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Panelists of The Updated WHO Policy on Xpert MTB/RIF assay: What is New and How it May Support Implementation and GHDonline staff

The Updated WHO Policy on Xpert MTB/RIF assay: What is New and How it May Support Implementation

Posted: 16 Jan, 2014   Recommendations: 34   Replies: 202

Dear Colleagues,

Various international parties have monitored Xpert MTB/RIF technology with interest since its WHO endorsement and global rollout in 2010. By the end of September 2013, close to 2,000 GeneXpert instruments and more than 4 million Xpert MTB/RIF cartridges were procured in the public sector in 95 countries eligible for concessional prices.

Experiences on the use of this technology have rapidly accumulated and have been regularly shared via peer-reviewed publications, systematic reviews, country and technical partner reports in several meetings of implementers organized by the WHO, as well as in previous GHDonline expert panel discussions. Taking stock of this new knowledge and experiences, a WHO Policy Update was issued in October 2013. It provides updated recommendations on the use of Xpert MTB/RIF assay for the diagnosis of pulmonary TB, pediatric TB, extrapulmonary TB and rifampicin resistance.

Please join us for a virtual Expert Panel discussion next week, from January 20 to 24, 2014 to discuss this new knowledge and the following topics:
- Selection of individuals to test using Xpert MTB/RIF and importance of risk assessment
- Interpretation of Xpert MTB/RIF results in different groups based on risk of DR-TB
- The best way to integrate Xpert MTB/RIF testing and the conventional methods
- How Xpert MTB/RIF and other rapid and sensitive TB tests may impact the dynamics of programmatic management of TB and DR-TB

I'm delighted to welcome the following panelists for this discussion and, together, we will answer these questions and more during our week long Expert Panel:
 - Christopher Gilpin, PhD, MPH, of the WHO.
- Armand Van Deun is a consultant with the International Union Against Tuberculosis and Lung Disease and a senior researcher for the Institute of Tropical Medicine, Antwerp.
- Professor Wendy Stevens is Head of the Department of Molecular Medicine and Haematology at the University of the Witwatersrand and Head of National Priority Programs at the National Health Laboratory Service, South Africa.
- Martin Colla was Cepheid’s marketing lead-person on the Xpert MTB/RIF development project and saw the product through to launch. He is now the Programme Manager Cepheid’s HBDC team Asia.
- Peter Saranchuk, MD, is a TB-HIV adviser for the Southern Africa Medical Unit (SAMU) of Médecins Sans Frontières (MSF).

How to Participate:

This virtual expert panel is free and open to all.

1. MDR-TB Treatment & Prevention community members: This Expert Panel is taking place in your community – this means that you will receive email notifications for this panel based on the email notification settings you’ve selected for these communities in your GHDonline profile. If you’d like to update your email notification settings for this Expert Panel, or any of your GHDonline communities, please log in to your GHDonline account (https://www.ghdonline.org/accounts/signin/) and select « Edit Email Settings » from the « My Profile » drop down.

2. Not a member? Click the « Join Expert Panel » button on the right to sign up for this Expert Panel.

Please feel free to start sharing questions and thoughts now. We look forward to this discussion.

Thank you.

Replies

 

Erlyn Rachelle Macarayan Replied at 7:54 PM, 16 Jan 2014

This is a really great topic! I am looking forward to the information shared by the panel and those who will join this discussion. I believe this will also accompany a variety of issues and will consider sociodeterminants of health, program monitoring and evaluation, and the various strategies that accompany this initiative's implementation.

Abebayehu Yilma Replied at 8:42 PM, 16 Jan 2014

Dear all,

I'm looking forward to join the discussion.

Stephen Muleshe Replied at 1:13 AM, 17 Jan 2014

Dear All
Happy New Year. This is indeed a great opportunity to discuss this
important topic. I look forward to the discussion

Rgds

Gemeda Abebe Replied at 2:02 AM, 17 Jan 2014

Dear All,

Happy New Year! This is an important topic and I will join the discussion.

Abdallah Mlwati Replied at 2:12 AM, 17 Jan 2014

It is indeed, a great opportunity to get involved on this wonderful topic about GeneXpert, i am looking forward to learn more from world class expert on this subject. Thanks.

Gidado Mustapha Replied at 2:36 AM, 17 Jan 2014

This is a good opportunity, as we are currently working in Nigeria to update our guidelines and SOP's based on the new policy. Already few questions asked by my colleagues on the new specimens (CSF, gastric fluids and tissues) on the practical procedure is this same with sputum? Are there SOS's for this already? Will it require change of modules?

febronie mushimiyimana Replied at 2:42 AM, 17 Jan 2014

Great opportunity for us to learn more as xpert is new in our country!

Leen Rigouts Replied at 2:45 AM, 17 Jan 2014

Idem

Fuad Mirzayev Replied at 3:30 AM, 17 Jan 2014

The pre-publication copy of the policy update if you haven't seen it yet is currently here: http://www.stoptb.org/wg/gli/assets/documents/WHO%20Policy%20Statement%20on%2...

Regards,

Fuad

Fuad Mirzayev Replied at 3:40 AM, 17 Jan 2014

The policy update will be complemented with the operational considerations, how-to's to be featured in the "Implementation manual" that is planned to be published in February-March. The Implementation manual will also have the SOP for for processing extrapulmonary samples (CSF, lymph nodes and other tissues). We can share the draft of this particular SOP during this panel discussion.
Regards,

Fuad

Christopher Gilpin, PhD, MPH Panelist Replied at 3:52 AM, 17 Jan 2014

A draft SOP (see attached) has been developed for specimen processing of selected extrapulmonary samples (CSF, lymph nodes and other tissues) for testing in the Xpert MTB/RIF assay. The final version of this SOP will be incorporated into the 2nd edition of the Implementation manual which will be published in Feb-March 2014.

Attached resource:

Dr. Daniela Cirillo, MD, PhD Replied at 3:58 AM, 17 Jan 2014

Thanks Fuad, the document and the SOPs will be extremely useful for all. Great work

Stephen Muleshe Replied at 4:21 AM, 17 Jan 2014

Many thanks Chris for the document

HAIDER AL-DARRAJI Replied at 4:54 AM, 17 Jan 2014

Thanks for your invitation, Fuad.
Looking forward to participate in this important discussion.

Alaine Umubyeyi Nyaruhirira Replied at 5:34 AM, 17 Jan 2014

Dear Panelists

That a great initiative and good time has many African countries are introducing this technology with some challenges due to not well coordinated implementation.
Particularly, I would like to bring in this session How to uses different ''guidelines'' releases by WHO and one e.g. is the placement of the Xpert machines and it maximum capacity.
The other point is the lack of clear treatment plan for MDRTB cases detected by Xpert and the time consuming waiting for a confirmatory results by proportion, liquid or LPA at the country level, availability of second line drugs and weak PMDT program etc.. They are a bit Gap between Guidelines/ recommendation and Implementation.

Mohammed suaudi Hassen Replied at 6:15 AM, 17 Jan 2014

It`s ok , i wanna to participate and i am one of it.

Manoj Yadav Replied at 9:15 AM, 17 Jan 2014

Looking forward to the discussion

Aamer Ikram Replied at 9:32 AM, 17 Jan 2014

Looking forward

Raju Pangeni Replied at 9:45 AM, 17 Jan 2014

Dear all, I will be looking forward to joining this forum and update my current understanding of gene xpert as a newer diagnostic tool and its limitations. Thanks

Honesty Ganu Replied at 11:47 AM, 17 Jan 2014

A great learning opportunity. looking forward to it

Gaddo Flego Replied at 11:59 AM, 17 Jan 2014

Dear all,
I'll join the panel discussion with great interest.
In many replies I've seen a concern about local implementation of Xpert MTB/RIF assay, that doesn't surprise me, being a typical issues of innovative technologies. As I'm more and more interested in the adoption of formal or informal Health Technology Assessment (HTA) procedures in Countries and health systems at various levels of income/development, I would be grateful if you could tell me if in your experiences the decision to implement Xpert MTB/RIF assay has followed any kind of evaluation of efficacy, impact on patients/organisation, general and specific sustainability and/or other issues.
Thank you, Gaddo.

DIMITRIOS PAPAVENTSIS Replied at 2:00 PM, 17 Jan 2014

Dear all,

This is a great opportunity to discuss the implementation of the Xpert MTB/RIF assay at local and international level.

While the financial situation is still deteriorating in Greece, the worst increase in unemployement for decades, increasing personal depth, weakened social protection programs and lack of data to demostrate health impacts of unprecedented austerity, have almost led to the collapse of the healthcare system. What is now expected is the sharp increase of the incidence of infectious diseases, esp. HIV, malaria (already recorded), tuberculosis, etc.

How are we suppossed to face the upcoming epidemic? We have no dedicated TB Programme and budget, no national TB control and elimination strategy, no national guidelines for implementation of TB control, ΤΒ human resources are not dedicated, plans for training and skills development of people working in TB control are lacking, Reference Centers are not officially nominated and are constantly underfunded, and TB is severely under-notified (<80% of cases according to recently published data).

Thus, sharing experiences on the use of this fascinating technology through this new GHDonline expert panel discussion will be extremely important for me and my colleagues in Athens. We have already gone through the new WHO Policy Update issued in October 2013 and at the momment we are updating our Xpert MTB/RIF SOP. The attached document here will be extremely useful, thank you Chris and the team for your great work!

Looking forward to next week's discussions.

Elizabeth Glaser Replied at 2:15 PM, 17 Jan 2014

Interesting innovation. In modeling studies , Xpert MTB/RIF was found to be cost effective, are there are real time studies to verify the model estimates?

Elizabeth

Regina Loprang Replied at 7:57 AM, 18 Jan 2014

This is very interesting topic.
Any experiences on using geneXpert for children?

Looking forward to join the discussion

Regina

edward chilolo Replied at 8:10 AM, 18 Jan 2014

Thanks team.
GX MTB/RIF is real an important innovation for detecting TB in its early stages and hence reducing the transmission in the community.
I will love to attend the discussion as in Tanzania we are already using the machines in some few selected health facilities.
Thanks also for the SOP as I thought only sputum sample is used for Gene Xpert testing.
Best regards,
Chilolo.

edward chilolo Replied at 8:22 AM, 18 Jan 2014

Dear Regina,
For Gene Xpert in children we usually do gastric aspiration. And the aspirate sample is sent for the GX machine testing.
The procedure for gastric aspiration is simple, can be done by non specialist personnel- a nurse, clinical officer provided they are trained/mentored to do the procedure. A morning specimen (aspirate) before a child has taken food is preferred.
This is what we are doing in Tanzania.
Best regards,
Chilolo.

Asif Mahmud Replied at 8:28 AM, 18 Jan 2014

A great initiative. Will be very helpful for clinicians in high burden countries like Bangladesh. Really look forward to deriving maximum benefit from the deliberation of the experts.
Asif Mujtaba Mahmud

Ellen Munemo Replied at 8:41 AM, 18 Jan 2014

Thabk you for the invitation, will definately participate. Thank you so much for the SOP for non sputum samples as it will aid us in paediatric patients. Looking firward to the fruitful discussions.
Ellen

Brenda Asiimwe Kateera Replied at 9:55 AM, 18 Jan 2014

This is a great and informative topic. I look forward to the rich discussion that will be held by the panelists and participants. Thanks for the SOP on use of specimens other than sputum in GeneXpert.
Brenda Asiimwe-Kateera

RAJNEESH TRIPATHI Replied at 10:08 AM, 18 Jan 2014

Dear,
Its great for the information.

Thanks and Regards
Rajneesh

Omotayo Salau Replied at 10:18 AM, 18 Jan 2014

Many thanks to the initiators of the up coming discussion,

beyond every doubt, its going to be mind blowing and highly informative with avenue to share in the experiences of the experts in TB control.

Looking forward to it... Great job!

Arnaud Trébucq Replied at 1:09 PM, 18 Jan 2014

Cost is primarily dependant on 2 things: the cost of the material and the
cost of the manpower. Obviously, the cost of the material is much higher
with Xpert than for the microscopic examinations. For the manpower, the
salaries are very high in high-income countries, and for sure Xpert is
cost-effective; in low-income countries where the salaries are low,
obviously microscopic examinations are more cost-effective.

Arnaud

Elizabeth Glaser Replied at 2:24 PM, 18 Jan 2014

There are costs for initial outlay,training modules and quality assurance to make sure that the results are accurate. In malaria , RDT also has been a major step forward but with caveats: 1. Clinicians may ignore results in favor of their and the patient's expectations,
2. Though simple to use, mistakes can be made so quality assurance has to be in place. 3.Maintaining training programs , 4. Stock outs of cartridges ( for genxpert) .etc these all incur costs in time and money.
Hopefully some if not most of these issues can be mitigated based on the lessons learned from large rollouts of RDT for malaria and rapid tests for HIV.
Elizabeth

CLAUDE RUTANGA Replied at 1:42 AM, 19 Jan 2014

Greetings to everybody,
Following the question raised by Gaddo regarding evaluations of Xpert technology in the public health practice, I would say there are some that have been made in some african countries as part of routine monitoring (at least those I'm aware of) not an official evaluation mission. Common challenges reported included:
- Frequent power shortages
- Poor quality of sputum specimen linked to inadequate capacity of staff, inadequate sputum collection procedures and storage
- Sample Transportation system particularly for remote sites, which secondarily affects the desired quality of samples
- Delayed calibration of Xpert machines due to lack of local capacity and poor communication between the local service provider (in the event there is one) and the Xpert implementing site.

Along the way of implementation of the Xpert technology, the concerned countries attempted to address those challenges by the following:
- Replacement of UPS procured with Xpert by Inverters that supported the full 2 hours cycle for the test. The Procured UPS with Xpert could not support full 2 hours cycle in some settings. This strategy was also looked at as more cost effective because of the price difference between the power Inverter and the UPS, which costed 850$ and 2500 $, respectively.
Noteworthy is also the reduction in number of the samples and cartridges that were thrown due to uncompleted/failed testings.
In some instances, power shortage was controlled by the use of brand new truck batteries that could support the full 2 hrs cycle.

- Use of cool box/ice packs to prevent deterioration of sample from remote areas or conservation of samples in alcohol based solution
- Staff training on data collection procedures and storage also reinforced the performance of Xpert in its implementation.
More strategies can be discussed or found during the expert panel

Regards

RUTANGA Claude, MD, MSc

CLAUDE RUTANGA Replied at 7:56 AM, 19 Jan 2014

Hi Fuad,
Along the coming one-week Expert panel discussion on the Updated WHO Xpert MTB/RIF assay, hopefully there will be much sharing on country based experiences in regard to operationalization of that new technology, from which challenges have been noted and solutions tried to overcome the latter.
Indeed, following the implementation of this at countries level, there is a feeling that patients' groups that should be targeted to keep the PPV (Positive Predictive Value) of this technique as high as possible have not been exhaustively explored by some TB control programs, reference made to TB diagnostic algorithms I have accessed and that have incorporated Xpert MTB/RIF.
Anyway, this is just one mentioned era, but more could come all along the discussion week.
Thank you

RUTANGA Claude, MD, MSc

Abdul ghafoor Replied at 12:09 AM, 20 Jan 2014

Thank you for starting a discussion on a very important and relevant topic. This discussion will add to the existing information and its interpretation in the local contexts. I llok forward for the discussion and comments.

Andrew Black Replied at 1:53 AM, 20 Jan 2014

Dear all,
Thank you for this opportunity, I have a few points that may need discussion.
1)With regards cost of cartridges, the actual cost and not the subsidised cost should be what is used, as the subsidy is in effect money that could be spent on Health care elsewhere.
2) The importance of Rif resistance prevalence in the area that the test is used needs to be stressed as the test will have a low positive predictive value in areas with low Rif resistance resulting in a number of false positives with possible significant consequences to misdiagnosed patients. A confirmatory test is imperative.
3) How should discordant genotypic results be interpreted, e.g. GXP Rif resistant and LPA sensitive? And how should discordant genotypic vs phenotypic results be interpreted?
4) In areas with high HIV/TB incidence where empiric TB therapy is often prescribed is repeating a GXP in HIV positive first GXP negative TB suspects of any value?
Look forward to the discussion

Armand Van Deun Panelist Replied at 2:47 AM, 20 Jan 2014

I am looking forward towards a useful discussion, particularly regarding the need to confirm a rifampicin resistant result when prevalence is low. As discussed in the attached paper this recommendation is highly debatable, as it was based on an imperfect gold standard, i.e. phenotypic DST which misses some low-level but clinically and epidemiologically relevant rifampicin resistance. Taking these into account the specificity is much higher than previously published and probably close to 100%, so that resistant results technically do not need confirmation. However, it remains true that pre- and post-analytical errors do occur, as for any test, the result may simply not belong to that patient. For this reason an unexpected resistant result should be confirmed, and in this sense prevalence may play. But fortunately confirmation can thus be obtained without referring samples or patients, just by repeating Xpert MTB/RIF on ANOTHER SAMPLE. In our experience other rapid tests (MGIT, LPA MTBDRPlus version 2) miss more rifampicin resistance than Xpert, so that it is also preferable to just repeat Xpert.

Attached resource:

Fuad Mirzayev Replied at 3:20 AM, 20 Jan 2014

Dear All,

We maintain a page on the WHO website compiling all useful information on implementation of this new technology, policy and 'how-to' documents, mapping availability worldwide and also the list of published evidence: http://www.who.int/tb/laboratory/mtbrifrollout/en/index.html
The list of published articles can be found there and in the section on impact and cost effectiveness of the assay you can find a number of articles discussing both models and routine clinical practice: http://www.stoptb.org/wg/gli/assets/documents/map/XpertPublications.pdf

Fuad Mirzayev Replied at 3:22 AM, 20 Jan 2014

On detection of paediatric TB
 Nicol MP et al. Xpert MTB/RIF Testing of Stool Samples for the Diagnosis of Pulmonary
Tuberculosis in Children. Clin Infect Dis. 2013 Apr 26. [Epub ahead of print]
http://cid.oxfordjournals.org/content/early/2013/04/25/cid.cit230.abstract
Updated 13 November 2013
 Sekadde MP et al. Evaluation of the Xpert MTB/RIF test for the diagnosis of childhood
pulmonary tuberculosis in Uganda: a cross-sectional diagnostic study. BMC Infect Dis. 2013
Mar 12;13:133. doi: 10.1186/1471-2334-13-133.
http://www.biomedcentral.com/1471-2334/13/133

 Nguyen TQ et al. Evaluation of Xpert MTB/RIF and MODS assay for the diagnosis of pediatric
tuberculosis. BMC Infect Dis. 2013; 13: 31.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562258/

 Walters E et al. Rapid Diagnosis of Pediatric Intrathoracic Tuberculosis From Stool Samples
Using the Xpert MTB/RIF Assay: A Pilot Study. Pediatr Infect Dis J. 2012 Dec;31(12):1316. doi:
10.1097/INF.0b013e318266c21c.
http://journals.lww.com/pidj/Citation/2012/12000/Rapid_Diagnosis_of_Pediatric...
acic.29.aspx

 Bates M et al. Assessment of the Xpert MTB/RIF assay for diagnosis of tuberculosis with
gastric lavage aspirates in children in sub-Saharan Africa: a prospective descriptive study.
Lancet Infect Dis. 2012 Nov 2. pii: S1473-3099(12)70245-1. [Epub ahead of print]
http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(12)70245-1/abs...

 Whittaker E and HJ Zar. Promising directions in the diagnosis of childhood tuberculosis.
Expert Rev Respir Med. 2012 Aug; 6(4): 385-95.
http://www.expert-reviews.com/doi/abs/10.1586/ers.12.36

 Zar HJ et al. Rapid molecular diagnosis of pulmonary tuberculosis in children using
nasopharyngeal specimens. Clin Infect Dis. 2012 Jul 2. [Epub ahead of print]
http://cid.oxfordjournals.org/content/early/2012/06/28/cid.cis598.abstract
 Rachow A et al. Increased and Expedited Case Detection by Xpert MTB/RIF Assay in
Childhood Tuberculosis: A Prospective Cohort Study. Clin Infect Dis. 2012 Apr 3. [Epub ahead
of print]
http://cid.oxfordjournals.org/content/early/2012/03/29/cid.cis190.abstract
 Nicol M et al. Accuracy of the Xpert MTB/RIF test for the diagnosis of pulmonary tuberculosis
in children admitted to hospital in Cape Town, South Africa: a descriptive study. Lancet Infect
Dis. 2011 Nov;11(11):819-24. Epub 2011 Jul 19.
http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(11)70167-0/ful...

Musarurwa Kwaramba Replied at 7:56 AM, 20 Jan 2014

Xpert MTB/RIF assay is a molecular technic which is able to detect mutations associated with even lower levels of phenotypic resistance. Such low - level resistance - associated mutations may represent an early stage in the development of high - level resistance. The ability to identify these mutations may therefore be clinical useful in optimizing treatment by switching to the more potent drug regimens. Is the Gene Xpert machine able to detect these low - level resistance (early detectation)? Development to high - level resistance is gradual, and TB programme sample collection for follow -up is at least monthly, are we not delaying the drug resistance diagnosis? How often do you recomend retesting the negatives (xpert MTB/RIF assay)?.

Thank you.

Kwaramba

Sophie Beauvais Replied at 8:39 AM, 20 Jan 2014

Dear All,

Welcome to the first day of our virtual expert panel on "The Updated WHO Policy on Xpert MTB/RIF assay: What is New and How it May Support Implementation." Many of you have already posted very interesting questions, and thank you Fuad for sharing so many interesting publications. Looking forward to hearing from our panelists and colleagues in this discussion about their experiences. A partial recap of some of the questions received so far is below - please all share your thoughts:

- Experiences on the decision to implement Xpert MTB/RIF assay has followed any kind of evaluation of efficacy, impact on patients/organisation, general and specific sustainability and/or other issues.

- In modeling studies , Xpert MTB/RIF was found to be cost effective, are there are real time studies to verify the model estimates?

- Experience using GeneXpert with children

- Is the Gene Xpert machine able to detect these low - level resistance (early detectation)? Development to high - level resistance is gradual, and TB programme sample collection for follow -up is at least monthly, are we not delaying the drug resistance diagnosis? How often do you recomend retesting the negatives (xpert MTB/RIF assay)?.

- How should discordant genotypic results be interpreted, e.g. GXP Rif resistant and LPA sensitive? And how should discordant genotypic vs phenotypic results be interpreted?

- In areas with high HIV/TB incidence where empiric TB therapy is often prescribed is repeating a GXP in HIV positive first GXP negative TB suspects of any value?

- Country experiences in regard to operationalization of that new technology, challenges encountered and solutions tried.

Best, Sophie

Armand Van Deun Panelist Replied at 9:34 AM, 20 Jan 2014

To answer Musarurwa Kwaramba
(Lab pro from Bostwana)
Is the Gene Xpert machine able to detect these low - level resistance (early detectation)? Development to high - level resistance is gradual, and TB programme sample collection for follow -up is at least monthly, are we not delaying the drug resistance diagnosis? How often do you recomend retesting the negatives (xpert MTB/RIF assay)?.

Xpert MTB/RIF has no problem detecting the low-level resistance mutations covered by the probes; there is at least one outside the covered area (572Phe). However, under standard TB programme conditions these low-level resistance mutations are on their own sufficient to cause bad treatment outcome, little different from the high-level resistance mutations. Development of higher level resistance because of acquisition of additional mutations can happen but does not seem to be the rule. The bottomline is that any rifampicin resistance detected by Xpert should prompt to MDR-TB treatment start, as recommended in the algorithm, except when in doubt regarding mis-identification. Re-testing should logically be done when patients respond to an indication because of continuing or recurring symptoms / signs, e.g. if still smear-positive at 3 months of re-treatment after being negative or susceptible at testing because of failure of primo-treatment.

To answer Andrew Black
(Physician, ZA)
3) How should discordant genotypic results be interpreted, e.g. GXP Rif resistant and LPA sensitive? And how should discordant genotypic vs phenotypic results be interpreted?

Resistant, if misidentification is unlikely. Xpert is the more sensitive test compared to LPA and rapid phenotypic DST, and in the average lab probably also more than slow DST. False resistance due to silent mutations is possible but very rare (less than 1% of the mutations in rpoB) and in our experience not even picked up by Xpert or LPA because it is usually hetero, mixed with wildtype. If picked up, silent mutations would be expected to yield the same resistant result by LPA, but not phenotypically.

4) In areas with high HIV/TB incidence where empiric TB therapy is often prescribed is repeating a GXP in HIV positive first GXP negative TB suspects of any value?

Yes, if you have the funds. But also think of non-TB mycobacteriosis which is most likely with positive smear and negative Xpert.

Fuad Mirzayev Replied at 10:57 AM, 20 Jan 2014

The decision to perform the Xpert MTB/RIF assay should be taken by a healthcare professional through a risk assessment of each individual approaching the health centre.
The updated WHO policy document recommends use of the assay for all individuals (adults and children) suspected of having TB. These two recommendations are conditional acknowledging significant resource implications when programmes decide to test all in this sizeable group. The recommendation for adults is based on the stronger body of evidence while the evidence for children was relatively weaker.
Another two recommendations in the updated policy strongly advise Xpert MTB/RIF be used as the initial diagnostic test in both adults and children at risk of MDR-TB or HIV-associated TB, and these two groups should be prioritized for Xpert MTB/RIF testing when resources are limited.
Policy recommendations also allow the use of Xpert MTB/RIF as a follow on test to microscopy in adults who are not considered to be at risk of either MDR or HIV-associated TB. This last recommendation in the updated policy acknowledges a body of evidence from systematic reviews showing a significant diagnostic superiority of Xpert MTB/RIF in terms of test accuracy and yield when compared to culture along with the sputum smear microscopy. However, this recommendation is not to be taken as a blanket rule to test all smear-negative individuals but rather a rule that allows programmes to test individuals still suspected to suffer from TB while smear microscopy failed to identify any acid-fast bacilli.

Fuad Mirzayev Replied at 11:03 AM, 20 Jan 2014

Some interesting country experiences were presented in the Xpert MTB/RIF implementers meeting last year. Country presentations can be found and viewed right here: http://www.stoptb.org/wg/gli/assets/documents/5th%20GLI%20meeting%20DRAFT%20A...
We expect to have more country experiences to be shared in the next Xpert MTB/RIF implementers meeting that is planned to take place in Geneva mid- April this year.

Martin Colla Panelist Replied at 11:07 AM, 20 Jan 2014

The ability of Xpert MTB/RIF to detect resistance emergence is partly dependent on whether the mutation results in no hybridisation with the probe (A,B,C,D or E) under which the mutation lies (the individual probe result will be negative) or if there is a partial hybridisation (the individual probe result will be a delayed positive relative to the other probes). In the former case resistance can be detected earlier, when fewer mutated organisms are present in the sampled mycobacterial population than the latter where almost all of the organisms in the sample may have to mutate before resistance will be signalled.

Blakemore et al J Clin Microbiol. 2010 Jul;48(7):2495-501. doi: 10.1128/JCM.00128-10. Epub 2010 May 26.
http://jcm.asm.org/content/48/7/2495.full

Md. Shamim Hossain Replied at 11:54 AM, 20 Jan 2014

It's really informative discussions. Thanks to all.

S M Mostofa Kamal Replied at 12:31 PM, 20 Jan 2014

Thanks for arranging such panel discussion on expert MTB/RIF A new molecular innovative which is going to replace conventional culture and DST (TAT 60 to 90 days). Meta analysis shows no false RIF resistance but there are 5% false RIF-sensitive in groups. However the following queries:
1. How Xpert will detect new sites of mutations? Is Cephid continuously monitoring this phenomenon? What is about mutation in rpoA region?
2. How to follow up spot positive TB cases? What will be the basis of declaration of cures in such a case(when microscopy is yet not done) ?
3. How much Xperts will be accurate in non converter group at the month of two, three, four, or fifth? Does FDA staining can supplement?
4. In case of reactive or relapse TB lymph node or another conceal TB cases when Xpert positive but Culture negative will TB treatment to be continued or to be rescheduled? I think more data is required is required.
5. If there any variation in cartridges from batch o batch or within the batch. I think there is little variation In internal control of the cartridges(MTB positive vs MTB negative in the same patient and again RIF resistance to RIF sensitive when re-tested).
6. If there any universal algorithm for Xpert use?

Andrew Black Replied at 1:01 PM, 20 Jan 2014

Thank you for the discussion and literature.
It does however raise a further question. We are seeing a number of patients with just a Xpert MTB/Rif result showing rif resistance with no other clinical samples available. How should these patients be treated? We currently treat them as MDR (4-6Km-Mfx-Eto-Trd/18Z-Mfx-Eto-Trd) PLUS H and E (most of our Rif mono's retain sensitivity to Ethambutol as opposed to our MDR cases which have a high level of E resistance) however this is a large pill burden and most of these patients will be MDR as a policy should these patients be considered and treated as MDR? A further anomaly our system has is if MDR is proven we admit the patient until culture conversion however if they just have a Rif resistant Xpert result we treat them as outpatients in the community.

Wendy Stevens Panelist Replied at 1:40 PM, 20 Jan 2014

Claude Ratunga: Rwanda:
Claude Ratunga:
Question: sharing on country based experiences in regard to operationalization of that new technology from which challenges have been noted and solutions tried to overcome the latter

I understood the question that you are looking for country based experiences to implement the GeneXpert System nationally. There are several countries that have begun and could assist you. The GLI meetings have been very useful in presenting country experiences As a South African, we have now implemented 289 in 207 centers and conducted over 3 million tests. We are happy to share our experiences and training material. There is no need to re-invent the wheel –we have a standardized approach for the implementation of all assays and it was no different for the GeneXpert. We are willing to share all data and training material.
We initiated the test in microscopy centers to speed up the process and began with 25 high burden districts.

Numerous challenges have been encountered along the way and have varied at different time points: early on the following were the problems:
• Temporary global shortage of cartridges
• Phased implementation: Incomplete access to testing: two algorithms in place (smear & GXP)
– Equity issues: rollout of instrumentation brought forward
– Confusion at lab and clinical level
- consensus on appropriate algorithm
• Non-adherence to algorithm / confusion regarding test requests
– No confirmatory testing for Rif resistant (20-40%)
– Multiple tests requested on one form
• Paediatric Testing
• Module failure: about 8%
• Extra-pulmonary samples
• Off-site calibration
• No EQA program
• Use at Point-of-care: feasibility


We now think we are reaching 100% coverage for presumed Tb cases and have completed the original plan. Genexpert positivity rates were 16-17% in high burden districts nationally; now national figures have settled at averages of 11-13%; we think this may be due to increased coverage and/or ARV program expansion; and/or fewer cases are treated empirically. Do not under-estimate how long it will take you to get consensus on an algorithm; this will also depend on both HIV and TB prevalence rates in-country. Error rates are relatively low stabilising at less than 2- 3 % nationally.

Many of these problems in the early phase have been addressed by the WHO guidelines: we are in the process of finalizing our EPTB policy.
Interestingly our own data mirrored the current WHO recommendations. We had an overall positivity rate of 18% across all sample types. In addition to our costing model (NTCM), we need to re-do the model to include the relevant costing for EPTB and pediatric testing which is not a small component. FNA on lymph nodes is very successful; we had sensitivities and specificities in pleural fluid of about 50%; CSF upon centrifugation better results; GXP done on residual sample so results will improve if this is upfront sample.

The greatest difficulties now are: 1) the need for health system strengthening: we know our algorithm is not being followed and the test is not being used appropriately everywhere; 2) the algorithm itself needs to be reviewed; 3) module failure beyond the 2 year warranty: costs not planned for but significant: Cepheid is doing R&D to reduce failure further; 4) LINKAGE TO CARE the biggest issue; 5) budgeting for fluctuations in exchange; rate; 6) what to do with the HIV positive GeneXpert negative; we spend over 100 million rand on this arm alone with a very small yield; 7) under-estimation of the clinical training and re-training required 8)ensuring sustainability with the costs being paid for from the National department of health budget.; 9) expansion of the program to high risk populations in prisons, mines and peri-mining communities

Solutions have included: 1) EQA done using dried culture spots; continuous monitoring is done through a remote connectivity system designed in collaboration with Cepheid; staff below can be contacted with respect to access to material; 2) algorithm under review: one study suggested using a second Xpert test in this scenario would be useful and cost effective; 3) calibration is now done on site; 4) SOPS are being developed for EPTB and the costing model is under review as this accounts for a significant number of sample ; 5) all pediatric cases are now being tested. Good results thus far using gastric aspirates, volumes for sputum are generally very low, however the assay doubles detection; testing on stool currently underway; 6) a simple solution to algorithm adherence has been sending two sputum specimens upfront that are reflexed by the laboratory. 7) Requisition forms and registers are being changed-don’t under-estimate how disruptive this process can be; 8) funds have been ring-fenced in national budget; 9) need to manage massive increase in MDR cases (consistently at about 7% of cases tested); 10) global fund money has been sourced to initiate programs with special needs: prisons and mines.

Further information can be obtained: www.nhls.ac.za; ; ;

I will dropbox some presentations and papers tomorrow that may be useful.

Andrew Black Replied at 1:40 PM, 20 Jan 2014

Greetings to all,
Other challenges we came across when using the machines outside laboratories were:
Power surges which resulted in costly damage to the equipment.
The need to provide regular updated virus protection and adequate security for the machines.
Samples of less than 5mls sputum were discarded or sent for AFB staining.
Poor stock management with over and under ordering of cartridges resulted in expired or no stock.
Technicians 'dedicated' to running samples often ended up doing other tasks in the clinic and ran samples at the end of the day thus defeating the object of same day results.
Results esp Rif resistant results were given to patients either as a print out or more often written on a piece of paper and without centralisation or a repository for the results referral centres receiving these patients were unable to get confirmation.
All the challenges can be overcome with money and training, but is there a need as even where extra staff have been employed to ensure same day results and treatment no clinical benefit has been shown.
I would suggest that it is the exceptional case where this technology should be placed outside a laboratory (large remote clinics) and that investment in improved transport systems to laboratories for testing may be more cost effective and be of benefit for all clinical samples not just sputa for TB suspects.

Andrew Black Replied at 3:55 PM, 20 Jan 2014

South Africa has achieved an amazing roll out of Xpert technology due to a lot of hard work and dedication of a very motivated team with the support of donors and government. Their experience is invaluable and a great resource for anyone considering the roll out of Xpert as part of their TB programme.
I think the impact on sensitive TB in SA has been diluted by a very low threshold to treat patients (particularly TB suspects with advanced HIV disease) with empiric therapy (in some large districts 30% of patients registered as PTB have had no sputum sent to the laboratory for any test). In our environment with such a large burden of TB I am unsure if a second Xpert for HIV infected Xpert negative patients would be of much value as few clinicians would withhold empiric treatment (rightly or wrongly) even if the second Xpert was negative (getting some clinicians to send the first test is often a challenge). The same holds true for EPTB, empiric treatment would be given to patients with HIV and a clinical picture of TB, very few people in South Africa would withhold TB treatment if the clinical picture and CSF biochem suggests TBM regardless of what the Xpert result is. Depending on the TB and HIV burden as well as the use of empiric TB treatment, algorithms will need to differ, if a test (which is not inexpensive) result will not change patient management is it necessary? I am always uncomfortable treating a patient with empiric TB treatment but given the high mortality and morbidity of untreated TB (one of our top causes of death in SA) I do not believe Xpert is sufficiently sensitive to rule out TB in patients with advanced HIV.
Where Xpert has had a large impact is the early diagnosis of resistant TB in patients where the diagnosis would previously been made late if at all, however the diagnosis is needs to be supported with linkage to care an appropriate treatment.
It is amazing how simple something can look on paper but be so complex in the clinical scenario, the technology alone cannot solve multiple health system problems. The Xpert roll out in SA has highlighted and focused attention on deficiencies that have existed in our health system for years and in addressing these deficiencies as part of the roll out has unquestionably changed our entire TB programme for the better.

Omar Sued Replied at 3:57 PM, 20 Jan 2014

Thank you!
The big problem for middle and upper middle countries like my country (Argentina) is that any donnors provide this machine, and even with price reduction, 17000 US continues being prohibitive for most hospital to access to, and they continue to using LJ culture media. In addition, this country does not consider TB as a priority, even when between 500 -1000 patients continues to day every year in Argentina. We urgently need access to this technology

DIMITRIOS PAPAVENTSIS Replied at 4:47 PM, 20 Jan 2014

I would also like to thank all participants for their contributions today, especially Sophie for setting the framework of discussions and Fuad for all useful information on implementation of the Xpert technology and valuable references.

However, I would like to emphasize the comment made by Omar from Argentina. The lack of progress in control efforts in recent years in many parts of the world (Europe included) is largely due to limitations of health systems and services.TB indeed is still not a priority in countries such as Argentina or Greece. Poverty, poor living conditions, unemployment, social injustice and political instability, corruption and increased migration, allow TB to spread faster in wider areas (esp. in the urban populations).

To improve early case detection, access barriers need to be addressed within a broader health system strengthening agenda, something that I feel is often underestimated. The financial crisis and imposed austerity measures dramatically pose major threats to health. Ιn such difficult times, what should be expected from international health organizations, the civil society and key local scientists, would be to stand up demanding the protection of the most vulnerable parts of the population. The question is: "Is anybody listening?"

Peter Saranchuk Panelist Replied at 10:05 PM, 20 Jan 2014

Greetings, everyone.

Regarding the use of Xpert in children, I would like to share some experience on behalf of Médecins Sans Frontières (MSF). Over the past 3 years, our medical humanitarian organization has introduced ~30 Xpert systems in resource-limited settings across ~15 countries. Unfortunately we have yet to see a large impact on detection of paediatric TB in these settings.

One of the reasons is, of course, the ongoing challenge in getting specimens for testing from sick children, especially in resource-limited settings. It’s good to read that one of the participants in this forum (Chilolo, post 27) is performing gastric aspiration in Tanzania. MSF has also tried to introduce sputum induction (SI) in a number of settings, though dare I say that this has proven to be more challenging than the introduction of the Xpert system itself in some of them (usually due to infection control concerns)!

While it is true that Xpert testing of respiratory samples (sputum, induced sputum, gastric lavage, nasopharyngeal aspirates) significantly increases the number of paediatric TB cases being detected compared to sputum smear microscopy, and in an equally rapid timeframe, Xpert is not as sensitive as culture and cannot confirm the diagnosis of TB in many children.

Preliminary results from Xpert testing on stool specimens (much easier to collect from children) are encouraging, but these need further validation. MSF has not (yet) been able to reproduce these promising results in the resource-limited settings that we support, perhaps in part because lab protocols to prepare stool specimens for testing are quite onerous. Does anyone have a straightforward protocol that they can share?

Since Xpert has been shown to perform well in detection of TB-associated lymphadenopathy, please consider needle aspiration of any enlarged lymph nodes in the evaluation of children with TB symptoms. This technique is often underutilized, despite being relatively easy to perform, especially in fluctuant nodes.

In this era of Xpert, detection of paediatric TB remains challenging. We urgently need additional diagnostic tools to meet the needs of children, including one that is truly point-of-care (POC). In the meantime, lab confirmation of paediatric TB can be improved by defining the optimal use of existing tools (including Xpert) in each setting, and by earlier identification of paediatric TB cases through robust contact tracing activities…

YAP BOUM II Replied at 12:00 AM, 21 Jan 2014

Are we going to consider eventually the Xpert as the Gold standard to Rif
resistance ?

Wendy Stevens Panelist Replied at 12:06 AM, 21 Jan 2014

Wendy Stevens
Andrew Black response:

Question: 1) How should discordant genotypic results be interpreted e.g. GXP rif resistant and LPA sensitive; and how should discordant genotypic versus phenotypic results be interpreted?

2) In areas with High HIV/TB incidence where empiric treatment is often prescribed is repeating a GeneXpert in HIV positive, first time negative TB suspects of any value?


Neither of the approaches GeneXpert and the DST and/or frequently LPA on culture, plain DST) are perfect and there are limitations to both assays in their current formats :( LPA: (sensitivity issues and missing a few mutations, differing performances in version 1 versus version2; in our settings high smear negative rates so LPA often done from culture) and (culture takes to long and is frequently not clinically relevant for a critically ill patient with a low CD4 count). The standardization and facilities required ensuring good quality assurance. The performance of culture varies upon methodologies used. Both providers of genotypic assays are performing continuous R&D there are no perfect tests yet. There is however a TB pipe-line of assays that may address some of these concerns in future. These do create problems for diagnostic confirmation that I am not sure we have the answers to yet. There are companies looking to provide a more sensitive test, which can be done since there is a sensitivity trade off when using as many probes as the Expert.

We do know that:
• Rifampicin: Lowest occurence of naturally occurring resistance mutations : 2.25x10 -10 vs. INH : 2.256X10-8
• RIF resistance ussually follows INH as protective effect is lost
• RIF resistance used as a surrogate for INH resistance and thus MDR reaches sentivities of over 85%; nearly 100% in Western Cape.
• INH genotypically far more polymorphic than RIF resistance: ? Under-detection by LPA
• Discordance between LPA and DST: LPA may under-detect INH by 9.6% , while phenotypic methods may under-detect Rifampicin resistance and contamination rates can be high
• Low-level Rif resistant cases frequently have bad clinical outcomes and should be viewed and managed as for high risk

In South Africa, the concordance varies by province and we know that:

• Rif concordance is good for both LPA and culture
• Concordance in the western Cape is reaching 90% in certain provinces
• Rif mono-resistance based on using culture as the gold standard occurs. We are however comparing to imperfect gold standards and DST misses some low level Rif mutations
• So called Rif mono-resistance in SA has
• Significant geographical variation
• Laboratory variation?
• Interpretation of LPA?
• How reliable is gold standard?
• Strain variation?
• No real link with HIV status
• Testing and clinical algorithms show variation across provinces: requiring standardisation

A long-winded way of ansering your question is that together with data and my gut feel is that a positive Rif resistant case should be managed as such and in most cases is generally correct when sequencing is done. - Treatment started and then full LPA and/or DST to confirm MDR and exclude XDR. Such patients should be referred to MDR centres for furthe management. Currently the Xpert test is more sesitive than LPA. False mutations are very rare unless there has been lab contamination.

2) Some of the bacground explains why the situation you are describing exists. Some clinical assessment of risk has to be made; If patient is extremely ill then empirical TB treatment may be started; if not an antibiotic trial can be undertaken. If no improvement on antibiotic trial, a second well collected specimen for GeneXpert could be run as a repeat which often increases the yield (currently not financially affordable for all patients in South Africa.). A specimen for culture DST/or LPA should be sent as per national guidelines, to also confirm MDR and look for XDR. These are expensive and despite delays someone needs to pick up these results. If there is any doubt that the patient and results do not match the test should be repeated. These cases are important to collect fpr sequencing and strain typing. In my peronal opinion and not respresenting the department of health a second Xpert may be better than culture.

sabira Tahseen Replied at 1:18 AM, 21 Jan 2014

In Pakistan, Xpert /MTB is mainly used as screening tool for diagnosis
of RRTB with exception of children under 15 yrs where Xpert /MTB rif is
also used for diagnosis of presumptive TB .

In 2012 total of 757 pediatric specimen were tested including 283 gastric
aspirates( 90% under 10 yrs) . Out of gastric aspirate tested 10 were both
smear and Xpert positive and additionally 9 cases were detected by Xpert
which were negative on smear . Thus increasing diagnostic yield by 90% with
consumption of approx 30 cartridges for every additional case diagnosed
.

It would have been interesting but we could not follow up these cases for
impact of bacteriological diagnosis on clinical management of patient to
see how many of bacteriologically diagnosed and the other smear negative
/Xpert negative clinically diagnosed were ultimately registered for
treatment .

Although Gastric are only few but is it really sustainable in HBC and
should it be continued ??

Armand Van Deun Panelist Replied at 2:15 AM, 21 Jan 2014

All the techniques miss some RMP resistance. To come near to a perfect gold
standard would require combining the best of the molecular + the best of the
phenotypic methods. For the molecular methods this is DNA sequencing, not
Xpert.

Wendy Stevens Panelist Replied at 2:49 AM, 21 Jan 2014

Regina Loprang: Wendy Stevens
Question: Experience using GeneXpert with children?
In paediatric populations, studies are limited and all have focused on laboratory based testing of Nalc/NaOH treated sputum specimens (1-4). In this type of specimen, Xpert has shown promising results with sensitivities ranging from 33.3% (2) to approximately 70% (3, 5) in smear negative, culture positive paediatric patients. Increased sensitivities of up to 75.9% could be achieved if two induced sputa were tested (2).
We performed a recent study on sputum specimens routinely obtained (by physiotherapy) from paediatrics patients, with the aim to assess the volumes of sputum obtained routinely from children <14 year of age in a primary healthcare facility, and determine whether specimens not meeting the Xpert minimum required testing volume could be manipulated at POC, as well as determine the performance of the Xpert MTB/RIF assay performed by a dedicated staff member, at the point-of-care, on raw sputum specimens.
To date: compared to culture on 374 specimens, smear generated a sensitivity and specificity of 33.3% and 99.5% respectively. And Xpert compared to culture had a sensitivity of 62.5% and specificity of 99%. Relative to smear, Xpert detected 3 additional M.tb positive cases. A weak correlation was observed between age and volume of specimens received (R2=0.49). Data from our study indicates that a large proportion of specimens received from children under 14 years of age were below the minimum required volume for Xpert testing and could either not be processed (4.1%) or had to be manipulated prior to Xpert testing (62.6%). Manipulation required weighing the specimen as an estimate of volume and then addition of a sterile saline solution using a pipette to make up the volume. This did not affect the Xpert result but required extra processing time and technical training for the person performing the testing. Patient age was associated with Xpert result reporting, with more MTB positives detected in older children. This was unrelated to volume of the specimen, but probably as a result of a higher bacillary load in these patients.
Overall, Xpert testing of sputum in paediatrics is not as successful as in adults, especially in younger children, and therefore additional specimen types such as gastric aspirates (or gastric lavage aspirates) (6) and stool are being investigated.

1. Nhu NTQ, Dang TM, Nguyen DA, Do DA, Tran ND, Nguyen DQ, Nguyen TN, Tran VQ, Nguyen TB, Vo TH, Do CG, Nguyen HD, Wolbers M, Farrar J, Caws M. 2013. Evaluation of Xpert MTB/RIF and MODS assay for the diagnosis of pediatric tuberculosis. BMC Infect Dis 13:31.
2. Nicol MP, Workman L, Isaacs W, Munro J, Black F, Eley B, Boehme CC, Zemanay W, Zar HJ. 2011. Accuracy of the Xpert MTB/RIF test for the diagnosis of pulmonary tuberculosis in children admitted to hospital in Cape Town, South Africa: a descriptive study. Lancet Infect Dis 11:819-824.
3. Sekadde MP, Wobudeya E, Joloba ML, Ssengooba W, Kisembo H, Bakeera-Kitaka S, Musoke P. 2013. Evaluation of the Xpert MTB/RIF test for the diagnosis of childhood pulmonary tuberculosis in Uganda: a cross-sectional diagnostic study. BMC Infect Dis 13:133.
4. Zar HJ, Workman L, Isaacs W, Munro J, Black F, Eley B, Allen V, Boehme CC, Zemanay W, Nicol MP. 2012. Rapid molecular diagnosis of pulmonary tuberculosis in children using nasopharyngeal specimens. Clin Infect Dis 55:1088-1095.
5. Rachow A, Clowes P, Saathoff E, Mtafya B, Michael E, Ntinginya EN, Kowour D, Rojas-Ponce G, Kroidl A, Maboko L, Heinrich N, Reither K, Hoelscher M. Increased and expedited case detection by Xpert MTB/RIF assay in childhood tuberculosis: a prospective cohort study. Clin Infect Dis 54:1388-1396.
6. Bates M, O'Grady J, Maeurer M, Tembo J, Chilukutu L, Chabala C, Kasonde R, Mulota P, Mzyece J, Chomba M, Mukonda L, Mumba M, Kapata N, Rachow A, Clowes P, Hoelscher M, Mwaba P, Zumla A. 2013. Assessment of the Xpert MTB/RIF assay for diagnosis of tuberculosis with gastric lavage aspirates in children in sub-Saharan Africa: a prospective descriptive study. Lancet Infect Dis 13:36-42.

Armand Van Deun Panelist Replied at 2:54 AM, 21 Jan 2014

As to

1: several companies are looking at improved molecular tests for TB drug
resistance. The problem is that our knowledge is far from sufficient to
develop the perfect test, rifampicin may actually be the best studied drug.
Initiatives are emerging to promote further studies.

2: microscopy is still recommended for treatment monitoring; as always,
without documentation by negative smears a patient who has taken the full
treatment course will be declared "treatment completed", not "cured"

3: any results is possible during treatment (fail, negative, TB
RMP_sensitive, TB RMP_resistant). It looks as if false resistance is not a
problem.

4. this needs further investigations (histo-patology); if not possible or
inconclusive, for gland TB a conservative, waiting attitude could be
justified

Regina Loprang Replied at 3:14 AM, 21 Jan 2014

Dear all
thank you for sharing us with the latest experiences using genexpert in children. we are planning to piloting the genexpert for children in 2 big hospitals in Indonesia, but we still discussing and arguing about the algorithm. And information through this discussion really inspiring and useful.
It is true that diagnosing TB in children remains challenging. Despite the increasing sensitivities achieved when we use 2 sputa, but in children we still need to perform induced sputum or gastric lavage/aspirat , which is not convenient for children, I am really interesting with use of stool as the media for diagnosing TB.
looking forward to hear the promising result.

Wendy Stevens Panelist Replied at 3:17 AM, 21 Jan 2014

IIMusauwa Kwaramba:

Question: Is the GeneXpert able to detect low level resistance mutations (early detection), development to high level resistance is gradual and the TB sample collection follow up is at least monthly, are we not delaying the drug resistance diagnosis? How often do you recommend testing the negatives?

The paper provided by Armand van Deun in the discussion suggests that the specificity is much higher than previous descriptions in the literature. In fact, our specificity in the practical setting has increased over time. I would treat any Rif resistance case detected on Xpert with low or high- level mutations. I think we can close the door on accuracy of Rif, particularly with the G4 cartridge that is superior to the previous G3 and created all the issues around false positives. The positive predictive value of the result however may be affected by the prevalence of TB in your region. In addition, because the Xpert positivity result is based on the detection of the Rif gene, a change in concentration of bacteria should not alter this result unless the load is too low in which case a Rif indeterminate or negative results will occur.

In our setting we start patients on treatment immediately (high burden of HIV and TB) and refer for culture DST and/or LPA: to document MDR and/or XDR. If culture or LPA facilities are not available a second GeneXpert test can be done. Emerging data suggests that Xpert may well be superior over other technologies for detecting Rif resistance. Our MDR cases confirmed on culture is currently over close to 90% and in some provinces 100%. It may be a more cost-effective approach to repeat the Xpert than follow the full culture-based process recommended in many national algorithms(1-3).

Your last question I think has been answered in the Andrew Black response from me.

1. Schnippel K, Meyer-Rath G, Long L, Stevens WS, Sanne I, Rosen S. 2013. Diagnosing Xpert MTB/RIF negative TB: impact and cost of alternative algorithms for South Africa. S Afr Med J 103:101-106.
2. Meyer-Rath G, Schnippel K, Long L, MacLeod W, Sanne I, Stevens W, Pillay S, Pillay Y, Rosen S. 2012. The impact and cost of scaling up GeneXpert MTB/RIF in South Africa. PLoS ONE 7:e36966.
3. Schnippel K, Meyer-Rath G, Long L, MacLeod W, Sanne I, Stevens WS, Rosen S. 2012. Scaling up Xpert MTB/RIF technology: the costs of laboratory- vs. clinic-based roll-out in South Africa. Trop Med Int Health 17:1142-1151.

Wendy Stevens Panelist Replied at 3:19 AM, 21 Jan 2014

Gaddo Flego
(MD, Italy)

Question:
I would be greatful if you could tell me in your experiences the decision to implement Xpert MTB Rif assay has followed any kind of efficacy, impact on patients and organizations, general and specific sustainability.

I apologise upfront for only discussing South africa’s program but this is what I am most familiar with:

South Africa has a huge burden of disease for HIV and TB; we really had no choice but to implement a test that in demonstration studies doubled detection rates, improved resistance detection; all within a short-time frame. Our smear positivity rates had dropped to 9-10%. Some background to why the decision was made to go for the test is mentioned below. For equity reasons this test had to be available to all South Africans and thus one national plan was conceived using Xpert as a replacement for microscopy

• 20% worlds reported HIV‐associated TB cases and 4th largest reported numbers of MDR.
• 70% TB suspects infected with HIV
• Overall TB rates 993/100,000 (2011)
• Mining populations 2500/100,000
• Correctional Services 4500/100,0000
• Increasingly smear negative (8-10% positivity) and extra-pulmonary TB(16%), microscopy not helpful for DR detection
• HIV background of 5.7 million infected individuals of which 1.4 million are receiving ARV therapy
• Diagnosis is made to late to avert mortality in HIV co-infected where smear sensitivity drops to 35-40%. Symptomatic screen not useful in 25% cases (Lawn. JID 2011)
• Mean annual risk of developing TB is ~ 10% (Corbett, 2003)
• Estimated 25-30% of individuals in CT initiating ARV treatment have unrecognisable TB (Holmes, JAIDS 2006)

Based on demonstration studies produced, our own data and the ministers’ instruction we implemented the test in 25 high burden districts (phase I) based on WHO recommendations. At the time, Several SA research studies emerged confirming the increase in laboratory detection, reduced time to diagnosis and treatment initiation and a reduction in empiric treatment and so we continued the rollout summarised below

“The new automated DNA test for TB should be used as the initial diagnostic test in individuals suspected of MDR-TB or HIV/TB” (i.e. Most TB suspects in SA)

• In March 2011, South Africa developed and initiated a National Plan for phased implementation of the technology, as a replacement for microscopy as the initial diagnostic screen for TB suspects
• Significant support from CDC, Global fund, BMGF, UNITAID, amongst others
• Reinforced by announcements of significant reduction in test cost
• In high burden districts, significant increase in case detection in suspects (8 to16%), significant increase in detection of drug resistance (7%)
• Several SA research studies emerged confirming the increase in
laboratory detection, reduced time to diagnosis and treatment
initiation and a reduction in empiric treatment

We proceeded with one national plan where costing for the laboratory services was done, as well as modeling the needs for South Africa taking into account all aspects that would be needed in the continuum of care such as treatment, MDR drugs etc. A phased implementation was thus done:

• Three phases of implementation in microscopy centres
• Phase I: Pilot in high burden districts (25 sites)
• Phase II: Completion of high burden districts
a. Full capacitation of Phase I labs
b. Full capacitation of high burden districts
• Phase III: XTEND Study (Aurum: BMGF funded, RCT) looking at impact was embedded in the rollout program.
a. Intervention arm
b. Control arm.

Completion of all sites in September 2013

• Full financial commitment attained for program was secured in 2011 and thus the national department of Health covers the costs of all tests thus transitioning from the donor funding upfront to ensure sustainability
• The same process will be undertaken for prisons and mines, initially evaluated as vertical programs with donor funding that will be integrated into the national program.

Costing activities needed are listed below:

• To estimate implementation costs for NHLS lab network
• To inform national-level budget requirements (2011-2017)
• To estimate the incremental national health service cost of replacing the existing pulmonary TB diagnostic algorithm with a new algorithm incorporating Xpert MTB/RIF molecular technology, under routine care conditions and at costs incurred by the government (Excel-based population level decision model) (NTCM): focused on entire process from TB suspects to TB cases and TB treatment.
• Built into Rollout the XTEND study (BMGF funded): cluster randomised trial design (phase 3a and b: to verify modelling and evaluate the cost-effectiveness and assess impact of the Xpert intervention in routine conditions was implemented. Early data from this study has been analysed and will be presented at CROI
• For timing reasons alone, early implementation decisions were based on (National TB costing model) NTCM model, especially the NHLS costing component
• Additional early modelling by the Xtend study produced similar results to those done initially by our partners the Hero group.

The National TB costing model (NTCM) first version predicted the following:
• Scale- up as planned would require the placement of 65 GX4, 169 GX16 and 4 GX48
– Leading to a total national test capacity of 11,428 tests per day.
– This will need re-costing as additional analysers are added for EPTB, paediatric samples; hence the addition of seven infinities
• Total capital cost (including instruments, additional space, security, and training) between 2011/12 and 2016/17 would be 149 million ZAR (20 million USD)
• Additional annual budget requirement (53-57%) or USD 48-70 million per year
– Altered by different rates of scale-up
• The NHLS (or laboratory) share of total diagnostic cost increases by
– Cost per TB diagnosis suspects to $ 54-63 USD
– Cost per TB case diagnosed: 277-360 USD
– Cost per TB case diagnosed and treated increased by 9% (797-873 USD)
• Clinic (decentralised placement) was 46% more expensive, with NDoH investment increasing as a result of additional GX4 instruments, space, air-conditioning and security, and staff time.

Several other studies suggested this approach was cost-effective and in South Africa and are listed below:

• Cost effectiveness of routine TB screening prior to ARV initiation (Andrews et al. AIDS 2012), using 4 different diagnostic scenarios: concluded that screening using 2 Xperts in all individuals initiating ART is very cost effective and had the greatest gain in life -months. Strategies using one Xpert or symptom screening were less effective (Modified CEPAC model)
• Cost effectiveness analysis of Xpert MTB/RIF: (Vassal et al: Plos Med 2011) investigated and demonstrated in 3 different prevalence settings. Xpert increased case finding, more cost-effective than base case of microscopy and clinical diagnosis.
• The context impacts the results dramatically: sensitivity and specificity of baseline TB diagnoses, HIV co-infected, number of false positives. Issues not addressed in most studies; systems strengthening needed, equity, campaign costs
• Other important commentaries
• Kirwan et al. Valid points made: inputs into models rely heavily on estimations. They have developed an Impact Assessment Framework (IAF) that includes: (effect, equity, health systems, ethical issues, linkage to care) Am. J. Trop. Med. Hyg., 87(2), 2012, pp. 197–201:

South Africa has begun to populate the original model with actual data. One of the problems identified immediately was that we had under-estimated the amount of empiric treatment being undertaken and this may be one of the reasons for Tb cases not increasing as expected by the model. Bacteriologically confirmed specimens in patients were thus being treated. The increase in detection of drug resistance is likely to be one of the greatest advantages of this assay in South Africa. The model will now include the EPTB specimen that is not an insignificant number (15%).

Wendy Stevens Panelist Replied at 3:41 AM, 21 Jan 2014

Reply to number 57: Dimitrios Papaventsis

This is one of the most important comments made. The full benefit of the assay is only ascertained if conducted in a healthcare system that can deal with the result. In South Africa, the laboratories are doing thousands of tests and we believe based on the laboratory adherence to algorithm that only 30-40% are probably getting the full benefit, this is especially relevant for linking MDR cases to care.
Strengthening the underlying healthcare system is the most important activity to consider when implementing testing in a program. Several studies are being undertaken to assess where the weaknesses are in our system and finding ways to change practice and link individuals. In addition, a huge amount of training and re-training of all cadre of health care workers is needed and costs of this are under-estimated.

Wendy Stevens Panelist Replied at 3:45 AM, 21 Jan 2014

Response to Omar Sued:

I agree completely with your statement. While the cartridges have a very reasonable, negotiated price they are useless if one can't afford the analysers which are very expensive especially if you go for models processing higher volumes of samples. Having to purchase the analysers is the single limiting factor to initial implementation. Leasing and/or maintenance contracts are far preferable.

Lal Mani ADHIKARI Replied at 4:10 AM, 21 Jan 2014

Dear Fuad,

Its very impressive discussion which is very useful who are concerned with
TB Diagnosis and care especially like us who are on Field mission, we are
dealt with a great enthusiasm. thank you for providing opportunity to be a
part in this Panel discussion.

with kindest regards,
Lal Mani Adhikari

Martin Colla Panelist Replied at 4:51 AM, 21 Jan 2014

Reply to Andrew Black,

Re: 1)With regards cost of cartridges, the actual cost and not the subsidised cost should be what is used, as the subsidy is in effect money that could be spent on Health care elsewhere.)

The ‘buy down’ agreement between PEPFAR, UNITAID, the Bill and Melinda Gates Foundation and Cepheid was a one-time payment rather than an ongoing subsidy. The intention was to enable a reduction in the cartridge price from $16.88 to $9.98. This in turn was expected to boost global cartridge uptake to a new level. A level which would allow Cepheid to bring down its manufacturing costs and be able to sustain the $9.98 price without further support. Cartridge volumes have risen to the anticipated levels so $9.98 (ex-works, pre-paid) is the definitive, sustainable base-price. The agreement sets this price for ten years. There is no continuing subsidy which might be allocated elsewhere. I hope this helps.

Gaddo Flego Replied at 5:21 AM, 21 Jan 2014

Dear Wendy Stevens, Claude Rutanga, Sophie Beauvais,
thank you for having contributed to/shared my question. That confirms my original idea that success of a program highly depends on the ability to address relevant public health issues, to make evidence based decisions, to try to evaluate various kind of impact and to manage an ongoing follow-up that can lead to correcting actions. Many issues can be addressed "without reinventing the wheel", if methodology, data, evaluations are shared, and the need of this kind of assessment is global; platforms like GHDonline con play a major role in this dissemination process. I will continue to watch fo further contributions and I hope to share with you some final considerations.
Best regards, Gaddo.

Fuad Mirzayev Replied at 5:27 AM, 21 Jan 2014

question of Moustofa Kamal about universal algorithm prompts to summarise some of the points on this important topic.

It is virtually impossible to have one and universal testing algorithm for any diagnostic technology that would fit to all possible situations both in terms of epidemiologic scenario and the availability of resources (both financial and human resources). Therefore, in the cases of Xpert MTB/RIF implementation, I'd suggest to approach this in two logical steps: 1. Define the rules for the selection of the individuals to be tested using Xpert and 2. Agree and define the interpretation of the Xpert MTB/RIF results depending on the patient/suspect risk group.
Linking these two steps will complete the diagnostic algorithm and make it relevant to your particular setting, will allow the healthcare workers/clinicians to make appropriate decisions on the interventions to follow both in relation to the

a) patient management (and let me highlight the importance of starting appropriate treatment early),

b) registration and

c) any additional laboratory workup that may still be required.
Obviously, all these will require training and follow up, also to ensure adherence to the developed algorithm, as clearly shown for example by experience of South Africa (please see comments by Wendy Stevens).
The selection of the individuals to test should be based on the risk assessment of the individual and is advised to follow the recommendations of the updated WHO policy document. As mentioned earlier, this will need to be based on the epidemiology of the disease (high or low prevalence of TB, DR-TB, HIV) and consider the groups to be tested (adults, children), whether Xpert is used as initial or a follow up test and if resources are available to test all suspected of having TB or limited to focus only on the risk groups (for example on those at risk of MDR-TB only).
When it comes to the interpretation of the test results, it depends obviously on the result itself but also considering the group of risk from which the patient originated. Interpretation is usually fairly easy when Xpert doesn't detect TB or detects TB with no rifampicin resistance.
Interpretation of the Xpert MTB/RIF detection of MTB and rifampicin resistance might represent a higher challenge as interpretation depends on the patient risk group vis-a-vis the risk of MDR-TB. Some discussion on this already came up in this forum so let me share with you our thinking on this particular topic focusing on a),b) and c) above.

- In patients originating from a group at high risk of MDR-TB, a WHO-recommended regimen for MDR-TB with the addition of isoniazid should be initiated, the patient should be registered as having bacteriologically confirmed rifampicin-resistant TB (RR-TB), and another sputum sample (taken immediately and prior to starting treatment) should be sent for phenotypic DST to at least isoniazid, quinolones and second-line injectables. Confirmatory testing of rifampicin resistance using another testing technology is not necessary in such cases (given high PPV for rifampicin resistance in this group). When, at a later stage, results of the DST are available, treatment can be modified based on the results and patient registration updated accordingly. Treatment modifications may include dropping isoniazid if resistance was shown, adding an appropriate quinolone or second-line injectable or, in case of XDR-TB, placing the patient on an appropriately designed regimen including group 5 drugs. Accordingly, the registration of the patient should be modified reflecting this new information and be notified as per national regulations.

- In patients originating from a group at low risk of MDR-TB, this result may be considered unexpected and naturally a clinician may be hesitant to enrol a patient on a treatment regimen requiring second-line drugs (mostly due to its length and toxicity). While the unexpected Xpert MTB/RIF result may be attributed to the possibly lower PPV for rifampicin resistance in a group with low underlying prevalence, it may also result from the non-systematic or random errors at pre- or post-analytical stages of the testing that are relatively frequent even in quality-assured laboratories. These include clerical errors when recording specimen information or test results, or administrative errors that result in specimens being mixed up, etc. While not addressing the lower PPV issue for detection of rifampicin resistance in this group, an immediately repeated Xpert MTB/RIF test on a fresh sample can be useful in improving a clinician's confidence when deciding on the treatment to be prescribed for this particular patient.

Fuad Mirzayev Replied at 5:36 AM, 21 Jan 2014

An important topic is raised by DIMITRIOS PAPAVENTSIS and I would like to highlight that the access issues and an outlook with a broader health systems strengthening agenda is clearly highlighted in the new, post-2015 Global TB Strategy. This new strategy developed by the global TB programme of the WHO I consultation with countries and partners is being discussed right now in the Executive board meeting and you can find more details on its main pillars and proposed components right here: http://www.who.int/tb/post2015_strategy/en/index.html

Wendy Stevens Panelist Replied at 5:36 AM, 21 Jan 2014

Response to Elizabeth Glazer: in modelling studies Xpert assay was found to be cost-effective. Are there real-time studies to verify the model estimates:

Apologies for the long story again:In modelling studies, Xpert MTB Rif was found to be cost-effective, are there real time studies to verify the model estimates?

An early cost-effectiveness analysis, based upon the demonstration study of Xpert (Boehme et al., 2011) found:
Our results suggest that Xpert is a cost-effective method of TB diagnosis, compared to a base case of smear microscopy and clinical diagnosis of smear-negative TB in low- and middle-income settings where, with its ability to substantially increase case finding, it has important potential for improving TB diagnosis and control. The extent of cost- effectiveness gain to TB programmes from deploying Xpert is primarily dependent on current TB diagnostic practices. Further work is required during scale-up to validate these findings.(Vassall et al., 2011)
Knowing that Xpert was cost-effective relative to smear microscopy and clinical diagnosis ((defined as the cost per DALY averted of each country’s per capita GDP; US$5,786 for South Africa(Vassall et al., 2011))was important, but not sufficient for the decision as to whether and how the National TB Programme in South Africa should adopt this technology.
A population-level decision model was built for South Africa, based on the national TB diagnostic guidelines (including microscopy, culture, x-rays, PCR (line probe assay) and clinical diagnosis) in place in 2011 compared to replacing initial smear microscopy for pulmonary TB with Xpert. The cost and health impact of different scenarios was compared and used for the planning of the national roll-out.(Meyer-Rath et al., 2012) The model is still in use and updated as needed, but not for the determination of cost-effectiveness. Instead, it is used for planning and budgeting of TB diagnostics and control in South Africa. Additional analyses from this model have been published looking at the appropriate placement of the geneXpert instruments in laboratories or clinics in South Africa (Schnippel et al., 2012) and alternative diagnostic algorithms for persons who are Xpert- and HIV+(Schnippel, Long, Stevens, Sanne, & Rosen, 2013). The cost of Xpert at the reduced international prices was already addressed in the initial model analysis (Meyer-Rath et al., 2012) and the updated costs of Xpert at clinic level were also published (Van Rie et al., 2013). This model was also parameterized specifically for improving diagnosis and control of TB in correctional facilities in South Africa, the results of which informed the successful interim request to the Global Fund for South Africa (http://www.sanac.org.za/global-fund).
Multiple studies have been and are being done looking at the impacts (and sometimes costs) of Xpert as it is implemented and it is clear that:
When implementing and scaling up the use of a new diagnostic tool, the operational context in which diagnosis and treatment take place needs to be considered.(Lin, Dowdy, Dye, Murray, & Cohen, 2012)

Boehme, C. C., Nicol, M. P., Nabeta, P., Michael, J. S., Gotuzzo, E., Tahirli, R., … Perkins, M. D. (2011). Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet, 377(9776), 1495–505. doi:10.1016/S0140-6736(11)60438-8
Lin, H.-H., Dowdy, D., Dye, C., Murray, M., & Cohen, T. (2012). The impact of new tuberculosis diagnostics on transmission: why context matters. Bulletin of the World Health Organization, 90(10), 739–747A. doi:10.2471/BLT.11.101436
Meyer-Rath, G., Schnippel, K., Long, L., MacLeod, W., Sanne, I., Stevens, W. S., … Rosen, S. (2012). The impact and cost of scaling up GeneXpert MTB/RIF in South Africa. (M. P. Nicol, Ed.)PLoS ONE, 7(5), e36966. doi:10.1371/journal.pone.0036966
Schnippel, K., Long, L., Stevens, W. S., Sanne, I., & Rosen, S. (2013). Diagnosing Xpert MTB / RIF-negative TB : Impact and cost of alternative algorithms for South Africa. South African Medical Journal, 103(2), 101–106. doi:10.7196/SAMJ.6182
Schnippel, K., Meyer-rath, G., Long, L., Macleod, W., Sanne, I., Stevens, W. S., … Author, C. (2012). Scaling up Xpert MTB / RIF technology : the costs of laboratory- vs . clinic-based roll-out in South Africa. Tropical Medicine & International Health, 17(9), 1142–1151. doi:10.1111/j.1365-3156.2012.03028.x
Van Rie, A., Page-Shipp, L., Hanrahan, C. F., Schnippel, K., Dansey, H., Bassett, J., … Sanne, I. (2013). Point-of-care Xpert® MTB/RIF for smear-negative tuberculosis suspects at a primary care clinic in South Africa. The International Journal of Tuberculosis and Lung Disease, 17(3), 368–72. doi:10.5588/ijtld.12.0392
Vassall, A., Kampen, S. Van, Sohn, H., Michael, J. S., John, K. R., Boon, S. Den, … Cobelens, F. (2011). Rapid Diagnosis of Tuberculosis with the Xpert MTB / RIF Assay in High Burden Countries : A Cost-Effectiveness Analysis. PLoS Medicine, 8(11). doi:10.1371/journal.pmed.1001120

Alaine Umubyeyi Nyaruhirira Replied at 6:16 AM, 21 Jan 2014

Dear All

Thx a lot for this important panel discussion. We have learn and we are sharing a lot of experience and have response and clear picture on challenge we are facing day to day with the implementation of this new technique. One area we have to look also is the early treatment of MDRTB cases identified, availability of second line drugs and a good PMDT program. It for me no sense to install a machine in a setting where these compound is missing. Even the success in SA implementation , they are still a Gap between Diagnostic and Treatment of MDRTB . This situation increase the high death rate in some region/ countries, particularly where TB/HIV is high.
Another challenge as highlighted by Dimitrios, the inequality on providing health services/ technologies. Thx to Fuad to share and confirm that this will be cover in the New STOP TB strategic post 2015.

Alaine Umubyeyi Nyaruhirira Replied at 8:39 AM, 21 Jan 2014

Dear Panelists,

What is the recommendation from WHO (GLI) regarding “the standardization and required good quality assurance for GeneXpert.

Dr mayank Ghedia Replied at 11:55 AM, 21 Jan 2014

Dear All,

Can any one share experience regarding MTB Negative by GeneXpert and sputum positive sample.

Sophie Beauvais Replied at 12:05 PM, 21 Jan 2014

Dear All,

Fantastic exchange so far, many thanks to all.

Gemeda Abebe in Ethiopia posted the following question in a separate thread so here it is again for all our panelists and colleagues:

In countries with wide geographic area and differing MDR-TB prevalence we often see a single diagnostic algorithm. In such cases you can have varying level of RIF mono resistance. How could you make use of the result from geneXpert in predicting MDRT-TB in a country with variable level of RIF mono resistance?

Also, a reminder to everyone: If you want to change your email notifications for this virtual expert panel, please do NOT reply to this email discussion, instead sign in to your GHDonline profile here: https://www.ghdonline.org/accounts/signin/ and edit your email settings.

Best, Sophie

Fulgence Nzabintwali Replied at 12:14 PM, 21 Jan 2014

Dear All,

That is possible with AFB positive (smear positive) , bacilli seen by microscope can be MTB or MOTT(NTM), with by Gene X pert you will have result negative (MTB not detected)

That is a challenge in using Gene X pert .

Conclusion AFB positive = MOTT/NTM= by Gene X pert no result = MTB not detected

Only culture or molecular test for MOTT can help you in this case


Fulgence



Le 21 janv. 2014 à 18:03, Dr mayank Ghedia via GHDonline <> a écrit :

Lucia Barrera Replied at 12:34 PM, 21 Jan 2014

Greetings to all

Regarding the considerations on the interpretation of discordant results and the article that Armand kindly provided to us. This article comment that the original publication introducing GXP presented 9 discordant phenotipically susceptible strains. Among them , 8 had clinical relevant mutations. So the proportion of true vs false GXP resistance among discordant results might be 8:1? This proportion is consistent with
‾ 10-13% of “disputed” resistance found in Bangladesh-Kinshasa among isolates with rpoB mutations which was interpreted to be true resistance
‾ 1% of silent mutations estimated to occur among all mutations present in the rpoB gene
What about mutations that are out of the region investigated by the GXP?

About the recommendation on the use of GXP to diagnose TB among suspects with history of TB treatment.. Is there knowledge on the persistence of a positive GXP results after cure?

On the recent SOP developed to test extrapulmonary specimens by GXP. When more than 5 ml of CSF is available, culturing part of the specimen should be also recommended

In relation to implementation challenges, I found in Latin America many of the challenges that were already mentioned by the participants . I would like consider the weak capacity to design algorithms considering the available resources and to calculate the cartridges accordingly s. This ended up with h shortage and overstock of supplies in some countries . A tool to calculate the supplies might be useful. Is there any? Other drawback is the lack of initiative to develop and pilot EQA exercises. I am concerned on the use of the technology in settings without enough training for very basic procedures and the pre and post analytical errors that were mentioned in this Expert panel discussion


Last, to add on the comment made by Omar Sued. The NTP in Argentina acknowledged the utility of the GXP technology and has been trying, during a year and a half, to get the MOH funds required to implement the GXP in laboratories that concentrate the diagnoses of MDRTB and HIV associated TBf. No results yet. Some countries in LatinAmerica, Argentina and others, cannot obtain the equipment and cartridges at reduced prices because the national regulations do not permit to the MOH to pay to the company before receiving the merchandise.

Lucia Barrera

Somsak Rienthong Replied at 8:59 PM, 21 Jan 2014

Dear all, I'm happy to join this expert panel in Xpert I have some question and hope I can get the answer or some explanation.
1. When the 1st Xpert show invalid or indetermine result and repeat the 2nd sample and still Xpert show indetermine or invalid again, what shall I do for this case?
2. For the protocol of Xpert performance, the sample : buffer = 1 : 2, in this case I found that some technician take out only 2 ml of sputum and add buffer 4 ml and some sample remain in the container. I suggest it should be use all sample, add buffer X times after mixed then pipetted only 2 ml into the cartridge. Do you take only 2 ml or take all sputum sample and then add buffer? Thank. Somsak

YAP BOUM II Replied at 11:20 PM, 21 Jan 2014

I will say they are very rare in our setting (Southwestern Uganda). Most of
the time these sample will turn culture positive and the MPT64 (SD Bioline)
will also agree that they are not MTB but most likely NTM

Julius manjengwa Replied at 1:41 AM, 22 Jan 2014

this is a very informative discussion. there are a lot of things which we had not really looked into in our GeneXpert implementation here in Swaziland .

Peter Saranchuk Panelist Replied at 1:54 AM, 22 Jan 2014

A good question from Gemeda Abebe in Post #77: In countries with wide geographic area and differing MDR-TB prevalence we often see a single diagnostic algorithm. In such cases you can have varying level of RIF mono resistance. How could you make use of the result from geneXpert in predicting MDRT-TB in a country with variable level of RIF mono resistance?

The short answer is that you can’t. Quality-assured culture and drug susceptibility testing (DST) is necessary to accurately determine the different levels of TB drug-resistance that exist in each setting, which should then be reflected in setting-specific algorithms for both diagnosis and treatment. If there are variable levels of RIF mono-resistance (or other types of resistance) within a country, this means that a number of different diagnostic/treatment protocols are needed within that country.

Related points that I would like to make include:
- An Xpert RIF+ result only tells you that drug resistance is present. Culture and DST should ideally be performed in each case in order to determine the true treatment needs of each patient.
- In settings where culture/DST are not currently accessible, steps must be taken to improve this.
- In settings where drug-resistant TB (DR-TB) strains are common, including baseline resistance to fluoroquinolones and some injectables (e.g. Mumbai), Xpert MTB/RIF essentially becomes just a SCREENING test for DR-TB. Culture/DST to both 1st and 2nd line anti-TB drugs are needed to determine the degree of resistance (i.e. mono vs. poly vs. MDR vs. ‘pre-XDR’ vs. XDR or higher) and treatment needs of each patient.

I can’t repeat this enough: Algorithms for diagnosis and treatment of DR-TB need to be SETTING-SPECIFIC!

Lal Mani ADHIKARI Replied at 2:31 AM, 22 Jan 2014

Dear All,

Can I ask what is the actual reason that Xpert MTB/rif gives rifampicin indeterminate result? is this due to low bacillary load in the sputum sample? does much more load is needed for rifampicin susceptibility result than with MTB detected result?

Wendy Stevens Panelist Replied at 3:02 AM, 22 Jan 2014

Reply to: Somsak Rienthong and Lai Mani Adhikari
1. Dear all, I'm happy to join this expert panel in Xpert I have some question and hope I can get the answer or some explanation.
1. When the 1st Xpert show invalid or indetermine result and repeat the 2nd sample and still Xpert show indetermine or invalid again, what shall I do for this case?
An invalid results shows the internal control has failed. If the repeat also is invalid it would seem the specimen has a PCR inhibitor. The best would be to send another specimen for culture as for traditional methods. Indeterminate in the package insert is only reported for the Rif detection, and shows the bacterial load in the specimen is low, but the patient is positive. I would treat as positive and follow up with DST to confirm the resistance susceptibility.
2. For the protocol of Xpert performance, the sample : buffer = 1 : 2, in this case I found that some technician take out only 2 ml of sputum and add buffer 4 ml and some sample remain in the container. I suggest it should be use all sample, add buffer X times after mixed then pipetted only 2 ml into the cartridge. Do you take only 2 ml or take all sputum sample and then add buffer? Thank. Somsak.

You should not take out an aliquot from the primary specimen, the Xpert kit comes with SR buffer up to 8ml, so you can add the whole amount of SR to the specimen and not try to aliquot.

Wendy Stevens Panelist Replied at 3:05 AM, 22 Jan 2014

Response to Lai Mani
Thank you for your reply and accordingly we are not using the Xpert for treatment monitoring response, instead clinicians recommend the test for suspecting of MDR TB. Although these cases are very few in number, it will be helpful to troubleshoot for geneXpert, if the DOT drugs interfere performance of Genexpert.
Response
The Xpert cartridge is designed to filter the liquefied and inactivated specimen first, so the whole bacteria are captured on the membrane and the rest goes to waste. This should ensure any inhibitors in the specimen will not be part of the PCR process and therefore should not inhibit the reaction.

Wendy Stevens Panelist Replied at 3:11 AM, 22 Jan 2014

Response to Lai Mani:

Apologies, I left out the second part of the question:

In Nepal DR TB is increasing and clinicians request frequent testing with GeneXpert after 2 months or 6 month of DOT therapy to exclude MDR TB from Sputum positive cases. So far we have mostly Error 5007 for those samples. we appreciate if you have more information on it.

The 5007 error is a probe check error, which most likely indicates an incorrect reagent volume that is likely due to too little or too viscous a fluid transferred into the cartridge. This error is not linked to any specific patient or treatment, but rather to poor technique. It is interesting that you use the Xpert on smear positive cases only at 2 and 6 months after treatment has already been given: the PCR will most certainly still be positive since smear positivity indicates the bacterial load in the patient sputum is at least 10 000cfu/ml, whereas the Xpert has a minimum detection of 130cfu/ml and will still be positive on whole but inactive (drug affected) bacteria. The only advantage would be to determine Rif susceptibility, which seems more important to perform immediately and not wait for 2 months before providing MDR treatment (my opinion). Reasons for errors can be found in the package insert.

Armand Van Deun Panelist Replied at 3:27 AM, 22 Jan 2014

I would like to remark that there are alternatives to Xpert, if costs are excessive and few cases need to be checked. The gold standard is still DNA sequencing, and this is what we prefer also in our lab in Belgium. Cheaper and more accurate, particularly using primers covering important mutations also outside the RRDR. DNA amplicons can be prepared in all labs in the industrialised world for a small cost; if sequencing can’t be done on site, these amplicons can easily be sent to a service offering sequencing commercially. Hardly any equipment cost involved, and the sequencing cost per sample is low (around 10 Euros in Belgium, but cheaper companies exist for instance in S. Korea).

Several other important drugs could be tested at the same time, not covered by Xpert.

Needs some training of technicians for correct reading though, and more trouble than an Xpert in your lab.

Ernest Ruttoh Replied at 3:32 AM, 22 Jan 2014

Dear Lal Mani, you are right that the bacillary load is low. This is for the reason that the method is amplification which will be be on the few bacilli present and therefore low chances of picking the resistant strains which will be less or missing in few bacilli present in the sample and yet present in the system of the patient.
Thanks

Ernest Ruttoh
Senior Technical Advisor, SPHLS
Management Sciences for Health
ACK Garden House, Nairobi-Kenya
P.O. Box 8700-00100
+254 - 722833768(mobile)
Email :
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Dr. Daniela Cirillo, MD, PhD Replied at 4:11 AM, 22 Jan 2014

I fully agree with Armand, the cost for sequencing is now very affordable and fast (considering the personnel time is in the range of 15-20E considering forward and reverse. For some SNPs/genes data on correlation to the response to therapy are still weak or missing. For pyrazinamide resistance, sequencing may become in the future the cheapest option

Shubhada Shenai Replied at 4:11 AM, 22 Jan 2014

Reply to Lal Mani Adhikari :
RIF Indeterminate due to low bacillary load
A sample is considered RIF indeterminate when the last probe returns a CT of >38 and the first probe has a CT value of >34.5 cycles because the assay terminates at cycle 38, and a ΔCT Max of >3.5 cannot be measured.

Minimum detection load of 130 CFU was reported with old version of cartridges (G2-G3). WHO report on performance of Xpert MTB/RIF version G4 assay reported detection load of 300 copies/run for wild type and mutant MTB strains except 533 ccg (500 copies/run)

http://www.stoptb.org/wg/gli/assets/documents/map/findg4cartridge.pdf

Fulgence Nzabintwali Replied at 9:19 AM, 22 Jan 2014

Yes

That is why you need to have other system for identification from culture positive , MPT64 negative ( = MOTT), e.g. using PNB or other methods, if you use solid media like LJ rapid growth, colony color, or AFB from culture (cord factor ) can help .






Le 22 janv. 2014 à 05:30, YAP BOUM II via GHDonline <> a écrit :

Christopher Gilpin, PhD, MPH Panelist Replied at 10:39 AM, 22 Jan 2014

The Global Laboratory Initiative currently recommends the following minimum requirements for quality assurance of the Xpert MTB/RIF assay
1. Instrument verification
Each module in the GeneXpert instrument should be evaluated as being “fit for purpose” through verification with known positive or negative material prior to commencing routine testing of clinical specimens. A single verification test should performed per module upon instrument installation and following calibration of instrument modules.
Verification panels are now routinely distributed by Cepheid with each new instrument and with recalibrated modules. The format of the verification panels is a card containing 5 Dried Culture Spots (DCS) of a known concentration of whole inactivated Mycobacterium tuberculosis (Rifampicin sensitive) bacilli.
2. Performance indicator monitoring
The GLI recommends that each instrument be monitored using the following minimum set of indicators to evaluate proper use.
o Number of tests performed per month per module
o Number and proportion of MTB positive results
o Number and proportion of MTB positive rifampicin resistant results
o Number and proportion of errors (disaggregated by type of error)
o Number and proportion of indeterminate results
o Number and proportion of invalid results

3. Internal quality control
3.1 Each cartridge includes a sample processing control (SPC) which contains non-infectious spores in the form of a dry spore cake that is included in each cartridge to verify adequate processing of MTB.
o Verifies that lysis of MTB has occurred if the organisms are present
o Verifies the specimen processing is adequate.
o Detects specimen associated inhibition of the real-time PCR assay.
o SPC should be positive in a negative sample and
o SPC can be negative or positive in a positive sample.

3.2 The Probe Check Control is a check undertaken before the start of the PCR reaction. The system measures the fluorescence signal from the probes to monitor bead rehydration, reaction-tube filling, probe integrity and dye stability.

Note : There is currently no consensus on the need nor the requirements for performing any additional periodic blinded testing using quality assurance panels.

Martin Colla Panelist Replied at 11:24 AM, 22 Jan 2014

Re: Chris Gilpin's post

1. Instrument verification
We will begin shipping to the Dried Culture Spot verification panel in the very near future. Some systems will be shipped during January with the current liquid panel. This is not an error, we are using up the remaining stock. Please do not be surprised should you receive this version of the verification panel.

2. Performance indicator monitoring
This should be simpler in the future. Cepheid is currently piloting 'Remote Xpert', cloud-based software designed to transmit data from sites using GeneXpert across the internet to a central server enabling the NTP to monitor the set of parameters Chris describes and more.

Indrajit Kumar Replied at 12:26 PM, 22 Jan 2014

Respected sir,
I am a lab technician in med. College hospital . Simply I want know that
1 - This machine is for Sputum based diagnosis only.
2- What is the role of SPC.
3- What is meaning of error2008& why its happen B4 block only in my machine.

Regards
Indrajit Kumar
Lab Technician.
CB NAAT LAB
JLNMCH BHAGALPUR
BIHAR INDIA.

Yamile Sandoval Replied at 1:38 PM, 22 Jan 2014

Hi Indrajit,

Answering your questions

1) The intended use of Xpert MTB/RIF test is direct sputum samples and BAL (Broncho alveolar lavages), only this 2 kind of samples are validated by cepheid.. You can find some publications related to extrapulmonar samples (in attachments) where the researchers describe good results...here in Panamá (PTY) I know some customers that have excelent results and corelation between extrapulmonar samples as: lymphnodes, hepatic biopsys, bone marrow, pleural liquid and CSF, beacuse they develop their own validation protocol based using the info of these papers.

2) The SPC or Sample addecuacy control is an internal QC wich is in all Xpert test´s. This control ensures that everything it´s ok inside the cartridge, and all the PCR steps where well done.

3) The error 2008 is related to an increase presure in the syringe or the cartridge...This is commonly associated to a pre analytical error, the most common: presence of mucus in the final sample (after you add the buffer)...The most important thing here is shake it very well (20 times or 20 seconds if you have a vortex, 2 times between each incubation) I attach a flyer where you can see it.
The other reason is that the module has a faillure... So 2 things I recomended you: Call you local cepheid distributor or send an e mail to , they can help you with all your enquires.

If you need something else feel free to contact me

Best regards,

Yamile Sandoval M.D.

Attached resources:

Armand Van Deun Panelist Replied at 2:36 PM, 22 Jan 2014

Dear Lucia,



Regarding accuracy of Xpert, not sure whether I understand your estimates correctly:

- False resistance due to technical causes, i.e. these silent mutations in rpoB: 1% is even more than what we actually found among 1000 or so rpoB mutations by sequencing; however, few of those were from new cases, and among new these might theoretically be relatively more frequent (not resistant, not yet eliminated by treatment); on the other hand silent is often mixed with wildtype DNA and for that reason not “seen” by Xpert (or LPA), also because they occur in unusual codons where Xpert would only see the mutation at 100%. Difficult to tell for new cases without doing large studies, but we start to have some info:

o so far we haven’t encountered any in a Pakistan DRS with parallel phenotypic DST and Xpert for all, mostly new cases, which is re-assuring. Overall I would think that pre- and post-analytical errors are going to be far more frequent

o rpoB sequencing over 1000 new cases from Bangladesh by way of DRS showed only 13 resistance mutations; interestingly, more than half of those were among the “disputed”, and again standard treatment outcomes bad; interestingly sequencing found 2 silent mutations in the RRDR; both were susceptible for Xpert MTB/RIF as well as MTBDRsl vs. 2

- Xpert does miss some resistance, as do all tests, and probably on average least. WHO algorithms do not recommend testing further by conventional DST if Xpert shows sensitive. Personally I would make an exception for groups with very high prevalence, such as retreatment failures and relapses.

Relapse is always difficult to diagnose if not smear-positive and patient not clinically ill with signs of TB re-activation. Dead DNA might still be found the first months after cure, though I guess exceptionally. The cycle threshold of the Xpert probes would then be very high, indicating an extremely low bacillary load. I think treatment could be postponed then with repeat check-up, or wait for culture, or send for bronchoscopy.



Chris explained to me that the culture part of the high-volume CSF was left out on purpose, to keep it simple. But supposed to be done on part of the sediment I imagine, before adding Xpert reagent.



My understanding from visits to countries is that the excesses of cartridges are due to unexpectedly slow rolling out of the method, and also too low uptake by clinicians. There is in many countries a fundamental problem of donor-driven deliverables that have to be satisfied to get more funds; one of them is perfect treatment results, so better not to see failures, late conversion etc.. This mentality has to change before technology will be truly useful to control MDR.

As for TB diagnosis: clinicians know Xpert is not fully sensitive, so they will still do X-Ray etc.. as they are used to. Why bother then to request Xpert?



I think Argentina also could go for DNA sequencing in- or outside the country and not invest in a network of Xpert. Besides, next year something newer and better may pop up again…



Hope all is well,

DIMITRIOS PAPAVENTSIS Replied at 3:06 PM, 22 Jan 2014

Thank you very much Chris,

This is really very helpful, esp. performance indicators. We will endorse
them in our quality management system.
Στις 22 Ιαν 2014 5:48 μμ, ο χρήστης "Christopher Gilpin, PhD, MPH via
GHDonline" <> έγραψε:

Omar Sued Replied at 3:59 PM, 22 Jan 2014

Thank you very much! I would ask about the comment from Shenail. "WHO report on performance of Xpert MTB/RIF version G4 assay reported detection load of 300 copies/run for wild type and mutant MTB strains except 533 ccg (500 copies/run)"

If this is true, is some way in which I can use Xpert to quantify TB bacillary load for research pourpuses (diluted sputum until negativize, etc?)

Thanks

Steve Schuyler Replied at 5:45 PM, 22 Jan 2014

67 Wendy Stevens,

Leasing is cheaper than buying but read the agreement carefully. It is different than most common reagent rental agreements.

Lucia Barrera Replied at 6:53 PM, 22 Jan 2014

Dear Armand
Thank you very much for the the information and opinion that you are sharing with us.
Best regards

Kathleen England Replied at 7:43 PM, 22 Jan 2014

Dear All,

This is one of the best resource sharing discussions. There have been so many questions answered during this session on various topics regard GX MTB/RIF. Can anyone share on newer rapid molecular technologies coming available in the next few years that may offer further impact for DRTB? There are several new prototype devices or devices in trials? Any information on progress and success at tackling other relevant resistant markers for other relevant TB drugs?

Kathleen England, PhD

Mahfuza Rifat Replied at 12:30 AM, 23 Jan 2014

Very informative discussion. Thank you Armand for the clarifications.

Peter Saranchuk Panelist Replied at 12:31 AM, 23 Jan 2014

Hi, Kathleen.

MSF recently looked at the current ‘TB diagnostic pipeline’ and summarized how well it is expected to respond to unmet needs in the attached document ‘Beyond the Microscope’. Please see page 10 for some thoughts related to your questions.

To quote: “While the pipeline continues to grow and some nucleic acid amplification technology (NAAT)-based products are promising, none are expected to have the necessary evidence base for endorsement in the next two to three years. Xpert MTB/RIF and available LPAs will therefore remain the leading rapid molecular assay tests for the near future.”

This document also contains on pages 3-7 ‘lessons learnt’ related to Xpert MTB/RIF and challenges that lie ahead...

Hope it is useful.

Attached resource:

Elizabeth Shipiki Replied at 12:59 AM, 23 Jan 2014

Thank you all for your positive contribution, this is very crucial indeed.

Elizabeth – Namibia.

Kind Regards,


Elizabeth Shipiki | Chief Medical Technologist | Windhoek TB

Namibia Institute of Pathology (NIP)

OOIEVAAR ST.WINDHOEK NORTH

P O Box 277 | Windhoek | Namibia

t +264 61 295 4015 | f +264 61 233 285 | m +264 81 149 5678

<mailto:> | www.nip.com.na

Alaine Umubyeyi Nyaruhirira Replied at 1:53 AM, 23 Jan 2014

Dear Peter

Can you resend the MSF resource (MSF-Beyond the Microscope), I can’t access to.
Or use my personal address : <mailto:>

Alaine Umubyeyi Nyaruhirira Replied at 2:46 AM, 23 Jan 2014

Dear Chris and Martin

Thx for the feedback on ''quality assurance program system ''in place for GeneXpert.

Really clear and helpful for Lab participants to this discussion forum.
I also support the initiative for distribute to sites Dried Culture Spot for instrument verification but also users / lab technician quality monitoring as you can detect deficiency from human or user due to power training or not all trained personnel.

Stéphanie Bjerrum Replied at 3:58 AM, 23 Jan 2014

Dear all,
My question is in regards to performance of GeneXpert on stored sputum-sediments: I’m working on a research project in Ghana diagnosing MTBC among HIV infected individuals. For a period I didn’t have access to GeneXpert cartridges and therefore stored the sputum sediments at -20 0C for 1 to 8 weeks. I now intend running the assay on the thawn sediments. How do you think this will affect the performance of the GeneXpert? The sediment was re-suspended in phosphate buffer before storage and I do not intend to process it further before running the assay. I will be happy for any comments you might have.
Stephanie Bjerrum, MD and PhD-student

Attached resource:

Olivier Marcy Replied at 4:42 AM, 23 Jan 2014

Dear all,

Many thanks for this initiative. It's great to read and follow these exchanges!
Looking forward to the answer to Stéphanie Bjerrum' s question. We an have identical situation in one of our lab partners in Burkina Faso.
Sample processing is not always optimal. In case samples have been kept in a refrigerator (+4°C) rather than frozen, how long could they still be tested with Xpert with reliable sensitivity?
Thank you in advance,

Olivier Marcy, MD, MPH, Epidemiology Unit, Institut Pasteur, Cambodia

Martin Colla Panelist Replied at 5:08 AM, 23 Jan 2014

In reply to Alaine,

Agreed. Monitoring of GeneXpert instrument / cartridge performance should be complemented with monitoring of the complete testing process. The DCS EQA programme in South Africa is an excellent initiative in this regard, one which other NTPs will no doubt be interested by.

Relating to this, my question would be 'When monitoring detects issues, who should be responsible for corrective action?'

Ideally, we (Cepheid HBDC) would encourage NTPs to develop a core of 'super-users' at the regional and central level to provide first-line support, to answer basic technical and hardware questions in local languages and ensure levels of competence are maintained. This would be more efficient operationally than relying solely on the supplier who, try as hard as we are able, cannot match the rapidity and programme-specific feedback provided by an internal support network.

This forum has been a good demonstration of how this can be done. I have been surprised how little I have had to contribute so far, because most of the technical questions relating to GeneXpert and Xpert MTB/RIF have been comprehensively and accurately answered by other participants (notably the head of the RSA programme) before I have finished reading the question!

Importantly, establishing internal resources of this kind will help Cepheid keep costs down for everybody.

Martin Colla Panelist Replied at 5:17 AM, 23 Jan 2014

Olivier,

From the Xpert MTB/RIF package insert:

8.2 Storage and Transport
Sputum sediment: Store resuspended sediments at 2 to 8 °C for up to 7 days.
Raw sputum: Transport and store specimens at 2 to 8 °C before processing whenever possible. If necessary, sputum specimens
can be stored at a maximum of 35 °C for up to 3 days and then at 2 to 8 °C for an additional 7 days.

Within these limits, there should be no adverse effect upon the test performance.

Eric Aborgah Replied at 8:01 AM, 23 Jan 2014

A very unique opportunity to draw upon the knowledge and experiences of each other.
Eric Aborgah, Ghana

Jean de Dieu IRAGENA Replied at 8:10 AM, 23 Jan 2014

Dear all,

With regard to the pipeline of commercial TB test, I take the opportunity to share with all of you the 2013 UNITAID semi-annual update on TB diagnostic technology and market landscape (see p. 6). From WHO web site, you can also have access to the "Factsheet on TB diagnostics" that summarises the "WHO diagnostic tools" :
1. recommended FOR USE
2. NOT recommended due to current insufficient evidence
3. recommended NOT TO USE

Attached resources:

Norah Vere Replied at 8:36 AM, 23 Jan 2014

We have heard a number of Module failures with our gene Expert machines and the faulty modules had to be replaced. I am not sure how we can prevent this happening in future. Are there probable causes why you end up with one module out of 4 malfunctioning. Any preventive action?

Eric Aborgah Replied at 8:54 AM, 23 Jan 2014

In some laboratories, re-suspended sputum sediments are stored beyond the recommended 7 days and at -20^C. Raw sputa are sometimes transported and stored at -20^ against the recommended temperature of 2-8^C. Thus conditions for longer storage times have been adhered to. Will these conditions affect the result in any way if these samples are processed for Xpert MTB/Rif test?
Eric Aborgah,
NPHRL, KBTH

Martin Colla Panelist Replied at 8:59 AM, 23 Jan 2014

Norah,

It should not be forgotten that the GeneXpert is a piece of sophisticated laboratory instrumentation which is being deployed in what are often quite harsh environments. By and large, the instrument and cartridges have proven to be very robust. Some failures are to be expected and for this reason, the system carries two years of warranty and extended warranty cover is available. Having said this, steps have been taken to improve the temperature tolerance of the systems with the bigger fans and filters on the current generation of instruments and we are currently taking a very close look at modules which have failed in India where the environment is particularly dusty and the power-supply exceptionally unstable. Once we have fully understood the root causes we will establish what measures can be taken to prevent this.

There are preventive-maintenance steps everyone can take to ensure that your system up-time is maximised . Guidance from our Cepheid HBDC training group is attached.

Attached resource:

Mulualem Agonafir Replied at 9:28 AM, 23 Jan 2014

Is there a way that Cepheid could provide the UPS with the system? I am saying this because aftrer the machines are bought facilities are expected to purchase the UPS. For many reasons, this may not happen and let us lose many cartridges (for nothing) in places where there is intermittent electricity.

Mulualem

Colleen Daniels Replied at 9:29 AM, 23 Jan 2014

Hi all,
These discussions have been incredible informative. I also wanted to bring
your attention to an open letter sent by the global TB Community Advisory
Board (CAB) and Treatment Action Group to Cepheid regarding pricing of
Xpert Mtb/Rif cartridges and machines and ask you all to be aware of
differential prices even though in most high burden countries you should be
able to access the buy down price of $9.98. You can read the letter at:
http://www.tbonline.info/media/uploads/documents/tb_cab_open_letter_to_cephei...

Please do let us know if you see extortionate pricing. To see if your
country can access the buy down price please see:
http://www.finddiagnostics.org/about/what_we_do/successes/find-negotiated-pri...

*The Global TB Community Advisory Board (TB CAB) and the Treatment Action
Group <http://www.treatmentactiongroup.org/@@ (TAG) sent an open letter
@@http://www.tbonline.info/media/uploads/documents/tb_cab_open_letter_to_cepheid_pricing_06january2014.pdf@@
to Cepheid raising the following concerns:*

1) high Xpert MTB/RIF cartridge and GeneXpert instrument concessional
pricing;

2) costs associated with warranty;

3) high pricing in the public sector in Russia; and

4) the costs of the GeneXpert modules and cartridges, lack of registration
of the Xpert MTB/RIF cartridges, and greater efforts to broaden access to
Xpert MTB/RIF particularly in all CDC, TB Control and Prevention Centers
and infectious diseases hospitals in China.

*The letter requests that Cepheid:*

*1. further decrease the price of Xpert MTB/RIF cartridges (below US $9.98
per cartridge) given the large volume already purchased and increased
procurement projections for 2014 and beyond, particularly in light of the
new WHO policy update*

*“More than a year after the initial but insufficient price reduction, and
with sales increasing exponentially, we urge you to decrease the price of
cartridges below US $9.98 based on volume-related thresholds.”*

*2. decrease the price of GeneXpert instruments from US $17,000-17,500 for
high burden countries*

*“As instrument sales have similarly risen, with over 1,800 instruments
purchased under concessional pricing, we urge you to lower the price of
GeneXpert instruments as well. Following up on previous communication in
April 2012 @@http://tbonline.info/posts/2012/4/16/tb-cab-open-letter/>, we
remain disappointed that the price of GeneXpert instruments has not been
reduced as requested from the high price of US $17,000 and $17,500.”*

*3. provide extended warranties free of charge due to the impact the
company’s proposed price increases will have on national TB and HIV
programs*

*“We find it unacceptable that Cepheid should profit from extended
warranties in high burden countries due to high module failure rates and
for a technology partly developed by public funds. Cepheid must remove any
additional warranty costs.”*

*4. clarify the differential pricing for Xpert MTB/RIF cartridges in Russia
and outline the company’s plans to rectify the situation to ensure that the
Russian public sector can access the negotiated buy-down price of US $9.98
per cartridge*

*“We are concerned that machines and cartridges purchased for public
institutions, but outside of the existing public procurement mechanism, are
now subject to extortionate prices. We call on you to ensure that all
public institutions go through the public procurement mechanism to ensure
access to the negotiated buy-down price.”*

*5. clarify the differential pricing for GeneXpert modules and Xpert
MTB/RIF cartridges in China*

*“China is one of the countries eligible for concessional pricing for
GeneXpert modules (US $17,000-17,500 per module) and cartridges (US $9.98
per cartridge). In China GeneXpert IV costs RMB1,100,000 (US $180,623.97),
GeneXpert II costs RMB700,000 (US $114,942.53) and the cartridges are being
sold for RMB300 (US $49.26). We would like to know why the modules are at
such exorbitantly high costs and why cartridges are almost five times the
concessional price?”*


*6. provide details on company's plans to register Xpert MTB/RIF cartridges
in China*

*“The GeneXpert I, GeneXpert IV and GeneXpert XVI were all registered in
2011 at the Chinese Food and Drug Administration but to date the Xpert
MTB/RIF cartridges have not been registered. We would like to know your
projected timeframe and plans for registration of the cartridges in China?”*

GeneXpert MTB/RIF has contributed to advances in the diagnosis of
tuberculosis (TB) and drug-resistant TB around the world. The use of Xpert
MTB/RIF is critical as a diagnostic tool in the fight against TB. In
various settings GeneXpert MTB/RIF has contributed to an increase in
multidrug-resistant tuberculosis (MDR‐TB) diagnosis, increasing the chance
of appropriately treating and curing more people.

Mulualem Agonafir Replied at 9:45 AM, 23 Jan 2014

We encountered a pateint who completed a full course TB treatment and got sick after some time. He was put on retreatment regimen. Four months after completion of the retreatment regimen, he got sick again. He gave a sputum and was checked by Xpert MTB/RIF test. The result was MTB detected/Susceptible to RIF. Any suggestions what to do next?

Martin Colla Panelist Replied at 10:10 AM, 23 Jan 2014

Mulualem,

Cepheid can supply a UPS system. However, they contain high-capacity batteries which are heavy so the shipping costs are relatively high. In addition, for repair, these units need to be returned to the supplier in Germany which is both costly in shipping and time-consuming.

Generally, it is a better solution if the UPS can be sourced locally (usually at a lower cost), thereby avoiding the shipping costs and enabling more rapid and convenient servicing. Cepheid is looking at suppliers with a broad presence in low- and middle- income countries with a view to avoiding shipping from France. Our training team who you know well, have evaluated a number of UPS providers in various countries and may be able to provide you with more guidance.

At the recent Paris meeting, delegates from Uganda mentioned that the use of inverters and batteries enabled them to sustain the power supply to the GeneXpert longer than with a UPS. Perhaps they can share their experiences with you.

Wendy Stevens Panelist Replied at 10:27 AM, 23 Jan 2014

Response to: Mulualem Agonafir number 117.

Can Cepheid supply the UPS with the system?

In South Africa:
A UPS with the right certifications is essential for all instrumentation. In South Africa this was supplied by Cepheid as per other suppliers. The model bought however was not adequate and only has a one year warranty, after which we had to replace them. We have to negotiate a better UPS going forward and are beginning to place them as they reach the end of their warranty which appears ridiculously short anyway for this type of instrument.

Fuad Mirzayev Replied at 10:31 AM, 23 Jan 2014

An interesting experience from Uganda using solar panels to power GeneXpert unit that was shared in one of the previous GHD expert panels
http://www.ghdonline.org/uploads/Uganda-GX-solar_for-website_190420111-SOLAR_...

CLEMENT ADESIGBIN Replied at 10:55 AM, 23 Jan 2014

Reply to Mulualem Agonafir question:
This is totally a clinical case. I do not think it
Is a challenge with any of the diagnostic tools.
The patient, I feel, you need to fully evaluate.
Could it be there is/are some systemic immuno-
Suppressive ailments? Could it be a case of re-
Infection? His close relatives possibly need to be
Evaluated?
Unfortuntely we do not know the age of the patient in
Question. From the history submitted as well nothing
Was suggestive of failure of the drugs. He gets well
Everytime he is treated.
Thanks

Wendy Stevens Panelist Replied at 10:56 AM, 23 Jan 2014

Answer to: Malulem Agonafir: 119

We encountered a pateint who completed a full course TB treatment and got sick after some time. He was put on retreatment regimen. Four months after completion of the retreatment regimen, he got sick again. He gave a sputum and was checked by Xpert MTB/RIF test. The result was MTB detected/Susceptible to RIF. Any suggestions what to do next?

Answer: This is an extremely difficult case and requires an extensive clinical work-up. My first instinct is to assess adherence as this may well be the cause. I would also ensure if HIV positive the patient is put on ART and high risk diseases for TB such as diabetes iare excluded. If you have Xray capabilities there are some patients we see that still have horrible cavitatory spaces left in lung following treatment that continue to give problems and where drastic steps such as survey can be done. I am surprised the patient is Rif negative and to be on the safe side a culture and LPA may be useful. Also check there has been no mis-identifaction.
Tracing contacts in his family and immediate environment may be useful.

Wendy Stevens Panelist Replied at 11:03 AM, 23 Jan 2014

Reply to
Norah Vere
We have heard a number of Module failures with our gene Expert machines and the faulty modules had to be replaced. I am not sure how we can prevent this happening in future. Are there probable causes why you end up with one module out of 4 malfunctioning. Any preventive action?

Our overall module failure in South Africa is 8% which we feel is to high. We will hopefully be able to work with Cepheid to iron out issues and as you see above they have been different approaches in the pipeline. We have a manuscript in preparation which discusses time to failure, no of failures per instrument etc. This document will aid sites as well as provide a body of evidence for troubleshooting. Interestingly, failures appears, in our setting to occur earlier rather than later. I will post once it is published.

Wendy Stevens Panelist Replied at 11:08 AM, 23 Jan 2014

In response to Marin Colla's comments about EQA.

We currently are producing the verification and EQA material and piloting a fabulous remote connectivity system monitoring instrument performance continually.

If you would like further assistance please contact my staff at`; ,

Jean de Dieu IRAGENA Replied at 11:14 AM, 23 Jan 2014

Dear all,
Please let me comment on UPS supply: I agree with Martin Colla that the best solution could be that UPS is provided locally. when countries choose this option, the issue is that unappropriate UPS devices (from local market) without adequate specifications to allow the GeneXpert instrument to function are used instead and I would be cautious in recommending this solution without knowing country capacity to get this locally even if it is the best solution to lower the shipping cost.
One should identify a local or regional provider of the UPS in low, middle-income countries is in my view as the best solution for sustainability and really time technical support to labs in the regions that may experience problems with UPS. Indeed the experience of Uganda using solar source devices (Thanks Fuad for sharing) is a great solution, but again the local/regional hub needs to be identified to allow countries in the regions (especially in Africa) to rely on that

Wendy Stevens Panelist Replied at 11:15 AM, 23 Jan 2014

Stephanie Bjerrum:

Answer:

Dear Stephanie,

Martin Colla above has provided temperatures for transport requirements and other short -term storage requirements for raw sputum
We have stored NALC/NAOH treated pellets which we store at -70 C and have not had difficulties producing the same results and use these samples for evaluation of Xpert and other TB testing candidates. We don't however have data at 20C.

Mulualem Agonafir Replied at 11:24 AM, 23 Jan 2014

Reply to Clement Adesigbin:
The patient is 60 yrs old male and seronegative to HIV. No member of his family had recent history of TB.

Martin Colla Panelist Replied at 11:36 AM, 23 Jan 2014

Reply to Colleen Daniels:

Cepheid will respond in the very near future to your open letter.

Re: ... "ask you all to be aware of differential prices even though in most high burden countries you should be able to access the buy down price of $9.98."

Whatever local pricing arrangements may have evolved in a small number of countries, the $9.98 (ex-works, advance payment) cartridge price is available to not most but all of the 145 High Burden Developing Countries without exception when procured directly from Cepheid HBDC.

Yamile Sandoval Replied at 11:46 AM, 23 Jan 2014

Hi Malulem Agonafir: Permalink 119

And what about other comorbidities such as Diabetes? this patients are very vulnerable to reinfection (In attachments: Association of diabetes and tuberculosis: impact on treatment and post-treatment outcomes Jimenez Corona et. al)... Other thing, what about the other antituberculous drugs, did you perform DST? He is Rif sensitive, but what about susceptibility to the others
I´m agree with Wendy Stevens about assess adherence...this may well be the cause (Here in Panamá is very common...they started feeling great so they quit the treatment)

Attached resource:

Wendy Stevens Panelist Replied at 11:48 AM, 23 Jan 2014

Response to Kathleen England number 102
Can anyone share on newer rapid molecular technologies coming available in the next few years that may offer further impact for DRTB? There are several new prototype devices or devices in trials? Any information on progress and success at tackling other relevant resistant markers for other relevant TB drugs?

Dear Kathleen, There are numerous technologies in the pipeline, both laboratory and non-laboratory based, high and/or low volume, with and without Resistance detection. At current time the Xpert is still first in class although fast followers are on their way. An updated TB diagnostic pipeline document produced by UNITAID in 2013 would provide you with more insight. It is on the UNIAID website.

Martin Colla Panelist Replied at 11:49 AM, 23 Jan 2014

Reply to Omar Sued #99,

For further information regarding the use of Xpert MTB/RIF for quantitation, my colleague Martin Jones has recommended the following article as a good starting point.

A Multisite Assessment of the Quantitative Capabilities of the Xpert MTB/RIF Assay
Blakemore et al: Am J Respir Crit Care Med. 2011 Nov 1;184(9):1076-84. doi: 10.1164/rccm.201103-0536OC.

Martin Colla Panelist Replied at 11:54 AM, 23 Jan 2014

Reply to Yamile (#96)

Cepheid is obliged to be very precise with regulatory matter so can I make a small correction? While there are a number of publications citing its use, Cepheid has not itself validated the assay for use with BAL.

Md. Shamim Hossain Replied at 12:02 PM, 23 Jan 2014

Module failure!! it's really a problem. We (NTRL, Bangladesh) have 2 xpert
machines containing 16 modules. Initial one was working with 15 modules
from the time of installation. This machine has been calibrated recently
and at that time another module was failure also. Finally it is working
with 14 modules.
The later one has been installed a few months ago which is also working
with only 15 modules. Besides the module number in the PC is not
correlating with the number in the machine during starting a test of this
machine.
Why these types of module problems are happening?

Yamile Sandoval Replied at 12:03 PM, 23 Jan 2014

Hi Martin (#134) Indrajit (#95),

Thank you for the correction, there are only 2 approved samples: sputum samples or concentrated sediments prepared from induced or expectorated sputa

Steve Schuyler Replied at 12:10 PM, 23 Jan 2014

Mulualem- How long was the patient on therapy for? What did the therapy consist of? Did he undergo DOT? We have had pts who do not properly absorb the medication.

Mulualem Agonafir Replied at 12:15 PM, 23 Jan 2014

Reply to Martin:
Thank you. I do agree to what you and Iragena said. However, I do believe that it would be nice if Cepheid negotiate with its local/regional distributors to identify good quality UPS providers and also look for better options like the ones indicated by Fuad. For instance, the UPSs found in our country are useless as mentioned by Wendy.

Wendy Stevens Panelist Replied at 12:22 PM, 23 Jan 2014

Response to Lucia Barrera,

Apologies I though my answer had bee posted yesterday-there may be some overlap with discussions above. However here goes?

Question:Regarding the considerations on the interpretation of discordant results and the article that Armand kindly provided to us. This article comment that the original publication introducing GXP presented 9 discordant phenotipically susceptible strains. Among them , 8 had clinical relevant mutations. So the proportion of true vs false GXP resistance among discordant results might be 8:1? This proportion is consistent with 
‾ 10-13% of “disputed” resistance found in Bangladesh-Kinshasa among isolates with rpoB mutations which was interpreted to be true resistance
‾ 1% of silent mutations estimated to occur among all mutations present in the rpoB gene
What about mutations that are out of the region investigated by the GXP?
Answer:
There may be value in performing full genome sequencing to detect these mutations, and others, and I believe there is an application and need for the new generation sequencing technology, which improves affordability in the near future.
Question:
About the recommendation on the use of GXP to diagnose TB among suspects with history of TB treatment. Is there knowledge on the persistence of a positive GXP results after cure?
Answer
In our experience in South Africa, where Xpert is not being used for monitoring, it is difficult to answer, however we do see on the laboratory information system some patients receiving several Xpert tests over time, but it is hard to link this to clinical information treatment and outcome. I am sure our clinical partners would have more experience in answering this.
Question:
On the recent SOP developed to test extrapulmonary specimens by GXP. When more than 5 ml of CSF is available, culturing part of the specimen should be also recommended.
This is a valuable specimen and also one of the most prevalent among EPTB specimens (30% in SA setting), however the diagnosis of TB or not in CSF is critical to be performed with rapid turnaround time to have clinical impact, and implementing a change in laboratory specimen processing (such as first take out 1ml minimum specimen and transfer to a second container to perform SR inactivation and follow up with culture on the residual) may not be easy to manage, especially in a large program and if Xpert testing is being performed outside of a laboratory environment. In our experience, majority of CSF specimens are <2ml, so the number of those with residual volume after Xpert testing would be few. In summary, we believe that the first specimen should be tested with Xpert and not as we have done to date on residual samples. The WHO guidelines will assist in getting this testing implemented
Question
In relation to implementation challenges, I found in Latin America many of the challenges that were already mentioned by the participants. I would like consider the weak capacity to design algorithms considering the available resources and to calculate the cartridges accordingly s. This ended up with h shortage and overstock of supplies in some countries . A tool to calculate the supplies might be useful. Is there any? Other drawback is the lack of initiative to develop and pilot EQA exercises. I am concerned on the use of the technology in settings without enough training for very basic procedures and the pre and post analytical errors that were mentioned in this Expert panel discussion.

These are valuable points, and quality monitoring of testing is critical to ensure good clinical laboratory practice. There are however initiatives to assist with EQA: 1) The University of the Witwatersrand and the National Health Laboratory Service in Johannesburg in South Africa have developed an EQA program specific to Xpert MTB/RIF using dried culture spots (DCS)(1). The DCS consists of inactivated M.tb that is quantified and spotted onto filter cards which are easily transported with the instruments and/or by local mail to Xpert testing sites. The spots are then tested like clinical specimens with the Xpert assay and are used to initially verify the GeneXpert instrumentation is fit for purpose. The CSV (comma separated file) from the GeneXpert instrument can then be uploaded to a website (www.tbgxmonitor.com) to automatically generate a verification report. This DCS material has also been developed into an EQA program which the NHLS and others like ACTG (AIDS Clinical Trials Group) run three times/year, with similar report management through tbgxmonitor. To date this program has been extended to 17 countries and recently the WHO (GLI) has requested the DCS replace their initial artificial sputum panel for use in verification and calibration for new sites. Cepheid has also agreed to assist by offering to distribute the verification DCS together with newly purchased instruments and calibration kits. In addition PATH (Program for Appropriate Technology in Health) is collaborating with the University and NHLS to commercialize the DCS program to ensure sustainability and manufacture scale up. Other EQA materials have also been developed by Vircell, MMQCI and the CDC (to support their research sites). (2) Apart from verification and EQA, it is more critical to ensure on-going quality monitoring and a remote monitoring solution is being developed by Cepheid (collaboration and alpha/beta testing with the NHLS in South Africa). This web-based application is loaded on each Gx instrument and users (site and program) can monitor the performance of the instrument remotely.

There are costing spreadsheets and models that have been developed in several countries, including South Africa that could be shared. It is essential to match number of presumed infected with size of analysers and likely throughput. This assist in forecasting which if done well should alleviate issues such as stockouts or too much stock.

Martin Colla Panelist Replied at 12:32 PM, 23 Jan 2014

Reply to Dr Shamim,

GeneXpert systems are trans-shipped from the US where they are manufactured to Europe and then on to your country. Occasionally we do see modules that are 'dead on arrival'. In your case, because there are sixteen modules, the probability of such an incident is unfortunately increased four-fold when compared to the GeneXpert IV.

The local Approved Service Provider will be able to replace the module as soon as we can get one to you. As the number of modules increases in a country, Cepheid will place a buffer stock of modules locally. We are also reviewing the siting of our service centres to shorten the supply line and ensure more rapid exchange of modules and system repairs.

Being a modular system, a GeneXpert module breakdown does not result in a total shutdown of the system. The situation you find yourself in is clearly not satisfactory and I would not seek to minimise it but patients can still be tested which might not be the case with a less modular system.

Andrew Black Replied at 1:14 PM, 23 Jan 2014

With the case mentioned I would consider 1) The patient, do they have risk factors for re infection (previous TB is in itself a risk factor, but HIV, diabetes, malignancy etc should all be looked for and excluded). Is there a source for re infection? Would do a thorough contact tracing to rule out a infective source. Compliance is always an issue where patients stop or take irregular treatment when they feel better and deteriorate as the mycobacterial load increases over time. A physical reason for persistent infection should be excluded e.g. a destroyed lung or cavitation which may result in suboptimal drug levels reaching the mycobacteria, in these cases surgery is an option if prolonged therapy doesn't clear the infection.
2) The drugs, if compliant are the doses correct for the patient's weight, are FDC's being used and is the manufacturer reliable. Is there malabsorption, chronic diarrhoea or other drugs that may decrease TB drug levels? 3) The bug, would repeat Xpert and do culture with DS/LPA to confirm a Rif sensitive strain and exclude INH mono resistance as well as exclude specimen mix ups.
In a fully sensitive mycobacteria would treat with R/H/Z/E as an aminoglycoside has poor lung penetration and decreased activity in acid environments such as cavities and doesn't add much other than side effects and increased patient reluctance to take therapy. INH mono resistance would require a prolonged course 9-12/12 R/Z/E, if available moxifloxacin could be used as an INH substitute. Z resistance would require a duration longer than the standard 6/12.
Hope this helps

Andrew Black Replied at 2:17 PM, 23 Jan 2014

With regards to a SOP for extrapulmonary specimens, what is the standpoint of advising the use of Xpert on specimens for clinical decisions rather than research where there is no regulatory approval? Should clinical laboratories be processing specimens with tests not approved for the specimen? Given the body of research that exists in this regard would it not be more appropriate to get regulatory approval prior to developing guidelines?

Armand Van Deun Panelist Replied at 3:01 PM, 23 Jan 2014

Answer to: Mulualem Agonafir: 119, and Wendy

Sorry to come back on this again, but if there are no other clear risk
factors for re-infection or relapse, and Xpert shows TB, these RMP
low-resistance strains are a possibility. I have seen them causing relapse
after relapse before I knew they existed, and found out only years later
moving from the field to the Antwerp SRL where there isolates were still
kept, some labeled sensitive to RMP...

Xpert does not cover the low-resistance mutation at codon 251 nor the one at
codon 572, but these are quite rare. And when we tested it on some 20
different strains with the 533Pro mutation, it missed one out of three to
one out of four, depending on dilution used. One such false susceptible has
also been published recently in JCM by others. This codon is located at the
complete end of the last probe, and the mutation is probably the most
frequent of these "rare, low-level" mutations, some 3-5% of all in series
from different countries (except if already missed by insensitive
pre-screening for phenotypic resistance).

If you want to find out and he is still smear-positive, we can help doing
the rpoB sequencing for you.

Jay Liu Replied at 9:59 PM, 23 Jan 2014

2 Questions to Cepheid:
1. Why CDCs in China are not procuring the Genexpert and its MTB/RIF cartridges directly from Cepheid with a price of $9.98, and through a local sales agent with much high price instead?
2. When do you expect the license from CFDA can be received for clinical use for MTB/RIF cartridges in China? And what are the barriers so far from your prospective?

Thanks!

sabira Tahseen Replied at 11:46 PM, 23 Jan 2014

Xpert Implementation Challenges in Pakistan
In Pakistan we have experienced problem with machine operation both due to high ambient temperature ( in most part of country) and also due to low temperature ( two sites in north) . Uninterrupted power supply for two hours is unusual as Country is facing severe power crises , so even though air-condition have been installed at all Xpert sites but there is no power to switch on the air conditioner or to maintain temperature in refrigerator supplied for storage of KITs , often there is not enough power to fully charge UPS to ensure 2 hours backup .These challenges exuberate in long summer months .
Transportation of Kits from central store to xpert sites in cold chain is also a challenge and in most of cases is not possible keeping in view the bulk of Kits. Transport time from central store to Xpert site vary from 24 hours to 72 hours and change in color of buffer is seen happening in extreme hot season even in 6 hours .
Availability of uninterrupted supply of stock is also challenging , no public sector funding is yet used for purchase of kits or equipment but direct transfer of funds is also not possible from country which has resulted in delays and ultimate solution was to establish a contract with local distributor / procurement agent resulting in increase in cost of Kits by 10% . We foresee more challenges in utilization of public funds (if made available at some time) for purchase of these KITs through direct contracting from international market .
Experience in training of staff also varies from area to area , laboratory staff having some knowledge of computers were definitely easy to train but in some area staff just had no experience on use of computers and training such staff required lot of time/effort on use of computers
Algorithm are developed but due to non established robust specimen transport system, specimen of all eligible patient donot reach the Xpert sites and only limited patient having direct access to Xpert sites are the one benefiting most.
Probably Xpert can be implemented successfully through donor funded project in few large cities on small scale but successful implementation of Xpert throughout the country with equity of access for all, in high burden resource poor country like Pakistan would remain a challenge because of poor health systems , weak infra-structure, compromised human resource , poor logistic and supply and lack of robust specimen transport systems .

Peter Saranchuk Panelist Replied at 1:36 AM, 24 Jan 2014

An interesting finding by MSF over the past 3 years: Although the use of Xpert MTB/RIF has invariably increased the percentage of patients with lab-confirmed TB in each setting where it has been implemented, the number of drug-sensitive TB patients being started on treatment has not necessarily increased. Thus, consider introducing active case finding strategies (e.g. screening of all household contacts of TB cases) in order to maximize the impact of this new technology in your setting...

Phasouk SENEPHANSIRI Replied at 3:20 AM, 24 Jan 2014

Dear all,
The updated SOP or guide will be useful for all and necessary for the new implementors
Best regards,
Phasouk SENEPHANSIRI

Christopher Gilpin, PhD, MPH Panelist Replied at 3:40 AM, 24 Jan 2014

WHO policy recommendations on TB diagnostics are based on a process of systematic evaluation of scientific evidence for the use of different technologies with different specimen types. Although the evidence presented to WHO on the performance characteristics of Xpert MTB/RIF with different specimen types can be used to obtain regulatory approval (through a different mechanism) for that test, regulatory approval is not a pre-requisite for the development of WHO evidenced based policy guidance on TB diagnostics.

Martin Colla Panelist Replied at 4:18 AM, 24 Jan 2014

Reply to Jay Liu:

1. Why CDCs in China are not procuring the Genexpert and its MTB/RIF cartridges directly from Cepheid with a price of $9.98, and through a local sales agent with much high price instead?

As is our policy, Cepheid HBDC provided a quotation at $9.98 (ex-works, advance payment) plus freight costs to the China CDC. Cepheid HBDC's quotation includes delivery to the nearest airport in China and does not cover import duty, customs clearance, delivery to the site and any other expenses that may be necessary. The local service provider also provided a similar quotation to that provided by Cepheid HBDC but including the additional elements to deliver to all sites.

The service provider's quotation was chosen. Cepheid is not in a position to impose a procurement choice on national programmes but we will advise them when consulted. The GDF team can be exceptionally helpful in this regard and are currently handling about half of the product shipped - outside of South Africa.

My current understanding of the China situation is that the contract with the local service provider has been re-discussed and the issues resolved.

2. When do you expect the license from CFDA can be received for clinical use for MTB/RIF cartridges in China? And what are the barriers so far from your prospective?

Cepheid expects this license imminently. There are no particular barriers. The time to register a product is long in countries with formal regulatory procedures because the responsible authorities need to be satisfied that a product performs to an acceptable standard. This requires supporting evidence to be generated in local studies on local strains isolated from the local population and reported in the local language. The same would apply to a product entering the United States for example. What might be helpful in accelerating the process would be greater harmonisation between regulatory bodies.

Martin Colla Panelist Replied at 5:48 AM, 24 Jan 2014

Reply to Sabira #145,

The GeneXpert will not operate outside of the acceptable temperature range as thermocycling becomes less efficient at the extremes of temperature. If you compare the time taken to process a cartridge, you may notice it can be slightly longer in the summer months since the system needs longer to cool the reaction mixture with each cycle. The latest (white) GeneXpert IV tolerates high ambient temperature better than the original (grey) model because of its larger fan. If you are using both models within the programme, it would be best to deploy the white systems in the warmer environments.

A solar-power solution as described by Fuad (#122) could help support the GeneXpert during power-outages though powering air conditioning and refrigeration would require significantly more panels and batteries as the load an a/c would represent can be up to 10x that of the GeneXpert.

The yellow buffer colour does not indicate a failure of any kind. This can happen over time but the buffer will continue to work satisfactorily.

Concerning procurement - this comment is general and not just for Pakistan. Cepheid HBDC likes to keep things as simple as possible. The size of our HBDC organisation is kept to a minimum to ensure costs remain low. This is essential as we are providing the products at a much lower cost than our commercial counterparts. We therefore try to avoid complex, cost-inflating arrangements involving currency exchange, financial instruments, delayed payment, part-payment, payment on inspection etc. If you feel you cannot procure directly and choose to ask a local service provider ito procure on your behalf then they will charge for the service rendered. The more comlex the arrangement and the greater the financial risk involved, the higher this price is likely to be.

Procurement directly from Cepheid with payment in USD is the simplest and least costly approach. If there are issues with converting local currency to USD and external funding is involved, consider discussing with the donor organisation concerned whether they could make the payment directly to Cepheid.

CLEMENT ADESIGBIN Replied at 5:55 AM, 24 Jan 2014

Reply to Mulualem A: 129

Thanks for the follow up history.
It has been over emphasised that it is purely clinical
Adherence issue has been raaised.
Also other chronic systemic diseases.

I feel should work with these and should be alright.

Lal Mani ADHIKARI Replied at 6:15 AM, 24 Jan 2014

Dear Panelist,

The Operational research on GeneXpert implementation is a rising concern as well as TB Reach Component. We have more than two years of Xpert implementation and focused on Operational research issue such as Coverage and accessibility, policy endorsement for GeneXpert in Country guidelines. We have the issues in roll up cases under treatment, mainstreaming in diagnostic tool as compared to Microscopy and many more such. Kindly advise what are the issues for Developing Countries like Nepal, we should focus so that it might be supportive in advocating Xpert implementation in the time to come.

hope to get feedback. Thank you.

Wessen Nega Replied at 7:38 AM, 24 Jan 2014

Dear all,

I am supervising TB diagnostic laboratory here in Ethiopia, GeneXPert is good diagnostic tool for drag resistances Tb bacilli. My concerns are Sample referral problem from remote sites, budget issue for supplies and maintenance problem. Those mentioned factors are rate limiting for proper utilization of the technology in resource poor setting. Therefor, it is better to be critical seen how we are using GeneXPert technology with a minimum cost for communities with high MDR/XDR TB prevalent areas.

Thanks

Armand Van Deun Panelist Replied at 8:44 AM, 24 Jan 2014

Regarding questions raised by Wessen Nega from Ethiopia:

- transport for molecular tests should in principle be easy, since
bacilli do not have to remain viable. We have extensive good experience with
molecular testing of smear-positive sputum preserved in ethanol at ambient
temperature, even years later (for research and surveys, not patient care of
course). Most important are hermetically closing vials; we used for this
cryovials with O-ring screw cap of 2 ml. To about 1 ml of 95% ethanol
(denatured alcohol) about 0.5 ml sputum is added (e.g. after spontaneous
liquefaction overnight). We have not documented this, but the final ethanol
concentration will be close to 70% and after sufficiently long contact time
the TB should be killed. For surveys we had over 90% recovery from such
samples, which is higher than usual with culture and conventional DST. We
used mostly DNA sequencing or LPA, but limited experience suggests that also
Xpert works well.

- If you want to test RMP resistant samples further by
culture-based DST, transport of sputum at ambient temperature is also
possible in 50 ml screw cap conical tubes (Falcon) which are typically used
in TB labs for decontamination and centrifugation of specimens, mixing the
sample with about equal volume 1% CPC (cetylpyridinium chloride). This
antiseptic is very well known for transport and decontamination of TB sputa,
with also about 90% recovery after prolonged transport delays (on average 3
weeks, but can be longer if AFB were not rare in the fresh sputum). Xpert
works from such samples, but I haven't seen results from larger scale
evaluations yet

Wessen Nega Replied at 9:24 AM, 24 Jan 2014

Dear Sir,
Many thanks for your sputum transportation update. I think your advice can apply for Tb culture testing but coming to the molecular technical needs detail study and evaluation, since there is high risk for contamination.

Martin Colla Panelist Replied at 10:36 AM, 24 Jan 2014

Further to Armand's transportation guidance,

Cepheid has no experience of the use of 95% ethanol to preserve samples in transit for testing. Neither are we aware of any related publications so we are unable to offer additional guidance.

CPC has been tested and found not to interfere with the Xpert MTB/RIF assay.

Mulualem Agonafir Replied at 12:04 PM, 24 Jan 2014

Reply to Steve Schuyler:

The patient did take primarily six months treatment (2RHZE/4RH) and again retreated for 8 months (2RHZES/RHZE/5RHE). He was on DOTs

Mulualem Agonafir Replied at 12:31 PM, 24 Jan 2014

Dear all,

Thank you for your feedback. This patient was on DOTs, with no recent close infectious source, took drugs brought by the NTLCP (I believe it is from reliable manufacturer). However, screening for DM and DST for other drugs were not done. This patient is found in a remote village where DST is not easily accessible. I shall discuss with my colleagues on all the suggestions provided. I thank again Dr Armand for the offer of sequencing. I will give updates.

Thank you

S M Mostofa Kamal Replied at 1:42 PM, 24 Jan 2014

Hi every panelists and participants! 
Greetings from NTRL Bangladesh, especially to Armand , Martin Colla, Fuad and Gilpin for their technical and policy based input. This online discussion is more productive than attending an international symposium.
 I may conclude and share our experience on the overall discussion as follows: 
Xpert- posses all the characters for equal & universal access. Though it is not superior to sequencing but better than LPA for large scale use.
Clinical evaluation(immune deficiency, drug diffusion and absorption) and TB-culture and DST(1st and 2nd line) will be needed when RIP result will not correlate with the suspects or taking surgical intervention.
 Our experiences suggest further development of last probe ( at Codons 252 & 572) and continuous monitoring to develop new probes. I also suggest to check variation of internal control in the cartridges from batch to batch. Cephid should take steps to replace inactive modules of Xpert machine. Calibration and post calibration control running can minimize analytical errors or discordant.
Our "unique" observation suggest to perform routine Xpert in all patients attending a tertiary chest disease hospital especially in a high TB burden country to detect TB from non-TB suspect and RR-TB from non-TB as well as from new-TB suspect(that Armand recently witnessed at NTRL).
Lastly I will be obliged if anybody posts any practicing SOP(not yet endorsed) for EP-TB, Urine and stool for Xpert.

Sophie Beauvais Replied at 4:07 PM, 24 Jan 2014

Dear All,

We are nearing the end of the last “official” day of our virtual Expert Panel on "The Updated WHO Policy on Xpert MTB/RIF assay: What is New and How it May Support Implementation."

There are still a few questions open for comments and also a colleague in Bangladesh asked if anyone has practical SOPs for EP-TB, Urine and stool for Xpert to post. Also, I wanted to share with you again the two key documents for our panel and if you have any questions or comments on these for our panelists and colleagues please post:

* The pre-publication copy of the updated WHO policy on Xpert MTB/RIF assay is available in PDF here: http://www.stoptb.org/wg/gli/assets/documents/WHO%20Policy%20Statement%20on%2... The final copy will be published in February-March 2014.

* The draft SOP is available in PDF here: http://www.ghdonline.org/uploads/GeneXpert_SOP_Xpert_processing_EPTB_specimen... and has been developed for specimen processing of selected extrapulmonary samples (CSF, lymph nodes and other tissues) for testing in the Xpert MTB/RIF assay. The final version will be incorporated in the manual to be published in Feb-March.

Last but not least, Creswell (WHO) et al have recently published a research article (open access) that might be of interest to participants here: Results from early programmatic implementation of Xpert MTB/RIF testing in nine countries (Bangladesh, Cambodia, DR Congo, Kenya, Malawi, Moldova, Mozambique, Nepal, Pakistan) http://www.biomedcentral.com/1471-2334/14/2

Please note that the entire conversation of this virtual Expert Panel is available online at this link: http://www.ghdonline.org/xpert-mtb-rif-jan2014/discussion/the-updated-who-pol... and will remain open to all for comments in the future so feel free to continue the conversation. We will also publish a peer-reviewed discussion brief summarizing key lessons learned and knowledge exchanged in the coming weeks.

Many thanks again to our wonderful panelists and to everyone who participated and shared critical information here.

Very sincerely, Sophie

Attached resource:

Victor Ombeka Replied at 8:46 PM, 24 Jan 2014

Very informative discussion. Ciao

sabira Tahseen Replied at 10:31 PM, 24 Jan 2014

Reply to Martin #150
yes Martin you are right number of errors were not more then usual in KIts with observed change in colour during transportation but we used these KITs on priority so we actually dont know how they would have behaved if left till end of shelf life .

Do we have any guideline for transportation of kits - Kits are also lying at room temperature while waiting for customs clearance

sabira Tahseen Replied at 10:43 PM, 24 Jan 2014

Policy guideline on need of DST laboratories
With Xpert used as screening tool for testing patient at risk of DRTB , Need for DST laboratories ( phenotypic) probably has changed from projected one for 10M population . Secondly proportion of MDR samples being tested at these laboratories has remarkably increased from around 20%to more than 90%, Safety of laboratory staff working in these laboratories is now even more of concern then before.

Armand Van Deun Panelist Replied at 5:47 AM, 25 Jan 2014

Thanks for bringing this up, Sabira. The policy on numbers of culture labs
and numbers of DST labs required still hasn't changed, but clearly needs a
revision since Xpert.

With Xpert decentralized screening, on average only 300-500 DST would be
needed for a 10 million population (10,000 TB detected, 3-5% RMP resistance
among new). This is a low workload for a DST lab, and surely it will be much
easier to create capacity for 5-10 times more in one lab than to build,
maintain and create proficiency in 5-10 labs. Same goes for safety.

Treatment response monitoring capacity of the MDR is often mentioned as the
reason to have a network of culture labs. In my opinion this is also not a
must:

- few labs can handle thousands of cultures per year, and with CPC
use transport should not be so problematic

- detecting MDR is now easier than treating them, as we heard in
this panel the capacity is not there where Xpert networks function well;
going for early detection of MDR treatment failures is then even more a
reversing of priorities. We need now highly effective regimens for MDR and
XDR that can be used large-scale and without difficult monitoring of
response

- the problem with treatment response monitoring by AFB microscopy
as well as Xpert is that these tests can't distinguish between live and dead
bacilli, not the sensitivity. I'm sure it must be possible to find solutions
for that with more efforts on research, rather than keep multiplying methods
that an NTP must develop as a network



The future is molecular, so why keep investing in methods from the past, for
which we already have the experience that for many NTPs it is not working in
spite of a lot of effort and money?

Salman Siddiqi Replied at 10:39 AM, 25 Jan 2014

Just a note on using CPC for sputum transportation. CPC is recommended for only egg-based medium culture. For Middlebrook medium including MGIT it does not work well as the residual CPC present in the inoculum inhibits growth of TB.
Salman Siddiqi

Martin Colla Panelist Replied at 4:17 AM, 27 Jan 2014

Reply to Sabira #162

The storage conditions for the GeneXpert MTB/RIF cartridges are 2-28C until the end of the stated shelf-life. We know from experience that higher temperatures - such as during transport - can be tolerated for a short period but this has not been documented. For the new 50 test kits which contain pouches of 10 cartridges, the stability of the cartridges once the pouch has been opened has been established to be 6 weeks at up to 45C. Unfortunately, we currently have no data for the closed pouches at these temperatures.

The GeneXpert performs multiple controls on each cartridge. These are designed to ensure that should some deterioration of the cartridge occur, the GeneXpert will report an error rather than an inaccurate result. One should expect that inappropriate storage would be accompanied by an increase in errors reported by the GeneXpert.

Phasouk SENEPHANSIRI Replied at 11:27 PM, 27 Jan 2014

It is very grateful for me to have a good chance to join the panel discussion on the WHO Updated policy on Xpert MTB , I got the variety opinion on the implementing the new technology and gain the updated information and hopefully to look forward to join the further discussion.
Thank you.

Phasouk SENEPHANSIRI Replied at 11:38 PM, 27 Jan 2014

I would like to share with the others for specimen transportation. 1.Is it possible to transport the sputum specimen by putting in to the normal envelop without any kind of the icepack or coolbox?2. could we use the NAOH or NACL -NAOH to decontaminate before loading or mixing with buffer and perform the xpert?
Thanks,

Andrew Black Replied at 11:55 PM, 27 Jan 2014

I would like to thank everyone for the opportunity of sharing in the panel discussion.

Fuad Mirzayev Replied at 3:19 AM, 28 Jan 2014

Many thanks for all who participated, for asking interesting questions and sharing your experiences. I would also want to thank our panellists for their time and valuable contributions to this online panel.
Special thanks to GHD, Sophie and Elise for preparing and hosting this panel discussion.
To the extent possible I will try to address some new questions and queries in the "Implementation Manual" to be released in February-March and inputs from this panel will help to guide the agenda of the Xpert MTB/RIF implementers meeting we plan in April. When dates are set we will announce them on the GLI website http://www.stoptb.org/wg/gli/ and also on the GHD.

Armand Van Deun Panelist Replied at 2:48 PM, 28 Jan 2014

Sputum mixed with CPC (cetylpyridinium chloride) MUST be transported at
ambient temperature, refrigerated the product will precipitate and become
inactive. Cepheid has confirmed that such samples can be tested by Xpert,
and they can also be used for culture on egg-based media.

Sputum in alcohol also does not need to be kept cool, we know it keeps at
without cooling very well for DNA sequencing, even for years, but it has not
been extensively tested for use with Xpert. We are also not sure that all
the TB bacilli have been killed after for instance just a few hours in the
alcohol.

JATA safety regulations might thus still make transport by air difficult.
However, for transport over land your local regulations will apply, which
are generally less heavy for clinical samples like sputum.

S M Mostofa Kamal Replied at 12:49 AM, 6 Feb 2014

Dear all
As per request  of Dr.
Paramacivan to FIND microbiologist, Mr. Michel Chakma(working at NTRL) a AMC
budget was  sent  to him and bellow is the  forwarded reply  mail from Dr. Paramacivan for your kind
information and needful initiative.

 Presently the  maintenance contract is the main challenge for
NTRL and RTRLs running that also mentioned in Dr. Armand every visit reports.
There is a funding gap regarding this activity. We were very much enthusiastic
hearing is mail and expecting to get thic budget as a LDC country.


In this regard cooperation from everybody will be highly appreciated.
Attachment is the AMC budget.
Thanks.

 
Best regards,
 
Dr. S. M. Mostofa Kamal
M.B.B.S, M.Phil.(Micro.DU)
Associate Professor 
Pathology and Microbiology
& Coordinator,NTRL
NIDCH,NTP, DGHS,MOH&FW

Mohakhali, Dhaka-1212.
Phone: +8801819-401900



On Wednesday, February 5, 2014 9:31 PM, C.N. Paramasivan <> wrote:


Dear Mikel,
 
Unfortunately EXPAND TB has no such provision  to cover this expense. NTP or NTRL shall approach partners such as URC or MSH and request for the support.
 
Regret that we are not in a position to support.
 
Best Wishes,
Param
 
C.N. Paramasivan
Ph.D., D.Sc., FAMS, FNASc.
Head of TB Programme FIND (India) & South East Asia
Tel: +91 (11) 40419517
Mobile: +91 9910007045
E-mail:
FIND (India)
Foundation for Innovative New Diagnostics
Flat No. 6-14(excluding No.7),
9th floor, Vijaya Building,
17-Barakhamba Road,
New Delhi – 110 001.
 
From:mikel chakma [mailto:]
Sent: Wednesday, February 05, 2014 3:19 PM
To: C.N. Paramasivan
Subject: Re: Estimates
 
Dear Dr. Param Sir,
 
I just received AMC quotation from one of the service provider STERLING Multi-Tech Ltd and plealse find attached PDF file quoting AMC cost by the same SP.
 
 
Row Labels Budget Required
Commodities USD 45445.00
Equipment Maintenance  USD 25200.00
 
Maintenance of ventilation system incl. BSC
Technical assistance  
 
Grand Total


 
Best regards


Mikel Chakma
Consultant Microbiologist
Foundation for Innovative New Diagnostics (FIND), Bangladesh
NTRL, NIDCH
Mohakhali, Dhaka,
Bangladesh
Mobile: +880 1821 889 714
 
On Wed, Jan 29, 2014 at 4:15 PM, mikel chakma <> wrote:
Dear Dr. Param Sir,
 
Sorry for being late to replay this mail & keep you waiting. After getting the quotation sample from Dr. Prabakaran, I discuss with Dr. Kamal about the AMC. According to his guide I contact with three Service Provider (SP) with the equipment's list. Among three one service provider came out with no result and other two SP inform me today that they still working on it and require more time especially for BSC certification and HVAC system maintenance. 
 
In this circumstances I have to wait for their feedback or other wise getting the quotation from India.
 
Here below attached only the commodities budget and the equipment's list -
 
With best regards
 
Mikel 
 
 
 
Row Labels Budget Required
Commodities USD 45445.00
Equipment Maintenance  
Maintenance of ventilation system incl. BSC  
Technical assistance  
 
Grand Total
 
 
 


 
 
On Sat, Jan 25, 2014 at 10:54 AM, Loganathan Prabakaran <> wrote:
Dear Mikel,
 
Hope everything is fine there, I am herewith sending the AMC Quotes received for the equipments in IRL Chennai, like this you can find the parties in Dhaka and get quotes (estimates) and send, in case you need from here I can help in getting it from Stericlean Chennai if you send me the list of equipments to be covered under AMC. Pl. be informed that in the attached list AMC for ventilation system is not covered.
 
For technical assistance as mentioned in the trailing mail you need not worry.
 
Awaiting for your response.
 
Thanks and regards.
Prabakar.
 
From:Mikel Chakma [mailto:]
Sent: 25 January 2014 06:56
To: Loganathan Prabakaran
Subject: Fwd: Estimates
 
Dear Dr. Prabakaran,
 
Good morning. May I have your assistance to fill up the following budget. I may able to figure out the commodities budget but other maintenance & technical assistance budget how to predict the cost? Looking forward your comments.
Best regards

Mikel Chakma
Consultant Microbiologist
Foundation for Innovative New Diagnostics (FIND), Bangladesh
NTRL, NIDCH
Mohakhali, Dhaka -1212
Bangladesh
Ph - +880 1821 889714
 
Sent from my iPad

Begin forwarded message:
From:"C.N. Paramasivan" <>
>Date: January 24, 2014 at 12:18:48 PM GMT+6
>To: mikel chakma <>
>Cc: Loganathan Prabakaran <>
>Subject: FW:  Estimates
Dear Mikel,

>Can you fill up the details as Daniel wanted. You can take 2013 supplies as a measure for your planning for 2014 and 2015. Perhaps a 10% increase may be considered. Consult Prabakar for any doubt.

>Best,
>Param

>C.N. Paramasivan
>Ph.D., D.Sc., FAMS, FNASc.
>Head of TB Programme FIND (India) & South East Asia
>Tel: +91 (11) 40419517begin_of_the_skype_highlighting +91 (11) 40419517FREE  end_of_the_skype_highlighting
>Mobile: +91 9910007045begin_of_the_skype_highlighting +91 9910007045FREE  end_of_the_skype_highlighting
>E-mail:
>FIND (India)
>Foundation for Innovative New Diagnostics
>Flat No. 6-14(excluding No.7),
>9th floor, Vijaya Building,
>17-Barakhamba Road,
>New Delhi – 110 001.

>From:Daniel Orozco
>Sent: Thursday, January 23, 2014 10:01 PM
>To: C.N. Paramasivan
>Subject: RE: Estimates

>Thanks Param
>Don’t worry about the technical assistance part, I can enter that
>You can focus on the equipment and supplies (+ estimates for maintenance)
>
>Daniel


>From:Daniel Orozco
>Sent: Thursday, January 23, 2014 9:47 PM
>To: C.N. Paramasivan
>Subject: FW: Estimates
>Importance: High

>Dear Param
>For next week’s meetings we need some preparations as discussed over the last weeks with Fuad (e-mails)
>One of the critical aspects of this is the estimates for the countries regarding supplies, equipment, maintenance, TA etc (such as  already done for other countries– see below)
>It would be very useful if you manage to come up with the estimates for the countries in your portfolio, as to facilitate the discussion.
>
>If you are developing now the info sheets, even better, but again, the main part that we need next week is that preliminary estimate (even though the  transitioning consultant has not yet visited all the countries)
>
>Let me know if you have any questions,
>
>Thanks
>
>Daniel


>Total gap to be filled post EXPAND TB support three laboratories
>Row Labels Budget Required
>Commodities  
>Equipment Maintenance  
>Maintenance of ventilation system incl. BSC  
>Technical assistance  
>Grand Total


>
>________________________________
>
>Daniel Orozco| Senior Project Manager – Head of Downstream Unit |FIND | Tel. +41 22 710 09 57 |Cel. +41 79 946 44 82

>

Phasouk SENEPHANSIRI Replied at 1:13 AM, 7 Feb 2014

Dear all,
I would like discuss with the all experts and consultants for the technical on the shipment the sputum samples from the provincial or district level to Xpert sites,and how to ship or how to pack? by triple packages or simple envelopes ? could we send to Expert site without putting in the cool box or not?
your recommendation is my requirements

Alaine Umubyeyi Nyaruhirira Replied at 1:52 AM, 7 Feb 2014

Dear Phasouk

I would like to share a ''summary of what was discussing during the GLI panels last two weeks regarding Transport, storage of samples for Xpert testing''. Hope it will help you.

Transport for molecular tests should in principle be easy, since bacilli do not have to remain viable. We have extensive good experience with molecular testing of smear-positive sputum preserved in ethanol at ambient temperature, even years later (for research and surveys, not patient care of course). Most important are hermetically closing vials; we used for this cryovials with O-ring screw cap of 2 ml. To about 1 ml of 95% ethanol (denatured alcohol) about 0.5 ml sputum is added (e.g. after spontaneous liquefaction overnight). We have not documented this, but the final ethanol concentration will be close to 70% and after sufficiently long contact time the TB should be killed. For surveys we had over 90% recovery from such samples, which is higher than usual with culture and conventional DST. We used mostly DNA sequencing or LPA, but limited experience suggests that also Xpert works well. If you want to test RMP resistant samples further by culture-based DST, transport of sputum at ambient temperature is also possible in 50 ml screw cap conical tubes (Falcon) which are typically used in TB labs for decontamination and centrifugation of specimens, mixing the sample with about equal volume 1% CPC (Cetylpyridinium chloride). This antiseptic is very well known for transport and decontamination of TB sputa, with also about 90% recovery after prolonged transport delays (on average 3 weeks, but can be longer if AFB were not rare in the fresh sputum). Xpert works from such samples, but I haven't seen results from larger scale evaluations yet.

Transport for molecular tests should in principle be easy, since bacilli do not have to remain viable. We have extensive good experience with molecular testing of smear-positive sputum preserved in ethanol at ambient temperature, even years later (for research and surveys, not patient care of course). Most important are hermetically closing vials; we used for this cryovials with O-ring screw cap of 2 ml. To about 1 ml of 95% ethanol (denatured alcohol) about 0.5 ml sputum is added (e.g. after spontaneous liquefaction overnight). We have not documented this, but the final ethanol concentration will be close to 70% and after sufficiently long contact time the TB should be killed. For surveys we had over 90% recovery from such samples, which is higher than usual with culture and conventional DST. We used mostly DNA sequencing or LPA, but limited experience suggests that also Xpert works well. If you want to test RMP resistant samples further by culture-based DST, transport of sputum at ambient temperature is also possible in 50 ml screw cap conical tubes (Falcon) which are typically used in TB labs for decontamination and centrifugation of specimens, mixing the sample with about equal volume 1% CPC (Cetylpyridinium chloride). This antiseptic is very well known for transport and decontamination of TB sputa, with also about 90% recovery after prolonged transport delays (on average 3 weeks, but can be longer if AFB were not rare in the fresh sputum). Xpert works from such samples, but I haven't seen results from larger scale evaluations yet.

Dr Alaine, MSH South Africa

Alaine Umubyeyi Nyaruhirira Replied at 1:59 AM, 7 Feb 2014

Dear Phasouk

I would like to share a ''summary of what was discussing during the GLI panels last two weeks regarding Transport, storage of samples for Xpert testing''. Experience from Dr Armand
Hope it will help you.

Transport for molecular tests should in principle be easy, since bacilli do not have to remain viable. We have extensive good experience with molecular testing of smear-positive sputum preserved in ethanol at ambient temperature, even years later (for research and surveys, not patient care of course). Most important are hermetically closing vials; we used for this cryovials with O-ring screw cap of 2 ml. To about 1 ml of 95% ethanol (denatured alcohol) about 0.5 ml sputum is added (e.g. after spontaneous liquefaction overnight). We have not documented this, but the final ethanol concentration will be close to 70% and after sufficiently long contact time the TB should be killed. For surveys we had over 90% recovery from such samples, which is higher than usual with culture and conventional DST. We used mostly DNA sequencing or LPA, but limited experience suggests that also Xpert works well. If you want to test RMP resistant samples further by culture-based DST, transport of sputum at ambient temperature is also possible in 50 ml screw cap conical tubes (Falcon) which are typically used in TB labs for decontamination and centrifugation of specimens, mixing the sample with about equal volume 1% CPC (Cetylpyridinium chloride). This antiseptic is very well known for transport and decontamination of TB sputa, with also about 90% recovery after prolonged transport delays (on average 3 weeks, but can be longer if AFB were not rare in the fresh sputum). Xpert works from such samples, but I haven't seen results from larger scale evaluations yet.

Transport for molecular tests should in principle be easy, since bacilli do not have to remain viable. We have extensive good experience with molecular testing of smear-positive sputum preserved in ethanol at ambient temperature, even years later (for research and surveys, not patient care of course). Most important are hermetically closing vials; we used for this cryovials with O-ring screw cap of 2 ml. To about 1 ml of 95% ethanol (denatured alcohol) about 0.5 ml sputum is added (e.g. after spontaneous liquefaction overnight). We have not documented this, but the final ethanol concentration will be close to 70% and after sufficiently long contact time the TB should be killed. For surveys we had over 90% recovery from such samples, which is higher than usual with culture and conventional DST. We used mostly DNA sequencing or LPA, but limited experience suggests that also Xpert works well. If you want to test RMP resistant samples further by culture-based DST, transport of sputum at ambient temperature is also possible in 50 ml screw cap conical tubes (Falcon) which are typically used in TB labs for decontamination and centrifugation of specimens, mixing the sample with about equal volume 1% CPC (Cetylpyridinium chloride). This antiseptic is very well known for transport and decontamination of TB sputa, with also about 90% recovery after prolonged transport delays (on average 3 weeks, but can be longer if AFB were not rare in the fresh sputum). Xpert works from such samples, but I haven't seen results from larger scale evaluations yet.

Dr Alaine, MSH South Africa

Fulgence Nzabintwali Replied at 2:22 AM, 7 Feb 2014

Dear Phasouk

Follow information from Dr Alaine.

If you still using Savanakhet and Luangnamtha Laboratoy it will not be a problem , Gene x pert is located to CCML or Mahosoth hospital NRL, or Regional lab also (SVK, LNT) ,normally for CCML they have long experience for that if necessary Dr Phimba can help for that.

IF resistant RIF by Gene X pert you will need fresh sputum lake what we have done during NTPS for culture for all DST on solid media or using CPC method (See comment Dr Alaine) do same method recommended by Dr Kim or look SOPS we had before or go to GLI web site and download or ask Dr Kim for other information you need (do you still using KIT SRL?).


Fulgence






Le 7 févr. 2014 à 08:26, Phasouk SENEPHANSIRI via GHDonline <> a écrit :

Indrajit Kumar Replied at 10:04 AM, 7 Feb 2014

Respected Sir,
I want to know if sputum is Negative and gene xpert test is also saying M TB NOT DECTED, but patient having coughing with blood or some time without blood and having other symtoms. He is previously taken ATT .
Then now he is a TB patient or not . Ihe is a patient then which regimine he will get ?
Secd thint to know can anyone do gene xpert from urine stool CSF Plural fluid materials like sputum and by which process.
With
Indrajit.

CLEMENT ADESIGBIN Replied at 10:47 AM, 7 Feb 2014

Response to I. Kumar:
More clinical work up is required. A comprehensive history to evaluate other causes of hemoptysis
Will help. Pathologies like bronchocarcinoma, aspergillosis even
Some atypical pneumonia to mention a few.

Depending on your natIional guideline, a TB culture/DST will help.
Best.

Arthur Lagos Replied at 10:05 PM, 7 Feb 2014

Dear Indrajit,
In addition to Clement's comments, I'd like to say that it is not unusual to see hemoptysis among TB patients even among those declared cured by NTP guidelines after treatment. One of the common causes for hemoptysis in this group of patients, is bronchiectasis (assuming TB relapse was ruled out). The condition is often associated with recurrent episodes of cough, usually productive, due to an inadequately treated upper or lower respiratory infection. It could also be due to an inflammatory condition, such as an inadequately treated allergic rhinitis, sinusitis, or pneumonitis, complicated by a secondary bacterial infection.

In a setting with limited diagnostic resources, an adequate history taking and physical examination will give you useful clues to the condition's underlying cause. If infection is suspected, then a round of broad spectrum antibiotics may suffice. It is also important to provide assurance to the patient because hemoptysis generates a lot of anxiety in the patient and the family, and sometimes, even among health workers. For massive hemoptysis, it is wise to bring the patient to a hospital to ensure adequate airway and circulatory support. It is also important to follow up these patients to while on treatment.

Arthur B. Lagos MD

CLAUDE RUTANGA Replied at 4:59 AM, 8 Feb 2014

Hello Kumar,
I would like to comment on your question by pointing on the need of further clinical documentation about such a patient (as much as it can be done), because the other symptoms that add on the hemoptysis (bloody cough) may add the likelihood of the positive screen of TB at the point of clinical diagnosis of TB first. Then, the patient history of previous treatment will classify the patient as a re treatment (assuming the first treatment course has successfully completed!). From a clinical investigation stand point, if TB is ruled out (based on a valid TB diagnostic algorithm), it's a wise step to investigate for other causes of hemoptysis with a wide range of tests and refer where adequate to take chance for test like CT Scan, IRM.
Regarding the regimen to prescribe to this patient (if Anti TB are the ultimate treatment given the other possible causes of hemoptysis have been ruled out with robust investigation methods), in presence of a negative Xpert MTB/RIF result, it's wiser to first seek the view of the in-country (national) MDR TB committee which is mandated as per your national MDR TB clinical management to initiate any MDR TB treatment in the country as elsewhere I think, which decides on whether or not to put on SLD treatment. If treatment is initiated in this case (which is an empirical treatment), the expert committee should have based on strong clinical, epidemiological arguments regarding TB in your region/county, province or county.
Again the regimen for SLD is already formulated in your national policy in case there is one, but I agree there should be some minor adaptations needed depending on the patient FLD regimen formulation, resistance profile in the patient residence or origin.
But still keep in mind to answer questions like:
-Prior to the first anti TB treatment, what was the sputum status (Pos or neg)
-Did the patient complete the first treatment course
-If not, after how long did the patient stop treatment (in terms of months so to classify her/him accordingly).
Answers to those may also simply and quickly in some instances tell you that the patient is a MDR TB suspect and therefore orient to a FLD for example, if the treatment has been abandoned or is a LTF (Lost to follow up).
Thank you

CLAUDE RUTANGA Replied at 6:46 AM, 8 Feb 2014

Hello Kumar,
I come back to you with a focus on your second point regarding Xpert process of EPTB specimens (you mentioned, urine, stools, CSF).
There are important links that have been shared during the one-week expert panel discussion on "The Updated WHO Policy on Xpert MTB/RIF assay: What is New and How it May Support Implementation", which ended one week ago and which you can access and download through important related documents. Follow the reply posted by Sophie Beauvais, on 24th January for instant access to the documents via their respective links.
Thanks to WHO and its collaborators for these insightful/guiding documents:
- The pre-publication copy of the updated WHO policy on Xpert MTB/RIF assay
- The Draft SOP for Xpert processing_extra pulmonary specimens
- Results from early programmatic implementation of Xpert MTB/RIF testing implementation in nine countries

As you go through the draft SOP doc, you will find interestingly the three key chapters followed as :
Principles : ..." These recommendations do not apply to stool, urine or blood, given the lack of data on the utility of Xpert MTB/RIF on
these specimens".
General considerations: ..."Tissues must be processed within a BSC given the risk of aerosol production while grinding and
homogenizing samples".
"CSF samples are paucibacillary and can be processed using the same precautions as for sputum
EXCEPT when concentrated by centrifugation".
"Decontaminate samples for culture using either 4% NaOH or NaOH-NALC depending on usual practice in
"the laboratory".
Specimen processing which is described for: - Lymph nodes and other tissues (Xpert MTB/RIF only)
- Lymph nodes and other tissues (Non sterile collection Xpert MTB/RIF and
culture)
- Lymph nodes and other tissues (Sterile collection Xpert MTB/RIF and culture)
- CSF
With a good and stable internet connection, you will get these readily available documents in a couple of few minutes.
Good week-end
Claude Rutanga

Dr Uzodinma Adirieje Replied at 8:49 AM, 8 Feb 2014

I find this rather interesting.

Any further references?

Dr. Uzodinma Adirieje
Executive Director
Afrihealth Information Projects/Afrihealth Optonet Association
Suite 216, Block G, FHA Cornershop, Lugbe, Airport Road, Abuja
P.O. Box 8880, Wuse Abuja, Nigeria
Ph: +234 9 291 4297; DL: +234 9 291 5732; Mobile: +234 803 472 5905
Emails: ,
Web: http://www.afrihealthoptonet.org
Web: http://www.afrihealthoptonetassociation.blogspot.com
Afrihealth's Health and Food Security Summits (HEFOSS):
http://hefossnigeria.blog.com
Facebook: www.facebook.com/afrihealth
Afrihealth's community of practice for health and community systems
strengthening: http://knowledge-gateway.org/afrihealth
Afrihealth's community of practice for vaccines and immunization
(COVIAN): http://knowledge-gateway.org/covianigeria
AFRIHEALTH - strengthening health and community systems to ensure
'Better-Life-for-All'


--
Afrihealth Information Projects/Afrihealth Optonet Association is a
community-focused national, civil society, not-for-profit,
non-religious, non-governmental organization (NGO)/Coalition of 600
community-based organizations, groups and stakeholders in the 36
States of Nigeria and the Federal Capital Territory and global south,
involved in Health Systems Strengthening, HIV/AIDS/TB and Malaria
[prevention, treatment, impact mitigation, care and support],
Vaccinations/Immunizations, Preventing/Controlling Poverty-Related
Diseases; Nutrition and Food Security; Energy and Environment; and
Empowerment, Gender, Good Governance and Human Rights. Incorporated in
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Partnerships (PPP), Advocacy and Mobilisation,
Research/Evidence-Generation (monitoring and evaluation, reviews,
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targeted beneficiaries include the poorest of the poor,
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communities.

Indrajit Kumar Replied at 9:04 AM, 8 Feb 2014

Respected Sirs,
Thanks a lot to reply me such a good way.
With regards,
Indrajit

CLAUDE RUTANGA Replied at 9:17 AM, 8 Feb 2014

Erratum: I meant if the patient is not a MDR TB and therefore orient to a FLD treatment... toward the end of the text. Thank you

Sent from Yahoo Mail on Android

Belayneh Dimah Replied at 9:04 AM, 5 Mar 2014

Thanks chris for the SOPs,it is very use full doc.
Best Regards

Belayneh Dimah Replied at 9:09 AM, 5 Mar 2014

Dear all
how can i get the SOPS LPA?
If you have please attached .
Thank you

Kedir Abdella Abdulsemed Replied at 9:52 AM, 5 Mar 2014

Dear all,
I am kedir from ethiopia. i need advanced information about the MDR-TB and XDR-TB inrelation to the all the responsible mutation for this strain and host-pathogen interaction in this strain.
thanks

Alaine Umubyeyi Nyaruhirira Replied at 10:46 AM, 5 Mar 2014

Dear Taye

Please send your personal mail and I can send requested material on LPA.

Belayneh Dimah Replied at 3:56 AM, 6 Mar 2014

Hi Alaine Umubyeyi;

Belayneh Dimah Replied at 4:09 AM, 6 Mar 2014

Hi Alaine Umubyeyi ;
Here it is my e mail
Regards

Kedir Abdella Abdulsemed Replied at 7:31 AM, 10 Mar 2014

Dear all,
How are you doing ? I need help from some body of group member who can help me the current WHO EQA giudeline

Thanks

Mohammed suaudi Hassen Replied at 7:51 AM, 10 Mar 2014

Dear
Kedir Hey how are you doing with your Research? for your question i
will provide for you WHO EQA Material.
so please send for me your email ok.

David Zavala Replied at 9:08 AM, 10 Mar 2014

Dear Mohammed:
Maybe in this website you could find your answer.

http://www.stoptb.org/wg/gli/

Kind regards,

David


2014-03-10 8:00 GMT-04:00 Mohammed suaudi Hassen via GHDonline <
>:

Wessen Nega Replied at 11:25 AM, 18 Mar 2014

Hello, Every one

I am kindly asking to give me information how do I get training on Gene Xpert training.

Natalie Lorent Replied at 10:30 PM, 18 Mar 2014

Hi Wessen, it is best to contact Cepheid directly. They can provide online training on Xpert or you can get organised with your NTP and maybe have on-site training done (not sure which country you are based on so actually not sure if you have an NTP :-)). That's what we experienced here in Cambodia. Training was well appreciated by our lab techs.
Natalie

Alaine Umubyeyi Nyaruhirira Replied at 2:26 AM, 19 Mar 2014

Dear Wessen



You can have online training organized by CEPHEID, Or visit the Web site of CEPHEID they have 2 training sessions organized in France at their Home office. Another option is to come to CEPHEID South Africa office .

The last option is in country training organized throught a request by the NTP when they have to install new machine.



Hope it will help,

Alaine Umubyeyi Nyaruhirira Replied at 2:32 AM, 19 Mar 2014

Dear Wessen

You can have online training organized by CEPHEID, Or visit the Web site of CEPHEID they have 2 training sessions organized in France at their Home office. Another option is to come to CEPHEID South Africa office .
The last option is in country training organized throught a request by the NTP when they have to install new machine.

Hope it will help,

Wessen Nega Replied at 3:40 AM, 19 Mar 2014

Dear Sir,
I would like to attend CEPHEID South Africa office but I can't afford to travel South Africa for the training. I kindly as king you that it there any ways to get my travel cost cover and attend the training.

Kind regards
Wessen

soundiram indira Replied at 3:59 AM, 19 Mar 2014

Dear Wessen,
Thanks for your request.

- Cepheid cannot afford your travel expenses for you to come.
The training is free and we take care of your meals and ground transportation during the training period.

- Depending on the country you are from, we have cepheid approved service providers that do installation and training of the users. Kindly tell us your location.

- If you cannot afford those costs you still have the possibility to follow a free web based training session (online) with one of our trainers.

- As a general recommandation, i would always advise National Programs to anticipate and include those costs in the implementation of the genexpert so you can come on training.

We have a website where you can always find all the training dates and complete information.
http://www.cepheidcares.com/tb/index.php/resources/tb-training/

Feel free to come back to us for more information,
Indira Soundiram
Customer Care&Training Manager
<mailto:>


Le 19 mars 2014 à 08:41, "Wessen Nega via GHDonline" <<mailto:>> a écrit :

Wessen Nega<http://email.ghdonline.org/c/ZD0zNzczJmk9MjAxNDAzMTkwNzQwMTEuMjY1MTEuMTI... replied to a discussion<http://email.ghdonline.org/c/ZD0zNzczJmk9MjAxNDAzMTkwNzQwMTEuMjY1M... in The Updated WHO Policy on Xpert MTB/RIF assay: What is New and How it May Support Implementation<http://email.ghdonline.org/c/ZD0zNzczJmk9MjAxNDAzMTkwNzQwMTEuM...:

Dear Sir,
I would like to attend CEPHEID South Africa office but I can't afford to travel South Africa for the training. I kindly as king you that it there any ways to get my travel cost cover and attend the training.

Kind regards
Wessen

Mohammed suaudi Hassen Replied at 7:03 AM, 19 Mar 2014

Dear Hi
you need Training on GeneXpert it`s good , if your real interested on
the training , you can come to ADAMA RRL We can provide you
with full application & instillation 0f Xpert machine.


King regard

Gemeda Abebe Replied at 7:28 AM, 19 Mar 2014

Dear Wossen,

There are lots options that you can have to do the geneXpert training without going abroad. You can come to Jimma University Laboratory of Mycobacteriology to have the training. Hope this can help.

Gemeda

Belayneh Dimah Replied at 10:35 AM, 19 Mar 2014

Dear all
I wander the one who answer the question of the training of GeneXpert.
Belayneh

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