The tuberculosis diagnostics pipeline

19 July 2014. Related: Pipeline report, TB coinfection.

By Colleen Daniels

Accurate diagnosis of tuberculosis (TB) is the gateway to treatment and—it is hoped—cure for people with latent TB infection (LTBI) or active TB disease. According to the Stop TB Partnership and the World Health Organization (WHO), 3 million of the 9 million people who develop TB disease every year are not recorded as diagnosed or treated. [1]

Sputum smear microscopy is still the most widely used TB diagnostic test, despite its lack of sensitivity, most notably among children and people living with HIV. There is still no simple, instrument-free, point-of-care diagnostic test for active TB. Products moving forward are listed in table 1.

*Unlike with the phase designations for drug development (i.e., phase I, IIa, IIb, III), there are no global standard definitions for the stages or definitions for diagnostics development. The European Union (E.U.), the U.S. Food and Drug Administration (FDA), [17, 18] and the WHO [19] each uses different definitions and terminology.

Only technologies with documented progress—data published in peer-reviewed journals —since the 2013 Pipeline Report are shown in table 1. Several sponsors claim that they have additional tests in development, but these have made no visible progress since 2012. After the approval of Xpert MTB/RIF by the WHO in 2010, the diagnostics pipeline for molecular technologies expanded. TB experts spoke hopefully of “fast followers,” hoping that these tests might be cheaper, faster, or easier to use than Xpert MTB/RIF. No such test has yet been validated by the WHO or a stringent regulatory authority.

Xpert MTB/RIF Implementation Science Moves Forward

Cepheid’s GeneXpert system was recommended by the WHO in 2010. It uses a rapid, automated, cartridge-based nucleic acid amplification test (NAAT) platform that detects the TB organism and some common rifampin-resistance mutations. The Xpert MTB/RIF assay is more accurate than smear microscopy and much faster than TB culture. Data from the implementation of Xpert MTB/RIF may have helped persuade more countries to use it. [20]

A 2013 Cochrane Review [21] analysis focusing on 18 studies reported a “pooled sensitivity of 88% and specificity of 98%” when Xpert MTB/RIF replaced smear microscopy as an initial test, and pooled sensitivity of “67% and specificity of 98%” when used as a follow-up test after a smear-negative culture result. The authors concluded that Xpert MTB/RIF can be used as an “initial diagnostic test for TB detection and [rifampin] resistance” and would be “valuable” as an add-on test. [22] In 2014, the Cochrane Review published an updated analysis of Xpert (27 studies), with highly consistent results. [23]

The WHO updated its policy guidance on Xpert MTB/RIF in October 2013, recommending that the assay be used for initial diagnosis in individuals suspected of having MDR-TB or HIV-associated TB. It added conditional recommendations regarding the assay’s use as a follow-up to microscopy, in “adults who are suspected of having TB but not at risk of MDR-TB or HIV-associated TB.” [24] The update provided recommendations on using Xpert MTB/RIF to detect TB in children. [25]

A systematic review and meta-analysis [26] determined that Xpert MTB/RIF performed well compared with culture and a composite reference standard in the detection of certain types of extrapulmonary TB. The WHO recommends using Xpert MTB/RIF rather than conventional tests for “diagnosis of TB in lymph nodes and other tissues, and as the preferred initial test for diagnosis of TB meningitis [tuberculous meningitis].” [27]

One of the many studies published in the past year and a half on Xpert MTB/RIF showed that nurses can administer the assay effectively in primary health care settings. [28] Rapid diagnosis allows more patients to start treatment the same day. Hanrahan and colleagues found that those who received an Xpert MTB/RIF–positive test at a primary health clinic had a median time of zero days time to treatment initiation. [29] In a study done in South Korea, the median turnaround time for the Xpert MTB/RIF assay was 0 and 6 days; the median time to treatment was 7 days compared with 21 days in those who did not have a diagnosis with Xpert MTB/RIF. [30]

In some of these studies, Xpert MTB/RIF was used to diagnose tuberculous meningitis; one in Vietnam showed that diagnosis was possible: Xpert MTB/RIF had a sensitivity of 59.3% when compared with microscopy (78.6%) and the Mycobacterial Growth Indicator Tube (MGIT) liquid culture system (66.5%). [31] Several studies also tried using samples other than sputum to detect TB using Xpert MTB/RIF. [32, 33] Among people with HIV, exhaled breath condensate, urine, saliva, and blood samples did not allow TB detection using Xpert MTB/RIF. [34] Another study found that Xpert MTB/RIF can be used as the initial diagnostic for HIV-associated lymph node tuberculosis. A single Xpert test had a 88.2% and a sensitivity of 93.3%, though this improved with decreasing CD4 cell count. All patients who had a positive Xpert MTB/RIF result initiated treatment within one day compared with those without an Xpert MTB/RIF result. [35] A study with Xpert using stool as a specimen for the diagnosis of pulmonary TB in HIV-positive children found that Xpert detected “8/17 (47%) culture-confirmed tuberculosis cases, including 4/5 (80%) HIV-infected and 4/12 (33%) HIV-uninfected children.” [36]

Many studies showed that Xpert MTB/RIF increased detection of TB, both drug-resistant and drug-susceptible. An active case-finding study in Phnom Penh, Cambodia, increased detection of drug-susceptible and drug-resistant TB by using a symptom screening followed by smear microscopy and targeted use of Xpert MTB/RIF. [37] At health centers in Adama Town and the Oromia region of Ethiopia, Xpert MTB/RIF was found to increase the TB detection rate by 47.4% (64 cases) compared with smear microscopy, especially in patients with advanced immunosuppression. [38] Results from the implementation of Xpert MTB/RIF in nine TB REACH projects show that Xpert MTB/RIF detected TB in a large number of people with TB that routine services failed to detect. In Kenya, Malawi, the Democratic Republic of Congo, and Nepal, diagnostic interventions that included Xpert MTB/RIF to test people who were sputum smear–negative found 2,833 people that would previously have been unidentified. [39]

Some published data suggest that Xpert MTB/RIF has not demonstrated a clear effect in improving patient outcomes. [40, 41] The TB NEAT [42] and TB Extend [43] studies concluded that Xpert MTB/RIF does not necessarily increase the number of people treated, but does increase the number of people diagnosed with microbiologically confirmed TB. In many countries, including South Africa, Xpert MTB/RIF testing is done through a laboratory service rather than in community clinics. If Xpert MTB/RIF was implemented at more peripheral levels of the health system, it would be possible for people to have a single visit to a health facility and start treatment the same day, thereby reducing loss to follow-up, morbidity, and mortality.

Current operational research studies on Xpert MTB/RIF listed on ClinicalTrials.gov focus on achieving the best clinical outcomes and reducing TB in HIV-positive adults and children, using Xpert MTB/RIF in mobile units, assessing Xpert MTB/RIF diagnosis at the point of treatment, and intensifying case finding with a package of diagnostic tools including Xpert MTB/RIF.

Xpert MTB/RIF is a major advance in TB diagnostics. Among the short-term priorities should be understanding how best to implement Xpert MTB/RIF in order to improve individual and public health, increasing the ruggedness of the instrument in order to ensure that it operates reliably in a variety of climates and settings, determining specimen processing and testing procedures that optimize yield from Xpert MTB/RIF testing of nonrespiratory specimens, and increasing the assay’s sensitivity to enable it to detect a greater proportion of paucibacillary TB.

Alere Determine LAM – A Useful Test in Advanced Immunosuppression

An important advance in assays over the past year is the Alere Determine TB LAM (lipoarabinomannan) lateral flow test. Several studies are assessing its ability to detect TB in severely immunosuppressed people with HIV, who are among the hardest to diagnose.

One of the key findings, presented at the Conference for Retroviruses and Opportunistic Infections in Boston, Massachusetts, in February 2014, is the importance of the Determine LAM urinary test as an add-on rather than a stand-alone test. Steven Lawn presented data showing an increase in detection from 26.6% to 80.6%, when the Determine LAM test was added to an Xpert MTB/RIF test. When combined, Determine TB LAM and Xpert MTB/RIF detected 69.1% of culture-confirmed cases, enabling them to find MTB infection in 85% of people with CD4 cell counts below 100/mm3. [44] In Uganda, a study showed that the sensitivity of Xpert MTB/RIF and Determine LAM, used together, is superior to that of either test alone. [45]

A study conducted in Ethiopia in people with HIV found that the Determine TB LAM assay worked best in those who had a CD4 cell count ≤100/mm3 and that it could be used with sputum microscopy in this group. [46] A study conducted in hospital and outpatient settings in Uganda and South Africa found that in HIV-positive adults with symptoms of TB who had a CD4 cell count ≤100/mm3, the assay detected over half of culture-positive tuberculosis samples in less than 30 minutes. [47] Getting sputum samples from children is difficult, so for them a urinary LAM test would be best for TB detection; however, a study in South Africa showed that the test has insufficient sensitivity and specificity to diagnose TB in children, whether they have HIV or not. [48]

Determine TB LAM tests can also be used to rule in TB in patients with advanced HIV-induced immunosuppression and lead to early treatment initiation. [49] The test is cheap, produces results in less than 30 minutes, and can be used at the point of care. The WHO must review available evidence on Determine TB LAM, and provide guidance so that this test, if appropriate, can be used widely in people with HIV and low CD4 counts, and possible TB.

Other Diagnostics Progressing

New additions to the 2014 table are the LiPA (Nipro), the FluoroType MTB (Hain Lifescience), the FluoroType MTB RNA (Hain Lifescience), and the Pure LAMP (Eiken Chemical). The LiPA is a drug susceptibility test (DST). A recent study found no difference between conventional DST and LiPA for rifampin, pyrazinamide, and levofloxacin, but it did find a difference in isoniazid susceptibility. [50] FIND is evaluating LiPA at two centralized laboratories. The FluoroType MTB is a semi-automated nucleic acid amplification test to detect MTB. A study evaluated the test in a laboratory in Germany and found it had a sensitivity of 99.2% (smear-positive 100%; smear-negative 56.3%) and a specificity of 98.9%. The authors concluded that the test results were comparable to non-nucleic acid amplification tests on the market. The FluoroType MTB RNA is a molecular platform that monitors therapy of people with TB. The assay is in development, and Hain Lifescience intends to publish its first clinical data this year. [51] There is a need for additional well-designed, quality-monitored studies to ensure the reproducibility of these results. The Pure LAMP is a manual TB detection tool based on loop-mediated isothermal amplification (LAMP) using a nucleic acid amplification method. A study at county-level TB laboratories in China found 92.12% sensitivity in smear-positive, culture-positive TB patients and 53.81% in smear-negative, culture-positive patients. Specificity was 98.32%. The study found that there was a lower contamination rate than in solid culture. [52]

The linear-after-the-exponential PCR (LATE-PCR) with Lights-On/Lights-Off probes is a test that can detect MTB and resistance to isoniazid, rifampin, ethambutol, fluoroquinolones, amikacin, kanamycin, and capreomycin in less than three hours. [53] Brandeis University licensed this technology to Hain Lifescience. Hain will work to develop assay versions to detect MDR and XDR-TB in one single-tube PCR assay.

The TREK Sensititre MYCOTB MIC plate is a culture-based technology for DST. A study conducted in the Republic of Korea and Uganda assessed the performance and feasibility compared to the agar proportion method (APM). Results between the MYCOTB and APM showed ≥92% for 7 of 12 drugs with respect to susceptible or resistant TB isolates when assessed with a strict definition. [54] Minimum inhibitory concentration (MIC) results are used to optimize therapy in a number of infectious diseases other than TB. The availability of a simple, commercially produced MIC plate for MTB testing that shows what drugs the person’s strain of TB is resistant to could facilitate individualized approaches to the management of highly drug-resistant TB.

Other studies currently under way are assessing the use of interferon gamma release assays (IGRAs), primarily Quantiferon TB Gold (QFT), for diagnosis of latent TB infection in health care workers in high- and middle-income countries and in children. Two studies (NCT00982969 and NCT00962676) are assessing the clinical use of QFT in the diagnosis of active TB in immunosuppressed and immunocompetent patients. The WHO recommends against the use of IGRAs for the detection of active TB in any setting. [55]

Three studies (NCT01301144, NCT01748357, NCT01379066) are looking at the efficacy of volatile organic compounds (VOC), with one study assessing the Siemens VOC breath analyzer. No published data on these studies were available in 2013.

Diagnostics from the 2013 Pipeline with No Reported Progress

The following tests from the 2013 Pipeline Report are not included in this year’s table, as no new data have been published: the Alere Q, B-Smart GeneXpert XDR cartridge, GenoType MTBDRsl, iCubate, Infiniti MTB, Loopamp TB detection, GenoType MTBDRplus 2.0, NATeasy, TruArray, Truenat, TB rapid screen, TBDx, BNP Middlebrook, MDR/XDR-TB Color Test, BreathLink, and the breathalyzer prototype. Of these, the GenoType MTBDRplus 2.0, iCubate System, EasyNAT TB Diagnostic Kit, and the Truenat MTB test are now available on the market. The GenoType MTBDRplus 2.0 and the Truenat had data published in 2007–2012 and 2012, respectively. The Truenat is currently included in a study (NCT01589289) on predictors of tropical diseases in neurological disorders in the Democratic Republic of the Congo. FIND and Applied Visual Life Sciences (Leesburg, Virginia) recently announced a collaboration to evaluate the TBDx automated platform.

The developer of Truenat, Bigtec Laboratories, states that it has tested the assay’s performance against Xpert MTB/RIF, is now evaluating the test in the public sector in India to inform national TB policy, is attempting to validate the Truenat MTB test for detection of TB in extrapulmonary samples, and is developing a resistance assay for detection of MDR-TB. Truenat said that it is developing a multicenter trial in collaboration with FIND. [56]

Basic Science and Biomarkers

Current limits on our understanding of the biology of TB infection and disease limit scientific approaches to developing better diagnostic tests. There is simply not enough research being funded and conducted in basic science and biomarker discovery for TB. A ClinicalTrials.gov search found only three studies (NCT01269268, NCT00023439, and NCT00212498) investigating potential TB biomarkers. [57]

Funding

Funding for TB diagnostic R&D remains grossly insufficient; there was a 23.4% decline in spending between 2011 and 2012 according to our most recent report on TB R&D resource tracking. [58] In 2012, US$42,429,160 was spent globally when the Global Plan to Stop TB 2011–2015 called for annual spending of US$340 million. [59] This serious inadequacy of funding is one of the main reasons for the lack of movement in the diagnostics pipeline.

Whole-Genome Sequencing: The Final Frontier?

Whole-genome sequencing is becoming cheaper and more widely used for a variety of scientific investigations, including disease diagnosis, staging, and response to therapy. [60] Current technologies available from Illumina, Oxford Nanopore Technologies, Life Technologies, and Integrated Nano-Technologies can be used for whole-genome sequencing for TB. South Africa uses whole-genome sequencing as part of its TB drug-resistance surveillance, and the United Kingdom uses it for management of patients with very difficult XDR-TB cases. If the technology can be developed, [61] there is potential to use whole-genome sequencing to manage patients with MDR- and XDR-TB. Whole-genome sequencing has the potential to help guide clinicians in the selection of regimens to which a patient’s TB organism is susceptible. However, additional basic-science research is needed to more fully delineate the mechanisms of resistance and the spectrum of genetic determinants of resistance for certain drugs.

Identifying High-Priority Target Product Profiles and Market Size Estimation

While much of the current activity is centered around scale-up of Xpert MTB/RIF and evaluation of newer molecular tests, there are many other gaps in TB diagnostics, including a simple, low-cost triage test to identify patients who need further testing; a simple, biomarker-based TB test for nonsputum samples; a molecular or nonmolecular smear replacement test at the microscopy-center level; and tests for systematic screening.

Kik and colleagues published a study [62] in which the greatest needs were identified using several criteria, with the engagement of stakeholder groups. A rapid, sputum-based, molecular test for microscopy centers (with the option of an add-on DST cartridge) ranked highest, followed by a rapid biomarker-based, instrument-free test for nonsputum samples (which also detects childhood and extrapulmonary TB).

Parallel efforts to estimate potential markets for new TB tests are ongoing. This information will be most helpful to product developers and could catalyze new investments. Kik and colleagues estimated that the potential market size for a smear replacement molecular test (costing US$5) to be 30.8 million tests annually, with a potential market value of US$154 million per year in 22 high-burden countries. [63]

An expert consensus group convened by the WHO, the Global Laboratory Initiative, the Stop TB Partnership, and FIND met in Geneva, Switzerland, in May 2014 to develop, review, and agree on the minimum requirements for products most urgently needed; a report is expected in late 2014.

Conclusion

The TB diagnostics pipeline is at a standstill. Several potentially promising technologies are stuck in early development with little funding and no cohesive strategy to develop and evaluate them faster and more effectively. The TB diagnostics pipeline needs to be coordinated, prioritized, and funded by the TB and research communities together.

Recommendations

1. Public- and private-sector R&D funders and research institutes must include more clinicians as researchers in the development process to ensure that basic science and biomarker research prioritizes needs based product development.
2. Public- and private-sector R&D funders, investigators, and civil-society must prioritize and fully fund the development of an accurate, fast, cheap, point-of-care diagnostic for TB.
3. Public- and private-sector R&D funders and investigators must prioritize and fully fund basic science, biomarker research, in order to gain a better understanding of TB disease.
4. Public- and private-sector R&D funders and policy makers setting the agenda for R&D must create new opportunities for investigators and developers to be able to translate findings from biomarker research into technologies.
5. Public- and private-sector R&D funders must fully fund specimen- and strain banks to increase their capacity and investigators’ access to them, and to facilitate technology development and early testing. They must develop standard operating procedures across initiatives so that samples and information can be shared.

Endnotes

1. Herbert N, George A, Baroness Masham of Ilton, et al. World TB Day 2014: finding the missing 3 million. Lancet. 2014 Mar 22;383(9922):1016–8. doi: 10.1016/S0140-6736(14)60422-0.
2. Castan P, Pablo A, Fernández-Romero N, et al. Point-of-care system for detection of mycobacterium tuberculosis and rifampin resistance in sputum samples. J. Clin. Microbiol. 2014 February;52(2):502–7. doi: 10.1128/JCM.02209-13.
3. Matsumoto T, Ogata H, Toyota E, et al. Clinical evaluation of a line probe assay kit for the identification of Mycobacterium species and detection of drug-resistant Mycobacterium tuberculosis. Kekkaku Journal. 2013 Mar;88(3):291–6.
4. Schito, Marco (National Institutes of Health, Bethesda, MD). Personal communication with: Colleen Daniels (Treatment Action Group, New York, NY). 2014 March 11.
5. Hofmann-Thiel S, Hoffmann H. Evaluation of FluoroType MTB for detection of Mycobacterium tuberculosis complex DNA in clinical specimens from a low-incidence country. BMC Infect Dis. 2014 Feb 5;14:59. doi: 10.1186/1471-2334-14-59.
6. Hain, David (Hain Lifescience, Nehren, Germany). Personal communication with: Colleen Daniels (Treatment Action Group, New York, NY). 2014 March 28.
7. Ibid.
8. Rice J, Rice L, Wangh L, et al. A four color, highly multiplexed, single-tube, quantitative end-point assay for M(X)DR-TB using LATE-PCR and allied technologies. Paper Presented at: European Society of Mycobacteria; 2013 July; Florence, Italy.
9. Rice J, Rice L, et al. Single-tube multiplex assay for M(X)DR-TB. Paper presented at: 18th Conference of the Union North American Region; 2014 February 27– March 1; Boston, MA.
10. Ou X, Li Q, Xia H, et al. Diagnostic accuracy of the PURE-LAMP test for pulmonary tuberculosis at the county-level laboratory in China. PLoS One. 2014 May 1;9(5):e94544. doi: 10.1371/journal.pone.0094544.
11. Boehme, Catharina. (Foundation for Innovative New Diagnostics, Geneva, Switzerland). Personal communication with: Colleen Daniels (Treatment Action Group, New York, NY). 2014 March 26.
12. Lawn SD, Kerkhoff AD, Vogt M, Wood R. HIV-associated tuberculosis: relationship between disease severity and the sensitivity of new sputum-based and urine-based diagnostic assays. BMC Med. 2013 Oct 29;11:231. doi: 10.1186/1741-7015-11-231.
13. Dhana AV, Howell P, Spender D. When smear and molecular diagnostics fail: identification of tuberculosis in advanced HIV infection using the newly developed urine lipoarabinomannan lateral-flow assay. BMJ Case Rep 2014. 2014 March 10. doi: 10.1136/bcr-2013-200696.
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18. Hojvat, Sally (U.S. Food and Drug Administration, Bethesda, MD). Personal communication with: Colleen Daniels (Treatment Action Group, New York, NY). 2014 June 19.
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20. Steingart KR, Schiller I, Horne DJ, Pai M, Boehme CC, Dendukuri N. Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev. 2014 Jan 21;1:CD009593. doi: 10.1002/14651858.CD009593.pub3.
21. Ibid.
22. Ibid.
23. Steingart KR, et al. Xpert MTB/RIF assay.
24. World Health Organization. Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF system for the diagnosis of pulmonary and extrapulmonary TB in adults and children: policy update. Geneva: World Health Organization; 2013. Available from: http://www.who.int/tb/laboratory/policy_statements/en/. (Accessed 2014 April 16)
25. Ibid.
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27. Ibid.
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32. Christopher DJ, Schumacher SG, Michael JS, et al. Performance of Xpert MTB/RIF on pleural tissue for the diagnosis of pleural tuberculosis. Eur Respir J. 2013 Nov;42(5):1427–9. doi: 10.1183/09031936.00103213.
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34. Shenai S, Amisano D, Ronacher K, et al. Exploring alternative biomaterials for diagnosis of pulmonary tuberculosis in HIV-negative patients by use of the GeneXpert MTB/RIF assay. J Clin Microbiol. 2013 Dec;51(12):4161–6. doi: 10.1128/JCM.01743-13.
35. Van Rie A, Page-Shipp L, Mellet K, et al. Diagnostic accuracy and effectiveness of the Xpert MTB/RIF assay for the diagnosis of HIV-associated lymph node tuberculosis. Eur J Clin Microbiol Infect Dis. 2013 Nov;32(11):1409–15. doi: 10.1007/s10096-013-1890-0.
36. Nicol MP, Spiers K, Workman L, et al. Xpert MTB/RIF testing of stool samples for the diagnosis of pulmonary tuberculosis in children. Clin Infect Dis. 2013 Aug;57(3):e18–21. doi: 10.1093/cid/cit230.
37. Lorent N, Choun K, Thai S, et al. Community-based active tuberculosis case finding in poor urban settlements of Phnom Penh, Cambodia: a feasible and effective strategy. PLoS One. 2014 Mar 27;9(3):e92754. doi: 10.1371/journal.pone.0092754.
38. Balcha TT, Sturegård E, Winqvist N, et al. Intensified tuberculosis case-finding in HIV-positive adults managed at Ethiopian health centers: diagnostic yield of Xpert MTB/RIF compared with smear microscopy and liquid culture. PLoS One. 2014 Jan 22;9(1):e85478. doi: 10.1371/journal.pone.0085478.
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40. Hanrahan C, et al. Time to treatment and patient outcomes.
41. Theron G, et al. Feasibility, accuracy, and clinical effect of point-of-care Xpert MTB/RIF testing.
42. Theron G, et al. Feasibility, accuracy, and clinical effect of point-of-care Xpert MTB/RIF testing.
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50. Matsumoto T, et al. Clinical evaluation of a line probe assay kit.
51. Hain, David (Hain Lifescience, Nehren, Germany). Personal communication with: Colleen Daniels (Treatment Action Group, New York, NY). 2014 March 28.
52. Ou X, et al. Diagnostic accuracy of the PURE-LAMP test.
53. Rice J, et al. A four color, highly multiplexed, single-tube, quantitative end-point assay for M(X)DR-TB
54. Lee J, et al. Sensititre MYCOTB MIC plate for testing Mycobacterium tuberculosis susceptibility
55. World Health Organization. Tuberculosis Diagnostics [Internet].
56. Nair, Chandrasekhar (Director and CEO, bigtec Labs, Bangalore, India). Personal communication with: Colleen Daniels (Treatment Action Group, New York, NY). 2014 April 26.
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59. Ibid.
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