An Integrated Tabletop Platform for Rapid Detection of XDR-RB in Clinical Samples
Funding Source: NIH 5R01AI111435-05
The goal of this project is to produce and deliver an integrated tabletop diagnostic platform for detecting extensively drug-resistant tuberculosis (XDR-TB) in sputum in less than eight hours using novel Gel Element Microarray (GEM) technology developed by our industry partner, Akonni Biosystems. There is currently no FDA approved rapid diagnostic for XDR-TB in the U.S., which is why the 2013 CDC fact sheet states that diagnosis of XDR-TB (a NIAID Category C priority pathogen) currently requires “6 to 16 weeks” to complete.1 XDR-TB is caused by Mycbacterium tuberculosis (Mtb) that is resistant to the two most effective first-line anti-TB medications, isoniazid (INH) and rifampin (RIF) as well as the most effective second-line medications including fluoroquinolones (FQ) and at least one of the injectable drugs, amikacin (AMK), kanamycin (KAN) and capreomycin (CAP). XDR-TB, which has been associated with up to 80% mortality,2 is considered “virtually untreatable” in many parts of the world and is threatening global TB control.3 In 2011 alone, over 6,000 new cases were reported to the World Health Organization (WHO) from 85 countries.4 WHO estimates this is number is likely <10% of the actual number of incident cases due to lack of global laboratory capacity to diagnose XDR-TB, the length of time necessary for diagnosis using available growth-based methods, and an absence of an approved molecular assay for rapidly detecting global XDR-TB.
Both domestically and abroad, U.S. civilians are at increased risk for exposure to XDR-TB from a growing list of potential transmission environments including contact with XDR-TB infected persons entering the US undetected,5 to airplane flights,6, 7 and increased exposure to TB in high prevalence countries during leisure and business travels. US troops are at increased risk of exposure from visitors to foreign and domestic military bases,8 and environments encountered on tactical and humanitarian missions.
There is a clear and critical need for an integrated, table-top platform for high sensitivity, high specificity, rapid diagnosis of drug resistant TB from direct patient samples. We propose to combine the experience, resources and existing diagnostic testing pipeline of the Global Consortium for Drug Resistant Tuberculosis Diagnostics (GCDD – NIAID U01AI082229) with the technological innovation and industry knowledge of our project partner, Akonni Biosystems to produce a rapid XDR-TB detection platform based on detection of resistance conferring mutations. Leveraging our combined resources, we will expand, verify, and field-test an existing prototype GEM platform (NIAID: RC3 AI089106 and R43 EB011274) to detect all of the clinically relevant single nucleotide polymorphisms (SNPs) that confer resistance in XDR-TB isolates. The proposed platform will be an integrated, table-top sized device, able to process sample to clinically relevant result in under eight hours, and will fill an unmet need in drug resistant TB diagnostics. The technical and clinical knowledge gained in this project will translate directly to the ultimate goal of a “sample-in, answer-out” system that is deployed closer to the point of need than current, diagnostics, enabling not only rapid diagnosis, but also rapid response to the threat posed by XDR-TB in healthcare and biodefense settings. Based on our extensive experience with the genetic basis of XDR-TB, and Akonni Biosystems’ high fidelity prototype platform for identifying specific SNPs in pathogens from clinical samples, we hypothesize that we will be able to detect Mtb isolates with clinically relevant phenotypic resistance to INH, RIF, FQ, AMK, KAN, and CAP from a direct sputum sample, with 90-98% sensitivity and ~100% specificity in under eight hours. We will achieve this goal with the following three aims:
Specific Aim 1: Expand and optimize an existing prototype Gel Element Microarray (GEM) platform to simplify the user interface and detect all of the clinically relevant resistant alleles found in XDR-TB isolates.
Specific Aim 2: Verify the expanded XDR-TB GEM platform performance in a controlled laboratory setting.
Specific Aim 3: Evaluate the XDR-TB GEM platform performance in the field with direct clinical samples.
The proposed project directly addresses a top research priority of the NIAID—the development of “technologies to rapidly diagnose TB and to identify drug resistance” and represents a significant advance in the field of rapid diagnostics. This team-based multidisciplinary project is based on existing partnerships, mature, well-established science and technology, and a proven diagnostics development and testing pipeline. and presents a low-risk, high-reward opportunity to produce a working, validated and field-tested integrated platform for rapid diagnosis of XDR-TB from sputum.
References
1. Centers for Disease Control and Prevention (CDC). TB Elimination: Extensively Drug-Resistant Tuberculosis (XDR TB). Centers for Disease Control and Prevention (CDC); 2013 [updated 2013; cited 2013 07 June]; Available from: http://www.cdc.gov/tb/publications/factsheets/drtb/xdrtb.pdf.
2. Gandhi NR, Shah NS, Andrews JR, Vella V, Moll AP, Scott M, Weissman D, Marra C, Lalloo UG, Friedland GH, Tugela Ferry C, Research C. HIV coinfection in multidrug- and extensively drug-resistant tuberculosis results in high early mortality. Am J Respir Crit Care Med. 2010;181(1):80-6. PubMed
3. Marris E. Extreme TB strain threatens HIV victims worldwide. Nature. 2006;443(7108):131. PubMed
4. World Health Organization (WHO). Global tuberculosis control 2012. 2012 [updated 2012 2013/04/29/; cited June 7, 2013]; Available from: http://www.who.int/tb/publications/global_report/en/index.html.
5. Government Acountability Office (GAO). Public Health and Border Security: HHS and DHS Should Further Strengthen Their Ability to Respond to TB Incidents. Washington DC 2008. GAO-09-58 p. 63.
6. Martinez L, Blanc L, Nunn P, Raviglione M. Tuberculosis and air travel: WHO guidance in the era of drug-resistant TB. Travel medicine and infectious disease. 2008;6(4):177-81. PubMed
7. Martinez L, Thomas K, Figueroa J. Guidance from WHO on the prevention and control of TB during air travel. Travel medicine and infectious disease. 2010;8(2):84-9. PubMed
8. Aaron CL, Fotinos MJ, West KB, Goodwin DJ, Mancuso JD. Tuberculosis among nonimmigrant visitors to U.S. Military installations. Military medicine. 2013;178(3):346-52. PubMed