Rapid Tests for Drug Resistance to Detect Extensively Drug-Resistant Tuberculosis

Funding Source:  NIH  5U01AI082229-05

The Global Consortium for Drug-resistant Tuberculosis Diagnostics (GCDD) was established in 2008 by an international collaboration of researchers, healthcare professionals, and tuberculosis experts to characterize the genetic basis of drug resistance and evaluate molecular and microbiological methods of detecting DR-TB quickly and efficiently. 

This 5 year grant (2008-2013) was funded by the National Institutes of Health with data collected from four international enrollment sites: India, Republic of Moldova, the Philippines, and South Africa, as well as from three domestic laboratory sites: Richmond, CA; Honolulu, HI; and San Diego, CA.

Drug-resistant tuberculosis, in general, and XDR-TB in particular, is an indisputable threat to global public health, with the potential to reverse the hard-won achievements of TB treatment and control made in the last decade. Drug-resistant TB can spread very quickly in local communities with high rates of HIV as well as to the world through global travel, commerce, and immigration. The scourge of drug-resistant TB can be managed successfully only if it is detected rapidly, allowing for prompt and appropriate treatment before patients develop further resistance, transmit the disease or die.  Faced with the possible reversal of hard-won TB control gains both globally and in the US, the National Institute of Allergy and Infectious Diseases (NIAID) placed the development of “technologies to rapidly diagnose TB and to identify drug resistance” at the top of their list of research priorities for 2008. Our primary aim in the proposed study was to leverage existing molecular and microbiological methods to quickly and efficiently produce a functioning product for the rapid detection of TB drug resistance in both high- and low-resource settings.

Aim 1: To reduce the average XDR-TB detection time from months to a week. We will compare the performance of one existing line probe assay (Hain GenoType®MTBDRplus and Hain GenoType®MTBDRsl) with a newly developed sequence-based assay (pyrosequencing) and an expanded Microscopic Observation Drug Susceptibility (MODS) phenotypic assay, to detect resistance to isoniazid and rifampin, ofloxacin, moxifloxacin, kanamycin, amikacin, and capreomycin.

Aim 2: To determine agreement between rapid tests and standard drug susceptibility test results. Results of rapid tests based on smear-positive sputum will be compared with those from the current gold-standard drug susceptibility test method, which is based on subculture of Mycobacterium tuberculosis growth in the MGIT 960 liquid culture system.

Aim 3: To identify the genetic basis of discordant results from Aim 2. Strains identified as drug resistant by the drug susceptibility test, but not by the gene-based molecular tests, will be further examined through sequencing target genes, neighboring genes, or the entire genomes of unique strain families.

Aim 4: To characterize XDR-TB strains globally. Genotypic, phenotypic, and epidemiological features, as well as geographical relationships of XDR-TB strains, will be characterized and compared with other drug-resistant and susceptible strains. We will explore the relationships between drug resistance, including XDR-TB, and patient risk factors and strain families of M. tuberculosis.

Secondary aims
Secondary Aim 1: Cost-effectiveness study. The costs associated with performing each rapid test will be compared with improvements in time and accuracy for detecting drug resistance and XDR-TB over standard drug susceptibility testing methods.

Secondary Aim 2: To determine the predictive value of resistance-associated mutations in determining sputum culture conversion.

Our main findings were published in this paper:

Catanzaro A, Rodwell TC, Catanzaro DG, Garfein RS, Jackson RL, Seifert M, Georghiou SB, Trollip A, Groessl E, Hillery N, Crudu V, Victor TC, Rodrigues C, Lin GS, Valafar F, Desmond E, Eisenach K. Performance Comparison of Three Rapid Tests for the Diagnosis of Drug-Resistant Tuberculosis. PloS one. 2015; 10(8):e0136861. PMID 26322781

Additional papers are listed below:

Bojorquez, Ietza; Salazar, Irais; Garfein, Richard S; Cerecer, Paris; Rodwell, Timothy C. 2018. Surveillance or support: The experience of direct observation during tuberculosis treatment. Glob Public Health 13(7): 804-818. PMID 27748157

Georghiou, Sophia B; Seifert, Marva; Catanzaro, Donald G; Garfein, Richard S; Rodwell, Timothy C. 2017. Increased Tuberculosis Patient Mortality Associated with Mycobacterium tuberculosis Mutations Conferring Resistance to Second-Line Antituberculous Drugs. J Clin Microbiol 55(6): 1928-1937. PMID 28404672

Catanzaro, Donald G; Trollip, Andre P; Seifert, Marva; Georghiou, Sophia B; Garfein, Richard S; Rodwell, Timothy C; Catanzaro, Antonino; Eisenach, Kathleen D. 2017. Evaluation of the microscopic observation drug susceptibility assay for the detection of first- and second-line drug susceptibility for Mycobacterium tuberculosis. Eur Respir J 49(4): PMID  28381434

Seifert, M; Ajbani, K; Georghiou, S B; Catanzaro, D; Rodrigues, C; Crudu, V; Victor, T C; Garfein, R S; Catanzaro, A; Rodwell, T C. 2016. A performance evaluation of MTBDRplus version 2 for the diagnosis of multidrug-resistant tuberculosis. Int J Tuberc Lung Dis 20(5): 631-7. PMID 27084817

Kambli, Priti; Ajbani, Kanchan; Nikam, Chaitali; Sadani, Meeta; Shetty, Anjali; Udwadia, Zarir; Georghiou, Sophia B; Rodwell, Timothy C; Catanzaro, Antonino; Rodrigues, Camilla. 2016. Correlating rrs and eis promoter mutations in clinical isolates of Mycobacterium tuberculosis with phenotypic susceptibility levels to the second-line injectables. Int J Mycobacteriol 5(1): 43471. PMID 26927983

Berrada, Zenda L; Lin, Shou-Yean Grace; Rodwell, Timothy C; Nguyen, Duylinh; Schecter, Gisela F; Pham, Lucy; Janda, J Michael; Elmaraachli, Wael; Catanzaro, Antonino; Desmond, Edward. 2016. Rifabutin and rifampin resistance levels and associated rpoB mutations in clinical isolates of Mycobacterium tuberculosis complex. Diagn Microbiol Infect Dis 85(2): 177-81. PMID 27036978

Georghiou, S B; Ajbani, K; Rodrigues, C; Rodwell, T C. 2016. Performance of a pyrosequencing platform in diagnosing drug-resistant extra-pulmonary tuberculosis in India. Int J Tuberc Lung Dis 20(2): 160-5. PMID 26792466

Nikam, C; Patel, R; Sadani, M; Ajbani, K; Kazi, M; Soman, R; Shetty, A; Georghiou, S B; Rodwell, T C; Catanzaro, A; Rodrigues, C. 2016. Redefining MTBDRplus test results: what do indeterminate results actually mean?. Int J Tuberc Lung Dis 20(2): 154-9. PMID 26792465

Seifert, Marva; Georghiou, Sophia B; Catanzaro, Donald; Rodrigues, Camilla; Crudu, Valeriu; Victor, Thomas C; Garfein, Richard S; Catanzaro, Antonino; Rodwell, Timothy C. 2016. MTBDRplus and MTBDRsl Assays: Absence of Wild-Type Probe Hybridization and Implications for Detection of Drug-Resistant Tuberculosis. J Clin Microbiol 54(4): 912-8. PMID 26763971

Conners, E; Garfein, R S; Rodwell, T C; Udwadia, Z F; Catanzaro, D G. 2016. Mobility patterns of persons at risk for drug-resistant tuberculosis in Mumbai, India. Int J Tuberc Lung Dis 20(12): 1633-1638. PMID 27931339

Georghiou, Sophia B; Seifert, Marva; Lin, Shou-Yean; Catanzaro, Donald; Garfein, Richard S; Jackson, Roberta L; Crudu, Valeriu; Rodrigues, Camilla; Victor, Thomas C; Catanzaro, Antonino; Rodwell, Timothy C. 2016. Shedding light on the performance of a pyrosequencing assay for drug-resistant tuberculosis diagnosis. BMC Infect Dis 16(): 458. PMID 27576542

Colman, Rebecca E; Anderson, Julia; Lemmer, Darrin; Lehmkuhl, Erik; Georghiou, Sophia B; Heaton, Hannah; Wiggins, Kristin; Gillece, John D; Schupp, James M; Catanzaro, Donald G; Crudu, Valeriu; Cohen, Ted; Rodwell, Timothy C; Engelthaler, David M. 2016. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study. J Clin Microbiol 54(8): 2058-67. PMID 27225403

Georghiou, S B; Seifert, M; Catanzaro, D; Garfein, R S; Valafar, F; Crudu, V; Rodrigues, C; Victor, T C; Catanzaro, A; Rodwell, T C. 2016. Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape. Antimicrob Agents Chemother 60(7): 3994-4004. PMID 27090176

Kambli, P; Ajbani, K; Nikam, C; Khillari, A; Shetty, A; Udwadia, Z; Georghiou, S B; Rodwell, T C; Catanzaro, A; Rodrigues, C. 2015. Determination of MICs of levofloxacin for Mycobacterium tuberculosis with gyrA mutations. Int J Tuberc Lung Dis 19(10): 1227-9. PMID 26459538

ElMaraachli, W; Slater, M; Berrada, Z L; Lin, S-Y G; Catanzaro, A; Desmond, E; Rodrigues, C; Victor, T C; Crudu, V; Gler, M T; Rodwell, T C. 2015. Predicting differential rifamycin resistance in clinical Mycobacterium tuberculosis isolates by specific rpoB mutations. Int J Tuberc Lung Dis 19(10): 1222-6. PMID 26459537

Kambli, Priti; Ajbani, Kanchan; Sadani, Meeta; Nikam, Chaitali; Shetty, Anjali; Udwadia, Zarir; Georghiou, Sophia B; Rodwell, Timothy C; Catanzaro, Antonino; Rodrigues, Camilla. 2015. Defining multidrug-resistant tuberculosis: correlating GenoType MTBDRplus assay results with minimum inhibitory concentrations. Diagn Microbiol Infect Dis 82(1): 49-53. PMID 25749461

Kambli, Priti; Ajbani, Kanchan; Sadani, Meeta; Nikam, Chaitali; Shetty, Anjali; Udwadia, Zarir; Rodwell, Timothy C; Catanzaro, Antonino; Rodrigues, Camilla. 2015. Correlating Minimum Inhibitory Concentrations of ofloxacin and moxifloxacin with gyrA mutations using the genotype MTBDRsl assay. Tuberculosis (Edinb) 95(2): 137-41. PMID 25522842

Torres, Jessica N; Paul, Lynthia V; Rodwell, Timothy C; Victor, Thomas C; Amallraja, Anu M; Elghraoui, Afif; Goodmanson, Amy P; Ramirez-Busby, Sarah M; Chawla, Ashu; Zadorozhny, Victoria; Streicher, Elizabeth M; Sirgel, Frederick A; Catanzaro, Donald; Rodrigues, Camilla; Gler, Maria Tarcela; Crudu, Valeru; Catanzaro, Antonino; Valafar, Faramarz. 2015. Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates. Emerg Microbes Infect 4(7): e42. PMID 26251830

Ajbani, Kanchan; Lin, Shou-Yean Grace; Rodrigues, Camilla; Nguyen, Duylinh; Arroyo, Francine; Kaping, Janice; Jackson, Lynn; Garfein, Richard S; Catanzaro, Donald; Eisenach, Kathleen; Victor, Thomas C; Crudu, Valeru; Gler, Maria Tarcela; Ismail, Nazir; Desmond, Edward; Catanzaro, Antonino; Rodwell, Timothy C. 2015. Evaluation of pyrosequencing for detecting extensively drug-resistant Mycobacterium tuberculosis among clinical isolates from four high-burden countries. Antimicrob Agents Chemother 59(1): 414-20. PMID 25367911

Garfein, R S; Catanzaro, D G; Rodwell, T C; Avalos, E; Jackson, R L; Kaping, J; Evasco, H; Rodrigues, C; Crudu, V; Lin, S-Y G; Groessl, E; Groessel, E; Hillery, N; Trollip, A; Ganiats, T; Victor, T C; Eisenach, K; Valafar, F; Channick, J; Qian, L; Catanzaro, A. 2015. Phenotypic and genotypic diversity in a multinational sample of drug-resistant Mycobacterium tuberculosis isolates. Int J Tuberc Lung Dis 19(4): 420-7.PMID 25859997

Seifert, Marva; Catanzaro, Donald; Catanzaro, Antonino; Rodwell, Timothy C. 2015. Genetic mutations associated with isoniazid resistance in Mycobacterium tuberculosis: a systematic review. PLoS One 10(3): e0119628. PMID 25799046

Avalos, Elisea; Catanzaro, Donald; Catanzaro, Antonino; Ganiats, Theodore; Brodine, Stephanie; Alcaraz, John; Rodwell, Timothy. 2015. Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates: a systematic review. PLoS One 10(3): e0120470. PMID 25816236

Colman, Rebecca E; Schupp, James M; Hicks, Nathan D; Smith, David E; Buchhagen, Jordan L; Valafar, Faramarz; Crudu, Valeriu; Romancenco, Elena; Noroc, Ecaterina; Jackson, Lynn; Catanzaro, Donald G; Rodwell, Timothy C; Catanzaro, Antonino; Keim, Paul; Engelthaler, David M. 2015. Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing. PLoS One 10(5): e0126626. PMID 25970423

Catanzaro, Antonino; Rodwell, Timothy C; Catanzaro, Donald G; Garfein, Richard S; Jackson, Roberta L; Seifert, Marva; Georghiou, Sophia B; Trollip, Andre; Groessl, Erik; Hillery, Naomi; Crudu, Valeriu; Victor, Thomas C; Rodrigues, Camilla; Lin, Grace Shou-Yean; Valafar, Faramarz; Desmond, Edward; Eisenach, Kathleen. 2015. Performance Comparison of Three Rapid Tests for the Diagnosis of Drug-Resistant Tuberculosis. PLoS One 10(8): e0136861. PMID 26322781

Hoshide, Matt; Qian, Lishi; Rodrigues, Camilla; Warren, Rob; Victor, Tommie; Evasco 2nd, Henry B; Tupasi, Thelma; Crudu, Valeriu; Douglas, James T. 2014. Geographical differences associated with single-nucleotide polymorphisms (SNPs) in nine gene targets among resistant clinical isolates of Mycobacterium tuberculosis. J Clin Microbiol 52(5): 1322-9. PMID 23784122

Rodwell, Timothy C; Valafar, Faramarz; Douglas, James; Qian, Lishi; Garfein, Richard S; Chawla, Ashu; Torres, Jessica; Zadorozhny, Victoria; Kim, Min Soo; Hoshide, Matt; Catanzaro, Donald; Jackson, Lynn; Lin, Grace; Desmond, Edward; Rodrigues, Camilla; Eisenach, Kathy; Victor, Thomas C; Ismail, Nazir; Crudu, Valeru; Gler, Maria Tarcela; Catanzaro, Antonino. 2014. Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations. J Clin Microbiol 52(3): 781-9. PMID 24353002

Lin, S-Y Grace; Rodwell, Timothy C; Victor, Thomas C; Rider, Errin C; Pham, Lucy; Catanzaro, Antonino; Desmond, Edward P. 2014. Pyrosequencing for rapid detection of extensively drug-resistant Mycobacterium tuberculosis in clinical isolates and clinical specimens. J Clin Microbiol 52(2): 475-82. PMID 24478476

Trollip, A P; Moore, D; Coronel, J; Caviedes, L; Klages, S; Victor, T; Romancenco, E; Crudu, V; Ajbani, K; Vineet, V P; Rodrigues, C; Jackson, R L; Eisenach, K; Garfein, R S; Rodwell, T C; Desmond, E; Groessl, E J; Ganiats, T G; Catanzaro, A. 2014. Second-line drug susceptibility breakpoints for Mycobacterium tuberculosis using the MODS assay. Int J Tuberc Lung Dis 18(2): 227-32. PMID 24429318

Hillery, Naomi; Groessl, Erik J; Trollip, Andre; Catanzaro, Donald; Jackson, Lynn; Rodwell, Timothy C; Garfein, Richard S; Lin, S-Y Grace; Eisenach, Kathleen; Ganiats, Theodore G; Park, Daniel; Valafar, Faramarz; Rodrigues, Camilla; Crudu, Valeriu; Victor, Thomas C; Catanzaro, Antonino. 2014. The Global Consortium for Drug-resistant Tuberculosis Diagnostics (GCDD): design of a multi-site, head-to-head study of three rapid tests to detect extensively drug-resistant tuberculosis. Trials 15(): 434. PMID 25377177

Georghiou, Sophia B; Magana, Marisa; Garfein, Richard S; Catanzaro, Donald G; Catanzaro, Antonino; Rodwell, Timothy C. 2012. Evaluation of genetic mutations associated with Mycobacterium tuberculosis resistance to amikacin, kanamycin and capreomycin: a systematic review. PLoS One 7(3): e33275. PMID 22479378