Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study.
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Zignol Matteo, Cabibbe Andrea Maurizio, Dean Anna S, Glaziou Philippe, Alikhanova Natavan, Ama Cecilia, Andres Sönke, Barbova Anna, Borbe-Reyes Angeli, Chin Daniel P, Cirillo Daniela Maria, Colvin Charlotte, Dadu Andrei, Dreyer Andries, Driesen Michèle, Gilpin Christopher, Hasan Rumina, Hasan Zahra, Hoffner Sven, Hussain Alamdar, Ismail Nazir, Kamal S M Mostofa, Khanzada Faisal Masood, Kimerling Michael, Kohl Thomas Andreas, Mansjö Mikael, Miotto Paolo, Mukadi Ya Diul, Mvusi Lindiwe, Niemann Stefan, Omar Shaheed V, Rigouts Leen, Schito Marco, Sela Ivita, Seyfaddinova Mehriban, Skenders Girts, Skrahina Alena, Tahseen Sabira, Wells William A, Zhurilo Alexander, Weyer Karin, Floyd Katherine, Raviglione Mario C
Аннотация
METHODS: Population-level surveys were done in hospitals and clinics in seven countries (Azerbaijan, Bangladesh, Belarus, Pakistan, Philippines, South Africa, and Ukraine) to evaluate the use of genetic sequencing to estimate the resistance of Mycobacterium tuberculosis isolates to rifampicin, isoniazid, ofloxacin, moxifloxacin, pyrazinamide, kanamycin, amikacin, and capreomycin. For each drug, we assessed the accuracy of genetic sequencing by a comparison of the adjusted prevalence of resistance, measured by genetic sequencing, with the true prevalence of resistance, determined by phenotypic testing.
FINDINGS: Isolates were taken from 7094 patients with tuberculosis who were enrolled in the study between November, 2009, and May, 2014. In all tuberculosis cases, the overall pooled sensitivity values for predicting resistance by genetic sequencing were 91% (95% CI 87-94) for rpoB (rifampicin resistance), 86% (74-93) for katG, inhA, and fabG promoter combined (isoniazid resistance), 54% (39-68) for pncA (pyrazinamide resistance), 85% (77-91) for gyrA and gyrB combined (ofloxacin resistance), and 88% (81-92) for gyrA and gyrB combined (moxifloxacin resistance). For nearly all drugs and in most settings, there was a large overlap in the estimated prevalence of drug resistance by genetic sequencing and the estimated prevalence by phenotypic testing.
INTERPRETATION: Genetic sequencing can be a valuable tool for surveillance of drug resistance, providing new opportunities to monitor drug resistance in tuberculosis in resource-poor countries. Before its widespread adoption for surveillance purposes, there is a need to standardise DNA extraction methods, recording and reporting nomenclature, and data interpretation.
FUNDING: Bill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.