Genomic Profiling of Mycobacterium tuberculosis Strains, Myanmar.

Htin Lin Aung,Peter J Lockhart,Yang Fong,Patrick J Biggs,Tsin Wen Yeo,Si Thu Aung,Gregory M Cook,Philip C Hill,Wint Wint Nyunt,Richard C Winkworth

doi:10.3201/eid2711.210726

Abstract

Multidrug resistance is a major threat to global elimination of tuberculosis (TB). We performed phenotypic drug-susceptibility testing and whole-genome sequencing for 309 isolates from 342 consecutive patients who were given a diagnosis of TB in Yangon, Myanmar, during July 2016‒June 2018. We identified isolates by using the GeneXpert platform to evaluate drug-resistance profiles. A total of 191 (62%) of 309 isolates had rifampin resistance; 168 (88%) of these rifampin-resistant isolates were not genomically related, indicating the repeated emergence of resistance in the population, rather than extensive local transmission. We did not detect resistance mutations to new oral drugs, including bedaquiline and pretomanid. The current GeneXpert MTB/RIF system needs to be modified by using the newly launched Xpert MTB/XDR cartridge or line-probe assay. Introducing new oral drugs to replace those currently used in treatment regimens for multidrug-resistant TB will also be useful for treating TB in Myanmar.

Highlights

Multidrug resistance is a major threat to global elimination of tuberculosis (TB)
Myanmar is recognized by the World Health Organization (WHO) as having high burdens of TB (338 cases/100,000 population), MDR TB (21 cases/100,000 population), and co-infections of TB and HIV (29 cases/100,000 population) [1]
Phenotypic drug-susceptibility testing (DST) of first-line or second-line drugs is rarely performed for new patients, and currently testing is based solely on the Xpert MTB/RIF (M. tuberculosis/rifampin) assay

Summary

Introduction

Multidrug resistance is a major threat to global elimination of tuberculosis (TB). We performed phenotypic drug-susceptibility testing and whole-genome sequencing for 309 isolates from 342 consecutive patients who were given a diagnosis of TB in Yangon, Myanmar, during July 2016‒ June 2018. A nationwide drug-resistant TB survey was conducted during 2012–2013 by the Myanmar National Tuberculosis Programme (NTP) to identify the drug susceptibility profile for first-line drugs (phenotypic drug susceptibility testing for second-line drugs was established during 2016) [2]. This survey identified MDR TB among 5% of new cases and 27.1% of previously treated cases, and the Yangon region was identified as a hotspot for drug-resistant TB [3]. Phenotypic drug-susceptibility testing (DST) of first-line or second-line drugs is rarely performed for new patients, and currently testing is based solely on the Xpert MTB/RIF (M. tuberculosis/rifampin) assay. Technological advances in next-generation, wholegenome sequencing (WGS) and downstream bioinformatic analyses enable comprehensive detection of drug resistance and provide an alternative to existing

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Conclusion