Genomic markers of drug resistance inMycobacterium tuberculosispopulations with minority variants

Abstract

AbstractMinority variants ofMycobacterium tuberculosisharbouring mutations conferring resistance can become dominant populations during tuberculosis (TB) treatment, leading to treatment failure. Our understanding of drug resistant within-host sub-populations and the frequency of resistance conferring mutations in minority variants remains limited.M. tuberculosissequences recovered from liquid cultures of culture-confirmed TB cases notified between January 2017 and December 2021 in New South Wales, Australia were examined. Potential drug resistance conferring minority variants were identified using LoFreq, and mixed populations of differentM. tuberculosisstrains (≥100 SNPs apart) were examined using QuantTB.A total of 1831 routinely sequencedM. tuberculosisstrains were included in the analysis. Drug resistance conferring minority variants were detected in 3.5% (65/1831) of sequenced cultures; 84.6% (55/65) had majority strains that were drug susceptible and 15.4% (10/65) had majority strains that were drug resistant. Minority variants with high confidence drug resistance conferring mutations were 1.5 times more common when the majority strains were drug resistant. MixedM. tuberculosisstrain populations were documented in 10.0% (183/1831) of specimens. Minority variants with high confidence drug resistance conferring mutations were more frequently detected in mixedM. tuberculosisstrain populations (2.7%, 5/183) than in single strain populations (0.6%, 10/1648; p=0.01).Drug resistant minority variants require careful monitoring in settings that implement routineM. tuberculosissequencing. The frequency with which drug resistant minority variants are detected is influenced by selective culture methods and culture-independent sequencing should provide a more accurate picture.