Genomic Analysis Identifies Mutations Concerning Drug-Resistance and Beijing Genotype in Multidrug-Resistant Mycobacterium tuberculosis Isolated From China

Abstract

Development of modern genomics provides us an effective method to understand the molecular mechanism of drug resistance and diagnose drug-resistant <i>Mycobacterium tuberculosis</i>. In this study, mutations in 18 genes or intergenic regions acquired by whole-genome sequencing (WGS) of 183 clinical <i>M. tuberculosis</i> strains, including 137 multidrug-resistant and 46 pan-susceptible isolates from China, were identified and used to analyze their associations with resistance of isoniazid, rifampin, ethambutol, and streptomycin. Using the proportional method as the gold standard method, the accuracy values of WGS to predict resistance were calculated. The association between synonymous or lineage definition mutations with different genotypes were also analyzed. The results show that, compared to the phenotypic proportional method, the sensitivity and specificity of WGS for resistance detection were 94.2 and 100.0% for rifampicin (based on mutations in <i>rpoB</i>), 90.5 and 97.8% for isoniazid (<i>katG</i>), 83.0 and 97.8% for streptomycin (<i>rpsL</i> combined with <i>rrs</i> 530 loop and 912 loop), and 90.9 and 65.1% for ethambutol (<i>embB</i>), respectively. WGS data also showed that mutations in the <i>inhA</i> promoter increased only 2.2% sensitivity for INH based on mutations in <i>katG</i>. Synonymous mutation <i>rpoB</i> A1075A was confirmed to be associated with the Beijing genotype. This study confirmed that mutations in <i>rpoB</i>, <i>katG</i>, <i>rrs</i> 530 loop and 912 loop, and <i>rpsL</i> were excellent biomarkers for predicting rifampicin, isoniazid, and streptomycin resistance, respectively, and provided clues in clarifying the drug-resistance mechanism of <i>M. tuberculosis</i> isolates from China.