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Development of modern genomics provides us an effective method to understand the molecular mechanism of drug resistance and diagnose drug-resistant  Mycobacterium tuberculosis . In this study, mutations in 18 genes or intergenic regions acquired by whole-genome sequencing (WGS) of 183 clinical  M. tuberculosis  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  rpoB ), 90.5 and 97.8% for isoniazid ( katG ), 83.0 and 97.8% for streptomycin ( rpsL  combined with  rrs  530 loop and 912 loop), and 90.9 and 65.1% for ethambutol ( embB ), respectively. WGS data also showed that mutations in the  inhA  promoter increased only 2.2% sensitivity for INH based on mutations in  katG . Synonymous mutation  rpoB  A1075A was confirmed to be associated with the Beijing genotype. This study confirmed that mutations in  rpoB ,  katG ,  rrs  530 loop and 912 loop, and  rpsL  were excellent biomarkers for predicting rifampicin, isoniazid, and streptomycin resistance, respectively, and provided clues in clarifying the drug-resistance mechanism of  M. tuberculosis  isolates from China.

frontiers in microbiology

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