Abstract
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.
Highlights
The World Health Organization’s (WHO’s) target is to end the tuberculosis epidemic by 2035 (Treatment Action Group and Stop Tb Partnership, 2018)
The isolates used for whole-genome sequencing (WGS) were obtained from 183 adult patients with pulmonary TB from 2005 to 2009 from institutes for tuberculosis control and prevention as well as tuberculosis hospitals distributed in 11 provinciallevel administration divisions (PLADs) of China; the numbers isolated from each PLAD were as follows: Beijing, 13; Fujian, 24; Guangdong, 8; Guizhou, 21; Henan, 6; Inner Mongolia, 5; Liaoning, 20; Shaanxi, 25; Shanghai, 26; Tibet, 30; and Xinjiang, 5
Synonymous mutations were universally acknowledged to be unrelated with drug resistance, we found that the prevalence of rpoB 1075 GCT-GCC (Ala-Ala) in RMP-resistant M. tuberculosis was higher than that in RMPsusceptible isolates, and the prevalence of gidB 205 GCA-GCG (Ala-Ala) in STR-resistant isolates was higher than that in STRsusceptible isolates
Summary
The World Health Organization’s (WHO’s) target is to end the tuberculosis epidemic by 2035 (Treatment Action Group and Stop Tb Partnership, 2018). Maningi et al (2018) reports that whole-genome sequencing (WGS) shows better concordance with the Lowenstein–Jensen (L-J) phenotypic assay than with Hain line probe assay in that many more mutations were found by WGS Many genes, such as ndh, efpA, kasA, iniABC operon (for INH resistance) (Sandgren et al, 2009; Nguyen, 2016); rpoC (RMP) (Farhat et al, 2013; Perdigao et al, 2020); embA, embC, ubiA (EMB) (Plinke et al, 2010; Zhao et al, 2015a; Farhat et al, 2016); and gidB (STR) (Nhu et al, 2012; Spies et al, 2011; Perdigao et al, 2014), are reported to correlate with drug resistance
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