Genetic Characterization Conferred Co-Resistance to Isoniazid and Ethionamide in <i>Mycobacterium tuberculosis</i> Isolates from Southern Xinjiang, China

Background Ethionamide (ETH), a structural analogue of isoniazid (INH), is used for treating multidrug-resistant tuberculosis (MDR-TB). Due to the common target InhA, INH and ETH showed cross-resistance in M. tuberculosis . This study aimed to explore the INH and ETH resistant profiles and genetic mutations conferring independent INH- or ETH-resistance and INH-ETH cross-resistance in M. tuberculosis circulating in south of Xinjiang, China. Methods From Sep 2017 to Dec 2018, 312 isolates were included using drug susceptibility testing (DST), spoligotyping, and whole genome sequencing (WGS) to analyze the resistance characteristics for INH and/or ETH. Results Among the 312 isolates, 185 (58.3%) and 127 (40.7%) belonged to the Beijing family and non-Beijing family, respectively; 90 (28.9%) were INH-resistant (INH R ) with mutation rates of 74.4% in katG , 13.3% in inhA and its promoter, 11.1% in ahpC and its upstream region, 2.2% in ndh , 0.0% in mshA , whilst 34 (10.9%) were ETH-resistant (ETH R ) with mutation rates of 38.2% in ethA , 26.2% in inhA and its promoter, and 5.9% in ndh , 0.0% in ethR or mshA ; and 25 (8.0%) were INH-ETH co-resistant (INH R ETH R ) with mutation rates of 40.0% in inhA and its promoter, and 8% in ndh. katG mutants tended to display high-level resistant to INH; and more inhA and its promoter mutants showed low-level of INH and ETH resistance. The optimal gene combinations by WGS for the prediction of INH R , ETH R , and INH R ETH R were, respectively, katG + inhA and its promoter (sensitivity: 81.11%, specificity: 90.54%), ethA + inhA and its promoter+ ndh (sensitivity: 61.76%, specificity: 76.62%), and inhA and its promoter+ ndh (sensitivity: 48.00%, specificity: 97.65%). Conclusion This study revealed the high diversity of genetic mutations conferring INH and/or ETH resistance among M. tuberculosis isolates, which would facilitate the study on INH R and/or ETH R mechanisms and provide clues for choosing ETH for MDR treatment and molecular DST methods in south of Xinjiang, China.