Abstract:

Objective: To analyze the characteristics of drug resistance-related gene mutations in Mycobacterium tuberculosis (MTB) isolated from five provinces in Northwest China, evaluate the efficacy of whole genome sequencing (WGS) technology in predicting phenotypic drug resistance, explore the applicability of existing rapid molecular diagnostic methods in this region, and provide scientific basis for the prevention and control of regional drug-resistant tuberculosis. Methods: From 2013 to 2022, 2125 clinical isolates of MTB were collected from Shaanxi Province, Gansu Province, Ningxia Hui Autonomous Region, Qinghai Province, and Xinjiang Uygur Autonomous Region. Phenotypic drug susceptibility testing was performed using the microplate method for 13 anti-tuberculosis drugs. Simultaneously, WGS and drug resistance gene mutation analysis were conducted. Taking the phenotypic drug susceptibility results as the gold standard, the sensitivity and specificity of WGS in predicting phenotypic drug resistance were analyzed. Additionally, the regional drug resistance mutation spectrum and sites not covered by rapid molecular diagnostic methods were analyzed. Results: Among the 1716 strains with phenotypic drug susceptibility results, the resistance rates of rifampin and isoniazid were 5.30% (91/1716) and 10.72% (184/1716), respectively. WGS predicted the sensitivity of rifampin, isoniazid, ethambutol, amikacin, kanamycin, levofloxacin, moxifloxacin, ethionamide, bedaquiline, clofazimine, and streptomycin to be 96.74% (89/92), 72.83% (134/184), 67.92% (36/53), 5/6, 7/8, 54.84% (17/31), 59.09% (13/22), 80.00% (24/30), 1/8, 23.08% (3/13), and 97.22% (35/36), respectively, with specificities all exceeding 98.34%. The most prevalent resistance mutations to rifampin and isoniazid in the northwest region were rpoB_Ser450Leu (58.16%, 57/98) and katG_Ser315Thr (68.71%, 101/147), respectively, but there were also some rare mutations such as rpoB_Ser450Trp, katG_Ser315Ile, katG_Pro429fs, rpoB_His445_Lys446delinsGln. The coverage rates of rapid molecular detection methods for resistance loci of rifampin, isoniazid, and fluoroquinolones were 97.94% (95/97), 93.01% (133/143), and 78.95% (15/19), respectively. Conclusion: WGS has a high predictive value for the resistance of MTB to traditional anti-tuberculosis drugs in Northwest China. The presence of numerous rare mutation sites in this region suggests the need to further expand the target coverage of molecular diagnostic methods to improve the accuracy of drug-resistant molecular diagnosis, thereby blocking the transmission of drug-resistant tuberculosis.

Key words: Mycobacterium tuberculosis, Drug resistance, Genes, Mutation