Characterization of Fluoroquinolone-Resistant and Multidrug-Resistant Mycobacterium tuberculosis Isolates Using Whole-Genome Sequencing in Tianjin, China.

Abstract

ObjectiveTuberculosis (TB) caused by Mycobacterium tuberculosis remains a global concern. This study aimed to determine the molecular characteristics of fluoroquinolone-resistant and multidrug-resistant M. tuberculosis strains using whole-genome sequencing to predict drug resistance in M. tuberculosis in Tianjin, China, which has not been established previously.MethodsTwenty-one fluoroquinolone-resistant and multidrug-resistant M. tuberculosis strains were isolated from sputum samples. Phenotypic drug resistance against 12 anti-tuberculosis drugs was determined using drug susceptibility testing. Whole-genome sequencing was performed to predict drug resistance in M. tuberculosis based on genome regions associated with drug resistance. The sensitivity of whole-genome sequencing for predicting drug resistance was calculated based on phenotypic drug susceptibility testing information.ResultsAmong the 21 isolates, mutations in 15 genome regions associated with drug resistance, including rpoB for rifampicin; katG and inhA promoter for isoniazid; gyrA and gyrB for ofloxacin and moxifloxacin; rpsL for streptomycin; rrs for streptomycin, amikacin, kanamycin and capreomycin; pncA and panD for pyrazinamide; embB, embC-embA, aftA, and ubiA for ethambutol; ethA for protionamide; and folC for para-aminosalicylic acid, were detected. Compared with traditional drug susceptibility testing results, the sensitivities for whole-genome sequencing of rifampin, isoniazid, ofloxacin, moxifloxacin, streptomycin, ethambutol, pyrazinamide, kanamycin, and amikacin resistance were 100%, 90.48%, 95.24%, 92.86%, 95.27%, 85.71%, 66.67%, 50%, and 50%, respectively. The sensitivities for whole-genome sequencing of capreomycin, protionamide, and para-aminosalicylic acid were not calculated because only one isolate showed phenotypic drug resistance. Mutations determined in drug susceptibility-associated genes can explain phenotypic drug resistance in most isolates. Notably, these mutations were absent in certain drug-resistant isolates, indicating other drug resistance mechanisms.ConclusionWhole-genome sequencing represents an effective diagnostic tool for fluoroquinolone-resistant and multidrug-resistant TB though it has some obstacles. Whole-genome sequencing should be used to predict drug resistance prior to performing traditional phenotypic drug susceptibility testing in Tianjin, China.