Identification of novel resistance-associated mutations and discrimination within whole-genome sequences of fluoroquinolone-resistant Mycobacterium tuberculosis isolates

Yingzhi Chong; Xueying Li; Yifei Long; Shengfei Pei; Qi Ren; Fumin Feng; Haibo Zhang

doi:10.1128/spectrum.03930-23

Identification of novel resistance-associated mutations and discrimination within whole-genome sequences of fluoroquinolone-resistant Mycobacterium tuberculosis isolates

Microbiol Spectr. 2024 Apr 30:e0393023. doi: 10.1128/spectrum.03930-23. Online ahead of print.

Authors

Yingzhi Chong^{1

2}, Xueying Li¹, Yifei Long¹, Shengfei Pei¹, Qi Ren^#¹, Fumin Feng^#¹, Haibo Zhang^{1

3}

Affiliations

¹ Hebei Coordinated Innovation Center of Occupational Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei Province, China.
² School of Public Health, Shandong Second Medical University, Weifang, Shangdong Province, China.
³ Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.

^# Contributed equally.

PMID: 38687077
DOI: 10.1128/spectrum.03930-23

Abstract

This study aims to elucidate additional mutation loci associated with fluoroquinolone (FQ) resistance and evaluate the discriminatory capacity of mutation loci and allele mutation frequencies in identifying FQ-resistant Mycobacterium tuberculosis (MTB) isolates. A random selection of isolates was extracted from an ongoing collection. Drug resistance was determined using the resazurin microtiter assay (REMA) as the gold standard. Mutation loci and the burden of mutations in the quinolone resistance-determining region (QRDR) were elucidated through whole-genome sequencing (WGS). Novel amino acid mutations, namely, G520D and G520T, were identified in the gyrB and associated with FQ resistance. In the context of distinguishing FQ-resistant isolates, the AUC for the QRDR mutation frequency burden (0.969) surpassed that of the mutation locus (0.929), and this difference was statistically significant (P = 0.03). Furthermore, using the resistance mutation locus as a reference, setting the QRDR mutation frequency burden threshold at 1.31% resulted in a 3.60% increase in the accuracy of classifying FQ-resistant isolates (NRI = 3.60%, P < 0.001). The QRDR mutation frequency burden appears to offer superior diagnostic efficacy in discriminating FQ-resistant isolates compared to qualitative detection of mutant loci.IMPORTANCEFluoroquinolone (FQ) drugs are recommended as second-line drugs for the treatment of multidrug-resistant tuberculosis. With the massive use of FQ drugs in the clinical treatment of tuberculosis (TB), there is an increasing rate of drug resistance to FQ drugs. In this study, we identified and demonstrated novel amino acid mutations associated with FQ resistance in Mycobacterium tuberculosis (MTB), and we quantified the mutation sites and identified the quinolone resistance-determining region (QRDR) mutation frequency burden as a novel diagnostic method for FQ resistance. We hope that the results of this study will provide data support and a theoretical basis for the rapid diagnosis of FQ-resistant MTB.

Keywords: Mycobacterium tuberculosis; fluoroquinolone; resistance; tuberculosis; whole-genome sequencing.