Evaluation of whole-genome sequence to predict drug resistance of nine anti-tuberculosis drugs and characterize resistance genes in clinical rifampicin-resistant Mycobacterium tuberculosis isolates from Ningbo, China

Yang Che; Yi Lin; Tianchi Yang; Tong Chen; Guoxin Sang; Qin Chen; Tianfeng He

doi:10.3389/fpubh.2022.956171

Frontiers in Public Health (Aug 2022)

Evaluation of whole-genome sequence to predict drug resistance of nine anti-tuberculosis drugs and characterize resistance genes in clinical rifampicin-resistant Mycobacterium tuberculosis isolates from Ningbo, China

Yang Che,
Yi Lin,
Tianchi Yang,
Tong Chen,
Guoxin Sang,
Qin Chen,
Tianfeng He

Affiliations

Yang Che: Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
Yi Lin: Center for Health Economics, Faculty of Humanities and Social Sciences, University of Nottingham, Ningbo, China
Tianchi Yang: Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
Tong Chen: Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
Guoxin Sang: Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
Qin Chen: Department of Disease Prevention and Health Promotion, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
Tianfeng He: Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China

DOI: https://doi.org/10.3389/fpubh.2022.956171
Journal volume & issue: Vol. 10

Abstract

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SettingControlling drug-resistant tuberculosis in Ningbo, China.ObjectiveWhole-genome sequencing (WGS) has not been employed to comprehensively study Mycobacterium tuberculosis isolates, especially rifampicin-resistant tuberculosis, in Ningbo, China. Here, we aim to characterize genes involved in drug resistance in RR-TB and create a prognostic tool for successfully predicting drug resistance in patients with TB.DesignDrug resistance was predicted by WGS in a “TB-Profiler” web service after phenotypic drug susceptibility tests (DSTs) against nine anti-TB drugs among 59 clinical isolates. A comparison of consistency, sensitivity, specificity, and positive and negative predictive values between WGS and DST were carried out for each drug.ResultsThe sensitivities and specificities for WGS were 95.92 and 90% for isoniazid (INH), 100 and 64.1% for ethambutol (EMB), 97.37 and 100% for streptomycin (SM), 75 and 100% for amikacin (AM), 80 and 96.3%for capreomycin (CAP), 100 and 97.22% for levofloxacin (LFX), 93.33 and 90.91% for prothionamide (PTO), and 70 and 97.96% for para-aminosalicylic acid (PAS). Around 53 (89.83%) and 6 (10.17%) of the isolates belonged to lineage two (East-Asian) and lineage four (Euro-American), respectively.ConclusionWhole-genome sequencing is a reliable method for predicting resistance to INH, RIF, EMB, SM, AM, CAP, LFX, PTO, and PAS with high consistency, sensitivity, and specificity. There was no transmission that occurred among the patients with RR-TB in Ningbo, China.

Published in Frontiers in Public Health

ISSN: 2296-2565 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Medicine: Public aspects of medicine
Website: https://www.frontiersin.org/journals/public-health

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