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

TITLE=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

JOURNAL=Frontiers in Public Health

VOLUME=Volume 10 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2022.956171

DOI=10.3389/fpubh.2022.956171

ISSN=2296-2565

ABSTRACT=SETTING: Programmatic management of drug-resistant tuberculosis in Ningbo, China.
OBJECTIVE: The comprehensive information of M.tuberculosis isolates by Whole-genome sequencing (WGS), especially Rifampicin-resistant tuberculosis (RR-TB) have not been studied in Ningbo, China. The goal of this study was to provide a baseline characterization of circulation known and putative drug resistance mutations, and to identify potential RR-TB transmission chains.
DESIGN: WGS was utilized to predict drug resistance using an online 'TB-Profiler' tool after phenotypic DST against nine anti-drugs among 59 clinical isolates. For each drug, the consistency, sensitivity, specificity, positive and negative predictive values of WGS were compared with those of the conventional drug susceptibility test.
RESULTS: The overall sensitivities and specificities for WGS were 95.92% and 90.00% for isoniazid (INH), 100.00% for rifampicin (RIF), 100.00% and 64.10% for ethambutol (EMB), 97.37% and 100.00% for streptomycin (SM), 75.00% and 100.00% for amikacin (AM), 80.00% and 96.30% for capreomycin (CAP), 100.00% and 97.22% for levofloxacin (LFX), 93.33% and 90.91% for prothionamide (PTO), 70.00% and 97.96% for para-aminosalicylic acid ( PAS), respectively. Around 89.83% isolates (n=53) and 6 (10.17%) belonged to lineage two (East-Asian) lineage four (Euro-American), respectively.
CONCLUSION: WGS 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 occurred among the RR-TB in Ningbo,China.