Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China.

Adult Amikacin / pharmacology Antitubercular Agents / pharmacology China Drug Resistance, Bacterial / genetics Ethambutol / pharmacology Humans Isoniazid / pharmacology Male Mycobacterium tuberculosis / drug effects Ofloxacin / pharmacology Rifampin / pharmacology Streptomycin / pharmacology Tuberculosis / microbiology Whole Genome Sequencing
Drug resistance Drug susceptibility testing Drug-resistant tuberculosis Whole-genome sequencing

Journal

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
ISSN: 1878-3511
Titre abrégé: Int J Infect Dis
Pays: Canada
ID NLM: 9610933

Informations de publication

Date de publication:
Jul 2020
Historique:
received: 28 01 2020
revised: 14 04 2020
accepted: 17 04 2020
pubmed: 28 4 2020
medline: 4 9 2020
entrez: 28 4 2020
Statut: ppublish

Résumé

To evaluate the performance of whole-genome sequencing (WGS) for predicting Mycobacterium tuberculosis (MTB) drug resistance. 276 rifampin-resistance tuberculosis (RR-TB) and 30 rifampicin-sensitive clinical isolates were randomly selected from patients with tuberculosis in Shanghai Pulmonary Hospital (SPH). Phenotypic drug susceptibility testing (DST) against six anti-TB drugs was performed, and WGS was used to predict the drug resistance using an online 'TB-Profiler' tool. Using phenotypic susceptibility as the gold standard, the overall sensitivities and specificities for WGS were 94.53% and 92.00% for isoniazid, 97.10% and 100.00% for rifampicin, 97.46% and 64.36% for ethambutol, 97.14% and 95.83% or streptomycin, 93.02% and 98.87% for ofloxacin, and 75.00% and 100.00% for amikacin, respectively. The concordances of WGS-based DST and phenotypic DST were: isoniazid (94.12%), rifampicin (97.39%), ethambutol (77.12%), streptomycin (96.73%), ofloxacin (96.41%) and amikacin (97.06%). WGS could be a promising approach to predict resistance to isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and amikacin.

Identifiants

DOI: 10.1016/j.ijid.2020.04.039 PMID: 32339720
pubmed: 32339720
pii: S1201-9712(20)30256-3
doi: 10.1016/j.ijid.2020.04.039
pii:
doi:

Substances chimiques

Antitubercular Agents 0
Amikacin 84319SGC3C
Ethambutol 8G167061QZ
Ofloxacin A4P49JAZ9H
Isoniazid V83O1VOZ8L
Rifampin VJT6J7R4TR
Streptomycin Y45QSO73OB

Types de publication

Evaluation Study Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

48-53

Informations de copyright

Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Auteurs

Xiaocui Wu (X)

Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China. Electronic address: wuxiaocui1210@163.com.

Rongliang Gao (R)

Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China. Electronic address: 1980gaooag@sina.com.

Xin Shen (X)

Shanghai Municipal Center for Disease Control and Prevention. Electronic address: shenxin@scdc.sh.cn.

Yinjuan Guo (Y)

Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China. Electronic address: 402873391@qq.com.

Jinghui Yang (J)

Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China. Electronic address: yangjh918@163.com.

Zheyuan Wu (Z)

Shanghai Municipal Center for Disease Control and Prevention. Electronic address: wuzheyuan@scdc.sh.cn.

Guangkun Tan (G)

Department of Clinical Laboratory, Shanghai University of Traditional Chinese Medical Attached Shuguang Hospital, Shanghai, China. Electronic address: tanguangkun1988@163.com.

Hongxiu Wang (H)

Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China. Electronic address: polerterwang@163.com.

Fangyou Yu (F)

Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China. Electronic address: wzjxyfy@163.com.

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Classifications MeSH

questionsmedicales.fr › Personnes › Tranches d'âge › Adulte › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Glucides › Hétérosides › Aminosides › Kanamycine › Amikacine › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Actions chimiques et utilisations › Actions pharmacologiques › Utilisations thérapeutiques › Anti-infectieux › Antibactériens › Antituberculeux › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Régions géographiques › Asie › Extrême-Orient › Chine › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Phénomènes physiologiques › Phénomènes pharmacologiques et toxicologiques › Phénomènes pharmacologiques › Résistance aux substances › Résistance microbienne aux médicaments › Résistance bactérienne aux médicaments › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Composés chimiques organiques › Amines › Polyamines › Diamines › Éthylènediamines › Éthambutol › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Composés hétérocycliques › Composés hétéromonocycliques › Pyridines › Acides isonicotiniques › Isoniazide › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Bâtonnets à Gram positif › Bâtonnets asporogènes à Gram positif › Bâtonnets asporogènes réguliers à Gram positif › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Composés hétérocycliques › Composés hétérocycliques à cycles fusionnés › Composés hétérobicycliques › Quinoléines › Quinolinone › Fluoroquinolones › Ofloxacine › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Composés polycycliques › Composés macrocycliques › Lactames macrocycliques › Rifamycine › Rifampicine › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Glucides › Hétérosides › Aminosides › Streptomycine › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Infection › Infections bactériennes et mycoses › Infections bactériennes › Infections bactériennes à Gram positif › Infections à Actinomycetales › Infections à Mycobacterium › Tuberculose › Use of whole-genome sequencing to predict...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › Use of whole-genome sequencing to predict...