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

Xiaocui Wu; Rongliang Gao; Xin Shen; Yinjuan Guo; Jinghui Yang; Zheyuan Wu; Guangkun Tan; Hongxiu Wang; Fangyou Yu

International Journal of Infectious Diseases (Jul 2020)

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

Xiaocui Wu,
Rongliang Gao,
Xin Shen,
Yinjuan Guo,
Jinghui Yang,
Zheyuan Wu,
Guangkun Tan,
Hongxiu Wang,
Fangyou Yu

Affiliations

Xiaocui Wu: 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
Rongliang Gao: 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
Xin Shen: Shanghai Municipal Center for Disease Control and Prevention
Yinjuan Guo: 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
Jinghui Yang: 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
Zheyuan Wu: Shanghai Municipal Center for Disease Control and Prevention
Guangkun Tan: Department of Clinical Laboratory, Shanghai University of Traditional Chinese Medical Attached Shuguang Hospital, Shanghai, China
Hongxiu Wang: 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; Corresponding author. Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Yangpu District, Shanghai 200433, People's Republic of China.
Fangyou Yu: 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; Corresponding author. Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Yangpu District, Shanghai 200433, People's Republic of China.

Journal volume & issue: Vol. 96
pp. 48 – 53

Abstract

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Objective: To evaluate the performance of whole-genome sequencing (WGS) for predicting Mycobacterium tuberculosis (MTB) drug resistance. Methods: 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. Results: 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%). Conclusions: WGS could be a promising approach to predict resistance to isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and amikacin.

Published in International Journal of Infectious Diseases

ISSN: 1201-9712 (Print); 1878-3511 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Medicine: Internal medicine: Infectious and parasitic diseases
Website: http://www.journals.elsevier.com/international-journal-of-infectious-diseases/

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