Use of whole-genome sequencing to predict mycobacterium tuberculosis drug resistance in Shanghai, China
International Journal of Infectious Diseases Apr 29, 2020
Wu X, Gao R, Shen X, et al. - Researchers examined predictive value of whole genome sequencing (WGS) for Mycobacterium tuberculosis (MTB) drug resistance. From patients with tuberculosis in Shanghai Pulmonary Hospital (SPH), they randomly selected 276 rifampin-resistance tuberculosis (RR-TB) and 30 rifampicin-sensitive clinical isolates. They conducted phenotypic drug susceptibility testing (DST) against 6 anti-TB drugs, and performed WGS to predict the drug resistance using an online ‘TB-Profiler’ tool. For WGS, they observed the overall sensitivity and specificity of 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. Whole genome sequencing-based DST and phenotypic DST had concordances as follows: isoniazid (94.12%), rifampicin (97.39%), ethambutol (77.12%), streptomycin (96.73%), ofloxacin (96.41%) and amikacin (97.06%). Observations support a promising utility of whole genome sequencing to predict resistance to isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin and amikacin.
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