Journal
BRIEFINGS IN BIOINFORMATICS
Volume 23, Issue 2, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbac030
Keywords
whole genome sequencing; drug-susceptibility testing; drug-resistant tuberculosis; transmission; nontuberculous mycobacteria
Funding
- Sanming project of Medicine in Shenzhen [SZSM201611030]
- National Natural Science Foundation of China [81661128043, 81871625]
- National Science and Technology Major Project of China [2017ZX10201302, 2018ZX10715012]
- Natural Science Foundation of Guangdong Province of China [2020A1515011086]
- China Postdoctoral Science Foundation [2019M661365]
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The study established a free, function-rich, user-friendly online platform (SAM-TB) for analyzing MTB WGS data, which includes drug-resistance prediction, genetic relationship analysis, and NTM species identification. SAM-TB shows high accuracy in predicting drug-resistance, can analyze the genetic relationships between multiple strains, and detect mixed MTB and NTM samples. The platform is of great significance in guiding treatment and epidemiological investigation.
Whole genome sequencing (WGS) can provide insight into drug-resistance, transmission chains and the identification of outbreaks, but data analysis remains an obstacle to its routine clinical use. Although several drug-resistance prediction tools have appeared, until now no website integrates drug-resistance prediction with strain genetic relationships and species identification of nontuberculous mycobacteria (NTM). We have established a free, function-rich, user-friendly online platform for MTB WGS data analysis (SAM-TB, ) that integrates drug-resistance prediction for 17 antituberculosis drugs, detection of variants, analysis of genetic relationships and NTM species identification. The accuracy of SAM-TB in predicting drug-resistance was assessed using 3177 sequenced clinical isolates with results of phenotypic drug-susceptibility tests (pDST). Compared to pDST, the sensitivity of SAM-TB for detecting multidrug-resistant tuberculosis was 93.9% [95% confidence interval (CI) 92.6-95.1%] with specificity of 96.2% (95% CI 95.2-97.1%). SAM-TB also analyzes the genetic relationships between multiple strains by reconstructing phylogenetic trees and calculating pairwise single nucleotide polymorphism (SNP) distances to identify genomic clusters. The incorporated mlstverse software identifies NTM species with an accuracy of 98.2% and Kraken2 software can detect mixed MTB and NTM samples. SAM-TB also has the capacity to share both sequence data and analysis between users. SAM-TB is a multifunctional integrated website that uses WGS raw data to accurately predict antituberculosis drug-resistance profiles, analyze genetic relationships between multiple strains and identify NTM species and mixed samples containing both NTM and MTB. SAM-TB is a useful tool for guiding both treatment and epidemiological investigation.
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