TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis.. Mycobacterium tuberculosis

Whole-genome sequencing (WGS) with next-generation DNA sequencing (NGS) is an increasingly accessible and affordable method for genotyping hundreds of Mycobacterium tuberculosis (Mtb) isolates, leading to more effective epidemiological studies involving single nucleotide variations (SNVs) in the core genomic sequences based on molecular evolution. We developed an all-in-one web-based tool for genotyping Mtb, referred to as Total Genotyping Solution for TB (TGS-TB), to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenes with core genomic single nucleotide variations (SNVs), IS6110 insertion sites, and VNTRs (our customized short TR on 43 loci) through a user-friendly simple click interface. In addition, this methodology is implemented with a KvarQ script to predict MTBC lineages/sublineages and potential antimicrobial resistance. Indeed, seven Mtb isolates in this study showing the same VNTR profile were accurately discriminated through median joining network analysis using specific SNVs unique to those isolates. Furthermore, an additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs. TGS-TB provides more accurate and discriminative strain typing for clinical and epidemiological investigations; NGS strain typing offers a total genotyping solution for Mtb outbreak and surveillance. TGS-TB web site: https://gph.niid.go.jp/tgs-tb.