title: TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing.
abstract: 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 core genomic sequences based on molecular evolution. We developed an all-in-one web-based tool for genotyping Mtb, referred to as the Total Genotyping Solution for TB (TGS-TB), to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface. This methodology is implemented with a KvarQ script to predict MTBC lineages/sublineages and potential antimicrobial resistance. Seven Mtb isolates (JP01 to JP07) in this study showing the same VNTR profile were accurately discriminated through median-joining network analysis using SNVs unique to those isolates. An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs. The results of in silico analyses using TGS-TB are consistent with those obtained using conventional molecular genotyping methods, suggesting that NGS short reads could provide multiple genotypes to discriminate multiple strains of Mtb, although longer NGS reads (≥ 300-mer) will be required for full genotyping on the TGS-TB web site. Most available short reads (~100-mer) can be utilized to discriminate the isolates based on the core genome phylogeny. TGS-TB provides a 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/.
authors.affiliation: Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku-ku, Tokyo, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Sekizuka
authors.affiliation: Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku-ku, Tokyo, Japan.
authors.forename: Akifumi
authors.initials: A
authors.lastname: Yamashita
authors.affiliation: Molecular Epidemiology Division, The Research Institute of Tuberculosis/Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan.
authors.forename: Yoshiro
authors.initials: Y
authors.lastname: Murase
authors.affiliation: Department of Infectious Diseases, Kobe Institute of Health, Chuo-ku, Kobe, Japan.
authors.forename: Tomotada
authors.initials: T
authors.lastname: Iwamoto
authors.affiliation: Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Mitarai
authors.affiliation: Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan.
authors.forename: Seiya
authors.initials: S
authors.lastname: Kato
authors.affiliation: Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku-ku, Tokyo, Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Kuroda
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods; D019070:Cell Lineage; D019295:Computational Biology / Q000379:methods*; D024881:Drug Resistance, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology / Q000379:methods; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014376:Tuberculosis / Q000382:microbiology*