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TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing.

Sekizuka T, Yamashita A, Murase Y, Iwamoto T, Mitarai S, Kato S, Kuroda M - PLoS ONE (2015)

Bottom Line: An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs.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.

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku-ku, Tokyo, Japan.

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/.

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Related in: MedlinePlus

The core genome phylogeny obtained by the maximum-likelihood method with x100 bootstrapping.
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pone.0142951.g003: The core genome phylogeny obtained by the maximum-likelihood method with x100 bootstrapping.

Mentions: In total, 21,805 core genome SNVs on the non-repetitive regions (S2 Table) are available in the TGS-TB, and 20,928 (95.98%) SNVs for the seven isolates (JP01 to JP07) were correctly extracted in the sample test (Fig 2). Additional query-specific novel SNVs can be identified in TGS-TB, and 219 additional strain-specific SNV sites can be implemented in the original dataset (21,805 core genome SNVs). A maximum-likelihood core genome phylogenetic tree is constructed based on the whole SNV dataset, including newly identified SNVs sites (Fig 3). The data for the original and query-specific SNVs can be downloaded as a tab-delimited file (summary_SNVs.txt) or fasta file (phylocoreGenome.fasta) for further phylogenetic analysis using more bootstrapping analyses or a Bayesian approach.


TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing.

Sekizuka T, Yamashita A, Murase Y, Iwamoto T, Mitarai S, Kato S, Kuroda M - PLoS ONE (2015)

The core genome phylogeny obtained by the maximum-likelihood method with x100 bootstrapping.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643978&req=5

pone.0142951.g003: The core genome phylogeny obtained by the maximum-likelihood method with x100 bootstrapping.
Mentions: In total, 21,805 core genome SNVs on the non-repetitive regions (S2 Table) are available in the TGS-TB, and 20,928 (95.98%) SNVs for the seven isolates (JP01 to JP07) were correctly extracted in the sample test (Fig 2). Additional query-specific novel SNVs can be identified in TGS-TB, and 219 additional strain-specific SNV sites can be implemented in the original dataset (21,805 core genome SNVs). A maximum-likelihood core genome phylogenetic tree is constructed based on the whole SNV dataset, including newly identified SNVs sites (Fig 3). The data for the original and query-specific SNVs can be downloaded as a tab-delimited file (summary_SNVs.txt) or fasta file (phylocoreGenome.fasta) for further phylogenetic analysis using more bootstrapping analyses or a Bayesian approach.

Bottom Line: An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs.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.

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku-ku, Tokyo, Japan.

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/.

Show MeSH
Related in: MedlinePlus