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

Area of Science:

• Genomics
• Molecular Epidemiology
• Bioinformatics

Background:

• Whole-genome sequencing (WGS) using next-generation sequencing (NGS) is becoming more accessible for Mycobacterium tuberculosis (Mtb) genotyping.
• Effective epidemiological studies rely on genotyping methods that can analyze single nucleotide variations (SNVs) within core genomic sequences.

Purpose of the Study:

• To develop and present an integrated web-based tool, the Total Genotyping Solution for TB (TGS-TB), for comprehensive Mtb genotyping.
• To facilitate multiple genotyping platforms including spoligotyping, SNV analysis, IS6110 insertion site detection, and variable number tandem repeat (VNTR) typing using NGS data.

Main Methods:

• Development of the TGS-TB web-based tool with a user-friendly interface.
• Implementation of KvarQ script for predicting MTBC lineages, sublineages, and antimicrobial resistance.
• Application of median-joining network analysis using unique SNVs for discriminating Mtb isolates with identical VNTR profiles.

Main Results:

• TGS-TB accurately discriminated seven Mtb isolates (JP01-JP07) with identical VNTR profiles using unique SNVs.
• An additional IS6110 insertion was identified in one isolate, providing supportive genetic information.
• In silico analysis results from TGS-TB were consistent with conventional genotyping methods, demonstrating the utility of NGS short reads for Mtb strain discrimination.

Conclusions:

• NGS short reads can effectively discriminate Mtb strains based on core genome phylogeny, complementing traditional methods.
• TGS-TB provides a more accurate and discriminative strain typing solution for Mtb clinical and epidemiological investigations.
• NGS-based strain typing, as facilitated by TGS-TB, offers a comprehensive genotyping solution for Mtb outbreak investigations and surveillance.