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GBS-SBG - GBS Serotyping by Genome Sequencing.

Suma Tiruvayipati1, Wen Ying Tang2, Timothy M S Barkham2

  • 1Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

Microbial Genomics
|December 13, 2021
PubMed
Summary

A new genome sequencing database, GBS-SBG, accurately identifies all Group B Streptococcus (GBS) serotypes, including subtypes. This tool simplifies and accelerates GBS serotyping by sequencing for researchers and clinicians.

Keywords:
Group B Streptococcus serotypesgenome sequencingmolecular epidemiologyshort read typing

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Area of Science:

  • Microbiology
  • Genomics
  • Infectious Diseases

Background:

  • Group B Streptococcus (GBS) is a significant cause of neonatal meningitis, adult sepsis, and emerging foodborne illness.
  • Bacterial polysaccharide capsules are crucial for serotyping, but existing whole-genome sequencing (WGS) methods for GBS lack complete serotype coverage and data type compatibility.
  • Current WGS-based serotyping systems for GBS do not cover all known serotypes, including serotype III subtypes, and are not compatible with both raw short reads and assembled sequences.

Purpose of the Study:

  • To develop a comprehensive and compatible whole-genome sequencing (WGS)-based serotyping database for Group B Streptococcus (GBS).
  • To create a tool that can accurately identify all described GBS serotypes, including serotype III subtypes, using both short-read and assembled sequence data.
  • To provide a publicly available package that simplifies and accelerates GBS serotyping by sequencing.

Main Methods:

  • Development of a novel serotyping database named GBS-SBG (GBS Serotyping by Genome Sequencing).
  • Creation of associated scripts and running instructions for the GBS-SBG database.
  • Validation of GBS-SBG using previously reported and newly generated strain data sets.

Main Results:

  • The GBS-SBG database successfully calls all currently described GBS serotypes, including serotype III subtypes.
  • Higher concordance was achieved using GBS-SBG on a dataset of 790 strains compared to existing methods.
  • Validation on a new set of 572 strains demonstrated 99.8% concordance with PCR-based molecular serotyping, irrespective of data type (short-read or assembly-based).

Conclusions:

  • The GBS-SBG package provides a robust and comprehensive solution for GBS serotyping by genome sequencing.
  • This tool enhances accuracy and compatibility, supporting both raw short reads and assembled sequences.
  • The public availability of GBS-SBG is expected to accelerate and simplify GBS serotyping, aiding research and diagnostics.