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Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus
A Friães1, R Mamede1, M Ferreira1
1Instituto de Microbiologia, Instituto de Microbiologia Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
Journal of Clinical Microbiology
|May 9, 2022
Summary
A new whole-genome multilocus sequence typing (wgMLST) schema improves Streptococcus pyogenes surveillance by providing high-resolution genetic analysis. This method overcomes limitations of older techniques for tracking this diverse pathogen.
Area of Science:
- Microbiology and Molecular Epidemiology
- Genomics and Bioinformatics
Background:
- Streptococcus pyogenes exhibits high genetic diversity due to recombination and horizontal gene transfer, complicating traditional surveillance methods like single nucleotide polymorphism (SNP)-based analyses.
- Existing typing methods such as pulsed-field gel electrophoresis (PFGE), superantigen gene profiling, and multilocus sequence typing (MLST) have limitations in resolving the genetic heterogeneity of S. pyogenes.
Purpose of the Study:
- To develop and validate a novel whole-genome multilocus sequence typing (wgMLST) schema for high-resolution typing of Streptococcus pyogenes.
- To assess the performance of the new schema against existing methods and SNP-based approaches for epidemiological surveillance.
Main Methods:
- A gene-by-gene approach was used to develop a wgMLST schema with 3,044 target loci based on 208 complete S. pyogenes genomes.
- The developed schema was applied to core-genome MLST (cgMLST) analyses of existing datasets and 265 newly sequenced draft genomes.
- cgMLST results were compared with pulsed-field gel electrophoresis (PFGE), superantigen gene profiling, MLST, and PopPUNK clustering.
Main Results:
- The novel wgMLST schema provides scalable cgMLST analysis, allowing for increased resolution with more loci for closely related isolates.
- cgMLST analysis revealed the genetic heterogeneity within many emm types and showed poor correlation with older typing methods, highlighting their limitations.
- cgMLST results were comparable to SNP-based methods in identifying emerging sublineages and clarifying isolate relatedness during outbreaks.
Conclusions:
- The developed wgMLST schema offers a robust framework for high-resolution typing and genetic variability analysis of Streptococcus pyogenes.
- The publicly available schema on the chewie-NS platform facilitates standardized and improved epidemiological surveillance of S. pyogenes.
- cgMLST represents a significant advancement over traditional methods for understanding the population structure and evolution of S. pyogenes.
