AI Article Synopsis

  • Researchers have developed a new pipeline that allows for the identification of all 29 serotypes of Streptococcus suis directly from whole-genome sequencing (WGS) data.
  • This automated system uses a custom database and differential alignment techniques, successfully differentiating between previously indistinguishable serotypes through specific genetic mutations.
  • The pipeline has shown high accuracy in identifying serotypes, with a 99% match to traditional methods and a 92% match using additional genomic data, thereby resolving a long-standing challenge in S. suis classification.

Article Abstract

Background: Streptococcus suis is divided into 29 serotypes based on a serological reaction against the capsular polysaccharide (CPS). Multiplex PCR tests targeting the cps locus are also used to determine S. suis serotypes, but they cannot differentiate between serotypes 1 and 14, and between serotypes 2 and 1/2. Here, we developed a pipeline permitting in silico serotype determination from whole-genome sequencing (WGS) short-read data that can readily identify all 29 S. suis serotypes.

Results: We sequenced the genomes of 121 strains representing all 29 known S. suis serotypes. We next combined available software into an automated pipeline permitting in silico serotyping of strains by differential alignment of short-read sequencing data to a custom S. suis cps loci database. Strains of serotype pairs 1 and 14, and 2 and 1/2 could be differentiated by a missense mutation in the cpsK gene. We report a 99 % match between coagglutination- and pipeline-determined serotypes for strains in our collection. We used 375 additional S. suis genomes downloaded from the NCBI's Sequence Read Archive (SRA) to validate the pipeline. Validation with SRA WGS data resulted in a 92 % match. Included pipeline subroutines permitted us to assess strain virulence marker content and obtain multilocus sequence typing directly from WGS data.

Conclusions: Our pipeline permits rapid and accurate determination of S. suis serotype, and other lineage information, directly from WGS data. By discriminating between serotypes 1 and 14, and between serotypes 2 and 1/2, our approach solves a three-decade longstanding S. suis typing issue.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4957933PMC
http://dx.doi.org/10.1186/s12866-016-0782-8DOI Listing

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