A Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae.

Frontiers in Cellular and Infection Microbiology
Lucia Gonzales-SilesMargarita Gomila

Abstract

Correct identifications of isolates and strains of the Mitis-Group of the genus Streptococcus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. Streptococcus pneumoniae and Streptococcus pseudopneumoniae are the most closely related species of the clade. In this study, publicly-available genome sequences for Streptococcus pneumoniae and S. pseudopneumoniae were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for S. pneumoniae and nine for S. pseudopneumoniae were identified. These species-unique gene marker candidates were verified by PCR assays for identifying S. pneumoniae and S. pseudopneumoniae strains isolated from clinical samples. All determined species-level unique gene markers for S. pneumoniae were detected in all S. pneumoniae clinical isolates, whereas fewer of the unique S. pseudopneumoniae gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, ta...Continue Reading

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Citations

Jul 28, 2020·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Ewa Sadowy, Waleria Hryniewicz

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Datasets Mentioned

BETA
70988

Methods Mentioned

BETA
PCR
proteotyping

Software Mentioned

Interactive Tree Of Life ( iTOL )
JSpeciesWS
Get
TCUP ( Typing and Characterization Using Proteomics )
Prokka
- Sequence Analysis ( MLSA )
BLAST
Homologues
Bionumerics
SPAdes

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