Streptococcal taxonomy based on genome sequence analyses

Cristiane C Thompson,Erica L Fonseca,Vanessa E Emmel,Michel A Marin,Ana Carolina P Vicente

doi:10.12688/f1000research.2-67.v1

Cristiane C Thompson, Erica L Fonseca + Show 3 more

Open Access

https://doi.org/10.12688/f1000research.2-67.v1

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Abstract

The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA), average amino acid identity (AAI), genomic signatures, genome-to-genome distances (GGD) and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance, S. pneumoniae, S. mitis, and S. oralis. A Streptococcus species can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.

Highlights

IntroductionDifferent strains of a single bacterial species sometimes have the ability to explore distinct niches, to be pathogenic or non-pathogenic and to present different metabolic pathways[1,2]
Bacteria are subjected to numerous forces driving their diversification
16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) The 16S rRNA gene sequences and the gene sequences used for MLSA were obtained from GenBank

Summary

Introduction

Different strains of a single bacterial species sometimes have the ability to explore distinct niches, to be pathogenic or non-pathogenic and to present different metabolic pathways[1,2]. In such a scenario, the identification of bacteria isolates to the species level is a hard task[1,2]. The genus Streptococcus comprises 99 recognized species, many of which are associated with disease in humans and animals (http://www.bacterio.cict.fr/s/streptococcus.html). The Mitis group currently includes the important pathogen S. pneumoniae and 12 other recognized species, S. australis, S. cristatus (formerly S. crista), S. gordonii, S. infantis, S.mitis, S. oligofermentans, S. oralis, S. parasanguinis (formerly S. parasanguis), S. peroris, S. pseudopneumoniae, S. sanguinis (formerly S. sanguis) and S. sinensis. The Anginosus group includes three recognized species, S. anginosus, S. constellatus (including two subspecies S. constellatus subsp. constellatus and S. constellatus pharyngis) and S. intermedius, and the Salivarius group includes S. salivarius, S. vestibularis, and S. thermophilus

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