Abstract
Viridans streptococci are a group of α-hemolytic streptococcal species. They are mainly commensals, most abundant in the mouth supporting oral health. But they also include important human pathogens such as Streptococcus pneumoniae. Identification and molecular typing of viridans group streptococci are challenging, especially for members of the salivarius group. In this study, we developed a single-locus molecular typing method that is able to differentiate among the highly phylogenetically related members of the salivarius group (S. salivarius, S. vestibularis and S. thermophilus) and might support differentiation in other groups as well. This typing approach is based on the amplification and sequence analysis of the housekeeping gene dephospho-coenzyme A kinase (coaE), a gene with unrecognized taxonomic potential to date. Here, we analysed coaE gene sequences of 154 publicly available genomes and of 30 salivarius group isolates of our own collection that together belong to 20 different gram-positive bacterial (sub) species. Our results revealed that the coaE phylogeny distinguished between streptococcal and non-streptococcal genomes and that coaE gene sequences were species-specific. In contrast to MALDI-TOF MS performance, the coaE typing was able to precisely identify the phylogenetically very closely related members of the salivarius group.
Highlights
The genus Streptococcus comprises 107 assigned species that diverge between commensals and pathogens to various animals and to humans
The phylogenetic tree based on the coenzyme A kinase (coaE) gene sequence of these 30 OMI-isolates and of the 37 publicly available salivarius group genomes was constructed using maximum likelihood (ML) method and Tamura 3-parameter substitution model with a discrete gamma distribution as it was shown by model testing to be the best-fit evolutionary model (BIC = 6398.365) (Figure 1A)
S. vestibularis had several phylogenetically distinct sub-clusters, differing by 31 single nucleotide polymorphisms (SNPs) in average, that were clearly located closer to the S. thermophilus than to the S. salivarius clade. This phylogenetic clustering was confirmed by a separate NJ phylogenetic method (Figure 1B), which revealed identical two clusters of S. salivarius, S. thermophilus and S. vestibularis with high bootstrap values comparable to those obtained from the ML method (Figure 1A)
Summary
The genus Streptococcus comprises 107 (validly published and correctly named) assigned species (http://www.bacterio.net/streptococcus.html) that diverge between commensals and pathogens to various animals and to humans. Previous studies based on 16S rRNA gene sequence analysis divided most members of the genus Streptococcus into six distinct phylogenetic groups, namely the mitis, anginosus, pyogenic, bovis, mutans, and salivarius group. The latter is composed of the oral and intestinal commensals S. vestibularis and S. salivarius while. With the introduction of high-throughput sequencing, whole-genome sequence (WGS) analysis has become a valuable typing method for bacterial species due to its high discriminatory power that is able to even differentiate between closely related bacterial isolates This method is still expensive and time-consuming
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