A New Species-Specific Typing Method for Salivarius Group Streptococci Based on the Dephospho-Coenzyme A Kinase (coaE) Gene Sequencing

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.

SVep1, a temperate phage of human oral commensal Streptococcus vestibularis

“…Previous studies have reported a close similarity between S. vestibularis and S. salivarius based on phylogenetic analysis of the 16S rRNA gene sequence ( Pombert et al, 2009 ). Here, we employed the coaE ( Abdelbary et al, 2021 ) gene-based phylogenetic tree to demonstrate a closer relationship between S. vestibularis and S. thermophilus.…”

“…Given their shared physiological traits and habitat, it is reasonable to assume that S. salivarius and S. vestibularis are more closely related to each other than to S. thermophilus. Recent phylogenetic analyses presented in a study strongly support the sister relationship between S. vestibularis and S. thermophilus, with S. salivarius diverging earlier at the base of the salivarius clade (Pombert et al, 2009;Abdelbary et al, 2021). Identifying and typing viridans group streptococci has proven challenging in multiple reports.…”

“…Similarly, due to the high similarity (>99%) of the 16S rRNA gene among the three species in the salivarius group ( Thompson et al, 2013 ), clear differentiation between them is typically difficult. In our study, we adopted a new typing approach that involves amplification and sequence analysis of the housekeeping gene coaE to identify these closely related members of the salivarius group ( Abdelbary et al, 2021 ). Our findings, which align with recent studies, indicate a closer relationship between S. vestibularis and S. thermophilus .…”

Impact of liver fibrosis on the relative abundance of a urease‐positive Streptococcus salivarius group from saliva in patients with chronic liver disease

“…20 The S. salivarius group of the genus Streptococcus is a cluster significantly supported by the data of sequence analysis using the 16S rRNA, rnpB, and coaE genes from the core streptococcal genome. 14 16S rRNA is widely used to determine the S. salivarius group. However, it is difficult to identify the group species using the 16S rRNA region.…”

“…PCR amplification in the coaE gene was performed using the following primers: forward primer coaE-SG-fwd 5 0 -TTAACAGGWGGYATTGCTTCAG-3 0 and reverse primer coaE-SG-rev 5 0 -CTTMACCTTCTYCTTCAAATCATC-3 0 were used. The PCR program involved an initial denaturation step at 94°C for 1 min, followed by 30 cycles (each cycle consisting of 94°C for 30 s, 51°C for 30 s, and 72°C for 1 min) of reactions terminated by a final extension step at 72°C for 4 min 14 Sequence analysis of the coaE gene was similar to that of the 16S rRNA gene described above. We also performed phylogenetic analysis to study the evolutionary relationships between organisms based on their genetic sequences.…”