Identification of species of Abiotrophia, Enterococcus, Granulicatella and Streptococcus by sequence analysis of the ribosomal 16S–23S intergenic spacer region

Abstract

The feasibility of sequence analysis of the ribosomal 16S-23S intergenic spacer region (ITS) was evaluated for identification of 24 species of Streptococcus, one species of Abiotrophia, 18 species of Enterococcus and three species of Granulicatella. As GenBank currently lacks ITS sequence entries for many species of these four genera, the ITS sequences of 38 type strains were first sequenced and submitted to GenBank to facilitate species identification of these genera. Subsequently, the ITS sequences of 217 strains (84 reference strains and 133 clinical isolates) were determined and species identification was made by BLAST search for homologous sequences in public databases. Species other than Streptococcus contained multiple ITS fragments and only the shortest fragment was analysed. A total of 25 isolates (11.5 %) produced discrepant identification by ITS sequencing. The 25 discordant strains were analysed further by sequencing of the 16S rRNA gene for species clarification, and 21 were found to be identified correctly by ITS sequence analysis. The correct identification rate by ITS sequencing was 98.2 % (213/217). Several closely related enterococcal and streptococcal species/subspecies contained specific ITS signature sequences that were useful for differentiating these bacteria. In conclusion, ITS sequencing provides a useful approach towards identifying this group of pathogens on a molecular platform alongside 16S rRNA gene sequencing.

Phylogenetic Analysis of Viridans Group Streptococci Causing Endocarditis

“…By the current and published standard, our unusual sequence variants could support several new species designations. In fact, prior investigators have proposed the assignment of new species based on isolated case reports or have claimed a greater accuracy of identification with sequencing of the 16S rRNA, rnpB, rpoB, sodA, and/or 16S-23S rRNA spacer targets (1,3,4,6,13,14). We have shown that both phenotype and hierarchy-of-sequence data are often discordant, and the relative ability of a particular DNA target to draw finer phylogenetic distinctions does not necessarily warrant the description of a new species or support greater accuracy of identification.…”

Associação entre a diminuição do nível de ferro salivar e a experiência de cárie em crianças

“…When there is a low availability of iron, certain bacterial species can achieve an ecological advantage [23]. Interestingly, Streptococci are bacteria that can grow under limited iron conditions [24], which may explain the caries experience in children with reduced salivary iron levels. Another hypothesis is that the lower availability of salivary iron does not inhibit the activity of the glycosyltransferase enzyme, which is responsible for producing insoluble extracellular polysaccharides that in turn confer an ecological advantage to cariogenic bacteria [25].…”

Streptococcus tigurinus sp. nov., isolated from blood of patients with endocarditis, meningitis and spondylodiscitis

“…This relatively high sequence demarcation of 1.3 % strongly suggested the recognition of a novel streptococcal species and an erroneous assignment of strain ATCC 15914, which was typed in 1977 based solely on phenotypic characteristics (Facklam, 1977). Moreover, the correct species assignment of strain ATCC 15914 was questioned recently by several reports on the basis of analyses of the housekeeping genes zwf and gki (Kiratisin et al, 2005) and the 16S-23S rRNA intergenic spacer region (Tung et al, 2006(Tung et al, , 2007. A retrospective analysis of our molecular database revealed three additional clinical streptococcal isolates (AZ_4a, AZ_7a, AZ_10) that displayed the closest 16S rRNA gene sequence similarity to strain ATCC 15914 in the public database.…”