Identification of Streptococci to Species Level by Sequencing the Gene Encoding the Manganese-Dependent Superoxide Dismutase

Abstract

We have used a PCR assay based on the use of degenerate primers in order to characterize an internal fragment (sodAint ) representing approximately 85% of the genes encoding the manganese-dependent superoxide dismutase in various streptococcal type strains (S. acidominimus,S. agalactiae, S. alactolyticus, S. anginosus, S. bovis, S. constellatus,S. canis, S. cricetus, S. downei,S. dysgalactiae, S. equi subsp.equi, S. equi subsp. zooepidemicus,S. equinus, S. gordonii, S. iniae,S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguis,S. pneumoniae, S. porcinus, S. pyogenes, S. salivarius, S. sanguis,S. sobrinus, S. suis, S. thermophilus, and S. vestibularis). Phylogenetic analysis of these sodAint fragments yields an evolutionary tree having a topology similar to that of the tree constructed with the 16S rRNA sequences. We have shown that clinical isolates could be identified by determining the positions of theirsodAint fragments on the phylogenetic tree of the sodAint fragments of the type species. We propose this method for the characterization of strains that cannot be assigned to a species on the basis of their conventional phenotypic reactions.

First report of Streptococcus iniae in red porgy (Pagrus pagrus, L.)

“…equisimilis. This misidentification has been reported by many researchers using Api 20 Strep or Rapid ID 32 Strep (Weinstein et al 1997;Poyart, Quesne, Coulon, Berche & Trieu-Cout 1998;Dodson, Maurer & Shotts 1999;Lau et al 2003;Facklam, Elliott, Shewmaker & Reingold 2005;Klesius et al 2006), BioMérieux Vitek (Weinstein et al 1997;Lau et al 2003;Facklam et al 2005), the ATB Expression System (Lau et al 2003) and the Microscan WalkAway System (Facklam et al 2005), which were unable to identify S. iniae because it was not in the corresponding databases of any of the automated devices. It is known that no commercial bacterial identification system includes S. iniae in its database (Agnew & Barnes 2007); however, the individual biochemical reactions read by these systems can still be used and compared to…”

A novel multiplex PCR/RFLP assay for the identification of Streptococcus bovis/Streptococcus equinus complex members from dairy microbial communities based on the 16S rRNA gene

“…The clear discrimination of SBSEC from other streptococcal groups is a clear advantage of the assay developed in our study considering the potential commensal microbial communities of raw dairy products. In contrast to other assays such as the general Streptococcus genus-specific assay targeting the sodA gene, the assay developed in this study does not require downstream sequencing for species identification (Poyart et al, 1998). Nevertheless, the primers developed in our study were designed to be compatible with the emerging wide availability of sequencing technologies.…”

Significance of bacterial identification by molecular biology methods

“…Some bacterial groups are very closely related and the sequence information within the gene is not sufficient to resolve these taxa with any certainty. Difficult Bacterial identification by molecular biology methods (sodA) is one such gene that has been successfully used to identify the oral streptococci, including the mitis group (18) and the coagulase-negative staphylococci (19). A number of other genes have been used to identify coagulase-negative staphylococci but not commonly within oral microbiology these are the hsp60 and rpoB.…”