title: rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella.
abstract: We developed a new molecular tool based on rpoB gene (encoding the beta subunit of RNA polymerase) sequencing to identify streptococci. We first sequenced the complete rpoB gene for Streptococcus anginosus, S. equinus, and Abiotrophia defectiva. Sequences were aligned with these of S. pyogenes, S. agalactiae, and S. pneumoniae available in GenBank. Using an in-house analysis program (SVARAP), we identified a 740-bp variable region surrounded by conserved, 20-bp zones and, by using these conserved zones as PCR primer targets, we amplified and sequenced this variable region in an additional 30 Streptococcus, Enterococcus, Gemella, Granulicatella, and Abiotrophia species. This region exhibited 71.2 to 99.3% interspecies homology. We therefore applied our identification system by PCR amplification and sequencing to a collection of 102 streptococci and 60 bacterial isolates belonging to other genera. Amplicons were obtained in streptococci and Bacillus cereus, and sequencing allowed us to make a correct identification of streptococci. Molecular signatures were determined for the discrimination of closely related species within the S. pneumoniae-S. oralis-S. mitis group and the S. agalactiae-S. difficile group. These signatures allowed us to design a S. pneumoniae-specific PCR and sequencing primer pair.
authors.affiliation: Unité des Rickettsies, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
authors.forename: Véronique
authors.initials: V
authors.lastname: Roux
authors.forename: Pierre-Edouard
authors.initials: PE
authors.lastname: Fournier
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics*; D016983:Enterococcus / Q000201:enzymology / Q000235:genetics*; D007777:Lactobacillaceae / Q000201:enzymology / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D040141:Staphylococcaceae / Q000201:enzymology / Q000235:genetics*; D013289:Streptococcaceae / Q000201:enzymology / Q000235:genetics*; D013291:Streptococcus / Q000201:enzymology / Q000235:genetics*
chemical_list: D017931:DNA Primers; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit