groESL Sequence Determination, Phylogenetic Analysis, and Species Differentiation for Viridans Group Streptococci

Abstract

The full-length sequences of the groESL genes (also known as cpn10/60) of Streptococcus anginosus, Streptococcus constellatus, Streptococcus gordonii, and Streptococcus sanguis and the near full-length sequence of the groESL genes of Streptococcus intermedius, Streptococcus bovis, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, and Streptococcus salivarius were determined. The lengths of the groES genes from the 10 species listed above ranged from 282 to 288 bp, and the full-length sequences of groEL determined for 4 species (S. anginosus, S. constellatus, S. gordonii, and S. sanguis) revealed that each was 1,623 bp. The intergenic region (spacer) between the groES and groEL genes varies in size (15 to 111 bp) and sequence between species. The variation of the groES sequences among the species tested was greater (62.1 to 95.1% nucleotide sequence identities) than that of the groEL sequences (77.2 to 95.2% nucleotide sequence identities). Phylogenetic analysis of the groES and groEL genes yielded evolutionary trees similar to the tree constructed by use of the 16S rRNA gene. The intraspecies variation of the spacer was minimal for clinical isolates of some species. The groESL sequence data provide an additional parameter for identification of viridans group streptococcal species.Viridans group streptococci (VGS) are the most common etiologic agents in subacute infective endocarditis and are known to be capable of causing many serious pyogenic infections (1,4,14). Since the clinical significance of VGS may differ between species, it is important to identify the individual species associated with diseases and to recognize their pathogenic traits (14). Moreover, increases in rates of antimicrobial resistance have been noted among VGS (25). The difference in susceptibilities between species of VGS indicates the importance of accurate identification. At present, the species of VGS can be divided into five major groups according to their 16S rRNA sequences (15). These are (i) the anginosus group (also called the milleri group), which includes At present, species identification of VGS is based on physiological and biochemical characteristics determined by conventional methods, which are time-consuming (6). Many clinical laboratories rely on manual or automated phenotypic test systems. However, there have been variations among physiological reactions within the same species, and misidentification has occurred, particularly for some species. S. mutans strains and strains of the anginosus and mitis groups are the most problematic (12, 29). Differentiation of species within the same group is often difficult (6, 27). Another approach to species identification may be the use of molecular methods. Several DNA-based techniques have been developed for the identification of VGS to the species level (3,7,8,13,16,21,23,24,28). The target genes have included 16S rRNA genes, the tRNA gene intergenic spacer, 16S-23S rRNA spacers, the gene for D-alanine-D-alanine ligase, and the gene for manganese-dependent superoxide ...

Use of Phylogenetic and Phenotypic Analyses To Identify Nonhemolytic Streptococci Isolated from Bacteremic Patients

“…As an alternative, sequencing of other housekeeping genes has been used to identify streptococci, e.g., the genes encoding D-alanine:D-alanine ligase (ddl) (19,32,36), glutamate dehydrogenase (gdh) (36,40), the ␤ subunit of RNA polymerase (rpoB) (15), and manganese-dependent superoxide dismutase (sodA) (32,41,42). Likewise, the sequences of the highly variable spacer region between the 16S and 23S rRNA genes and the groESL genes have been used for identification of streptococci (10,48). It is reported that these methods enable reliable identification of Streptococcus isolates to the species level, but they have not been applied to the whole spectrum of Streptococcus species.…”

A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

“…However, it involves more inputs and selection of other genes out of a few thousand genes within the genome is not an easy task. In spite of the fact that around 23 genes have been used frequently in many studies carried out for identifying Streptococcus, no consensus gene has been identified [3,4,11,[21][22][23][24][25][26][27][28][29][30][31][32][33][34][35]. It has also not been realized that except recA, the rest of the 22 genes are not present in all the species of Streptococcus.…”

“…Streptococcus poses a big challenge as most pathogenic strains are genetically very close to each other and have multiple copies of rrs per genome. A few genes which are frequently used for the identification of Streptococcus include genes: cpsA, gdh, groESL, lytA, ply, psaA, pspA, recA, recN, rpoA, rpoB, sodA, tuf, wzg, 16S-23S ribosomal DNA spacer region, and the DNA fragment Spn9802 [3,4,11,[22][23][24][25][26][27][28][29][30][31]. Optochin susceptibility testing (CO 2 atmosphere) in combination with amplification of Spn9802 fragment and the autolysin genes: lytA, rpoB, and tuf, have proved effective in identifying S. pneumoniae [32].…”

Characterization of thermophilic streptococci isolated from rustic white cheese

“…Studies on the microbiota of traditional cheeses in the Mediterranean agro-zones have indicated that enterococci are of a significant importance in cheese ripening and contribute to its typical taste and flavor probably through proteolysis, lipolysis, and citrate breakdown (Felis and Dellaglio, 2007;Manolopoulou et al, 2003). S. thermophilus and other thermophilic streptococci, including E. faecalis ABOU YOUNES,and SHARABI and E. faecium, are among the dominant members of the microflora of many cheeses produced with natural cultures (Teng et al, 2002). Traditional bacterial classification methods based on morphology, physiology and biochemical tests could be time-consuming and misleading (Yanagida et al, 2007).…”