Identification of Clinically Relevant Nonhemolytic Streptococci on the Basis of Sequence Analysis of 16S-23S Intergenic Spacer Region and Partial
            <i>gdh</i>
            Gene

Nielsen, Xiaohui Chen; Justesen, Ulrik Stenz; Dargis, Rimtas; Kemp, Michael; Christensen, Jens Jørgen

doi:10.1128/jcm.01449-08

Cited by 33 publications

(30 citation statements)

References 45 publications

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“…Thus, evidence of exchange of homologous gene sequences between species invalidates the many suggested identification procedures based on sequence comparisons of single housekeeping genes such as sodA, gdh, rpoA, recA, recN, etc. (11,12,22,28,31,34,41).…”

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confidence: 99%

Novel Molecular Method for Identification of Streptococcus pneumoniae Applicable to Clinical Microbiology and 16S rRNA Sequence-Based Microbiome Studies

2012

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The close phylogenetic relationship of the important pathogen Streptococcus pneumoniae and several species of commensal streptococci, particularly Streptococcus mitis and Streptococcus pseudopneumoniae , and the recently demonstrated sharing of genes and phenotypic traits previously considered specific for S. pneumoniae hamper the exact identification of S. pneumoniae . Based on sequence analysis of 16S rRNA genes of a collection of 634 streptococcal strains, identified by multilocus sequence analysis, we detected a cytosine at position 203 present in all 440 strains of S. pneumoniae but replaced by an adenosine residue in all strains representing other species of mitis group streptococci. The S. pneumoniae -specific sequence signature could be demonstrated by sequence analysis or indirectly by restriction endonuclease digestion of a PCR amplicon covering the site. The S. pneumoniae -specific signature offers an inexpensive means for validation of the identity of clinical isolates and should be used as an integrated marker in the annotation procedure employed in 16S rRNA-based molecular studies of complex human microbiotas. This may avoid frequent misidentifications such as those we demonstrate to have occurred in previous reports and in reference sequence databases.

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confidence: 99%

Novel Molecular Method for Identification of Streptococcus pneumoniae Applicable to Clinical Microbiology and 16S rRNA Sequence-Based Microbiome Studies

2012

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“…Other molecular-based identification methods for VGS species assignment have employed single-gene targets, such as rpoA, rpoB, rnpB, rodA, sodA, and gdh, with varied success (8,(17)(18)(19)(20)(21)(22)(23)(24). Although a single-gene approach is practical, problems with singlegene techniques in VGS stem from a highly diverse population undergoing extensive rates of inter-and intraspecies homologous recombination and horizontal gene transfer, which minimizes the utility of identification procedures based on any one particular gene tested to date (3,8,9,(25)(26)(27)(28)(29)(30).…”

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confidence: 99%

GyrB Polymorphisms Accurately Assign Invasive Viridans Group Streptococcal Species

et al. 2014

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Viridans group streptococci (VGS) are a heterogeneous group of medically important bacteria that cannot be accurately assigned to a particular species using conventional phenotypic methods. Although multilocus sequence analysis (MLSA) is considered the gold standard for VGS species-level identification, MLSA is not yet feasible in the clinical setting. Conversely, molecular methods, such as sodA and 16S rRNA gene sequencing, are clinically practical but not sufficiently accurate for VGS species-level identification. Here, we present data regarding the use of an ϳ400-nucleotide internal fragment of the gene encoding DNA gyrase subunit B (GyrB) for VGS species-level identification. MLSA, internal gyrB, sodA, full-length, and 5= 16S gene sequences were used to characterize 102 unique VGS blood isolates collected from 2011 to 2012. When using the MLSA species assignment as a reference, full-length and 5= partial 16S gene and sodA sequence analyses failed to correctly assign all strains to a species. Precise species determination was particularly problematic for Streptococcus mitis and Streptococcus oralis isolates. However, the internal gyrB fragment allowed for accurate species designations for all 102 strains. We validated these findings using 54 VGS strains for which MLSA, 16S gene, sodA, and gyrB data are available at the NCBI, showing that gyrB is superior to 16S gene and sodA sequence analyses for VGS species identification. We also observed that specific polymorphisms in the 133-amino acid sequence of the internal GyrB fragment can be used to identify invasive VGS species. Thus, the GyrB amino acid sequence may offer a more practical and accurate method for classifying invasive VGS strains to the species level.V iridans group streptococci (VGS) are a genetically heterogeneous group of commensal bacteria that cause a wide range of infections in humans, particularly in persons with hematologic disease or neutropenia as a result of chemotherapy (1, 2). Although Ͼ25 VGS species have been described, rapid and reliable identification to the species level eludes this group of organisms (3, 4). Accurate species identification is pertinent not only for epidemiological purposes but has potential implications for the clinical management of VGS infections. For example, recent studies show that Streptococcus mitis strains cause a higher incidence of severe clinical disease and have higher rates of resistance to penicillin and fluoroquinolones than do other VGS species (2, 4-6). Additionally, other VGS species have predilections to cause distinct types of infections, such as endocarditis by Streptococcus sanguinis and gastrointestinal infections by Streptococcus anginosus (2, 6).Routine tests and commercial kits used in clinical practice based on the phenotypic and biochemical traits of individual species, such as API Rapid ID32 Strep, Vitek 2, and Streptogram, have only a 30% to 80% accuracy rate for VGS, depending on the species (7-10). The inherent problems with these approaches lie in the variability of traits within V...

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…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].…”

Section: Introductionmentioning

confidence: 99%

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

Kalia

Kumar

et al. 2015

Indian J Microbiol

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The use of rrs (16S rRNA) gene is widely regarded as the ''gold standard'' for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4-7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.

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Identification of Clinically Relevant Nonhemolytic Streptococci on the Basis of Sequence Analysis of 16S-23S Intergenic Spacer Region and Partial gdh Gene

Cited by 33 publications

References 45 publications

Novel Molecular Method for Identification of Streptococcus pneumoniae Applicable to Clinical Microbiology and 16S rRNA Sequence-Based Microbiome Studies

Novel Molecular Method for Identification of Streptococcus pneumoniae Applicable to Clinical Microbiology and 16S rRNA Sequence-Based Microbiome Studies

GyrB Polymorphisms Accurately Assign Invasive Viridans Group Streptococcal Species

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

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