Phylogenetic diversity of Streptococcus suis strains of various serotypes as revealed by 16S rRNA gene sequence comparison

Chatellier, Sonia; Harel, Josée; Zhang, Ying; Gottschalk, Marcelo; Higgins, Robert; Devriese, Luc; Brousseau, Roland

doi:10.1099/00207713-48-2-581

Cited by 62 publications

(52 citation statements)

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“…Indeed, it has been reported that phylogenetic studies are severely limited by 16S rDNA heterogeneity and that analysis of distinct rRNA operons within the same microbial strain may lead to different results (5,7,36). Finally, for S. suis and S. mitis, differential branching could be the result of previously reported greater genetic variation within these two species (4,13,23,43,46). Phylogenetic analysis using either tuf or 16S rDNA sequences revealed that three clinically important streptococcal phenotypic species groups (i.e., mitis, pyogenes, and mutans) are composed of three to five phylogenetic clusters and that the groups anginosus and salivarius were monophyletic.…”

Section: Discussionmentioning

confidence: 99%

“…Phylogenetic analyses of streptococci conducted using several conserved genes, including those coding for 16S rRNA, heat shock proteins, glucose pyrophosphorylase, and superoxide dismutase, have been reported (4,13,23,33,43). All of these phylogenetic studies demonstrated the usefulness of genetic approaches to improve the accuracy of streptococcal species identification.…”

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Use of tuf Sequences for Genus-Specific PCR Detection and Phylogenetic Analysis of 28 Streptococcal Species

et al. 2004

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A 761-bp portion of the tuf gene (encoding the elongation factor Tu) from 28 clinically relevant streptococcal species was obtained by sequencing amplicons generated using broad-range PCR primers. These tuf sequences were used to select Streptococcus-specific PCR primers and to perform phylogenetic analysis. The specificity of the PCR assay was verified using 102 different bacterial species, including the 28 streptococcal species. Genomic DNA purified from all streptococcal species was efficiently detected, whereas there was no amplification with DNA from 72 of the 74 nonstreptococcal bacterial species tested. There was cross-amplification with DNAs from Enterococcus durans and Lactococcus lactis. However, the 15 to 31% nucleotide sequence divergence in the 761-bp tuf portion of these two species compared to any streptococcal tuf sequence provides ample sequence divergence to allow the development of internal probes specific to streptococci. The Streptococcus-specific assay was highly sensitive for all 28 streptococcal species tested (i.e., detection limit of 1 to 10 genome copies per PCR). The tuf sequence data was also used to perform extensive phylogenetic analysis, which was generally in agreement with phylogeny determined on the basis of 16S rRNA gene data. However, the tuf gene provided a better discrimination at the streptococcal species level that should be particularly useful for the identification of very closely related species. In conclusion, tuf appears more suitable than the 16S ribosomal RNA gene for the development of diagnostic assays for the detection and identification of streptococcal species because of its higher level of species-specific genetic divergence.

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Section: Discussionmentioning

confidence: 99%

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Use of tuf Sequences for Genus-Specific PCR Detection and Phylogenetic Analysis of 28 Streptococcal Species

et al. 2004

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“…For the phylogenetic analyses, the nucleotide residues with a gap or with an ambiguity were removed from the alignment. Evolutionary distance values were estimated using the DNADIST program of the PHYLIP, Phylogeny Inference Package, version 3.573c, and the neighbor-joining trees were constructed by the NEIGHBOR program of the PHYLIP as described previously [6]. Using the program package, the topologies of the trees were evaluated by a bootstrapping method.…”

Section: Methodsmentioning

confidence: 99%

Differentiation between Bovine and Ovine Strains of Histophilus somni Based on the Sequences of 16S rDNA and rpoB Gene

Tanaka

Hoshinoo

Hoshino

et al. 2005

The Journal of Veterinary Medical Science

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ABSTRACT. Nucleotide sequences of 16S rDNA and rpoB gene of 25 bovine and 6 ovine Histophilus somni strains were determined to detect subtle differences between the host animal species. The 1465 nucleotide residues of the 16S rDNA exhibited levels of sequence similarities of 99.4% or more. The high sequence similarity of the 16S rDNA of recently described species H. somni was confirmed in the 31 strains from cattle and sheep. These results suggested that the intra-specific diversity of 16S rDNA was limited in bovine and ovine strains of H. somni. The specific association of strains was also observed in the 311 bp region of rpoB gene which sequence similarities were 98.6% or more. However, the phylogenetic tree analysis of the rpoB gene showed that the ovine strains appeared to form a subgroup recovered in 70% of the bootstrap trees. In the 311 bp region of the ovine strains, a HincII restriction endonuclease site was detected. The PCR-amplified rpoB DNA of 46 bovine and 20 ovine H. somni strains were examined for the digestion with HincII. As the results, 17 strains of ovine strains were cleaved by the enzyme but none of the bovine strains appeared to possess the restriction site. The restriction enzyme analysis of rpoB gene may be useful to differentiate ovine strains from bovine strains of H. somni. H. somni was a recently described bacterial species as a combination of "Haemophilus somnus", "Haemophilus agni" and "Histophilus ovis" [1]. The organisms can be pathogens responsible for substantial economic losses in cattle and sheep industries due to a variety of diseases, such as thrombotic meningoencephalitis, pneumonia, myocarditis, and reproductive disorders in cattle [17,18,27] as well as mastitis, septicemia, and reproductive disorders in sheep [4,18,38]. H. somni is also distributed in nasopharyngeal tracts and reproductive organs of healthy animals [8-11, 19, 20, 29, 41, 45]. Based on the profiles of outer membrane protein, a restriction endonuclease analysis, PCR-based fingerprinting analyses and a DNA reassociation analysis, it has been suggested that there are host-specific subgroups in the organisms [3,23,46,47]. Up to the date, however, no simple mean to differentiate between bovine and ovine strains of H. somni has been available. Such a method reflecting on the boundary can be a useful tool for understanding the epidemiology of the organisms. Based on the phylogenies of the 16S rDNAs, H. somni strains are clearly distinguished from the related taxa in the family Pasteurellaceae [1]. In addition to the use of 16S rDNA sequencing for taxonomic purposes, subtle sequence differences in the 16S rDNA sequence were recently reported to be useful for species identification [34,39] and for subtyping and identifying hyper-virulent bacterial clones [5,31,33]. For the same purposes, the rpoB gene encoding the β-subunit of RNA polymerase has been studied for many bacterial species, such as Bacillus [24] although sequence stretches or cluster groups corresponding to the host-specific subgroups were not clear d...

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“…Corresponding to these results, no intraspecies variations were reported in the 16S rRNA genes of S. agalactiae (1,17) and S. porcinus (3). However, a variation in the sequence of the 16S rRNA gene was observed for S. suis (8) and for S. equi subsp. zooepidemicus (2).…”

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Evaluation of PCR Methods for Rapid Identification and Differentiation of Streptococcus uberis and Streptococcus parauberis

et al. 2001

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Streptococcus uberis and Streptococcus parauberis reference strains and isolates obtained from routine diagnostics were investigated by PCR with oligonucleotide primers designed according to species-specific parts of the 16S rRNA gene, the 23S rRNA gene, and the 16S-23S rRNA intergenic spacer region of both species. All three primer pairs allowed an identification of 67 isolates as S. uberis and 4 isolates as S. parauberis.The use of PCR as a diagnostic tool for the detection of bacterial pathogens has become more frequent during the past few years. The PCR technique allows the amplification of preselected, species-specific DNA regions which can be used for genotypic identification of bacteria. A molecule most suited for these purposes appears to be the gene encoding the 16S rRNA. According to Bentley et al. (4) and Bentley and Leigh (6), the sequence variability of the V2 region of the 16S rRNA allows a differentiation of 31 species of the genus Streptococcus, including the species S. uberis and S. parauberis. Both species, formerly classified as S. uberis types I and II (19), are well known as causative agents of bovine mastitis. According to biochemical and serological characteristics, the two species are almost indistinguishable (19). A molecular identification of both species can be performed by analysis of restriction fragment length polymorphisms (RFLPs) of the 16S rRNA gene (13,14,18) or by the use of species-specific oligonucleotide probes (5, 6). A major disadvantage of these procedures is the additional manipulation of the samples subsequent to the PCR and the time-consuming preparation of the gene probes. In the present study, species-specific regions of the 16S and 23S rRNA genes and the 16S-23S rRNA intergenic spacer region of S. uberis and S. parauberis were used to construct speciesspecific oligonucleotide primers. These oligonucleotide primers were used to identify and differentiate both species.A total of 17 S. uberis and 2 S. parauberis strains were used in this study, all of which were obtained from the Institute's strain collection. The cultures were identified and differentiated into both species as described previously (15, 18). In addition, 51 streptococci obtained from routine mastitis diagnostics and also S. parauberis strain 94/16 were included. The latter, kindly obtained from J. F. Fernández-Garayzábal (Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain), was originally isolated from a diseased turbot (9). The cultures isolated from routine diagnostics were preliminarily identified as S. uberis by using conventional methods (15, 16). These methods included carbohydrate fermentation tests for arabinose, fructose, inulin, lactose maltose, mannitol, raffinose, ribose, saccharose, salicin, sorbitol, and trehalose; esculin and sodium hippurate hydrolysis; determination of arginine hydrolysis; and analysis of the enzymes ␤-D-glucuronidase, pyrrolydonylaminopeptidase, and hyaluronidase. The ␤-D-glucuronidase and pyrrolydonylaminopeptidase enzyme activities were inves...

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Phylogenetic diversity of Streptococcus suis strains of various serotypes as revealed by 16S rRNA gene sequence comparison

Cited by 62 publications

References 29 publications

Use of tuf Sequences for Genus-Specific PCR Detection and Phylogenetic Analysis of 28 Streptococcal Species

Use of tuf Sequences for Genus-Specific PCR Detection and Phylogenetic Analysis of 28 Streptococcal Species

Differentiation between Bovine and Ovine Strains of Histophilus somni Based on the Sequences of 16S rDNA and rpoB Gene

Evaluation of PCR Methods for Rapid Identification and Differentiation of Streptococcus uberis and Streptococcus parauberis

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