Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences

Otto-von-Guericke University, Clinical Microbiology, Leipziger Str. 44, Magdeburg, Germany.
Journal of clinical microbiology (Impact Factor: 3.99). 04/2008; 46(3):1019-25. DOI: 10.1128/JCM.02058-07
Source: PubMed


The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci.
However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot
always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (∼931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal
species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities
of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (∼97%), rpoB (∼86%), hsp60 (∼82%), and sodA (∼78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification.

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Available from: Brigitte König, Oct 10, 2015
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    • "The study of genes other than 16S rRNA, has been considered for species discrimination. Thus, the 23S rRNA, the DNA gyrase b subunit (gyrB) (Chen and Tsen, 2002; La Duc et al., 2004), the RNA polymerase b subunit (rpoB) (Drancourt and Raoult, 2002; Qi et al., 2001) and the TU elongation factor (tuf) (Ghebremedhin et al., 2008) genes have been considered for the identification of certain bacterial taxons. Such genes may provide well conserved regions with potential usefulness for the design of primers and molecular probes for identification purposes in Bacillus spp. "
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    ABSTRACT: Bacillus genus includes foodborne pathogenic and spoilage-associated species, such as Bacillus cereus, Bacillus licheniformis, Bacillus subtilis and Bacillus pumilus. Bacillus is also a heterogeneous genus that includes closely related species that are difficult to discriminate among, especially when well-conserved genes such as 16S rRNA and 23S rRNA are considered. The main goal of the present work was to study the usefulness of three housekeeping genes, the TU elongation factor (tuf), the DNA gyrase β subunit (gyrB) and the RNA polymerase β subunit (rpoB) genes, for use in differentiating among the most important foodborne Bacillus spp. sequences from 20 foodborne isolated Bacillus strains, and sequences belonging to different Bacillus spp. retrieved from the GenBank were analysed. In general terms, gyrB, rpoB and tuf gene regions for the strains considered in this study exhibited interspecific similarities of 57.8%, 67.23% and 77.66% respectively. Novel tufGPF and tufGPR universal primers targeted to the tuf gene were designed and proved to be useful for the amplification of all Bacillus spp considered. In conclusion, the tuf gene can be considered to be a good target for the differential characterisation of foodborne Bacillus species, especially for differentiating B. subtilis and B. cereus from other closely related species.
    Food Microbiology 04/2015; 46:288–298. DOI:10.1016/ · 3.33 Impact Factor
    • "At present, one of the preferred approaches, along with whole genome sequencing, is the multi-locus sequence typing (MLST), a sequence analysis of multiple genes [24] [45] [63]. In most cases, house-keeping genes have been proven to be efficient genetic markers for these analyses [24] [28] [55]. Among cyanobacteria, the order Oscillatoriales comprises filamentous , non-heterocystous and non-branching morphotypes. "
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    ABSTRACT: Twenty strains of Planktothrix and five of 'Oscillatoria' were characterized by a polyphasic approach, for clarification of their taxonomic relationships. Emphasis was given to the strains (17) of the Pasteur Culture Collection of Cyanobacteria (PCC). Phenotypic characters analyzed comprised morphology, phycobiliprotein composition, temperature and salinity tolerance. The gvpA gas vesicle gene was detected by PCR in all strains, and transmission electron microscopy confirmed gas vesicle formation in the strains of 'Oscillatoria'. MALDI-TOF mass spectrometry revealed 13 chemotypes, nine of which produce microcystins. A multi-locus sequence typing (MLST) analysis was conducted using individual and concatenated nucleotide sequences of the 16S rDNA, internal transcribed spacer (ITS), gyrB, rpoC1 and rpoB. The results highlighted an unexpected diversity within the genus Planktothrix, showing that the five strains of 'Oscillatoria' need to be included in this taxon. Consequently, the genus consists of seven phylogenetic clusters, three of which represent new species, named Planktothrix paucivesiculata sp. nov.(ICNP) (type strain: PCC 8926(T)), Planktothrix tepida sp. nov.(ICNP) (type strain: PCC 9214(T)) and Planktothrix serta sp. nov.(ICNP) (type strain: PCC 8927(T)). These, together with the emended genus Planktothrix and its type species P. agardhii, valid taxa under the ICN, are described/re-described for gaining nomenclatural standing under the ICNP. Copyright © 2015 Elsevier GmbH. All rights reserved.
    Systematic and Applied Microbiology 02/2015; 38(3). DOI:10.1016/j.syapm.2015.02.004 · 3.28 Impact Factor
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    • "However, in three cases, S. capitis 35661, S. warneri 49454 and S. xylosus 29971 T , the fragment sequenced showed 99% or 100% similarity with the sequences of other species. Ghebremedhin et al. (2008) reported that some Staphylococcus taxa have the same 16S rRNA gene sequences in variable regions, including S. capitis subsp. urealyticus and S. caprae. "
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    ABSTRACT: Staphylococci isolated from bovine milk and not classified as Staphylococcus aureus represent a heterogeneous group of microorganisms that are frequently associated with bovine mastitis. The identification of these microorganisms is important, although it is difficult and relatively costly. Genotypic methods add precision in the identification of Staphylococcus species. In the present study, partial 16S rRNA sequencing was used for the species identification of coagulase-positive and coagulase-negative staphylococci isolated from bovine mastitis. Two hundred and two (95%) of the 213 isolates were successfully identified at the species level. The assigning of an isolate to a particular species was based on ≥99% identity with 16S rRNA sequences deposited in GenBank. The identified isolates belonged to 13 different Staphylococcus species; Staphylococcus chromogenes, S. aureus and Staphylococcus epidermidis were the most frequently identified species. Eight isolates could not be assigned to a single species, as the obtained sequences showed 99% or 100% similarity to sequences from two or three different Staphylococcus species. The relatedness of these isolates with the other isolates and reference strains was visualized using a cladogram. In conclusion, 16S rRNA sequencing was an objective and accurate method for the proper identification of Staphylococcus species isolated from bovine mastitis. Additional target genes could be used in non-conclusive cases for the species-level identification of these microorganisms. Copyright © 2015 Elsevier B.V. All rights reserved.
    Veterinary Microbiology 02/2015; 176(3-4). DOI:10.1016/j.vetmic.2015.01.024 · 2.51 Impact Factor
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