Complex genomic and phenotypic characterization of the related species Staphylococcus carnosus and Staphylococcus piscifermentans

Pantůček, Roman; Sedláček, Ivo; Doškař, Jiřı́; Rosypal, Stanislav

doi:10.1099/00207713-49-3-941

Cited by 11 publications

(7 citation statements)

References 67 publications

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“…Routine identification of coagulase‐negative staphylococci to the species level remains problematic in the clinical microbiology laboratory. One reason for this is the rapidly evolving taxonomy of the genus Staphylococcus [3,5–8]. In addition, most laboratories use commercial systems that are based on biochemical reactions.…”

Section: Introductionmentioning

confidence: 99%

“…Ribotyping, or rRNA restriction fragment length polymorphism analysis [21,22], is based on differences in the genes encoding the 16S, 5S and 23S rRNA and flanking DNA. This technique can be applied both for typing and for species‐level identification purposes [23–25]; in particular, it has been used in the study of staphylococci for both molecular epidemiology [13,26–29] and identification and taxonomic purposes [5,13,14,27,30–35]. High‐quality databases of ribotyping profiles, including representative strains of nearly all described CoNS species and subspecies, have been constructed and are useful for identification of unknown isolates [14].…”

Section: Introductionmentioning

confidence: 99%

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Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping

Carretto

Barbarini

Couto

et al. 2005

Clinical Microbiology and Infection

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As routine identification of coagulase-negative staphylococci is problematic, the performance of automated ribotyping was evaluated for identification of coagulase-negative staphylococci other than Staphylococcus epidermidis. In total, 177 isolates were tested, comprising 149 isolates from blood samples, 15 isolates that were not identified by internal transcribed spacer (ITS)-PCR in a previous study, and 13 reference strains. The identification results were compared with those obtained by the API 20 Staph system, with standard phenotypic and molecular methods as reference. Most (n = 166; 93.8%) isolates were identified correctly by automated ribotyping. For 61 isolates, API 20 Staph and ribotyping were in agreement, but for 105 isolates, ribotyping provided correct identification and API 20 Staph did not. Four isolates not identified by automated ribotyping were recognised correctly by API 20 Staph. The remaining seven isolates could not be identified by either of the two methods. Automated ribotyping was able to distinguish Staphylococcus capitis reliably from Staphylococcus caprae. The results demonstrate the value of automated ribotyping for identification of coagulase-negative Staphylococcus (CoNS) isolates from human sources and may help to clarify the clinical relevance of CoNS species. In addition, automated ribotyping was able to detect polymorphisms that may be useful for epidemiological purposes within S. capitis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus simulans, S. caprae, Staphylococcus warneri, Staphylococcus lugdunensis, Staphylococcus schleiferi, Staphylococcus sciuri, Staphylococcus pasteuri and Staphylococcus xylosus.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping

Carretto

Barbarini

Couto

et al. 2005

Clinical Microbiology and Infection

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“…A comparative 16S and 23S rRNA analysis shows that S. carnosus forms together with S. piscifermentans and S. condimentii in a cluster (23,57,62). S. carnosus TM300 is one of the strains used in the food industry and is phenotypically indistinguishable from the type strain DSM20501.…”

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confidence: 99%

Genome Analysis of the Meat Starter Culture BacteriumStaphylococcus carnosusTM300

Rosenstein

Nerz

Biswas

et al. 2009

Appl Environ Microbiol

120

107

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The Staphylococcus carnosus genome has the highest GC content of all sequenced staphylococcal genomes, with 34.6%, and therefore represents a species that is set apart from S. aureus, S. epidermidis, S. saprophyticus, and S. haemolyticus. With only 2.56 Mbp, the genome belongs to a family of smaller staphylococcal genomes, and the ori and ter regions are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5 Mbp). The events leading up to this asymmetry probably occurred not that long ago in evolution, as there was not enough time to approach the natural tendency of a physical balance. Unlike the genomes of pathogenic species, the TM300 genome does not contain mobile elements such as plasmids, insertion sequences, transposons, or STAR elements; also, the number of repeat sequences is markedly decreased, suggesting a comparatively high stability of the genome. While most S. aureus genomes contain several prophages and genomic islands, the TM300 genome contains only one prophage, ⌽TM300, and one genomic island, SCA1, which is characterized by a mosaic structure mainly composed of species-specific genes. Most of the metabolic core pathways are present in the genome. Some open reading frames are truncated, which reflects the nutrient-rich environment of the meat starter culture, making some functions dispensable. The genome is well equipped with all functions necessary for the starter culture, such as nitrate/nitrite reduction, various sugar degradation pathways, two catalases, and nine osmoprotection systems. The genome lacks most of the toxins typical of S. aureus as well as genes involved in biofilm formation, underscoring the nonpathogenic status.It has been known for a long time that staphylococci play a role in the fermentation of dry sausage (52). At first, they were regarded as micrococci, but it turned out that these micrococci were wrongly classified and were in fact staphylococci. Based on DNA/DNA hybridization, biochemical properties, and cell wall composition, these staphylococci formed a new species, which was named Staphylococcus carnosus because the bacteria can be isolated from meat fermentation products and have been used since the 1950s as a starter culture (64).One of the main advantages of starter cultures in fermentedfood processing is that the fermentation and ripening process can be carried out under controlled conditions. In this way, food poisoning and food spoilage microorganisms can be suppressed, and the course of the fermentation process and its termination can be more reliably monitored. During the ripening process of dry sausage, S. carnosus exerts several desired functions (5, 14, 40). First, S. carnosus gradually reduces nitrate to nitrite (50). The advantages of this reaction are that the nitrate concentration is lowered and that nitrite can combine with myoglobin to form nitrosomyoglobin, which results in the typical red color. In the second step, nitrite is then further reduced to ammonia, thus lowering the unbound nitrite concentration (51). Other advantages are d...

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“…Ribotyping was done according to Pantůček et al [17] with minor modifications. Briefly, all strains were cultivated overnight in 10 ml of Todd–Hewitt broth (OXOID) at 37°C.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of ribotyping for characterization and identification ofEnterococcus haemoperoxidusandEnterococcus moraviensisstrains

Švec

Sedláček

Pantůček

et al. 2001

FEMS Microbiology Letters

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Seven Enterococcus moraviensis and 16 Enterococcus haemoperoxidus as well as nine reference cultures of other enterococcal species obtained from the Czech Collection of Microorganisms were characterized using ribotyping with EcoRI and HindIII in the present work. The ribopatterns obtained by both restriction enzymes clearly distinguished all E. moraviensis and E. haemoperoxidus strains from the other enterococci (E. faecalis, E. faecium, E. avium, E. raffinosus, E. pseudoavium, E. malodoratus) and they differentiated both species from each other as well. Although all strains were isolated from different sampling sites, many strains shared the same band patterns. E. moraviensis formed four ribogroups using EcoRI and two ribogroups using HindIII restriction enzyme. E. haemoperoxidus gave six different patterns with EcoRI and five using the HindIII restriction enzyme.

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Complex genomic and phenotypic characterization of the related species Staphylococcus carnosus and Staphylococcus piscifermentans

Cited by 11 publications

References 67 publications

Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping

Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping

Genome Analysis of the Meat Starter Culture BacteriumStaphylococcus carnosusTM300

Evaluation of ribotyping for characterization and identification ofEnterococcus haemoperoxidusandEnterococcus moraviensisstrains

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