Recommended minimal standards for description of new staphylococcal species

Freney, J.; Kloos, Wesley E.; Hájek, Václav; Webster, John; Bes, Michèle; Brun, Y.; Vernozy-Rozand, C.

doi:10.1099/00207713-49-2-489

Cited by 119 publications

(78 citation statements)

References 80 publications

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“…Aerobic, endospore-forming bacteria (Logan et al, 2009) Anoxygenic phototrophic bacteria (Imhoff & Caumette, 2004) Genus Brucella (Corbel & Brinley Morgan, 1975a, b) Family Campylobacteraceae (Ursing et al, 1994) Family Flavobacteriaceae (Bernardet et al, 2002) Order Halobacteriales (Oren et al, 1997) Family Halomonadaceae (Arahal et al, 2007;Arahal et al, 2008) Genus Helicobacter (Dewhirst et al, 2000) Methanogenic bacteria (Archaea) (Boone & Whitman, 1988 (Bøvre & Henriksen, 1976) Genus Mycobacterium (Lévy-Frébault & Portaels, 1992) Family Pasteurellaceae (Christensen et al, 2007) Root and stem nodulating bacteria (Graham et al, 1991) Staphylococci (Freney et al, 1999) Genus Streptomyces (not a minimal standard, but a standard reference work, Shirling & Gottlieb, 1966) …”

Section: Minimal Standardsmentioning

confidence: 99%

Notes on the characterization of prokaryote strains for taxonomic purposes

Tindall

Rosselló‐Móra

Busse

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

1,230

959

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Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers. INTRODUCTIONThe characterization of a strain is a key element in prokaryote systematics. Although various new methodologies have been developed over the past 100 years, both the newer methodologies and those considered to be 'traditional' remain key elements in determining whether a strain belongs to a known taxon or constitutes a novel one. In the case of a known taxon, a selected set of tests may be used to determine whether a strain has been identified as a member of an existing taxon. However, in the case of a strain or set of strains shown to be novel taxa, they should be characterized as comprehensively as possible. The goal of this characterization is to place them within the hierarchical framework laid down by the Bacteriological Code (1990 revision) (Lapage et al., 1992), as well as to provide a description of the taxa. Strains should be allocated to species (and/or subspecies), but the nature of the 'species name' (a binomial or combination) dictates that it must also be assigned to a genus. The genus may be either an existing or a novel genus. The Bacteriological Code also recommends that the placement of a genus in a family should be mentioned, and this can be extended to the other hierarchical levels as these become defined. Although this approach may appear novel, with much emphasis currently being placed on the species, the advent of 16S rRNA gene sequencing forces us to choose between primers that are specific for members of the Archaea or for members of the Bacteria, so the first step in that direction is already routine in many laboratories. However, such a classification system is only possible if strains are comprehensively and properly characterized. A further key element is the way in which datasets are compared and it is here too that some degree of guidance and a discussion of the potential problems needs to be provided. In the case of species, various recommendations have been made with respect to the ways in which species may be delineated and it is important to consider these aspects when considering how new strains are to be placed in novel species. However, far too little attention has been paid to the way in which taxa above the rank of species should be characterized a...

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Section: Minimal Standardsmentioning

confidence: 99%

Notes on the characterization of prokaryote strains for taxonomic purposes

Tindall

Rosselló‐Móra

Busse

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

1,230

959

View full text Add to dashboard Cite

show abstract

“…The experimental documentation for the existence of species at the genotypic level 'requires analysis of large populations of each candidate species and not just one or a few reference isolates ' (Hanage et al, 2005). A certain minimum number of strains has also been mentioned in other minimal standards (Graham et al, 1991;Freney et al, 1999;Bernardet et al, 2002). For members of the Pasteurellaceae, descriptions have to be based on as many strains as possible (inclusion of at least five strains is highly desirable), representing different sources with respect to geography and ecology to allow proper characterization both phenotypically and genotypically, to establish the extent of diversity of the cluster to be named (Christensen et al, 2001).…”

Section: Selection Of Isolatesmentioning

confidence: 99%

Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Christensen

Kuhnert

Busse

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

115

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4Rødding Tvaervej 3, 6630 Rødding, DenmarkPrinciples and guidelines are presented to ensure a solid scientific standard of papers dealing with the taxonomy of taxa of Pasteurellaceae Pohl 1981. The classification of the Pasteurellaceae is in principle based on a polyphasic approach. DNA sequencing of certain genes is very important for defining the borders of a taxon. However, the characteristics that are common to all members of the taxon and which might be helpful for separating it from related taxa must also be identified. Descriptions have to be based on as many strains as possible (inclusion of at least five strains is highly desirable), representing different sources with respect to geography and ecology, to allow proper characterization both phenotypically and genotypically, to establish the extent of diversity of the cluster to be named. A genus must be monophyletic based on 16S rRNA gene sequence-based phylogenetic analysis. Only in very rare cases is it acceptable that monophyly can not be achieved by 16S rRNA gene sequence comparison. Recently, the monophyly of genera has been confirmed by sequence comparison of housekeeping genes. In principle, a new genus should be recognized by a distinct phenotype, and characters that separate the new genus from its neighbours should be given clearly. Due to the overall importance of accurate classification of species, at least two genotypic methods are needed to show coherence and for separation at the species level. The main criterion for the classification of a novel species is that it forms a monophyletic group based on 16S rRNA gene sequence-based phylogenetic analysis. However, some groups might also include closely related species. In these cases, more sensitive tools for genetic recognition of species should be applied, such as DNA-DNA hybridizations. The comparison of housekeeping gene sequences has recently been used for genotypic definition of species. In order to separate species, phenotypic characters must also be identified to recognize them, and at least two phenotypic differences from existing species should be identified if possible. We recommend the use of the subspecies category only for subgroups associated with disease or similar biological characteristics. At the subspecies level, the genotypic groups must always be nested within the boundaries of an existing species. Phenotypic cohesion must be documented at the subspecies level and separation between subspecies and related species must be fully documented, as well as association with particular disease and host. An overview of methods previously used to characterize isolates of the Pasteurellaceae has been given. Genotypic and phenotypic methods are separated in relation to tests for investigating diversity and cohesion and to separate taxa at the level of genus as well as species and subspecies. et al., 1992). However, it makes no sense to name a novel taxon without having considered its specific properties and evaluated how it differs from related taxa. To ensure the optimal circumscript...

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“…The South American squirrel monkey (Saimiri sciureus L.) is an arboreal, small-sized, non-human primate from equatorial South America; it has always been a common sight in zoos, and laboratory-bred squirrel monkeys have long been used as an animal model in various fields of biomedical research (Rosenblum & Coe, 1985). (Freney et al, 1999; Pantů ček et al, 1999;Mannerová et al, 2003). Additional biochemical profile data were obtained by using the ID32 Staph, API Staph and API ZYM systems (bioMérieux).…”

mentioning

confidence: 99%

“…During an outbreak of diarrhoeal disease in squirrel monkeys in a zoo in Olomouc, Czech Republic, staphylococcal strains with atypical features were isolated from both ill and healthy animals. The South American squirrel monkey (Saimiri sciureus L.) is an arboreal, small-sized, non-human primate from equatorial South America; it has always been a common sight in zoos, and laboratory-bred squirrel monkeys have long been used as an animal model in various fields of biomedical research (Rosenblum & Coe, 1985 Morphological and physiological characteristics of the tested cultures, as well as susceptibility to furazolidone (100 mg), novobiocin (1?6 mg), bacitracin (0?04 U), polymyxin B (300 U) and lysostaphin (200 mg l 21 ) were examined by using conventional key tube or plate tests as described previously (Freney et al, 1999;Pantů ček et al, 1999;Mannerová et al, 2003). Additional biochemical profile data were obtained by using the ID32 Staph, API Staph and API ZYM systems (bioMérieux).…”

mentioning

confidence: 99%

Staphylococcus simiae sp. nov., isolated from South American squirrel monkeys

Pantůček

Sedláček

Petřáš

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

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Eight coagulase-negative, oxidase-negative and novobiocin-susceptible staphylococcal strains were isolated from the gastrointestinal tracts of South American squirrel monkeys (Saimiri sciureus L.). These strains were differentiated from known staphylococcal species on the basis of 16S rRNA gene and hsp60 gene sequencing, and from the most closely related species by using DNA-DNA hybridization, ribotyping, whole-cell protein profiles and biotyping. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that these strains are members of the Staphylococcus aureus species group (99 % similarity) but are biochemically similar to Staphylococcus piscifermentans, from which they can be phenotypically distinguished by resistance to polymyxin B, acid production from D-mannitol, the inability to hydrolyse aesculin and DNA and the absence of a-glucosidase. On the basis of these analyses, a novel species of the genus Staphylococcus is described, for which the name Staphylococcus simiae sp. nov. is proposed, with CCM 7213 T (=LMG 22723 T ) as the type strain.Staphylococci are among the most widespread of the pathogenic and opportunistic pathogenic bacteria (Kloos et al., 1992). At present, 36 staphylococcal species are known: nine of them include two subspecies, and one of them includes three subspecies (Garrity et al., 2004;Spergser et al., 2003;Place et al., 2003; Švec et al., 2004). Several Staphylococcus species have been isolated from non-human primates and in some cases were associated with illness and mortality, particularly in newly imported animals (Padovan & Cantrell, 1983;Crouch et al., 1984;Stasilevich et al., 1986). An unnamed coagulase-negative and novobiocin-resistant 'Staphylococcus sp. 5' isolated from skin of squirrel monkeys has been reported previously by Kloos et al. (1976). During an outbreak of diarrhoeal disease in squirrel monkeys in a zoo in Olomouc, Czech Republic, staphylococcal strains with atypical features were isolated from both ill and healthy animals. The South American squirrel monkey (Saimiri sciureus L.) is an arboreal, small-sized, non-human primate from equatorial South America; it has always been a common sight in zoos, and laboratory-bred squirrel monkeys have long been used as an animal model in various fields of biomedical research (Rosenblum & Coe, 1985). (Freney et al., 1999; Pantů ček et al., 1999;Mannerová et al., 2003). Additional biochemical profile data were obtained by using the ID32 Staph, API Staph and API ZYM systems (bioMérieux). Susceptibility to other antibiotics was determined on Mueller-Hinton agar (Oxoid) by using a standard diffusion technique with a standard set of antibiotic discs for staphylococci (Oxoid).The characteristics of the novel isolates are summarized in the species description below. The squirrel monkey strains are phenotypically close to S. piscifermentans (Tanasupawat et al., 1992; Pantů ček et al., 1999) but differ from the latter in terms of the following biochemical characteristics: aesculin hydrolysis, DNA hydrolysis, a-and b-glucosid...

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Recommended minimal standards for description of new staphylococcal species

Cited by 119 publications

References 80 publications

Notes on the characterization of prokaryote strains for taxonomic purposes

Notes on the characterization of prokaryote strains for taxonomic purposes

Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Staphylococcus simiae sp. nov., isolated from South American squirrel monkeys

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