Abstract
Minute 3. Minutes of the meeting held in Auckland, New Zealand, on 13 October 1999
In accordance with Minute 3 of the meeting held in Auckland, the minutes of that meeting had previously been checked via e-mail and subsequently approved for publication [Int J Syst Evol Microbiol 53 (2003), 913914].
Minute 4. Retirement of members
The members were informed of the retirement from the subcommittee of members J. Henrichsen, V. Hájek, W. Köhler and J. M. Hardie. A formal letter will be sent to each expressing thanks for the services they have given to the subcommittee.
Minute 5. Current position regarding species epithet changes recently proposed within Streptococcus and Staphylococcus
Following several name (species epithet) changes effected on the grounds of grammatical correctness, particularly within the genus Streptococcus [Trüper & de' Clari, Int J Syst Bacteriol 47 (1997), 908909; Trüper & de' Clari, Int J Syst Bacteriol 48 (1998), 615], and subsequent arguments against this, particularly with regard to older established names [Kilian, Int J Syst Evol Microbiol 51 (2001), 723724], M. Kilian reported that his formal request for the retention of older, well-established names had been rejected by the Judicial Commission of the International Committee on Systematics of Prokaryotes and that, inevitably, a line would be drawn under the matter with the eventual appearance of the new names in the forthcoming 2nd edition of Bergey's Manual of Systematic Bacteriology.
It was also noted that, in future, all names published on the Approved Lists of Bacterial Names and appearing in Validation and Notification Lists would be regarded as permanent, as stated in the Amendment to Rule 61 of the Bacteriological Code [Minute 7, Session 1, of the meeting of the Judicial Commission held on 14, 15 and 18 August 1999, Sydney, Australia; Int J Syst Evol Microbiol 50 (2000), 22392244].
It was agreed that there is a need for any nomenclatural changes within the remit of the subcommittee to be voted by the members, and the collective opinion passed on to the International Committee on Systematics of Prokaryotes.
Minute 6. Species described since the previous meeting (October 1999)
An overview was given of the species listed within Macrococcus, Staphylococcus (K.-H. Schleifer) and Streptococcus (M. Kilian), in particular those species described since the previous meeting. The new taxa included:
(i) Macrococcus gen. nov., including Macrococcus bovicus sp. nov., Macrococcus carouselicus sp. nov., Macrococcus equipercicus sp. nov. (type species) and Macrococcus caseolyticus comb. nov. [Kloos et al., Int J Syst Bacteriol 48 (1998), 859877];
(ii) Staphylococcus carnosus subsp. carnosus subsp. nov. and subsp. utilis subsp. nov. and Staphylococcus condimenti sp. nov., from soy-sauce mash [Probst et al., Int J Syst Bacteriol 48 (1998), 651658], Staphylococcus fleurettii sp. nov., isolated from goat's milk cheeses [Vernozy-Rozand et al., Int J Syst Evol Microbiol 50 (2000), 15211527], Staphylococcus hominis subsp. hominis subsp. nov. and subsp. novobiosepticus subsp. nov., from human blood [Kloos et al., Int J Syst Bacteriol 48 (1998), 799812], Staphylococcus lutrae sp. nov., isolated from otters [Foster et al., Int J Syst Bacteriol 47 (1997), 724726] and Staphylococcus succinus sp. nov., isolated from 2535 million year old Dominican amber [Lambert et al., Int J Syst Bacteriol 48 (1998) 511518]. Staphylococcus pulvereri has been reported as probably synonymous with Staphylococcus vitulinus on the basis of biochemical characteristics, but requiring molecular analyses for confirmation [Petrá, Int J Syst Bacteriol 48 (1998), 617618];
(iii) Streptococcus australis sp. nov., from the human oral cavity [Willcox et al., Int J Syst Evol Microbiol 51 (2001), 12771281], Streptococcus constellatus subsp. constellatus subsp. nov. and subsp. pharyngis subsp. nov., from the human oral cavity, respiratory tract and clinical specimens [Whiley et al., Int J Syst Bacteriol 49 (1999), 14431449], Streptococcus didelphis sp. nov., from opposums with suppurative dermatitis and liver fibrosis [Rurangirwa et al., Int J Syst Evol Microbiol 50 (2000), 759765], Streptococcus pluranimalium sp. nov., from clinical specimens of several animals and birds [Devriese et al., Int J Syst Bacteriol 49 (1999), 12211226], Streptococcus entericus sp. nov., from the intestines of cattle suffering from catarrhal enteritis [Vela et al., Int J Syst Evol Microbiol 52 (2002), 665669], Streptococcus infantarius subsp. infantarius subsp. nov. and subsp. coli subsp. nov., responsible for endocarditis and isolated from human blood and faeces and from food products [Schlegel et al., Int J Syst Evol Microbiol 50 (2000), 14251434], Streptococcus lutetiensis sp. nov. and Streptococcus pasteurianus sp. nov., within the bovis species group or complex, reported as sp. nov. on the basis of the superoxide dismutase gene (sodA) sequences [Poyart et al., Int J Syst Evol Microbiol 52 (2002), 12471255], although the former is synonymous with S. infantarius subsp. coli; Streptococcus orisratti sp. nov., from the mouths of laboratory rats [Zhu et al., Int J Syst Evol Microbiol 50 (2000), 5561], Streptococcus ovis sp. nov., isolated from clinical specimens from sheep [Collins et al., Int J Syst Evol Microbiol 51 (2001), 11471150], Streptococcus sinensis sp. nov., isolated from patients with endocarditis [Woo et al., J Clin Microbiol 40 (2002), 805810; included in Validation List no. 87, Int J Syst Evol Microbiol 52 (2002), 14371438], and Streptococcus urinalis sp. nov., from human urine of patients with cystitis [Collins et al., Int J Syst Evol Microbiol 50 (2000), 11731178].
The emergence by 16S rDNA sequence analysis of a hitherto unnamed species group centred on Streptococcus hyovaginalis and also including Streptococcus thoraltensis and Streptococcus pluranimalium was noted.
Within the Streptococcus bovis/Streptococcus equinus complex, it was agreed that Streptococcus bovis is a junior synonym of Streptococcus equinus. Streptococcus waius is a synonym of Streptococcus macedonicus [Manachini et al., Int J Syst Evol Microbiol 52 (2002), 945951] and Streptococcus intestinalis is indistinguishable from Streptococcus alactolyticus on the basis of biochemical characteristics and SDS-PAGE of whole-cell proteins [Vandamme et al., Int J Syst Bacteriol 49 (1999), 737741]. There was some discussion as to the validity of the proposal by Poyart et al. [Int J Syst Evol Microbiol 52 (2002), 12471255], for the inclusion of strains previously named Streptococcus gallolyticus, Streptococcus macedonicus and Streptococcus waius within a single species, to be named Streptococcus gallolyticus. It was agreed that the data presented in the paper, particularly from the DNADNA hybridization experiments, were somewhat open to reinterpretation, as relatedness values consistently below 70 % were reported, and that it is more likely that, while Streptococcus macedonicus and Streptococcus waius together represent a single species, Streptococcus gallolyticus should remain a separate species. The latter interpretation had in fact been considered to be a possibility by the authors themselves in the discussion within that paper.
Minute 7. Author for Staphylococcus chapter in Bergey's Manual of Systematic Bacteriology, 2nd edition, vol. 3
K.-H. Schleifer reported that at present there is an outstanding requirement for someone to undertake the chapter on Staphylococcus for vol. 3 of the 2nd edition of Bergey's Manual of Systematic Bacteriology. The subcommittee notes that this is a matter of some urgency and that a suitable author needs to be found as soon as possible.
Minute 8. Streptococcal serogroup reference strains
M. Kilian pointed out the continuing requirement for a list of reference strains of streptococci as representatives of serological groups from which standard antisera could be derived. R. Facklam said that he would assist by sending his list of candidate strains from the CDC and pointed out that three new serological group antigens had been found within Streptococcus porcinus. M. Kilian remarked that work carried out by himself and colleagues had revealed that the Lancefield group O antigen of Streptococcus mitis biovar 1 was, in fact, identical to the C-polysaccharide antigen of Streptococcus pneumoniae [Bergström et al., Eur J Biochem 267 (2000), 71477157].
R. Facklam raised the issue of the problem of serological cross-reaction shown by some strains (i.e. non-monospecific reactions) and gave the example of Lancefield group B reaction with strains of Streptococcus porcinus. He considered that adsorption of antisera was a prerequisite for reliable use and that, in his opinion, one could not have confidence in some commercial antisera due to inadequate adsorption procedures. R. Facklam stated that he has raised this issue in several of his published papers.
T. Ezaki pointed out that, in Japan, there was less emphasis on Lancefield serological grouping for routine purposes and that strains were usually tested only against groups A, B, C, D, F and G.
Minute 9. Discussion of vitality of the subcommittee and its role
M. Kilian remarked on the danger of dormancy in taxonomic subcommittees and the underlying problem of a lack of identity and awareness of the remit of subcommittees by their members and the problems they should be addressing.
The idea of setting up a properly functioning e-mail group for the dissemination of material in preparation (for example, key text-book chapters where opinions from the membership would be valuable) and for maintaining general discussion and group identity within this subcommittee was raised and agreed in principle.
Minute 10. Description of new species based on a single strain
The practice of publishing descriptions of new species based on single strains was discussed. It was generally agreed that this was a bad practice and that as many strains as was practicable should be incorporated into proposals.
M. Kilian stated that, although strictly speaking the International Code of Nomenclature of Bacteria did not forbid the description of new species based on single isolates, it was unwise to do so in practice as there was no way of knowing whether a single strain could be guaranteed to constitute a representative of a separate species (i.e. a well-defined and genetically distinct population), particularly when considering the weight of scientific evidence that demonstrates that bacterial species comprise populations of genetically dissimilar clones, or strains, and that the overall population structure of species can be profoundly affected by horizontal gene transfer events.
T. Ezaki made the general point that, in the case of organisms isolated from remote environments, it may not be possible to obtain more strains and that the Judicial Commission was of the opinion that a case-by-case approach should be adopted. A. Bouvet pointed out that, where new, clinically important species were involved, it was right to publish a description even based on a single strain if that was all that was available. R. Facklam advised caution on this matter and quoted the example of the clinically important species Aerococcus sanguinicola [Lawson et al., Int J Syst Evol Microbiol 51 (2001), 475479], which had been described from a single isolate that was later found to be atypical when further strains were obtained and compared phenotypically. He pointed out that less haste would have resulted in a more accurate description in this case.
The subcommittee thought that the system practiced by the CDC, of numbering novel single strains until further isolates are found, instead of assigning a name, was a sensible one and makes the recommendation that this protocol should be generally adopted by those working with the taxa falling under the remit of the subcommittee.
A. Bouvet reminded members that the report of the ad hoc committee for re-evaluation of the species definition in bacteriology [Stackebrandt et al., Int J Syst Evol Microbiol 52 (2002), 10431047] recommended polyphasic approaches and encouraged applicable genomic methods, provided that there was demonstrated congruence between the technique used and DNADNA reassociation using reference strains. Multilocus sequence typing (MLST) was one of the promising techniques that offered an alternative to DNADNA hybridization. M. Kilian was of the opinion that MLST provided a valuable technique that would eventually be widely used when databases were available. R. Facklam gave the example of M-protein gene (emm) typing and the CDC database available on-line, where approximately 2000 hits' per month were being recorded.
Minute 11. Use of commercially available test kits versus conventional testing for characterizing strains and for taxonomic descriptions
R. Facklam was of the opinion that commercial test kits should not be used for these purposes and that initial descriptions of species should be based on characteristics determined using conventional biochemical and physiological tests, while commercial test kits could be used for routine identification purposes if required. He also pointed out that, in his professional capacity, he was not at liberty to endorse commercial products. M. Kilian was of the opinion that, whatever methods are employed in species descriptions, the reproducibility of the results is the decisive point and that methods should be clearly described. M. Kilian showed some unpublished data showing that, while there was often close agreement between commercial and conventional test formats, there were instances where marked disagreement occurred and, therefore, that these two sets of data thus derived should be treated as independent of each other while hopefully remaining consistent within individual species. These data would be sent to a leading commercial test kit manufacturing company with the suggestion that this cautionary note be included in the accompanying kit information.
Minute 12. Minimal standards for species descriptions
The minimum standards already published for staphylococcal species [Freney et al., Int J Syst Bacteriol 49 (1999), 489502] were discussed with regard to detail of characterization and the general availability of methods required. Some of the recommendations are possibly impractical in certain cases, particularly the requirement for peptidoglycan types to be determined, as this could probably only be carried out in a specialist laboratory. T. Ezaki commented that, in his laboratory, only molar ratios of peptidoglycan components were determined and not the type. R. Facklam reported that he had drafted the minimum standards for Enterococcus and would be grateful to receive comments. It was generally agreed that determination of G+C content should be included in the requirements and M. Kilian added that sequences of highly conserved housekeeping genes, such as those examined by MLST, are representative of the G+C content of DNA.
M. Kilian and R. Whiley are due to produce the minimum standards for streptococcal species descriptions and agreed to circulate a list of proposed tests for the subcommittee members to comment on.
Minute 13. Any other business
There was continuing concern over the increasing number of newly described genera with close relationships to those genera within the remit of this subcommittee. It was agreed that the taxa to be covered by the subcommittee needed clarification and that a list of the genera in question was required.
Minute 14. Next meeting of the subcommittee
A date for the next subcommittee meeting was not highlighted, and it was thought best if a list of relevant candidate scientific meetings be circulated to the membership before a decision is taken.
Minute 15. Adjournment
The meeting was adjourned at 17 : 15 on 31 July 2002.