Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.

This guidance document is intended to assist the applicant in the preparation and the presentation of an application, as foreseen in Article 7.6 of Regulation (EC) No 1831/2003, for the authorisation of additives used in animal nutrition. It specifically covers the assessment of the safety for the environment.

Sequences of the gene encoding the b-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases the rpoB phylogeny was in better agreement with DNA-DNA hybridization studies than the phylogeny derived from 16S rDNA. The rpoB gene is strongly conserved within the various species of the family of Pasteurellaceae. Hence, rpoB gene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of the Pasteurellaceae and may also prove useful for reorganizing the current taxonomy of this bacterial family.The family Pasteurellaceae Pohl 1981 currently comprises 57 named bacterial species which have been isolated from man and various animals. The three genera Haemophilus, Actinobacillus and Pasteurella which originally formed the family have recently been joined by new genera, the most prominent being Mannheimia, which contains the species Mannheimia haemolytica (formerly Pasteurella haemolytica) (Angen et al., 1999). Three genera are currently formed by single species, these are Phocoenobacter uteri (Foster et al., 2000), Lonepinella koalarum (Osawa et al., 1995) and Histophilus somni (Angen et al., 2003). The latter genus has been proposed to include the three species incertae sedis 'Haemophilus somnus', 'Haemophilus agni' and 'Histophilus ovis'. Finally, Christensen et al. (2003a) have described the genus Gallibacterium, which currently consists of one species and one genomospecies.Members of the Pasteurellaceae are generally isolated from mucosal membranes and tissue of birds, turtles and mammals, including man. They show a strong host association and have probably co-evolved with their corresponding hosts (Bisgaard, 1993). While most of the species are commensals, there are a few that act as pathogens . These include the human pathogens Haemophilus influenzae, which causes neonatal meningitis and otitis media, and Actinobacillus actinomycetemcomitans, which causes juvenile periodontitis. Important animal diseases are caused, for example, by M. haemolytica (shipping fever of cattle), Pasteurella multocida (atrophic rhinitis in swine and fowl cholera) and Actinobacillus pleuropneumoniae (pleuropneumonia in pigs). In many of the pathogenic species of Pasteurellaceae, specific toxins belonging to the RTX toxin family are found . These toxins are often associated with specifically pathogenic isolates and seem to determine to some extent the host range of the pathoge...

Results indicated a separate evolution for plasmid- and chromosomally-encoded blaZ. Although a common gene pool seems to exist among staphylococci, exchange of blaZ between strains and species is judged to be an extremely rare event.

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