The French specific 85-kb type II virulence plasmid (Ribeiro et al., 2005) was not detected either in organic or in environmental samples (Fig. 1). In addition to the classical vapA-carrying virulence plasmid, we identified, during plasmid extraction and RFLP analysis, seven strains harbouring smaller or larger plasmids with unknown function (Table S1). These plasmids, generally designated as cryptic plasmids (Makrai

et al., 2002), were identified in 1.6% of clinical, 9.1% of organic and 30.8% of environmental samples. Four strains harboured only cryptic plasmids, while another three Sirolimus strains carried both virulence and cryptic plasmids. The prevalence of cryptic plasmids in our strains (7.3%) is comparable to the prevalence of cryptic plasmids (>5%) reported in Japanese R. equi strains (Takai et al., 1994). Because they are less prevalent in clinical click here samples than in environmental samples, cryptic plasmids do not appear to be related to virulence. However, they may potentially constitute a gene reservoir for the virulence plasmid. Finally, to better understand the basis of the genetic diversity between vapA-carrying virulence-associated plasmids, we sequenced the second most frequently isolated virulence plasmid type: an 87-kb type I plasmid. Widespread throughout the world, the 87-kb type I virulence plasmid type has already been identified in horse-related environments in France, Italy, Turkey, North and South America

and Australia (Makrai et al., 2002) and, surprisingly, from a cutaneous lesion of a cat in Australia (Farias et al., 2007). We extracted the 87-kb type I plasmid from the strain MBE116 (Table S1) and designated it as pVAPA116. This plasmid is 83 100 bp in size and contains 77 coding sequences, including six pseudogenes, equivalent to a coding density of 76.6% (Table S2). Although pVAPA116 is 2490 bp larger than pVAPA1037 – an 85-kb type I plasmid – the overall structure is highly conserved in both plasmids (95.8% DNA sequence identity), and the CURV modular arrangement (found in pVAPA1037) (Letek et al., 2008) is also found in pVAPA116 (Fig. 2). The divergences between pVAPA116 and pVAPA1037

are concentrated ADP ribosylation factor in three major allelic exchange loci (Fig. 2). The first locus corresponds to the insertion of pVAPA_0041 in the generally conserved conjugation region. The pVAPA_0041 gene product (185 amino acids) shares 32% identity (47% similarity) over 107 amino acids, with the protein of unknown function RHOER0001_1517 from Rhodococcus erythropolis. As this similarity suggests horizontal DNA exchange between different Rhodococcus species, it would be interesting to assess the conjugation capacity of virulence plasmids from each species. The second allelic exchange locus occurs in the variable region downstream from the invA-like DNA invertase/resolvase gene pVAPA_0810 and corresponds to the insertion of pVAPA_0811 and pVAPA_0812 and the deletion of pVAPA_0830 (Table S2 and Fig. 2).