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Background   Clostridium sordellii  can cause severe infections in animals and humans, the latter associated with trauma, toxic shock and often-fatal gynaecological infections. Strains can produce two large clostridial cytotoxins (LCCs), TcsL and TcsH, related to those produced by  Clostridium difficile, Clostridium novyi  and  Clostridium perfringens , but the genetic basis of toxin production remains uncharacterised.    Results  Phylogenetic analysis of the genome sequences of 44 strains isolated from human and animal infections in the UK, US and Australia placed the species into four clades. Although all strains originated from animal or clinical disease, only 5 strains contained LCC genes: 4 strains contain  tcsL  alone and one strain contains  tcsL  and  tcsH.  Four toxin-positive strains were found within one clade. Where present,  tcsL  and  tcsH  were localised in a pathogenicity locus, similar to but distinct from that present in  C. difficile . In contrast to  C. difficile , where the LCCs are chromosomally localised, the  C. sordellii tcsL  and  tcsH  genes are localised on plasmids. Our data suggest gain and loss of entire toxigenic plasmids in addition to horizontal transfer of the pathogenicity locus. A high quality, annotated sequence of ATCC9714 reveals many putative virulence factors including neuraminidase, phospholipase C and the cholesterol-dependent cytolysin sordellilysin that are highly conserved between all strains studied.    Conclusions  Genome analysis of  C. sordellii  reveals that the LCCs, the major virulence factors, are localised on plasmids. Many strains do not contain the LCC genes; it is probable that in several of these cases the plasmid has been lost upon laboratory subculture. Our data are consistent with LCCs being the primary virulence factors in the majority of infections, but LCC-negative strains may precipitate certain categories of infection. A high quality genome sequence reveals putative virulence factors whose role in virulence can be investigated.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1613-2) contains supplementary material, which is available to authorized users.

Clostridium sordellii genome analysis reveals plasmid localized toxin genes encoded within pathogenicity loci