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Background  Most recent studies of  Clostridium perfringens  plasmids have focused on toxin-encoding or antibiotic resistance plasmids. To cause intestinal disease, a toxigenic strain must grow in the intestines to levels allowing for sufficient toxin production and this in vivo growth often involves overcoming the normal intestinal microbial population. For this purpose, bacteriocin production might be important.    Results  In this study, as the first step in the genetic analysis of a co-existing plasmid with an enterotoxin gene ( cpe )-encoding plasmid, the bacteriocin gene-encoding plasmid, pBCNF5603, was completely sequenced. This plasmid has some homology with two previously sequenced  C. perfringens  plasmids, namely, pCP13 carrying a  cpb2  gene and pIP404 carrying a  bcn  gene. Using recombinant plasmids, the  rep  gene homologous to the PCP63 gene on pCP13 appeared to be functional. Comparative genomics indicated that the identified  rep  gene homologs were found on two additional toxin plasmids, pCP-OS1 and pCP-TS1. While functional analysis using recombinant plasmids indicated that pBCNF5603 and pCP13 are likely to be incompatible, the plasmid replication and partitioning region of pBCNF5603 alone was insufficient for stable maintenance of this plasmid.    Conclusions  These findings suggest that pBCNF5603 evolved from recombination events between  C. perfringens  plasmids and inter-species mobile genetic element(s). In addition, the  bcn -encoding plasmid, pBCNF5603, is likely to be included in the Inc family, which includes pCP13 and two variant  iota -encoding plasmids. Furthermore, the  bcn  gene on pBCNF5603 could contribute to gastrointestinal disease induced by enterotoxigenic  C. perfringens .    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-015-0443-3) contains supplementary material, which is available to authorized users.

Identification of the replication region in pBCNF5603, a bacteriocin-encoding plasmid, in the enterotoxigenic Clostridium perfringens strain F5603