BMC Genomics 2007, 8:110 http://www.biomedcentral.com/1471-2164/8/110 21 wild duck isolate, strain 670, contains at least parts of two of the mobile elements reported previously in C. jejuni RM1221 (CMLP1 and CJIE4) [9,26]. CMLP1 is a Mu-like bacteriophage and wasn't identified in any of the other tester strains used in this study. CJIE4 carries sequences similar to a putative prophage encoded by C. lari (CLIE1) [9]. Strain 670 alone also carried multiple sequences matching the related pTet or pCC31 plasmids reported previously in C. jejuni 81–176 and C. coli respec- tively [27,28]. SSH data also indicated that the ST-21 cat- tle isolate strain 504 carries the prophage-like element CJIE4 (18 matching SSH sequences). However, none of the strain 504 SSH sequences matched plasmid sequences. In fact, other than those matching CJIE4, most of the SSH sequences from strain 504 matched hypothet- ical proteins of unknown function (Table 1). The SSH sequences from strains 1967, 629 and 961, each repre- senting a different MLST type, contained no matches to the genomic islands of strain RM1221 and very few matches to either bacteriophage or plasmid-related sequences (Table 1). Using dot-blot hybridization we determined the distribu- tion of the sequence 670-D7 as an indicator of the preva- lence of the pTet/pCC31 plasmid amongst our strain panel (Table 1). The sequence was found in three isolates from the ST-21 complex and four isolates from the ST-61 complex. Plasticity regions and variable genes Most of the subtractions identified variations in loci pre- viously reported as variable amongst C. jejuni strains. It has been reported that variable genes (absent or highly divergent) in the Campylobacter genome map to discrete areas, termed variously plasticity regions, hypervariable regions or plasticity zones [16,17,21,29]. Indeed the gen- otypes of C. jejuni strains have been shown to be inher- ently unstable, and recombination events occur between unrelated strains both in vitro and in vivo even in the absence of selective pressure [30]. Pearson et al. [16] iden- tified seven hypervariable plasticity regions (PR1-7) in the genome of C. jejuni NCTC11168. PR6 contains the cap- sule biosynthesis locus, flanked by capsule transport genes. Twelve SSH sequences in all matched capsule- related proteins. PR7 contains numerous putative outer membrane proteins but also carries a divergent gene encoding a probable flagellar hook protein [16]. Other motility-related genes, including flagellin and flagellin- glycosylation genes, are carried by PR5, along with LOS biosynthesis genes. SSH sequences matching flagellar hook proteins (FlgE), flagellins, flagellin glycosylation proteins and LOS biosynthesis proteins were all identified amongst the SSH sequences in our study. PR4 includes glycosyltransferases and galactosyltransferases of unknown functions as well as genes involved in the sia- lylation of LOS. SSH sequences matching proteins with similar putative functions were found with both the strain 961 and strain 1967 subtractions. In addition, the 629 subtracted library included one sequence matching both the NCTC11168 gmhA gene (from PR4) and a polysaccha- ride-related protein (SSH629-21). RM systems protect bacteria from foreign DNA and may impact on the transfer of genes responsible for virulence or host colonisation. It has also been demonstrated previ- ously that RM genes vary in Campylobacter spp. [15] and RM genes were amongst those identified in a previous study using SSH [24]. The first three subtractions in our study all identified RM-related SSH sequences. Ahmed et al. [24] also identified subtracted sequences relating to arsenite-metabolising genes as present in strain 81–116 but absent from strain NCTC11168, noting that phenylar- sonic compounds have been used in poultry feed and may have contaminated agricultural lands on which poultry litter has been used as manure. We identified an SSH matching the arsenical resistance protein of RM1221 in the subtracted library of strain 629 (SSH629-23), a rabbit isolate. In addition, Ahmed et al. [24] identified a putative γ-glutamyl transpeptidase gene in their subtraction. Equivalent genes have been implicated in a role in coloni- zation of the gastric mucosa by Helicobacter pylori [31,32]. We also identified SSH sequences matching a γ-glutamyl transpeptidase protein in strain 629. It has been reported that C. jejuni 81–176 carries a putative gene encoding a serine protease belonging to the autotransporter family [10]. The SSH indicates that this gene is also present in the cattle isolate 1967 (SSH1967-A5 and SSH1967-G6). C. jejuni 81–176 and isolates 1967 are both members of the ST-42 clonal complex. We determined the distribution of SSH1967-A5 amongst our strain panel. All ST-42 isolates were positive for SSH1967-A5. Of the other isolates, only one ST-45 cattle isolate contained SSH1967-A5 (Tables 3 and 4). We also determined the distribution of the SSH sequence SSH961-A9, which matches an enzyme from C. jejuni subsp. doylei (Table 2). With the exception of three iso- lates, the distribution was also restricted to the clonal complex of the tester strain (ST-61 complex; Tables 3 and 4). Metabolic genes When oxygen levels are low C. jejuni has the capacity to utilise a wide range of electron acceptors, including fuma- rate, nitrate, nitrite, sulfite, trimethylamine-N-oxide (TMAO) and dimethyl sulfoxide (DMSO) [33-35]. In strain NCTC11168 PR1 contains genes encoding the transport apparatus for molybdenum, which has a puta- tive role in the reduction of nitrate as an alternative termi- nal electron acceptor [33]. Just upstream of PR1 lies the gene (Cj0264c) encoding the reductase responsible for reduction of TMAO and DMSO under oxygen limiting Page 7 of 11 (page number not for citation purposes)