aureus (198 human isolates and 55 animal isolates) using microarray. Presence or absence of each gene (listed on left) in each isolate is depicted by colour. The colour is an indicator of test signal over reference signal ratio. Thus, (i) yellow indicates presence of the gene in both test strain and reference strain, (ii) red indicates presence of the gene in the test strain but not in the reference strain, (iii) blue indicates absence in the test strain but not the reference strain,

and (iv) grey indicates absence in both the test and reference strains. Genes with white signals are very low intensity and regarded as negative for both strains. The colour intensity is an indicator of signal intensity, and this can differ Selleck PLX-4720 because (i) the homology of the probe, which can be hundreds of base pairs long, and DNA may vary, and (ii) copy numbers may vary. Isolates BIBW2992 price (represented vertically) are clustered into lineages [14]. For each isolate, its mammalian host of origin and its lineage (clonal complex) are shown at the bottom of the figure. Human isolates are coloured light blue (invasive) and dark blue (carriage). Animal isolates are coloured red (cow), pink (horse), maroon (sheep and goat) and white (camel). The figure shows

that rep genes and resistance genes are distributed in a lineage dependent manner. We also assessed the distribution of other plasmid genes between S. aureus lineages. The presence of plasmid conjugation transfer (tra)A-M genes was rare amongst the S. aureus isolates in our collection and was not associated with lineage (Figure 2). Interestingly, antimicrobial resistance genes and heavy metal resistance genes were associated to lineage. arsC was common in MRSA CC22 and CC30 isolates, but rare amongst other lineages.

blaZ was common in all human lineages of S. aureus but was rare in animal lineages of S. aureus. cadA presence was associated with MRSA CC22, CC30 and CC239 lineages, whilst cadDX was widely distributed and associated with 9 different selleck compound lineages. ermA presence was associated with CC8 and CC239 lineages. qacA was associated with CC239 lineage. 2 of 9 (ble and tetM) resistance genes represented on the microarray are rare in the isolates we have analysed and were not distributed in a lineage dependent manner. We note that some of these genes may be carried on other elements or on integrated plasmids and this cannot be determined by microarray alone, for example tetM can also be carried on transposons such as Tn5801. Discussion In this study we extended a previously proposed plasmid classification system to characterise rep genes from 243 plasmids that appear in the public domain [11]. We characterised 21 rep families, of which 13 are newly described in this study. Whilst performing this analysis we noted that many plasmids carried more than one rep gene, we therefore assigned plasmids into groups based on the combination of rep genes carried.