104 Chapter 6 Plasmid Analysis In the hybrid assembly of fourteen sequences, both the IncI1–pST12 replicon gene and blaCMY-2 gene were located on a single circular contig ranging in size from 98,410 to 98,999 bp. No additional antimicrobial resistance or virulence genes were detected on any of the extracted plasmids. The number of SNP’s detected between the fourteen plasmids ranged from zero to nine SNPs (Table 2). When comparing the plasmids extracted from the selected isolates to a publicly available IncI1–pST12 blaCMY-2 genecontaining plasmid extracted from the GenBank (accession number: MH472638.1), the number of SNPs detected ranged from 0 to 7 (Table 2). A small SNP difference was seen between epidemiologically related strains with a maximum difference of two SNPs. The range of SNP differences overlapped between epidemiologically related and unrelated plasmids (Table 3). The median number of SNP differences of plasmids in a different domain or different location, but the same domain was higher than in the other three pairwise comparison groups. The total number of genes detected in the fourteen plasmids was 113, of which 112 were detected in all plasmids. One gene was present only in one plasmid (pEC11) and encoded for a hypothetical protein. An alignment of coding regions of the fourteen plasmids revealed no rearrangements between the described plasmids (Figure 2). However, progressive MAUVE alignment of non-coding regions revealed a small highly variable region of 519 to 1096 bp in all plasmids (Figure S1). This hypervariable region and approximately 2125 bp of the flanking sequence were extracted from all plasmids. The genes PilV and rci were detected in the flanking regions of the hypervariable region of all plasmids (Table 4). Moreover, in all plasmids, either one (B) or two (A, B) shufflon segments were detected in the extracted hypervariable region of the various plasmids (Table 4). No rearrangements were detected in any of the other regions.
RkJQdWJsaXNoZXIy MTk4NDMw