166 Chapter 9 genes. Furthermore, the range of SNPs overlapped among plasmids with different epidemiological links, suggesting that distinguishing between epidemiologically related and unrelated plasmids based solely on plasmid sequence is unlikely. Previous studies have shown the conserved sequences of IncI1-pST12 plasmids; however, these studies utilized either gene presence/absence-based analysis or SNP-based analysis, potentially missing subtle differences between various plasmid (Roer et al. 2019; Shirakawa et al. 2020; Castellanos et al. 2019). The current analysis, which combines long-read and shortread sequence data for a comprehensive plasmid analysis, including the identification of rearrangements, demonstrates the added value of this approach. Nevertheless, further studies with larger sample sizes are necessary to validate these results. As discussed in the thesis introduction, plasmid-encoded ampC genes are not the sole mechanism of AmpC resistance in E. coli. Another mechanism involves the occurrence of mutations in the promoter region of the ampC beta-lactamase gene, leading to hyperproduction of the chromosomally-encoded beta-lactamase. These promoter mutations are associated with various degrees of resistance against beta-lactam antibiotics (Tracz et al. 2007). While previous research has predominantly focused on the chromosomal AmpC resistance mechanism and its impact on AmpC hyperproduction, there is a knowledge gap regarding the evolutionary origin of these promoter/attenuator variants. Chapter 7 aims to address this gap by conducting an investigation into the homoplasy and association of the ampC promoter/attenuator region in E. coli with cefotaxime resistance. The study involves a genome-wide analysis of homoplasy, which examines the occurrence of identical mutations in different lineages, combined with a comprehensive examination of polymorphisms associated with cefotaxime resistance. By analysing the mutations occurring in the reference chromosome and determining their distribution within the phylogeny, the study reveals a remarkable level of homoplasy at the −42 position of the ampC promoter. Specifically, the presence of a T nucleotide at the −42 position, instead of the wild-type C nucleotide, was found in 24 instances, resulting from 18 independent C>T mutations across five phylogroups. These findings shed light on the complex evolutionary dynamics and genetic diversity within the ampC promoter region and its association with cefotaxime resistance in E. coli. Complexity of AmpC-Mediated Resistance Mechanisms The diversity of mechanisms and phenotypic variations associated with AmpC-mediated resistance is an intriguing characteristic. Different types of ampC genes, such as blaCMY,
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