18 Chapter 1 The third objective focuses on investigating the relatedness between plasmids containing the blaCMY-2 gene in epidemiologically linked and unrelated Enterobacterales isolates from humans and livestock. The aim is to explore the feasibility of accurately distinguishing related samples from unrelated ones based solely on plasmid sequencing data. The fourth aim of this thesis is to examine whether mutations occurring in the ampC promoter/attenuator region of E. coli are homoplastic and whether these homoplastic mutations are associated with cefotaxime resistance. This investigation sheds light on the relationship between specific mutations and antibiotic resistance. The fifth aim of this thesis was to compare the sequencing depth between chromosomal household genes and plasmid-encoded scaffolds containing the blaCMY-2 gene, as well as to utilize the ratio as an estimated plasmid copy number. This analysis aimed to provide insights into the abundance of plasmids carrying the blaCMY-2 gene within the studied isolates. Furthermore, the relationship between the estimated plasmid copy number and the minimal inhibitory concentrations of cefotaxime, ceftazidime, and piperacillin-tazobactam was investigated. This examination allowed for a deeper understanding of the association between plasmid presence and the level of resistance to these specific antibiotics.
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