102 Chapter 6 Results Isolate Characteristics A total of 2508 human cases from four different hospitals and 119 broilers from 14 different farms were screened for the presence of plasmid encoded AmpC genes, e.g blaCMY-2 (Table S1). In 107 isolates, an AmpC phenotype was confirmed based on the D68C AmpC & ESBL Detection Set. Sixteen of 107 isolates contained both an IncI1 pST12 and a blaCMY-2 gene (Table S1). Based upon the above-mentioned selection criteria, fourteen isolates were included for long-read sequencing analysis, i.e., thirteen E. coli and one Salmonella enterica, serotype Kentucky (Table 1). Nine of the E. coli isolates were from one broiler farm; the other isolates were from human origin. The E. coli isolates included five different MLSTs and fim types. Based on wgMLST analysis, four different clusters could be identified (Figure 1, Table 1, and Table S2). Additional information regarding antimicrobial resistance phenotype and genotype of the included isolates is provided in Table S3. Figure 1 Neighbor-joining tree representing the whole-genome multi locus sequence type (wgMLST) analysis of the different E. coli isolates included in the study. Isolates belonging to the same clonal clusters are represented in the identical colours.
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