150 Chapter 8 Accession numbers All raw reads were previously submitted to the European Nucleotide Archive (ENA) of the European Bioinformatics Institute (EBI) under the study accession number PRJEB64326. Results All genome assemblies met the previously described quality criteria for coverage, number of scaffolds, N50, maximum scaffold length, and percentage of expected genome size (Supplementary table S1) (Marjolein F Q Kluytmans-Van Den Bergh et al. 2016). Table 1 shows the results of antimicrobial susceptibility testing of the twenty CMY-2 positive E. coli isolates. The MIC values for CTX, CAZ, and TZP showed a bimodal distribution (Figures 1, 2, and 3). Based on this bimodality, isolates were divided into a low-MIC and high-MIC group using the highest MIC in the detectable range as a cut-off value (≥256 mg/L). The distribution of ePCN between the low-MIC and highMIC groups differed consistently (Figure 4). Isolate 16 showed low resistance for CTX but a high ePCN and formed the only exception (Figure 4.). Median ePCN was 1.98 (Interquartile Range (IQR) 1.60-4.76) for the CTX low-MIC group vs. 7.22 (IQR 4.249.61) for the CTX high-MIC group (p=0.012); 1.89 (IQR 1.57-4.12) for the CAZ low-MIC groups vs. 7.22 (IQR 4.78-9.83) for the CAZ high-MIC group (p<0.0005); 1.86 (IQR 1.53-2.80) in the TZP low-MIC-group vs. 6.06 (IQR 4.23-9.61) in the TZP high-MIC group (p<0.0005). A significantly higher CMY-2 ePCN was detected in the isolates with high MIC values for CTX, CAZ, and TZP compared to the isolates with low MIC values.
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