In silico estimates of plasmid copy number are associated with increased resistance to cefotaxime, ceftazidime, and piperacillin/tazobactam in CMY-2-producing Escherichia coli
The blaCMY-2 gene is the most prevalent plasmid-encoded ampC gene found in Escherichia coli. The production of blaCMY-2 ß-lactamases is associated with resistance to third-generation cephalosporins and most ß-lactam/ß-lactamase inhibitor combinations. However, the minimal inhibitory concentrations for cephalosporins tend to vary between different CMY-2-producing isolates. Differences in plasmid copy number may be causing this variation in ß-lactam susceptibility. The objective of the present study was to identify determinants of increased resistance to cefotaxime, ceftazidime and piperacillin-tazobactam for E. coli isolates that encode blaCMY-2 without co-expression of extended-spectrum beta-lactamase (ESBL), carbapenemase genes or chromosomal AmpC hyperproduction. The present study compared sequencing depth between chromosomal and plasmid-encoded scaffolds from whole genome sequencing data of twenty blaCMY-2 encoded E. coli isolates.  The ratio was used as an estimated plasmid copy number. A significantly higher estimated plasmid copy number was found in CMY-2 producing E. coli isolates with high MIC values for cefotaxime, ceftazidime, and piperacillin-tazobactam as compared to E. coli isolates with low MIC values. These results provide evidence that whole genome sequencing data not only confirms the presence of resistance genes but also supports evidence that plasmid copy numbers are related to the MICs of the bacterium.