Antimicrobial resistance and molecular characterization of Escherichia coli isolated from Ontario chickens

Abstract

In Canada, there is a lack of data regarding broad-spectrum β-lactamase producing E. coli in chickens. This thesis aimed to identify and characterize broad-spectrum β-lactamase producing E. coli in chickens coming from small and large-scale flocks. Chickens coming from small-scale flocks are not included as part of the Canadian national antimicrobial resistance surveillance program. We performed our study on this understudied bird population to identify broad spectrum β-lactamase producing E. coli. Following PCR and DNA sequencing in order to identify resistance genes, isolates were further characterized by PFGE to determine their relatedness. A subset of samples was subjected to MLST to determine if human resistance pandemic clones (E. coli ST131) were present in this chicken population. CTX-M-1 and CMY-2 were identified as predominant ESBL and AmpC β-lactamase genes. The population was genetically heterogeneous, only 32 out of 226 isolates formed clusters. None of the isolates were tested by MLST were ST131. We also conducted a comparative study of archived samples from chickens raised in large-scale flocks; stored samples were screened for 3rd generation cephalosporin resistance using CHROMagar ESBL (selective media). The results of this testing were compared to the findings of CIPARS to determine the value of including selective media in resistance surveillance programs. Following antimicrobial susceptibility testing by microbroth dilution, isolates resistant to 3GC were screened for ESBL and AmpC producing genes using PCR. The majority of the isolates were multi-drug resistance. Like chickens from small-scale flocks, CTX-M-1 and CMY-2 were found to be the predominant broad-spectrum β-lactamases.