Resistance to extended-spectrum cephalosporins in Escherichia coli and other Enterobacterales from Canadian turkeys

The goal of this study was to determine the frequency of resistance to extended-spectrum cephalosporins (ESCs) in Escherichia coli and other Enterobacterales from turkeys in Canada and characterize the associated resistance determinants. Pooled fecal samples were collected in 77 turkey farms across British Columbia, Québec, and Ontario. Isolates were obtained with and without selective enrichment cultures and compared to isolates from diagnostic submissions of suspected colibacillosis cases in Ontario. Isolates were identified using MALDI-TOF and susceptibility to ESCs was assessed by disk diffusion. The presence of bla(CMY), bla(CTX-M), bla(TEM,) and bla(SHV) was tested by PCR. Transformation experiments were used to characterize bla(CMY) plasmids. Genome sequencing with short and long reads was performed on a representative sample of bla(CTX-M)-positive isolates to assess isolates relatedness and characterize bla(CTX-M) plasmids. For the positive enrichment cultures (67% of total samples), 93% (587/610) were identified as E. coli, with only a few other Enterobacterales species identified. The frequency of ESC resistance was low in E. coli isolates from diagnostic submission (4%) and fecal samples without selective enrichment (5%). Of the ESC-resistant Enterobacterales isolates from selective enrichments, 71%, 18%, 14%, and 8% were positive for bla(CMY), bla(TEM,) bla(CTX-M,) and bla(SHV), respectively. IncI1 followed by IncK were the main incompatibility groups identified for bla(CMY) plasmids. The bla(CTX-M-1) gene was found repeatedly on IncI1 plasmids of the pMLST type 3, while bla(CTX-M-15), bla(CTX-M-55), and bla(CTX-M-65) were associated with a variety of IncF plasmids. Clonal spread of strains carrying bla(CTX-M) genes between turkey farms was observed, as well as the presence of an epidemic bla(CTX-M-1) plasmid in unrelated E. coli strains. In conclusion, Enterobacterales resistant to ESCs were still widespread at low concentration in turkey feces two years after the cessation of ceftiofur use. Although bla(CMY-2) is the main ESC resistance determinant in E. coli from Canadian turkeys, bla(CTX-M) genes also occur which are often carried by multidrug resistance plasmids. Both clonal spread and horizontal gene transfer are involved in parallel in the spread of bla(CTX-M) genes in Enterobacterales from Canadian turkeys.