Diversity of blaCTX-M-1-carrying plasmids recovered from Escherichia coli isolated from Canadian domestic animals.

Conserved IncI1 and IncHI1 plasmids carrying blaCTX-M-1 have been found circulating in chickens and horses from continental Europe, respectively. In Canada, blaCTX-M-1 is overwhelmingly the most common blaCTX-M variant found in Escherichia coli from chicken and horses and can be recovered at lower frequencies in swine, cattle, and dogs. Whole-genome sequencing has identified a large genetic diversity of isolates carrying this variant, warranting further investigations into the plasmids carrying this gene. Therefore, the objective of this study was to describe the genetic profiles of blaCTX-M-1 plasmids circulating in E. coli from Canadian domestic animals and compare them to those recovered in animals in Europe. Fifty-one blaCTX-M-1 positive E. coli isolates from chicken (n = 14), horses (racetrack horses n = 11; community horses n = 3), swine (n = 7), turkey (n = 6), dogs (n = 5), beef cattle (n = 3), and dairy cattle (n = 2) were selected for plasmid characterization. Sequences were obtained through both Illumina and Oxford Nanopore technologies. Genomes were assembled using either Unicycler hybrid assembly or Flye with polishing performed using Pilon. blaCTX-M-1 was found residing on a plasmid in 45 isolates and chromosomally located in six isolates. A conserved IncI1/ST3 plasmid was identified among chicken (n = 12), turkey (n = 4), swine (n = 6), dog (n = 2), and beef cattle (n = 2) isolates. When compared against publicly available data, these plasmids showed a high degree of similarity to those identified in isolates from poultry and swine in Europe. These results suggest that an epidemic IncI1/ST3 plasmid similar to the one found in Europe is contributing to the spread of blaCTX-M-1 in Canada. A conserved IncHI1/FIA(HI1)/ST2 plasmid was also recovered from nearly all racetrack horse isolates (n = 10). Although IncHI1/ST2 plasmids have been reported among European horse isolates, IncHI1/ST9 plasmids appear to be more widespread. Further studies are necessary to understand the factors contributing to these plasmids' success in their respective populations.

Presence and Diversity of Extended-Spectrum Cephalosporin Resistance Among Escherichia coli from Urban Wastewater and Feedlot Cattle in Alberta, Canada.

A recent preliminary study from our group found that extended-spectrum cephalosporin-resistance determinants can be detected in the majority of composite fecal samples collected from Alberta feedlot cattle. Most notably, blaCTX-M genes were detected in 46.5% of samples. Further isolate characterization identified blaCTX-M-15 and blaCTX-M-27, which are widespread in bacteria from humans. We hypothesized that Escherichia coli of human and beef cattle origins share the same pool of blaCTX-M genes. In this study, we aimed to assess and compare the genomic profiles of a larger collection of blaCTX-M-positive E. coli recovered from fecal composite samples from Canadian beef feedlot cattle and human wastewater through whole-genome sequencing. The variants blaCTX-M-55, blaCTX-M-32, blaCTX-M-27, blaCTX-M-15, and blaCTX-M-14 were found in both urban wastewater and cattle fecal isolates. Core genome multilocus sequence typing showed little similarity between the fecal and wastewater isolates. Thus, if the dissemination of genes between urban wastewater and feedlot cattle occurs, it does not appear to be related to the expansion of specific clonal lineages. Further investigations are warranted to assemble and compare plasmids carrying these genes to better understand the modalities and directionality of transfer.

Determinants of virulence and of resistance to ceftiofur, gentamicin, and spectinomycin in clinical Escherichia coli from broiler chickens in Québec, Canada.

Antimicrobials are frequently used for the prevention of avian colibacillosis, with gentamicin used for this purpose in Québec until 2003. Ceftiofur was also used similarly, but voluntarily withdrawn in 2005 due to increasing resistance. Spectinomycin-lincomycin was employed as a replacement, but ceftiofur use was partially reinstated in 2007 until its definitive ban by the poultry industry in 2014. Gentamicin resistance frequency increased during the past decade in clinical Escherichia coli isolates from broiler chickens in Québec, despite this antimicrobial no longer being used. Since this increase coincided with the use of spectinomycin-lincomycin, co-selection of gentamicin resistance through spectinomycin was suspected. Therefore, relationships between spectinomycin, gentamicin, and ceftiofur resistance determinants were investigated here. The distribution of 13 avian pathogenic E. coli virulence-associated genes and their association with spectinomycin resistance were also assessed. A sample of 586 E. coli isolates from chickens with colibacillosis in Québec between 2009 and 2013 was used. The major genes identified for resistance to ceftiofur, gentamicin, and spectinomycin were blaCMY, aac(3)-VI, and aadA, respectively. The aadA and aac(3)-VI genes were strongly associated and shown to be located on a modified class 1 integron. The aadA and blaCMY genes were negatively associated, but when present together, were generally located on the same plasmids. No statistical positive association was observed between aadA and virulence genes, and virulence genes were only rarely detected on plasmids encoding spectinomycin resistance. Thus, the use of spectinomycin-lincomycin may likely select for gentamicin but not ceftiofur resistance, nor for any of the virulence-associated genes investigated.