Antibiotic resistance

Antibiotic resistance remains a hot topic both in animal and human health. Increased awareness of the problem has brought some welcome changes in our use of antibiotics in animals. For instance, the use of antibiotics critically important for human medicine such as extended-spectrum cephalosporins (ESCs) has now been discontinued in poultry. This has resulted in an encouraging decrease of ceftiofur resistance in E. coli and Salmonella from chicken. However, the genes encoding resistance to these critically important antibiotics may still be lingering at low frequency in bacteria from chicken and may be ready to surge again if selected. Since antibiotic resistance genes are often linked together, it is also possible that the use of less critical antibiotics may contribute to maintaining resistance to the critical ones.

Dr. Patrick Boerlin

To address such questions, Patrick Boerlin and his graduate (MSc) student Pauline Zhang have conducted studies on the frequency of carriage of ESC-resistant bacteria in chicken in Ontario, using enrichment methods able to detect very small numbers of resistant bacteria hiding in the intestine of chicken. The results of this study conducted in 2015-2016 show that 98% of chicken harbor ceftiofur-resistant E. coli in their ceca at slaughter (Zhang, 2017). This contrasts with results obtained by CIPARS using conventional methods without enrichment and suggests that these resistant bacteria are persisting only at low concentration in the gut of chicken. Most of these resistant E. coli were carrying the commonly reported ceftiofur resistance gene blaCMY (Martin et al., 2012). However, 8% of the isolates were carrying a blaCTX-M gene. Previous studies that the Boerlin lab had conducted in collaboration with the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) had shown that this gene, widespread in bacteria from farm animals in Europe, had probably emerged in 2011 in Canadian poultry. Thus, this new ceftiofur resistance gene is now well established in intestinal bacteria from chicken in Ontario.

In another study on antibiotic resistance and colibacillosis in broiler chicken in Québec, Patrick Boerlin and his collaborators demonstrated that spectinomycin and gentamicin resistance genes were located on the same mobile genetic element in avian pathogenic E. coli. This provided a likely explanation for the recent surge of gentamicin resistance observed by the provincial diagnostic laboratory in this province (Chalmers et al., 2017) despite the absence of gentamicin use.

As an evidence of their high mobility, these two genes were shown to be located on a transposon distributed across a large a diversity of plasmids (the genetic elements responsible for the transfer of resistance genes between bacteria). This is of concern because gentamicin is also an antibiotic considered by the World Health Organization as critically important for human medicine. Fortunately, only very few of these spectinomycin-gentamicin resistance plasmids were also carrying virulence genes able to increase the pathogenicity of E. coli for chicken. Interestingly, the study also showed that blaCTX-M had emerged in avian pathogenic E. coli from Québec in 2011, at the same time as it had emerged in generic intestinal E. coli in Canadian poultry (see above).

These studies demonstrate that although the restrictions in the use of critically important antibiotics have positive effects, bacteria resistant to these agents are still lingering in the gut of chicken and that other less important antibiotics present the potential to maintain and possibly even increase their prevalence. Efforts to continuously improve and adjust our use of antibiotics in animals are definitely warranted.


  • Zhang P. L. C. 2017. Resistance to extended-spectrum cephalosporins in Enterobacteriaceae from chickens, dogs, and pigs in Ontario. MSc thesis, University of Guelph.
    >> Go to Thesis
  • Martin L. C., Weir E. K., Poppe C., Reid-Smith R. J., Boerlin P. 2012. Characterization of blaCMY-2 plasmids in Salmonella and Escherichia coli isolates from food animals in Canada. Appl Environ Microbiol. 78:1285-7.
  • Chalmers G., Cormier A. C., Nadeau M., Côté G., Reid-Smith R. J., Boerlin P. Determinants of virulence and of resistance to ceftiofur, gentamicin, and spectinomycin in clinical Escherichia coli from broiler chickens in Québec, Canada. Vet Microbiol. 2017 203:149-157.
Posted in 2017 News, Research - Boerlin, Research Stories.