Tracking Antibiotic Resistance in Feedlot Pathogens

Background

The Public Health Agency of Canada’s (PHAC) Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) has conducted antimicrobial resistance (AMR) surveillance in cattle entering packing plants and retail beef since the mid-2000s. The surveillance of antimicrobial use (AMU) and resistance in feedlot cattle started in 2019. Given that PHAC is primarily focused on human health, its surveillance efforts are directed toward AMR in bacteria found in the intestinal tracts of both livestock and humans (e.g., E. coli, Campylobacter, Enterococcus). However, feedlots use antimicrobials to combat veterinary pathogens, including the normally commensal bacteria involved in bovine respiratory disease (BRD). Understanding the prevalence of and trends in antimicrobial resistance in BRD-associated bacteria is critical to informing responsible antimicrobial stewardship in feedlot animal health programs.

Objectives

1. Provide representative national estimates of AMU and AMR in the Canadian finishing feedlot sector.
2. Monitor trends in AMU and AMR over time and in the context of changes to veterinary practice.
3. Assess the potential risks associated with AMU in feedlots on the effectiveness of antimicrobials in animals and humans.

What they did

Feedlots were enrolled by participating veterinary clinics according to particular inclusion criteria and a pre-specified sampling frame. Enrolled feedlots were de-identified by their clinic and assigned a unique code, which was used to link data or samples submitted from that operation.

With respect to the BRD component of the project, deep nasal swabs (deep guarded nasopharyngeal) samples were collected in every surveillance year from 16 animals in each of the enrolled feedlots at entry processing and then again at re-handling. The same pen of cattle (though not necessarily the same individual animal) was sampled at both time points. Samples were transported by courier in an insulated cooler to the Prairie Diagnostic Services (PDS) laboratory in Saskatoon for the culture and identification of Mannheimia haemolytica, Pasteurella multocida and Histophilus somni. Recovered bacterial isolates were tested for sensitivity to a standard panel of antimicrobial drugs.

Information collected at sampling included: the veterinary clinic and feedlot codes, date of sample, cattle breed type (beef, dairy), cattle age category (calf, yearling), BRD risk category (high, low), sample number and ear tag of the animal sampled.

Antimicrobial susceptibility data, adjusted for isolate clustering by feedlot, are presented for each organism as complete annual and temporal data. Susceptibility data are further stratified and reported by animal age (i.e., calf, yearling).

What They Learned

The key findings include:

1. Recovery of each of the BRD organisms varied by the time of the sample.

• P. multocida was the primary organism recovered at both arrival and re-handling.
• M. haemolytica was the second most commonly isolated species on arrival.
• H. somni was the second most commonly isolated species at re-handling.

2. Antimicrobial resistance increased between arrival and re-handling for all three organisms.

At arrival:

• 93% of the M. haemolytica isolates from all surveillance years were susceptible to all tested antimicrobials.
• 80% of the total P. multocida were susceptible to all tested antimicrobials.
• 64% of the total H. somni isolates were susceptible to all tested antimicrobials.
• In 2024, there was a significant increase in resistance to several antimicrobials for P. multocida isolates at arrival. Of particular concern was the increase for key antimicrobials used in feedlot medicine, including tetracycline, enrofloxacin (e.g., Baytril), tildipirosin (e.g., Zuprevo) and tulathromycin (e.g., Draxxin).

By re-handling:

• There was a 37% decrease in the percentage of susceptible M. haemolytica isolates between arrival and rehandling, across all surveillance years.
• There was a 39% decrease in the percentage of susceptible P. multocida isolates
• There was a 12% decrease in the percentage of susceptible H. somni isolates.
• Increases in resistance between time points were most commonly observed for the macrolide and tetracycline classes of antimicrobials, irrespective of the BRD organism.
• P. multocida isolates exhibit the largest decrease in susceptibility between sampling time points. Significant increases in resistance to the fluoroquinolone (e.g., A180, Baytril) antimicrobials in P. multocida isolates were detected at rehandling.

3. Antimicrobial resistance in isolates from calves is higher than in isolates from yearlings.

• There is greater multidrug resistance (i.e., resistance to three or more antimicrobial classes) in isolates from calves than from yearlings.
• The percentage of fully susceptible M. haemolytica isolates from calves at re-handling was approximately half that of isolates from yearlings.
• The percentage of fully susceptible P. multocida isolates from calves at re-handling was less than one-quarter that of isolates from yearlings.
• The percentage of multidrug-resistant P. multocida isolates from calves at re-handling was approximately four times higher than for isolates from yearlings.

What it Means

The surveillance results indicate:

1. The decrease in susceptibility of respiratory isolates over the feeding period is primarily driven by resistance acquisition in BRD organisms from calves.
2. Rising resistance to fluoroquinolones (Category I drugs of critical importance) is concerning. Maintaining very low resistance to these Category I antimicrobials should be a priority for the feedlot industry.
3. Increased resistance to macrolides over the feeding period may be due to selective pressure from AMU in the feedlot, the transmission of AMR between bacteria and/or animals, or both. This could reduce the effectiveness of BRD prevention and control.
4. Increased resistance to key feedlot antimicrobials in P. multocida isolates at arrival could impact the effectiveness of BRD treatment early in the feeding period and needs continued monitoring. The reason for this shift is unclear but may reflect changes to antibiotic use practices in cow-calf herds.
5. Surveillance data offers insights into the strategies and/or management practices that might best support animal health and preserve the effectiveness of currently available antimicrobials.