What is the Risk of Antibiotic Resistance in Weaned Calves?

Background

Earlier research conducted by this team through the Western Canadian Cow-Calf Surveillance Network found that respiratory disease was a leading cause for antibiotic use in calves before (and after) weaning. Subsequently, the BCRC supported a follow-up project to look at antibiotic use and resistance based on fecal samples collected from cows and calves in Western Canadian herds participating in the Canadian Cow Calf Surveillance Network. This project will add a component to that project, looking at respiratory disease bacteria.

Objectives

•  describe antibiotic resistance in respiratory pathogens in cow-calf herds using traditional culture techniques,
• assess the potential association between antibiotic use in cow-calf herds and antibiotic resistance in BRD pathogens in calves before entering the feedlot,
• evaluate emerging metagenomics tools to identify opportunities for more cost effective surveillance, and
• assess the potential association between key management variables in cow-calf herds and BRD pathogens and AMR in BRD pathogens for calves entering the feedlot.

What they Did

Local veterinarians collected nasal swabs from 26 calves at or near weaning, in most of the participating 27 cow-calf herds. The swabs were cultured in the lab to identify respiratory pathogens (Mannheimia haemolytica, Histophilus somnus and Pasteurella multocida) and then tested for antibiotic resistance using the same laboratory and protocols that CIPARS uses in its feedlot antimicrobial resistance surveillance initiative. Antibiotic resistance in the respiratory pathogens was compared to that reported previously reported for cow-calf herds and feedlot cattle in western Canada. The team also examined whether genomic testing with metagenomic sequencing of a subset of the samples could provide cost-effective information on respiratory bacteria, antimicrobial resistance genes and respiratory viruses to complement and enrich the data provided by culture and susceptibility testing. Data on antimicrobial use and vaccine practices for participating herds were obtained as part of the Canadian Cow-Calf Surveillance Network.

What They Learned

The most common bacteria was Pasteurella multocida, recovered in 28% of calves overall, and from at least one calf in all 27 participating herds. Mannheimia haemolytica was isolated from 10% of calves overall, and from at least one calf in 19 different herds. Histophilus somni was isolated from 2% of calves overall, and from at least one calf in 5 different herds. Time from sample collection to arrival at the lab was important – the longer it took for the sample to arrive at the lab, the less likely Mannheimia haemolytica was found.

Nine percent of Pasteurella multocida isolates from 2% of calves sampled were resistant to at least one class of antimicrobials. Resistance was reported to penicillin (ampicillin), tetracycline, (macrolides (gamithromycin, tildipirosin, tulathromycin), and aminocyclitol (spectinomycin) antibiotics. Multiclass resistance, including resistance to macrolides, tetracyclines, and aminocyclitols, was identified in one herd and in 1% of all BRD isolates. No Mannheimia haemolytica or Histophilus somni isolates were resistant to any of the antimicrobials tested.

Bacterial metagenomic analysis on a subset of samples from each herd were completed in a regional diagnostic laboratory. In addition to identifying Pasteurella multocida, Mannheimia haemolytica and Histophilus somni, metagenomic analysis also identified Mycoplasma bovis and Bibersteinia trehalosi.

The analysis also identified antimicrobial genes of interest on individual sequence reads from Pasteurella multocida, Mannheimia haemolytica and Histophilus somni including genes for the antimicrobial classes identified in the traditional culture and susceptibility analysis. Further analysis of the results categorized the Mannheimia haemolytica isolates by serotype reflecting their potential association with clinical disease.

Finally, a smaller subset of the samples was also analyzed with a slightly modified metagenomic protocol to detect respiratory viruses. The most commonly identified respiratory viruses were bovine coronavirus, influenza D virus and bovine rhinitis B. In contrast, PI3, BRSV, IBR and BVD Types 1 and 2 viruses were much less common, likely because 93% of the operations had vaccinated against them.

What It Means

Antimicrobial resistance was observed in 2% of respiratory bacteria in sampled calves. Multiclass resistance was only observed in three isolates from one herd. The culture and susceptibility results of this study are consistent with the few other published reports of antimicrobials resistance in beef calves in cow-calf herds. However, this study is unique in the number of calves and herds sampled on the farm of origin and before feedlot entry. The results of this study were complemented by metagenomic testing that described additional respiratory bacteria of interest, antimicrobial resistance genes on the respiratory bacteria, genes associated with bacterial serotype, and respiratory viruses.