Reduced antibacterial drug resistance and blaCTX-M β-lactamase gene carriage in cattle-associated Escherichia coli at low temperatures, at sites dominated by older animals and on pastureland: implications for surveillance

Abstract Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g. CTX-M □-lactamase-positive Escherichia coli). Here, we collected samples, monthly over a two-year period, on 53 dairy farms in the South West of England, and data for 610 variables concerning antimicrobial usage, management practices and meteorological factors. We detected E. coli resistant to amoxicillin, ciprofloxacin streptomycin and tetracycline, respectively, in 2754/4145 (66%), 263/4145 (6%), 1475/4145 (36%) and 2874/4145 (69%) of all samples from faecally contaminated sites. E. coli positive for blaCTX-M were detected in 224/4145 (5.4%) of samples. Multilevel, multivariable logistic regression showed antibiotic dry cow therapeutic choice (including use of cefquinome or framycetin) to be associated with increased odds of blaCTX-M positivity. Low temperature was associated with reduced odds of blaCTX-ME. coli positivity in samples and to reduced odds of finding E. coli resistant to each of the four test antibacterials. This was additional to the effect of temperature on total E. coli density. Furthermore, samples collected close to calves had increased odds of having E. coli resistance to each antibacterial or positive for blaCTX-M. Samples collected on pastureland had reduced odds of having E. coli resistant to amoxicillin or tetracycline, and being positive for blaCTX-M. Importance Antibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including to track the impacts of interventions aimed at reducing the prevalence of resistance. In this epidemiological survey of dairy farm antibacterial resistance, we show that local temperature, as it changes over the course of a year, is associated with the prevalence of antibacterial resistant E. coli. Also, that prevalence of resistant E. coli is higher in indoor environments and in environments inhabited by young animals. These findings have profound implications for routine surveillance and for surveys carried out for research. They provide important evidence that sampling at a single time-point and/or single location on a farm is unlikely to be adequate to accurately determine the status of the farm with regard to the presence or number of resistant E. coli.