Antimicrobial Resistance of Escherichia coli in Dairy Calves: A 15-Year Retrospective Analysis and Comparison of Treated and Untreated Animals

SIMPLE SUMMARY: In dairy production, antimicrobial resistance (AMR) is both a health and economic issue that may lead to treatment failures and the spread of multidrug-resistant pathogens. Epidemiological and farm data on AMR are instrumental for selecting the appropriate therapy. However, such data are not always available. We investigated the AMR profile of 2612 Escherichia coli strains isolated from cases of calf diarrhea over a 15-year period (2002–2016). Furthermore, the AMR profiles and major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves were examined, with a comparison made between those treated with antimicrobials (n = 406) and not treated (n = 99) as well as between the two age groups to evaluate the potential effects of treatments on AMR and pathogenicity. Resistance to tetracycline was the most common, followed by resistance to sulfamethoxazole/trimethoprim and flumequine. Treated calves showed a higher rate of AMR and virulence genes. These results highlight the risk of the frequent use of antimicrobials on calf microflora in leading to potentially ineffective treatments. A higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol was found in 1-week-old calves, suggesting the environment as a possible AMR source. In conclusion, measures such as improved hygiene in the calving pen, antimicrobial stewardship, and monitoring for resistant pathogens in manure should be promoted to prevent the spread of AMR. ABSTRACT: The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies; however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period of 15 years (2002–2016) from calf enteric cases were analyzed to determine the presence of resistance and their temporal dynamics. Furthermore, the AMR profiles and the presence of the major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves, 406 treated with antimicrobials and 99 untreated, were analyzed and compared to investigate the potential effects of treatment on AMR and strain pathogenicity. Resistance to tetracycline (90.70%) was the most common, followed by resistance to sulfamethoxazole/trimethoprim (77.70%) and flumequine (72.10%). The significantly higher percentage of AMR and virulence gene expression recorded in treated calves, combined with the statistically higher resistance to sulfamethoxazole/trimethoprim in E. coli with K99, corroborates the notion of resistance being induced by the frequent use of antimicrobials, leading to treatments potentially becoming ineffective. The significantly higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol in isolates from 1-week-old calves suggests the role of the environment as a source of contamination that should be investigated further.