Extended-spectrum beta-lactamases from French veal calves: WGS-based data will help build targeted AMR mitigation strategies

Antimicrobial resistance (AMR) is an important One Health issue affecting the three human, animal, and environmental sectors. The occurrence of Escherichia coli resistant to extended-spectrum cephalosporins (ESC-R) is considered a relevant marker for the estimation of the AMR burden. In the dairy industry, veal calves present the highest proportions of ESC-R compared to adults. Since little is known in France about the AMR dynamics from birth to the fattening farm, our observational study determined the proportion of ESC-R E. coli using selective media, and characterized by whole-genome sequencing. Bacterial isolates identified at the farm level and at the sorting center, before being sent to the fattening farms. The proportion of ESC-R-positive calves coming from farms in which waste milk was given to calves (30.3%) was higher than in the ones where it was discarded (13.1%). Overall, 12.5% of the veal calves were ESC-R carriers in their farm of origin, and 6.2% of the additional animals became carriers during their transport to the sorting center. Over the 176 ESC-R E. coli isolates sequenced, 55.1% ( n = 97) presented an extended-spectrum beta-lactamase phenotype conferred by a bla _CTX-M gene, while 44.9% ( n = 79) presented an AmpC phenotype due to chromosomal mutations. A few specific clones (ST8095 and ST117) were identified as responsible for AMR dissemination across farms. Our results showed that AMR in dairy calves results from cumulative effects of all risk factors along the whole production chain, including feeding calves with antibiotic residues-containing waste milk, animal grouping, and insufficient biosecurity measures in dairy farms.

IMPORTANCE

Despite the implementation of national action plans, the presence of Escherichia coli resistant to extended-spectrum cephalosporins (ESC-R), mainly due to the presence of extended-spectrum beta-lactamases or AmpCs, is still high in many veal-producing countries. In France, previous studies reported antimicrobial resistance (AMR) data during the fattening period and at the slaughterhouse, but data are still scarce on the AMR status of veal calves on their farm of origin. This study aimed at determining the proportion of ESC-R E. coli and characterizing bacterial isolates identified at the farm level and at the sorting center, just before being sent to the fattening farms. This is of utmost importance since mathematical models showed that minimizing AMR prevalence upon arrival in the fattening farm is an important factor to mitigate ESC-R carriage during the fattening process. In addition, we are providing important WGS data from the veal calf sector, which can be compared to already-existing data.