Evaluation of the level of antimicrobial resistance in two dairy cow farms with different antimicrobial consumption

Antimicrobial resistance is a natural phenomenon resulting from the exposure to the active ingredients. Antibiotic consumption in veterinary medicine is strictly ruled and farms are classified on the basis of the veterinary medical prescriptions. The aim of the present study was to assess the antimicrobial resistance level in two dairy herds using different quantities of antimicrobials. Faeces from all the animal categories of dairy farms, milk and colostrum underwent bacteriological examinations in order to isolate bacterial species considered indicators of antimicrobial resistance (Escherichia coli and Enterococcus sp) and metagenomics to analyse circulating antimicrobial resistance genes (ARG) and their relative abundance. The susceptibility of E. coli and Enterococcus sp strains against a panel of antimicrobials was tested through the determination of the minimum inhibitory concentration (MIC). The presence of ARGs was detected in pooled samples through NGS shot-gun sequencing and some selected ARGs were subsequently quantified by means of the digital PCR method. All the E.coli strains tested were susceptible to critical important antimicrobials (CIA) and resistant to sulphonamides. The highest MIC values of aminoglycosides, fluoroquinolones and amphenicols and most of the multidrug-resistant (MDR) E. coli strains were isolated from calves and colostrum. All Enterococcus sp strains were susceptible to betalactams, linezolid, teicoplanin and, most importantly, vancomycin. All the isolates were resistant to tigecycline and gentamicin, while 11/20 strains were resistant to erythromycin. All Enterococcus sp strains isolated from calves were resistant to streptomycin. The ARGs quantitatively more relevant in the farms were ermB, sul2 and blaTEM, conferring macrolides-lincosamine-streptogramine B resistance, sulphonamidesresistance and betalactams resistance respectively. Genes not detected in either farms were: blaCTXM, qnrS, mcr-1 and VanA. Although the differences in the antimicrobial consumption the results do not show relevant differences between farms, since the antimicrobial resistance indexes (ARI) were comparable. Dairy farms could be considered a hotspot of ARGs, comprising those classified as the highest risk for human health (ermB and blaTEM). Furthermore, this study identified the role of calves as the main source of ARGs and "non-wild" bacterial strains in dairy farms. Also, the presence of MDR E. coli in colostrum could represent a risk for early intestinal colonization and subsequent dissemination of resistant strains.