REDUCING ANTIMICROBIAL RESISTANCE RISKS AND ANTIBIOTIC USAGE IN DAIRY FARMING: MICROBIOLOGICAL INSIGHTS AND ALTERNATIVE STRATEGIES

Antimicrobial resistance (AMR) has become a significant global threat, ranking among the top 10 human health risks worldwide. It was identified as being responsible for approximately 1.27 million deaths internationally in 2019, but the annual impact of AMR-related deaths might eclipse 10 million by 2050. Therefore, there is a need for comprehensive research to address AMR and reduce antibiotic use in food animals, especially in dairy livestock systems. This thesis summarizes four research projects that investigate the impact of AMR in both animals and humans and explore the reduction of antibiotic use in intramammary infections, dairy farms, and livestock. The first study provides an overview of Staphylococcus (S.) aureus genotypes associated with AMR and virulence profiles in dairy pasture systems. The study revealed that RS-PCR analysis of S. aureus identified 12 genotypes within 8 clusters, with GTRI being the most prevalent (61%) and GTB at 14%. High penicillin resistance (69%), especially in CLR strains (88%), was observed, along with 51% resistance to amoxicillin plus clavulanate. All strains were susceptible to cephalosporins and oxacillin, with low macrolide resistance (4%) and multidrug resistance (6%). AMR genes were linked to susceptibility, with blaZ present in 94% of CLR strains, which also exhibited biofilm formation and virulence factors. The second study was designed to evaluate the effect of an approved cefazolin-based intramammary treatment on the milk microbiota of Alpine dairy goats during the dry and early lactation periods. The study found that the somatic cell count was decreasing over time at T3 compared to T1 after treatment with cefazolin. However, cefazolin treatment did not significantly impact alpha and beta diversity. The third study aimed to investigate genetic diversity and AMR genes, specifically for tetracycline (TET) and erythromycin (ERY) resistance in Enterococcus spp. isolates from a dairy farm with low antibiotic usage. The study found that E. faecalis exhibited high resistance to TET and ERY, with the tetM gene found in all isolates. The tetL gene was prevalent in E. faecalis (85% in environmental samples, 66% in milk) and rare in E. hirae (3.2%). The tetS gene was primarily in E. malodoratus (62.2%). The ermB gene was present in all E. faecalis isolates, and the int gene was found in 44.4% of E. faecalis and 6.4% of E. hirae. RAPD-PCR showed identical patterns in E. faecalis, indicating a predominant strain. The fourth study aimed to determine the effects of different commercial Lime-Based Bedding Conditions (LBCs) on the physical-chemical properties, microbial counts, and Clostridium spp. spore counts of anaerobically digested manure solids (ADMS). The significant finding of the study was that Product 1, with 100% lime, was the most effective at increasing pH and reducing bacterial counts, achieving a peak pH increase at T2 and reducing coliform bacteria and E. coli by up to 75%. It also decreased DM content by about 15% at a 20% concentration. Product 2 (20% lime) exhibited similar but less pronounced effects, characterized by lower pH increases and reduced microbial suppression. Product 3 (30% lime) demonstrated gradual improvements in pH and microbial reduction, particularly at T2, but had minimal impact on moisture reduction. Product 4 (20% lime and 10% gypsum) was the least effective overall, with weaker microbial suppression and pH increases, especially at lower concentrations. Overall, the findings of the studied project will help dairy farmers and policymakers take initiatives to reduce antibiotic use for intramammary infections on dairy farms and in livestock, and to adopt alternative treatment and management strategies, such as LBCs in bedding materials or dry cow or dry goat treatment in dairy farms.