Comprehensive exploration of antibiotic use in dairy cows Investigating milk and curd microbiota, antimicrobial resistance gene in native versus crossbreeds

Abstract

The indiscriminate use of antibiotics in dairy farming has raised serious concerns regarding antimicrobial resistance (AMR), food safety, and variations in dairy microbiota. This study aimed to analyze antibiotic usage patterns in dairy cows, investigate the microbiota composition of milk and curd from native and crossbred cows and assess the occurrence of antimicrobial resistance gene in milk samples. A structured questionnaire survey revealed that 69.6% of stakeholders expressed concerns regarding antibiotic use in dairy cows. Significantly, 87.5% acknowledged the devastating consequences of antibiotic overuse, and 76.8% agreed that minimizing antibiotic use is vital for controlling AMR. Mastitis was identified as the most common condition treated with antibiotics (86.79%), with tetracycline (47.6%), gentamycin (38%) and penicillin (30.9%) being the most frequently prescribed antibiotics. Physicochemical analysis revealed relatively stable values across different samples of milk, starter culture and curd. Nanopore sequencing of milk, curd, and starter culture samples generated good-quality reads, enabling comprehensive microbiome profiling. Taxonomic analysis showed dominance of the phylum Firmicutes across all fermented samples, while genus level varied among breeds, with Lactococcus, Streptococcus, and Bacillus being predominant. Native breeds, particularly Gir and Malnad gidda, exhibited higher microbial richness and diversity in milk samples. The AMR gene (mecA) analysis in milk samples confirms the presence of AMR resistance, indicating a potential link between antibiotic usage practices and resistance. Broadly, the findings highlight the very essential need for improved antibiotic supervision and promotion of ethno-veterinary practices in disease management protocols to mitigate AMR in the Indian dairy sector.