Comparative genomic analysis of Multi-Drug Resistance and Virulence Determinants of Escherichia coliSKN 649 and Staphylococcus ureilyticusSKN 217 isolated and characterized from milk and milk products in Anand, Gujarat, India

Abstract

Antimicrobial resistance (AMR) in dairy-associated pathogens presents a significant public health and food safety concern. This study examined 100 raw milk and fermented milk (buttermilk) samples collected from cattle farms in Anand, Gujarat, India, between January 2022 and December 2023, to assess the AMR patterns and genetic determinants. The bacterial isolates were identified using selective culturing and MALDI-TOF mass spectrometry, and their antibiotic susceptibility was determined through standard testing methods. Whole-genome sequencing (WGS) was performed on two extensively drug-resistant (XDR) strains, Escherichia coli SKN 649 and Staphylococcus ureilyticus SKN 217, to elucidate key resistance genes and mechanisms. E. coli SKN 649 showed high resistance to multiple antibiotic classes, including β-lactams, aminoglycosides, and macrolides, while retaining sensitivity to tetracycline and chloramphenicol. S. ureilyticus SKN 217 exhibited similar resistance patterns, particularly against penicillin and cephalosporins, with 90 % of isolates showing resistance to multiple antibiotics. Genomic analysis revealed resistance mechanisms mediated by efflux pumps and target alterations, with major AMR genes identified, such as kdpE, vanG, rsmA, and emrB in E. coli and norC, salE, sepA, sdrM, vanT, and FusF in S. ureilyticus. These findings underscore the urgent need for genomic surveillance in dairy farming and highlight the potential transmission risks of AMR bacteria through the food chain. The misuse and overuse of antibiotics in the veterinary sector is a critical factor driving AMR, with implications that extend beyond dairy production to human health. This growing threat emphasizes the need for a One Health approach, linking human, animal, and environmental health to address AMR. The global spread of resistant pathogens underscores the necessity for stricter regulations, better antibiotic stewardship in veterinary practices, and continuous monitoring to prevent the further emergence of AMR strains. Future research should focus on developing effective control strategies and mitigating the global AMR threat to safeguard both public health and the sustainability of dairy farming.