Sequencing-based molecular epidemiology of mesophilic Aeromonas in dairy environments and water systems

This study investigated the prevalence, virulence gene distribution, antimicrobial resistance, and molecular epidemiology of mesophilic Aeromonas species from milk, dairy farm environments, and drinking water systems in Kashmir, India. Aeromonas prevalence varied between sample sources, with environmental samples having the highest detection rate (51.96%), followed by water sources (46.60%) and milk (36.15%). Following pasteurization and disinfection, prevalence in milk samples was significantly reduced, demonstrating the efficacy of hygiene measures in minimizing contamination. Higher detection rates were found in environmental sources like soil, cow dung, and milkers’ hands, suggesting their role as potential sources of contamination. The Aeromonads exhibited a wide distribution of virulence determinants; species-associated variations were noted for the ahc and ast genes, while the fla gene was ubiquitous among isolates. Virulence gene distribution differed between species, with Aeromonas hydrophila exhibiting the most varied virulence profiles. Antimicrobial resistance patterns were generally comparable among the mesophilic Aeromonas species, and multidrug resistance was detected in 45.8% of the isolates. Analysis of gyrA , gyrB , and rpoD genes based on sequencing distinguished isolates into species-specific clades, with gyrB providing the highest intra-species resolution, suggesting its utility as an informative marker for molecular epidemiological investigations of Aeromonas . These results show that water systems and dairy environments are significant sources of genetically diverse Aeromonads carrying virulence and antimicrobial resistance determinants. IMPORTANCE Aeromonas species are widely distributed in aquatic environments and are increasingly recognized as emerging opportunistic pathogens, yet their role in dairy production systems remains poorly understood. The prevalence and genetic relatedness of mesophilic Aeromonas spp. across milk, dairy farm environments, and drinking water systems remain underexplored. By integrating prevalence data from a large and diverse collection of samples with virulence profiling, antimicrobial resistance characterization, and sequencing-based molecular epidemiology, the present study provides a comprehensive assessment of Aeromonas populations across these interconnected compartments. The findings underscore the importance of hygienic practices during milk production and the need for routine monitoring of environmental and water sources associated with dairy systems. Improved understanding of the genetic diversity and distribution of Aeromonas can support more effective surveillance strategies and help mitigate potential risks to food safety and public health.