Microbial Diversity and Resistome in Milk of Cows with Subclinical Mastitis in a Coastal District of Odisha, India

Mastitis is a globally prevalent bacterial disease of lactating cows. Prevention and control of this multi-etiological complex disease relies upon administration of antibiotics. This has led to the emergence of newer multi-drug resistant strains. In the current study, milk samples from subclinical mastitis cows and their healthy counterparts were subjected to Illumina-based whole genome metagenome sequencing to explore bacterial communities and antibiotic resistance genes associated with mastitis-affected and healthy udder. Bovine milk microbiome in subclinical mastitis-affected cows were dominated by pathogenic bacteria such as Acinetobacter baylyi , Acinetobacter pittii , Streptococcus agalactiae , Streptococcus suis , Streptococcus uberis , Aeromonas hydrophila , Aeromonas enteropelogenes , Lactococcus lactis , Corynebacterium resistens and Kocuria rhizophila . We observed higher bacterial abundance and diversity in milk of cows suffering from subclinical mastitis as compared to apparently healthy cows. Resistant genes against fluoroquinolones, peptides, β-lactams, tetracyclines and macrolides were detected in the subclinical group. In contrast, genes resistant to aminoglycosides, penams and β-lactams were found in healthy cow milk. The findings of the study expand our knowledge of bacterial diversity and associated resistant genes found in the milk of mastitis-affected and healthy cow milk.