Cervico-vaginal microbiota and antimicrobial resistance patterns in relation to different reproductive statuses in cattle: a field study from Nepal

Vaginal bacterial communities are increasingly recognized as key determinants of fertility in cattle. This study explored bacterial communities in the cervico-vaginal mucus of healthy heifers, cows with cervicitis, repeat-breeding, and cows within the 35-day postpartum period using the microbiological culture method (n=35) and sequencing of the V3-V4 hypervariable regions of 16S rRNA gene (n=18), along with antimicrobial susceptibility testing. Micrococcus spp. and Enterobacter spp. were the top two bacteria isolated across the groups. Alarmingly, antimicrobial sensitivity tests revealed a high prevalence of multidrug resistance (71.7%) and elevated multiple antibiotic resistance indices in the isolated bacteria; none of the isolates were sensitive to all the tested bacteria. From 16S rRNA sequencing, a total of 1,047,482 sequences and 2,366 operational taxonomic units (OTUs) were generated. All groups shared 434 OTUs, and they did not differ in alpha diversity and beta diversity except for healthy heifers and cervicitis cattle. Bacillota, followed by Pseudomonadota, Fusobacteriota, Actinomycetota, Bacteroidota, and Mycoplasmatota dominated the vaginal microbiota across all groups. Genus-level comparisons revealed the following group-specific enriched taxa: Chryseobacterium with a linear discriminant analysis (LDA) score > 3 in cervicitis, Filifactor (LDA score > 2) in repeat breeding cow, and Histophilus (LDA score > 3.5) in healthy heifers. These findings offer important insights into the structure of bovine vaginal microbial communities while highlighting the urgent need to monitor antimicrobial resistance. This study lays the groundwork for defining the core vaginal microbiota and its potential implications for reproductive health and disease. To the best of our knowledge, this is the first study in Nepal to investigate cervico-vaginal microbiota and antimicrobial resistance patterns in cattle across different reproductive statuses using both culture-dependent methods and 16S rRNA gene sequencing.