Association of Staphylococcus aureus bovine-adapted lineages with within herd prevalence of subclinical mastitis in Irish dairy herds
To investigate the genetic variability of bovine Staphylococcus aureus and determine if herd-level and individual cow milk quality parameters are associated with specific intramammary pathogens or S. aureus genotypes, 20 Irish dairy herds were studied. These herds were classified as problem herds i.e. high within-herd prevalence of sub-clinical mastitis based on cow level somatic cell count (SCC) measures (n = 10) or control, i.e., low within-herd prevalence of sub-clinical mastitis (n = 10). Milk samples were collected from putatively infected primiparous and multiparous cows and subjected to microbiological, milk composition and milk processing analysis. The major pathogens identified were non-aureus Staphylococci (37%), streptococci (17%) and S. aureus (13%) with no microorganism recovered from 29% of samples. There was a higher prevalence of S. aureus infection in problem herds compared to controls. The majority of S. aureus isolates belonged to Clonal Complex (CC) 97 or CC151 and S. aureus lineage was significantly associated with farm status; CC97 was 10 times more likely to be isolated from a problem than a control herd. SCC was dependent on the nature of the infecting agent. For all bacterial species, positive samples had significantly higher SCC than samples that were bacteriologically negative, with milk containing S. aureus having significantly higher SCC than all other groups. Infectious agent was also associated with total solids, lactose percentage and rennet coagulation time, although there were no differences between S. aureus lineages in any milk composition or processing parameters. Antimicrobial resistance was rare among the S. aureus isolates, although CC97 and CC8 isolates were resistant to penicillin and ampicillin. Comparative genomic analysis of the S. aureus isolates identified lineage-associated virulence genes. Pan-genome analysis identified a small number of CC97 and CC151 unique genes although no functional enrichment of the unique genes was identified. A number of the lineage-unique genes were associated with mobile genetic elements.