Longitudinal analysis reveals transitions in pathogen profiles associated with mastitis in dairy cows

Mastitis is a multifactorial infection of the udder potentially caused by many pathogens of varying severity and prevalence and it is one of the most common diseases on dairy farms. Limited information exists about the ecological interactions among pathogens in mastitis infections. This study aims (1) to identify the potential sources of the mastitis-causing pathogens at the farm level, (2) to analyse the statistical associations and dynamics of these pathogens over time in the milk microbiota, and (3) to assess their impact on somatic cell count (SCC) fluctuation. To address these objectives, two 4-month longitudinal studies were conducted on cows of six dairy farms in the Auvergne region of France. Milk and faeces were collected from a total of 33 cows, along with environmental samples (bedding and milk filter). A commercial qPCR kit (PathoProof ^™ ) was used to quantify 15 mastitis-causing pathogens in these samples. The data were then processed using Principal Component Analysis, the Ward clustering method and discrete-time Markov chain models. Clustering analyses of quarter milk samples revealed distinct profiles of pathogen distribution associated with specific SCC and cow recovery dynamics. Notably, profiles involving Corynebacterium bovis , though considered a minor pathogen, were associated with persistent infections and variable SCC levels. We also described co-infections between C. bovis and Streptococcus uberis . Non- aureus staphylococci (NAS) were associated with a wide range of effects on udder health, as they constitute a diverse bacterial group, and detection of this group in the udder might generally not be sufficient to confirm a mastitis diagnosis. We highlight the importance of considering multi-pathogen associations and longitudinal dynamics in udder health management.