Longitudinal analysis reveals transitions in pathogens 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 is one of the most common diseases on dairy farms. Limited information exists about the interactions among pathogens in mastitis infections. This study aims (1) to identify the potential sources of the mastitis-causing pathogens at farm level, (2) to analyse the 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 four-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 (PathoProofTM) 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 different SCC and cow recovery dynamics. Notably, profiles with Corynebacterium bovis, though considered a minor pathogen, were associated with persistent infections and limited antibiotic responses in our data. These results challenge the pathogenic status of bacteria such as the non-aureus staphylococci (NAS) group, typically also considered a minor pathogen. We highlight the complexity of mastitis infections and underscore the importance of considering multi-pathogen associations and longitudinal dynamics in udder health management.