Longitudinal comparison of animal and environmental microbiota, Coxiella burnetii detection frequency, and seroconversion in two goat herds following a Q fever outbreak and whole-herd vaccination

Two goat herds were longitudinally monitored following the implementation of a whole-herd vaccination protocol after a Q fever outbreak. Faecal, milk, vaginal, preputial, nasopharyngeal, environmental (qPCR and 16 S rRNA ), and blood samples (serology) were analysed. Before vaccination, over 70% of animals were seropositive, with qPCR positivity samples in 52% of the study animals. Seroconversion was complete after primary vaccination, accompanied by an approximately 40% reduction in qPCR-positive animals. Seropositivity remained high during the subsequent two kidding seasons (86% and 93%), while C. burnetii detection declined to 10% of goats at the second kidding and to a single goat (3%) from one herd at the third. The persistent presence of qPCR-positive animals and environmental contamination supports early, whole-herd vaccination as a long-term strategy at least two years. Frequent nasopharyngeal detection of C. burnetii DNA supports its potential for Q fever surveillance and further investigation of respiratory involvement. Metabarcoding revealed a significant reproductive impact, with vaginal microbiota richness remained lower in aborted goats together with Fusobacteriota dominance in the next kidding after the Q fever outbreak. These results underscore the importance of preventing C. burnetii infection in caprine herds due to its reproductive and productive consequences, which remain partly unknown.