Impact of whole-herd vaccination on a caprine coxiellosis outbreak: a longitudinal study of Coxiella burnetii shedding, serology, and host microbiota.

This longitudinal study investigated C. burnetii dynamics and the associated microbiota after vaccination in aborted and normal-delivery goats and bucks following a Q fever outbreak. Fecal, milk, vaginal, preputial, nasopharyngeal, environmental (qPCR and 16S rRNA), and blood samples (16S rRNA and serology) were analyzed. Before vaccination, over 70% of animals were seropositive, with qPCR positivity in all females and half of the males. Seroconversion remained complete until the second kidding season and reached approximately 90% by the third kidding season. After primary vaccination, a significant 60% reduction in shedders was observed, with shedding remaining absent during the two consecutive kidding seasons. Nasopharyngeal samples showed the highest and most persistent positivity, highlighting their diagnostic and epidemiological relevance. The first detection of C. burnetii in the buck prepuce underscores the potential role of males in disease maintenance. Persistent environmental contamination further supports early, whole-herd vaccination as a long-term strategy. Metabarcoding revealed significant shifts in microbial diversity across all anatomical sites over time, including vaginal community structure, suggesting local dysbiosis after abortion. The DNA detection of C. burnetii in blood and its significantly higher vaginal abundance in aborted females may contribute to abortion. A reduction in vaginal pathogen load (p < 0.05) may suggest a reproductive microbiota modulation associated with increased Firmicutes, considering it as a potentially health biomarker.