Assessing the Risk of Spreading Clostridioides difficile and Its Toxins Within the Dairy Farm

<i>Clostridioides difficile</i> currently constitutes a major pathogen of the gastrointestinal tract, which poses a significant growing burden on medicine and veterinary medicine in many regions. A farm was assessed (feed table, silage pit, and feces (healthy animals, emaciated animals, and animals with mastitis)) for the presence of <i>C. difficile</i> toxins using the PCR method and for the microbiome in cow feed and feces using NGS technology, one month apart. <i>C. difficile</i> toxin A and binary toxin were detected in feed samples. <i>C. difficile</i> toxin genes were found in the feces of sick animals two to three times more often than in healthy animals. Analysis of the microbial community of cow feces revealed that, during the month, the animals experienced major changes in the community structure associated with the accumulation of pathogenic bacteria, in particular <i>Paeniclostridium</i> sp., as well as with the development of methanogenic archaea of the Methanobacteriaceae and associated microorganisms (Lachnospiraceae and Anaerovoracaceae), which may speak of a decrease in feed efficiency and, subsequently, animal productivity. Thus, it seems likely that <i>C. difficile</i> enters the gastrointestinal tract of animals through feed, while animals weakened by diseases are more sensitive to the reproduction of pathogens in the GIT due to a weakened organism.