Diarrhea is a significant cause of morbidity and mortality in foals. Our hypothesis is that foals with diarrhea have a greater prevalence of ≥2 organisms causing coinfections. We investigated the major microorganisms associated with diarrhea in 200 foals up to 1-y-old (100 diarrheic and 100 non-diarrheic). Fecal samples were analyzed by real-time PCR (rtPCR) for the detection of Clostridioides difficile and toxin genes tcdA and tcdB, Clostridium perfringens (genotyping for toxin-encoding genes), Salmonella spp., Rhodococcus equi, Lawsonia intracellularis, Neorickettsia risticii, Enterococcus durans, Giardia duodenalis, and Cryptosporidium spp. Rotavirus A and coronavirus were detected using reverse-transcription rtPCR. Fecal bacterial culture was also performed for Clostridioides difficile and Clostridium perfringens, and isolates were submitted for the detection of toxin-encoding genes (conventional multiplex PCR). At least one enteric agent was detected by rtPCR in 85% and 70% of diarrheic and non-diarrheic foals, respectively. Co-detection was significantly more frequent in the diarrheic group (27 singly detected organisms vs. 58 co-detected organisms) than in the non-diarrheic group (37 singly detected organisms vs. 33 co-detected organisms; p = 0.008). Salmonella spp., C. difficile (and toxigenic C. difficile), and Cryptosporidium spp. were significantly associated with foal diarrhea. Our detection of multiple agents in diarrheic foals highlights the diagnostic complexity and potential interactions among agents in the multifactorial etiology of foal diarrhea.
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