Brazil study examines enteric pathogens in foals with and without diarrhea

Version 2 — Full analysis

A newly published study in the Journal of Veterinary Diagnostic Investigation focuses on a practical question for equine clinicians: how often are potential enteric pathogens found in diarrheic versus non-diarrheic foals in Brazil, and do coinfections help explain which foals get sick? The paper, by Roberta Martíns Basso, Fabrício Moreira Cerri, and Pollyana Rennó Campos Braga, evaluated 200 foals up to 1 year of age, including 100 with diarrhea and 100 without, using real-time PCR testing for key enteric organisms and toxin genes. Based on the abstract provided, the authors expected diarrheic foals to show a higher prevalence of two or more organisms, a hypothesis that speaks directly to how equine practices now use multiplex fecal testing. (us.sagepub.com)

The study lands in a field where interpretation is often harder than detection. Earlier Brazilian work in foals found that enteric pathogens and coinfections were common in both diarrheic and non-diarrheic animals, underscoring that fecal detection alone may not prove disease causation. In that earlier São Paulo cohort, Salmonella spp., Strongyloides, C. perfringens type A, and virulence-associated E. coli markers were among the organisms detected in diarrheic foals, while clinically normal foals also shed several potential pathogens. The authors of that paper reported no significant association between specific coinfections and the presence of diarrhea, even though mortality was high among Salmonella-positive diarrheic foals. (pmc.ncbi.nlm.nih.gov)

That broader context aligns with expert guidance from the American Association of Equine Practitioners. AAEP’s rotavirus resource describes equine rotavirus as one of the most common causes of foal diarrhea worldwide, particularly in breeding settings, and its infectious diarrhea guidance continues to place rotavirus, Salmonella spp., and Clostridioides difficile among the core pathogens to consider. AAEP’s clostridial diarrhea flowchart also advises clinicians to respond initially from a worst-case biosecurity standpoint, effectively treating suspect cases as if Salmonella could be involved until proven otherwise. (aaep.org)

Additional research reinforces why that caution matters. A retrospective study of 233 diarrheic foals found rotavirus was the most frequently detected infectious agent, followed by C. perfringens and Salmonella spp. (pmc.ncbi.nlm.nih.gov) Meanwhile, more recent work highlighted by UC Davis found that, in one foal cohort tested by qPCR, rotavirus was the only pathogen significantly more common in foals with diarrhea, while Salmonella enterica, Neorickettsia risticii, Lawsonia intracellularis, Rhodococcus equi, and equine coronavirus were not detected in that study population. UC Davis researchers concluded that even expanded C. perfringens toxin-gene panels could not definitively distinguish healthy from sick foals. (ceh.vetmed.ucdavis.edu) A 2025 microbiome study added another layer, noting that pathogen-positive diarrheic foals showed altered fecal microbial diversity, but also warning that intermittently shed organisms such as Salmonella can be missed without repeat testing. (bmcresnotes.biomedcentral.com)

Hospital outbreak data add an important real-world reminder that Salmonella risk is not limited to obviously classic cases. In a South African equine veterinary academic hospital outbreak reported in Veterinary Sciences, Salmonella was isolated from 25% of patients, along with environmental contamination in stables and clinic areas; Salmonella Typhimurium was the dominant serotype across patients and the hospital environment. Longer hospitalization and repeated fecal sampling were significantly associated with infection, but syndromic clinical presentation was not. In other words, Salmonella-positive equine patients could not be reliably identified just by looking for a “typical” salmonellosis picture. The report also documented probable zoonotic impact, including four students with symptoms and one hospitalization with a positive fecal culture, reinforcing why surveillance and strict infection prevention matter in equine facilities. This is highly relevant to foal diarrhea workups, where a positive or suspected Salmonella result can affect not just treatment choices but stall assignment, staff precautions, environmental monitoring, and decisions about repeat testing.

There doesn’t appear to be a dedicated institutional press release or broad industry reaction yet for the new Brazilian paper based on available search results. Still, the study fits squarely within an active diagnostic conversation in equine practice: how to use increasingly sensitive PCR panels without overcalling the clinical importance of every positive result. Commercial and academic laboratories now routinely offer equine diarrhea panels that include rotavirus, Salmonella, C. difficile, and C. perfringens targets, reflecting both the utility and the interpretive challenge of syndromic testing. (idexx.com)

Why it matters: For veterinarians, this is less about finding a new pathogen than about sharpening diagnostic judgment. Foal diarrhea remains a major cause of morbidity, and in referral or breeding-farm settings the stakes include dehydration, sepsis risk, outbreak control, staff exposure, and disruption for pet parents and farm managers. Studies like this can help clinicians understand local pathogen ecology, but they also reinforce that test results have to be read alongside age, clinical severity, exposure history, and herd-level patterns. If the Brazilian data show substantial overlap between diarrheic and non-diarrheic foals, that would support a more cautious interpretation of single-agent PCR positives and a continued emphasis on isolation, repeat testing when indicated, and targeted therapy rather than reflexive treatment. That last point is especially relevant for Salmonella and clostridial suspects, where infection control may matter as much as the medication plan. The South African outbreak experience sharpens that message further: because syndromic signs did not reliably identify infected patients, biosecurity and surveillance cannot depend on clinical appearance alone. (aaep.org)

What to watch: The next key step is the full article’s detailed breakdown of which organisms were most prevalent, whether coinfections truly clustered in diarrheic foals, and whether age or management factors changed the signal. If those data identify clearer patterns, they could inform how equine practices in Brazil and elsewhere triage fecal PCR results, choose isolation protocols, and counsel pet parents during foal diarrhea workups. They may also help clarify when repeat fecal sampling is worth pursuing for suspected Salmonella, especially in hospital settings where missed shedders can have consequences beyond the individual foal. (us.sagepub.com)