Brazil foal study highlights limits of one-off enteric test results

CURRENT FULL VERSION: A new report on enteric pathogens in Brazilian foals highlights a diagnostic challenge equine veterinarians know well: the organism you detect may not be the organism driving the case. The study, published in the Journal of Veterinary Diagnostic Investigation, examined diarrheic and non-diarrheic foals in Brazil and focused on whether diarrheic foals were more likely to carry multiple potential enteric pathogens. That question matters because fecal testing panels are increasingly sensitive, but sensitivity alone doesn’t resolve causation. (us.sagepub.com)

The background here is important. Foal diarrhea remains a major cause of morbidity and mortality, and the differential list is broad, spanning infectious and non-infectious causes. AAEP’s current field diagnostic guidance for acute infectious diarrhea in horses lists Clostridioides difficile, Clostridium perfringens, Escherichia coli in neonates, equine rotavirus types A and B, gastrointestinal parasites, Lawsonia intracellularis, Rhodococcus equi, and Salmonella spp. among foal infectious differentials. At the same time, AAEP notes that several of these agents, including Salmonella spp. and C. difficile, carry contagious or zoonotic implications, making test interpretation a herd health and workplace safety issue, not just an individual patient question. (aaep.org)

Additional context from earlier work in the same São Paulo foal population helps frame the new study’s significance. In that cohort of foals up to 90 days of age, enteric pathogens were found in 87% of diarrheic foals and 80% of non-diarrheic foals. Coinfections were more frequent in diarrheic foals, 46%, than in non-diarrheic foals, 33%, while monoinfections were actually somewhat more common in non-diarrheic foals. The study also identified Salmonella serotypes in both groups, found Cryptosporidium parvum and Giardia duodenalis at low levels, detected coronavirus only rarely, and did not detect rotavirus in the sampled animals. The authors concluded that the presence of pathogens alone, with the exception of some toxin-associated findings, did not sharply distinguish diarrheic from non-diarrheic foals. (repositorio.unesp.br)

That nuance aligns with more recent microbiome work in foals. A 2025 BMC Research Notes study comparing pathogenic and non-pathogenic diarrhea samples found that diarrheic foals positive by qPCR for C. difficile and/or C. perfringens had distinct microbial population changes, but the authors also stressed limitations of narrow diagnostic panels and noted that intermittently shed pathogens such as Salmonella can be missed without repeat testing. In other words, a single positive result may overstate significance, and a single negative result may understate risk. (bmcresnotes.biomedcentral.com)

Industry and guideline sources point in the same direction on biosecurity. AAEP’s diarrhea guidance recommends precautions for suspected infectious cases because of zoonotic exposure risk, and its salmonellosis guidance notes that clinically normal horses can transiently shed Salmonella, especially during stress, illness, feed change, transportation, or hospitalization. Foals are also more likely than adults to develop severe systemic illness from salmonellosis, including hemorrhagic diarrhea, pneumonia, meningitis, physitis, and septic arthritis. That’s one reason surveillance findings in apparently healthy foals deserve attention from ambulatory and hospital-based teams alike. (aaep.org)

A related South African hospital epidemiology study underscores the operational stakes. Reviewing isolates from 2012 to 2019 at a veterinary academic hospital, investigators found 715 Salmonella isolates, with 67.6% from animals and 32.4% from environmental samples; most positive animal cases came from equine clinics, and environmental contamination was identified as a major source of spread. A separate outbreak investigation at the same equine academic hospital during October to December 2016 sharpened that message: Salmonella was isolated from 25% of patients, S. Typhimurium was the dominant serotype in patients, stables, and clinic areas, and syndromic clinical signs were not associated with Salmonella infection. Longer hospitalization and repeated fecal sampling were significantly associated with detection, four students reported symptoms consistent with salmonellosis, and one had a positive fecal culture and required hospitalization. While that outbreak paper addressed a different setting and question than the Brazilian foal prevalence study, together they support a practical inference: equine practices can’t assume that only clinically obvious diarrhea cases contribute to pathogen pressure in the barn or hospital, and continuous patient-plus-environment surveillance matters. (bohrium.com)

Why it matters: For veterinary professionals, the study is less about any single pathogen than about diagnostic interpretation. Broad fecal panels can identify organisms in both sick and clinically normal foals, so positive results should be weighed against signalment, age, toxin or virulence-factor data, exposure history, outbreak context, and the possibility of coinfection. The South African outbreak data add a useful reminder that syndromic presentation alone may miss Salmonella-positive patients and that prolonged hospitalization can increase operational risk. That has consequences for antimicrobial stewardship, isolation decisions, cleaning protocols, staff protection, and discussions with pet parents and breeders about what a test result does, and doesn’t, mean. It also supports a more disciplined approach to repeat sampling, environmental monitoring, and herd-level assessment when Salmonella or clostridial disease is on the table. (repositorio.unesp.br)

What to watch: The next step is better stratification, which combinations of organism detection, toxin genes, age windows, or clinical markers most reliably predict clinically meaningful disease. If future studies can separate background shedding from actionable infection more clearly, they could sharpen how equine veterinarians use multiplex diagnostics, when they isolate foals, and how aggressively they respond at the farm or hospital level. Just as important, more data on repeat fecal sampling and routine environmental surveillance could help define when biosecurity escalation is warranted even if classic salmonellosis signs are absent. (repositorio.unesp.br)