The pictures aren’t pretty, and the condition is serious. But what truly stinks about foal diarrhea is that in more than half the cases, veterinarians never identify the underlying cause. Yet, according to Nathan Slovis, DVM, Dipl. ACVIM, CHT, director of the McGee Center at Hagyard Equine Medical Institute, in Lexington, Kentucky, that scenario is changing. Developing technologies—and even the use of certified sniffer dogs that can identify Clostridium difficile in humans—are making it faster and easier to diagnose whether the culprit is viral, bacterial, protozoal, or something else.

Twenty percent of foals will get some form of infectious diarrhea, Slovis said during his presentation at the 2020 American Association of Equine Practitioners’ Convention, held virtually. And because so many possible causes exist, veterinarians often find themselves treating symptoms without really knowing what they’re up against. Pathogens such as rotavirus, clostridium, and salmonella can proliferate in neonates with lethal speed. Fortunately, veterinarians can now use real-time polymerase chain reaction (PCR) testing to swiftly identify viruses, bacteria, and protozoa by amplifying fragments of genetic material in blood and fecal samples. Slovis explained that by recording how many cycles it takes to replicate the DNA to a trillion copies, the test also offers a way to quantify infectious loads.

For too long, veterinarians had to rely on what they could see under the microscope or what they could culture in a petri dish. Cultures are often misleading, because potentially harmful bacteria can be found everywhere, even in perfectly healthy horses. “Real-time PCR has been a diagnostic game-changer in both human and veterinary medicine,” he said.

Routinely treating foals with antibiotics has become controversial, Slovis acknowledged. Antibiotics are ineffective against viruses, and there’s growing concern about antibiotic-resistant bacteria, including multidrug resistant strains of salmonella. Genetically engineered “bacteria-eating” viruses known as bacteriophages hold future promise for treating some of these antibiotic-resistant infections, but more research is needed.

Antibiotics do change the gastrointestinal (GI) tract microbiome, leaving researchers to wonder whether they simply make diarrhea worse. Nonetheless, Slovis generally favors giving sick foals a broad-spectrum antibiotic even when he suspects and confirms rotavirus.

“Neonates are different than adults,” he said. “Bacteremia (bacteria in the bloodstream) occurs in 50% of foal diarrhea cases.” Because endotoxins can be deadly, his strategy is to quell any primary or secondary bacterial infections before the foal’s body is overwhelmed.

Slovis also made a strong pitch for vaccinating pregnant mares against rotavirus and salmonella. A two-dose vaccine for Salmonella typhimurium and agona (conditional license in Kentucky) can be given to mares at nine and 10 months of gestation or to foals of unvaccinated mares during their first month of life. The rotavirus vaccine requires three doses administered at eight, nine, and 10 months of gestation.

Studies show the rotavirus vaccine:

1. Reduces infection rates by 50%;
2. Reduces the duration of diarrhea from seven days to less than two days; and
3. Prevents virus shedding in mares and foals.

Unfortunately, the currently available rotavirus vaccine only protects from the G3 strain, not the G14 strain that’s becoming more common in Kentucky and elsewhere, Slovis said. He hopes a pharmaceutical company might be persuaded to work on a vaccine offering crossover protection between these two equine strains.

Rotavirus hits young foals hard and fast, with a one- to two-day incubation period. The virus invades the GI tract and impacts the production of lactase, which interferes with milk digestion, leading to diarrhea and painful bloating. Using PCR is the best way to diagnose it. Immunoassay tests can also be helpful, he noted, but they must be validated for horses, because human rotavirus antigen tests can provide false negatives in equines. Therapies include providing fluids, ulcer medication, pain relievers, and lactase to support digestion, reduce bloating, and calm the bowels.

Rotavirus shedding can continue for up to 10 days after the baby’s manure firms up, and the virus can persist in the environment for up to nine months, he cautioned. Bleach is not an effective disinfectant against the virus, whereas alcohol and hydrogen peroxide formulations are, he said.

Bacteria can also plague young foals, with C. difficile, C. perfringens, and Salmonella common culprits. Slovis warned that types A and C of C. perfringens are associated with fatal foal necrotizing enterocolitis (damage and death of cells in the small intestine and colon), so there’s no time to waste. By the time a positive culture comes back from the lab, it could be too late. Again, he said PCR is the new gold standard for identifying bacterial loads, possibly providing results within hours.

Lateral flow enzyme immunoassay tests that screen for both antigens and toxins are also useful. They’re quick and easy, but sometimes produce ambiguous results, such as indicating positive for antigens but negative for toxins.

“We used to believe that if we didn’t see that a test was positive for a C. difficile toxin, then it wasn’t significant,” Slovis said. Yet after studying many antigen-positive/toxin-negative foals (all of which had diarrhea, and all which responded to the antibiotic metronidazole), he found PCR tests confirmed more than three-quarters of them did have C. difficile infections.

Yet PCR isn’t the only trending diagnostic development. Slovis noted that canines are being trained and certified to “sniff out” C. diff and other infections. These special technicians, however, are currently in short supply in human medicine.

Hygiene is hugely important in preventing or reducing foal diarrhea outbreaks. If barns are potentially infected, he suggests foaling mares outdoors until all stall surfaces, tack, and equipment have been thoroughly disinfected. Foaling kits should contain only single-use items and equipment that can be sterilized between uses. Slovis also recommended using disposable udder wipes to cleanse the mare’s udder and hindquarters before her baby nurses. A bath before or after foaling might also be in order. He also emphasized proper handwashing for those handling mares and foals. Soap and towels (preferably touchless), along with hand sanitizer, should be within easy reach and installed where they won’t be contaminated, which means not just sitting on the counter next to the sink.

His recommendations also include:

• Wearing disposable boot covers, gowns, and gloves, and changing between horses;
• Doing away with “dip pans” used to disinfect footwear;
• Replacing leather halters, muzzles, and tack with nylon ones that can be disinfected after use; and
• Quarantining mares and foals until they are symptom-free and test negative for the pathogen as recommended by your veterinarian.

Not every case of foal diarrhea is preventable. But faster, more accurate diagnostics reduce guesswork regarding treatment, leading to better outcomes for babies.