Nearly 94% of pigs tested on Ontario farms carried the genetic makeup that makes them susceptible to E. coli F18, according to a new study published in Veterinary Microbiology by researchers from the University of Guelph, Université de Montréal and collaborating institutions. The finding sharpens the case for genetics-informed decisions in herds battling post-weaning diarrhea.

The research team, led by Chantelle I. Major and Abdolvahab Farzan, set out to answer two practical questions: which virulence genes circulate in E. coli from diarrheic versus non-diarrheic pigs, and how many animals on a given farm are genetically predisposed to infection with the two major post-weaning pathogens, E. coli F4 and F18. The study ran on a subset of farms in Ontario, Canada.

The design was straightforward. On each farm, researchers cultured rectal swabs from 10 diarrheic pigs and 5 non-diarrheic pigs, then genotyped the recovered isolates. Blood samples served to determine genetic susceptibility to F4 and F18 through the MUC4 and CHCF1 markers.

In total, the team recovered 199 E. coli isolates carrying at least one virulence gene. Carriage was nearly evenly split between sick and healthy animals: 55% of diarrheic pigs and 46% of non-diarrheic pigs shed such isolates, a difference that did not reach statistical significance (P=0.14). The same held for enterotoxigenic E. coli (ETEC), defined here as isolates carrying at least one fimbriae or AIDA-I gene plus at least one enterotoxin gene — 24.5% of diarrheic pigs and 17.0% of non-diarrheic pigs were positive (P=0.14).

That non-significant gap carries a message for practitioners: healthy pigs in the same barn shed virulence-gene-carrying E. coli at rates close to those of their diarrheic penmates. Diagnostics, not clinical presentation alone, identify the pathogen profile on a farm.

Two enterotoxin genes did separate the groups. Diarrheic pigs were significantly more likely to shed E. coli carrying STb (P=0.03) or LT (P=0.02). The most prevalent enterotoxin gene overall was EAST1, found in 35.7% of isolates, followed by STb at 24.7% and LT at 24.3%. Among fimbrial genes, F4 led at 9.0% and F18 followed at 8.3%.

The diversity was striking. Across the isolates, the researchers identified 52 distinct virotypes. The five most common were F4:STa:STb:Paa (5.5%), AIDA-I:LT:STb:EAST1 (5.5%), F4:LT:STb:Paa:EAST1 (4.0%), F18:LT:STb:Paa:EAST1 (3.0%) and F18:STa:STb (3.0%). The authors note that multiple enterotoxigenic E. coli were associated with the outbreak of post-weaning diarrhea under investigation — a reminder that outbreaks on a single farm may not have a single causative strain, which matters when selecting or designing a vaccine.

The susceptibility data may prove the most consequential part of the paper for breeding decisions. Based on the MUC4 marker, 42.7% of pigs were susceptible to E. coli F4; based on CHCF1, 56.3% were susceptible. For F18, susceptibility reached 93.7%. Crucially, the two F4 markers disagreed: the study found significant disagreement between MUC4 and CHCF1 results (P<0.001), leaving practitioners and breeders without a single reliable test for F4 susceptibility.

Despite that disagreement, the markers still predicted shedding. Pigs classified as F4-susceptible by MUC4 were more likely to shed E. coli F4 (OR=3.3; P=0.02); those classified by CHCF1 showed a similar trend (OR=2.8; P=0.06). Genetic susceptibility, in other words, translated into a measurable microbiological outcome.

For swine practitioners, the study offers three take-homes. First, virulence-gene carriage is widespread in apparently healthy pigs, so control programs built solely around clinical cases will miss reservoirs. Second, the virotype diversity — 52 profiles in a single study population — argues for farm-level genotyping before committing to autogenous or commercial vaccines, an area with no new regulatory action noted here but direct relevance to vaccine selection. Third, with F18 susceptibility approaching universality in this population and F4 susceptibility between roughly 43% and 56% depending on the marker used, genetic selection for resistant animals is a realistic lever, as the authors themselves conclude.

The researchers state that the findings will help develop an effective E. coli vaccine and can support breeding of E. coli-resistant pigs. With the F4 marker discrepancy now documented, resolving which test better predicts field susceptibility stands as the next step toward putting that tool in practice.