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OHEJP Project: BIOPIGEE Pigs are a reservoir of hepatitis E virus (HEV), which causes hepatitis in humans. To study the epidemiology of HEV in pig farms, sampling methods are currently used that cause discomfort to pigs, such as rectal sampling. In line with the 3Rs principle, we aimed to evaluate non-invasive methods to detect pens with HEV-shedding pigs. Twenty-eight pens of one farm were sampled cross-sectionally. Individual rectal swabs (IRS) were collected to determine prevalence within pens. Four pen-level samples were compared: a pool of IRS per pen (P), boot socks (BS), oral fluid (OF) and pooled faecal droppings (FD). Each sample was tested by RT-PCR and the sensitivity and specificity of each method was determined by Bayesian latent class analysis. According to IRS, 19/28 pens were HEV positive. BS had a sensitivity of 95% and detected HEV in pens with 10% of pigs shedding; however, specificity was below 30%. FD were comparably accurate to P, with a sensitivity and specificity of 94% and 86%, respectively. BS sampling is thus advised to detect early shedding of HEV or pen contamination, and FD to determine the duration of shedding. This study demonstrates that non-invasive sampling can replace rectal swabs in research on HEV in pigs.

Background. The use of antibiotics in food production selects for resistant bacteria and may cause a threat to human and animal health. Belgium and the Netherlands have one of the highest densities of broilers and pigs in Europe, making active monitoring of antibiotic use and resistance in this region vital. Objectives. This study aimed to quantify ESBL-producing (ESBL-E. coli), carbapenem- and ciprofloxacin-resistant (CiproR) Escherichia coli in animal feces on broiler and pig farms with a history of high antibiotic use in Belgium and the Netherlands. Methods. A total of 779 broiler and 817 pig fecal samples, collected from 29 conventional broiler and 31 multiplier pig farms in the cross-border region of Belgium and the Netherlands, were screened for the presence of antibiotic-resistant E. coli using selective culturing. Results. Carbapenem-resistant E. coli were not detected. ESBL-E. coli were remarkably more prevalent in samples from Belgian than Dutch farms. However, CiproR-E. coli were highly prevalent in broilers of both countries. The percentage of samples with ESBL- and CiproR-E. coli was lower in pig compared to poultry farms and varied between farms. No clear association with the on-farm antibiotic use in the year preceding sampling was observed. Multidrug resistance was frequently observed in samples from both countries, but ESBL-production in combination with ciprofloxacin resistance was higher in samples from Belgium. Conclusions. This study demonstrated marked differences in antibiotic resistance between countries, farms and within farms. The observed variation cannot be explained straightforward by prior quantity of antibiotic use suggesting that it results from more complex interactions that warrant further investigation.

Hepatitis E virus (HEV) can be transmitted from pigs to humans and cause liver inflammation. Pigs are a major reservoir of HEV and most slaughter pigs show evidence of infection by presence of antibodies (ELISA) or viral RNA (PCR). Reducing the number of HEV infected pigs at slaughter would likely reduce human exposure, yet how this can be achieved, is unknown. We aimed to identify and quantify the effect of biosecurity measures to deliver HEV negative batches of pigs to slaughter. A case-control study was performed with Dutch pig farms selected based on results of multiple slaughter batches. Case farms delivered at least one PCR and ELISA negative batch to slaughter (PCR−ELISA−), indicating absence of HEV infection, and control farms had the highest proportion of PCR and/or ELISA positive batches (PCR+ELISA+), indicating high within-farm transmission. Data about biosecurity and housing were collected via a questionnaire and an audit. Variables were selected by regularization (LASSO regression) and ranked, based the frequency of variable selection. The odds ratios (OR) for the relation between case-control status and the highest ranked variables were determined via grouped logistic regression. Thirty-five case farms, with 10 to 60% PCR−ELISA− batches, and 38 control farms with on average 40% PCR+ELISA+ batches, were included. Rubber and steel floor material in fattening pens had the highest ranking and increased the odds of a PCR−ELISA− batch by 5.87 (95%CI 3.03–11.6) and 7.13 (95%CI 3.05–16.9) respectively. Cleaning pig driving boards weekly (OR 1.99 (95%CI 1.07–3.80)), and fly control with predatory flies (OR 4.52 (95%CI 1.59–13.5)) were protective, whereas a long fattening period was a risk. This study shows that cleaning and cleanability of floors and fomites and adequate fly control are measures to consider for HEV control in infected farms. Yet, intervention studies are needed to confirm the robustness of these outcomes.