Morgane Salines

Le virus de l’hépatite E (HEV) est un agent zoonotique dont les porcs représentent le principal réservoir dans les pays industrialisés. Le présent projet de recherche a combiné études épidémiologiques, modélisation mathématique et sciences sociales pour proposer des leviers de réduction du risque d’exposition humaine au HEV par consommation de produits à base de porc. Deux essais expérimentaux et une étude en conditions naturelles ont mis en évidence le rôle majeur des co-infections immunomodulatrices dans la dynamique de l’infection par le HEV chez le porc, ces pathogènes intercurrents conduisant à une infection chronique par le HEV et à un risque augmenté de présence du virus dans le foie, le sang et les muscles des animaux abattus. Le développement d’un modèle intra-élevage, stochastique, individu-centré et multi-pathogènes, a permis de dégager des pistes de maîtrise à la fois zootechniques et sanitaires pour réduire la prévalence du virus en élevage. En complément, la conception d’un modèle inter-troupeaux a rendu possible l’analyse des facteurs de diffusion du virus dans un réseau d’élevages français. L’ensemble de ces mesures de gestion du HEV a été soumis à l’avis des organisations publiques et privées et des acteurs individuels de la filière porcine (éleveurs, conseillers, vétérinaires) par des approches de sciences humaines et sociales. Finalement, ce projet transversal et multi-disciplinaire a permis de définir des axes d’action tangibles et réalisables de gestion du HEV dans la filière porcine tout en apportant des contributions méthodologiques significatives en épidémiologie et en modélisation.

Interventions from lairage to the chilling stage of the pig slaughter process are important to reduce microbial contamination of carcasses. The aim of this systematic review and meta-analysis was to assess the effectiveness of abattoir interventions in reducing aerobic colony count (ACC), Enterobacteriaceae, generic Escherichia coli, and Yersinia spp. on pig carcasses. The database searches spanned a 30 year period from 1990 to 2021. Following a structured, predefined protocol, 22 articles, which were judged as having a low risk of bias, were used for detailed data extraction and meta-analysis. The meta-analysis included data on lairage interventions for live pigs, standard processing procedures for pig carcasses, prechilling interventions, multiple carcass interventions, and carcass chilling. Risk ratios (RRs) for prevalence studies and mean log differences (MDs) for concentration outcomes were calculated using random effects models. The meta-analysis found that scalding under commercial abattoir conditions effectively reduced the prevalence of Enterobacteriaceae (RR: 0.05, 95% CI: 0.02 to 0.12, I² = 87%) and ACC (MD: −2.84, 95% CI: −3.50 to −2.18, I² = 99%) on pig carcasses. Similarly, significant reductions of these two groups of bacteria on carcasses were also found after singeing (RR: 0.25, 95% CI: 0.14 to 0.44, I² = 90% and MD: −1.95, 95% CI: −2.40 to −1.50, I² = 96%, respectively). Rectum sealing effectively reduces the prevalence of Y. enterocolitica on pig carcasses (RR: 0.60, 95% CI: 0.41 to 0.89, I² = 0%). Under commercial abattoir conditions, hot water washing significantly reduced ACC (MD: −1.32, 95% CI: −1.93 to −0.71, I² = 93%) and generic E. coli counts (MD: −1.23, 95% CI: −1.89 to −0.57, I² = 61%) on pig carcasses. Conventional dry chilling reduced Enterobacteriaceae prevalence on pig carcasses (RR: 0.32, 95% CI: 0.21 to 0.48, I² = 81%). Multiple carcass interventions significantly reduced Enterobacteriaceae prevalence (RR: 0.11, 95% CI: 0.05 to 0.23, I² = 94%) and ACC on carcasses (MD: −2.85, 95% CI: −3.33 to −2.37, I² = 97%). The results clearly show that standard processing procedures of scalding and singeing and the hazard-based intervention of hot water washing are effective in reducing indicator bacteria on pig carcasses. The prevalence of Y. enterocolitica on pig carcasses was effectively reduced by the standard procedure of rectum sealing; nevertheless, this was the only intervention for Yersinia investigated under commercial conditions. High heterogeneity among studies and trials investigating interventions and overall lack of large, controlled trials conducted under commercial conditions suggest that more in-depth research is needed.

Hepatitis E virus is a zoonotic pathogen for which pigs are recognized as the major reservoir in industrialised countries. A multiscale model was developed to assess the HEV transmission and persistence pattern in the pig production sector through an integrative approach taking into account within-farm dynamics and animal movements based on actual data. Within-farm dynamics included both demographic and epidemiological processes. Direct contact and environmental transmission routes were considered along with the possible co-infection with immunomodulating viruses (IMVs) known to modify HEV infection dynamics. Movements were limited to 3,017 herds forming the largest community on the swine commercial network in France and data from the national pig movement database were used to build the contact matrix. Between-herd transmission was modelled by coupling within-herd and network dynamics using the SimInf package. Different introduction scenarios were tested as well as a decrease in the prevalence of IMV-infected farms. After introduction of a single infected gilt, the model showed that the transmission pathway as well as the prevalence of HEV-infected pigs at slaughter age were affected by the type of the index farm, the health status of the population and the type of the infected farms. These outcomes could help design HEV control strategies at a territorial scale based on the assessment of the farms’ and network’s risk.

Hepatitis E virus (HEV) is a zoonotic pathogen, in particular genotype 3 HEV is mainly transmitted to humans through the consumption of contaminated pork products. This study aimed at describing HEV infection patterns in pig farms and at assessing the impact of immunomodulating co‐infections namely Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Porcine Circovirus Type 2 (PCV2), as well as other individual factors such as piglets’ immunity and litters’ characteristics on HEV dynamics. A longitudinal follow‐up was conducted in three farrow‐to‐finish farms known to be HEV infected. Overall, 360 piglets were individually monitored from birth to slaughter with regular blood and faecal sampling as well as blood and liver samples collected at slaughterhouse. Virological and serological analyses were performed to detect HEV, PCV2 and PRRSV genome and antibodies. The links between 12 explanatory variables and four outcomes describing HEV dynamics were assessed using cox‐proportional hazard models and logistic regression. HEV infection dynamics was found highly variable between farms and in a lower magnitude between batches. HEV positive livers were more likely related to short time‐intervals between HEV infection and slaughter time (< 40 days, OR=4.1 [3.7‐4.5]). In addition to an influence of piglets’ sex and sows’ parity, the sequence of co‐infections was strongly associated with different HEV dynamics: a PRRSV or PCV2/PRRSV pre‐ or co‐infection was associated with a higher age at HEV shedding (Hazard Ratio=0.3 [0.2‐0.5]), as well as a higher age at HEV seroconversion (HR=0.5 [0.3‐0.9] and HR=0.4 [0.2‐0.7], respectively). A PCV2/PRRSV pre‐ or co‐infection was associated with a longer duration of shedding (HR=0.5 [0.3‐0.8]). Consequently, a PRRSV or PCV2/PRRSV pre‐ or co‐infection was strongly associated with a higher risk of having positive livers at slaughter (OR=4.1 [1.9‐8.9] and OR=6.5 [3.2‐13.2], respectively). In conclusion, co‐infections with immunomodulating viruses were found to affect HEV dynamics in the farrow‐to‐finish pig farms that were followed in the present study.