Monitoring of prevalence and persistence of Salmonella and resistant E. coli strains isolated from pig farms

Salmonella is the second most commonly reported zoonotic. Pork is considered, one of the major sources of human infections. Salmonella control on-farms remains a significant challenge, therefore the first objective of this thesis was to address the role of wild birds and environmental contamination in the epidemiology of Salmonella in one outdoor pig farm. This study suggests that wild bird populations are capable of recycling the infection and contributing to the persistence of Salmonella between batches of pigs. Additionally, the results showed that the environment itself can become a potential source of infection for subsequent batches of pigs and wildlife. To help monitor Salmonella, a literature review was conducted on alternative diagnostic media to blood samplings, such as oral fluid (OF) and meat juice. This review highlighted the promising use of the OF for diagnosis and surveillance of important in pig farms. Therefore, two more field studies were conducted aiming to adapt a commercial ELISA test for the detection of anti-Salmonella antibodies in pigs OF and to assess the reliably of the results against the gold standard. These two investigations provide evidence that OF may represent a simple, cheap and non-invasive, alternative to serum for the diagnosis of anti-Salmonella IgG in pigs. This thesis also provides valuable additional information on resistant bacteria. The last study of this thesis is a longitudinal field investigation aimed to investigate the prevalence and mechanisms of antimicrobial resistance(AMR) in E. coli strains recovered from a pig farm, following the suspension of group antibiotic treatment. The current study shows encouraging evidence of reductions in resistant E. coli strains. However, WGS analysis uncovered evidence of the presence in environmental samples of clones circulating in the animals, indicating a possible role of the environment might in the persistence of AMR bacteria in pig farms.