Salmonella in Irish pig farms; prevalence, antibiotic resistance and molecular epidemiology

The objective was to examine the prevalence of Salmonella in manure from 30 Irish pig farms and to characterize any recovered isolates in order to assess potential risks and epidemiological relationships. Salmonella was detected in the manure from finisher pigs in 50% of the herds investigated. S. Typhimurium was the predominant serotype recovered and the most common phage types were DT104 and DT104b. Nineteen of the 29 Salmonella isolates recovered were resistant to one or more antibiotics and 15 of these (all Typhimurium) were multi-resistant. Molecular analysis revealed 19 PFGE types and facilitated tracking of isolates across farms. Overall, Salmonella prevalence correlated well with Irish findings from an EU-wide study of pig production holdings conducted in 2008 (47.7%). The high level of antibiotic resistance observed among the porcine isolates is a concern, but not uncommon in S. Typhimurium. Introduction Pigs are well recognized as carriers of Salmonella and transmission of the pathogen to humans via carcass contamination at slaughter is a major food safety concern (Boyen et al., 2008). A number of baseline surveys have been conducted to determine the prevalence of Salmonella in pigs. In 2008, a European Food Safety Authority (EFSA) study found that 33.3% of pig production holdings in the EU were positive for Salmonella (EFSA, 2009). However, Ireland had a much higher prevalence (47.7%); in fact it was the third highest in the EU. Because of the high prevalence of Salmonella in pigs, a number of countries have introduced Salmonella surveillance and control programmes. In Ireland, a monitoring and control programme was first established in 2002. Monitoring is based on determining the Salmonella status of pig herds by serological testing of meat juice at slaughter and not bacteriological testing. In the past, if less than 10% of samples were positive the herd was classed as Category 1; if 11-49% of samples were positive it was categorized as 2 and if greater than 50% of samples were positive it was a category 3 herd. However, a revised national pig Salmonella control programme was implemented in Ireland in January 2010. Monitoring is still based on serological testing of meat juice samples but there are now only two categories; 1 (< 50% prevalence) and 2 (> 50% prevalence). While some studies have investigated Salmonella carriage in Irish pig herds, none to date have performed molecular as well as phenotypic analysis on the Salmonella recovered. The objectives of this study were (1) to determine the prevalence of Salmonella in finisher pigs from a sample of Irish pigs farms representing different Salmonella categories and (2) to characterize any Salmonella isolates recovered, both phenotypically and genotypically in order to identify predominant isolates and thereby assess potential risks as well as epidemiological relationships. Materials and Methods Pig manure sampling A total of 30 manure samples were collected from the finisher houses of commercial pig farms in Ireland between January 2009 and March 2010. Farms were chosen based on their categorization within the initial (pre-2010) Irish National Salmonella Control Programme. It should therefore be noted that any reference to farm categories in this study refers to this historical categorization system (as outlined above). Ten farms were sampled from each of Categories 1, 2 and 3. Samples (~100 ml) were obtained from manure storage tanks situated directly underneath finisher houses at a depth of