Outbreaks of salmonellosis in Danish pig herds caused by Salmonella Choleraesuis var. Kunzendorf – the use of pulsed-field gel electrophoresis and whole genome sequencing for outbreak investigation

So far, most epidemiological investigations on S. Choleraesuis have been done using biotyping and pulsed-field gel electrophoresis (PFGE) (ref). More recently, also the use of multilocus sequence typing (MLST) has been suggested as a replacement for serotyping, but in general MLST typing is more applicable for population genetic studies than for outbreak investigations (Achtman et al,. 2012). The genome of strains of S. Choleraesuis has been sequenced (Chiu et al., 2005; Richardson et al., 2011). Results by Chiu et al. (2005) showed that S. Choleraesuis has a genome size of 4.6 Mb and contains several pseudogenes, which suggests host adaptation. In the present study we describe outbreaks of salmonellosis in pig farms in Denmark, and the use of both PFGE and whole genome sequencing as tools for the outbreak investigation. In has neither in relation to the Danish outbreak in 1999 (Baggesen et al., 2000) nor to the outbreaks in 2012/2013 been possible to identify the primarily introduction of infection to the Danish pig herds. This may have been coursed by limitation in the epidemiological information available but also by an insufficient resolution of isolates by the epidemiological typing methods applied (mainly PFGE). The main goal of this study is therefore to evaluate whether application of whole genome sequence based analysis can improve the resolution of isolates in a way where the outbreak investigation on S. Choleraesuis is strengthened.