A Danish Salmonella Bareilly outbreak investigated by the use of whole genome sequencing

In 2012, we saw an increase of the Salmonella serotype Bareilly isolated from human infections. Bareilly is a rare serotype in Denmark, isolated from human infections between 2 and 9 times annually over the last 10 years. As a routine in rare serotypes, we use PFGE as the molecular method for cluster analysis, outbreak investigations, comparison with food and animal isolates as well as making international inquiries. In this case, we found Bareilly with the same PFGE profile from 8 patients. Seven of the cases could be traced back to an unknown food source served at a specific restaurant. At the same time four broiler flocks flocks were tested positive for Bareilly. Bareilly is also rare in the Danish food production, and it was the first time in more than 10 years that Bareilly was isolated in broiler flocks. PFGE was performed on these isolates as well and the profiles from humans and broilers differed by two bands
When using PFGE in outbreak investigation there are some interpretative implications that have to be considered. There are differences on how important band changes are when defining clusters of different serotypes. Some outbreaks have been reported to include PFGE profiles with several band changes and others are defined by one PFGE profile thereby excluding closely related profiles. We decided to investigate whether whole genome sequencing (WGS) could resolve this issue and be useful in outbreak investigations.
Several analyses were performed, including a SNP tree based on the core genome, MLST profiles and detection of phages in the genome. The human cluster and the broiler isolates belonged to the same ST, but the isolates were divided into two groups, 9 SNPs apart, according to an MP phylogeny. When using PHAST, we found that two phage regions were a 100% similar and present in both groups, whereas a third phage region was only present in the human isolates. These data indicate a close common ancestor between the two groups. However, the positive broiler flocks does not seem to be the direct source of the human outbreak.