Core genome multilocus sequence typing reveals an endemic Salmonella Enteritidis infection common to fox, cattle, and swine farms in Finland

Salmonella Enteritidis infections started to appear in fox farms in Finland in 2002, but it was not until 2014 when S. Enteritidis emerged on cattle and swine farms. S. Enteritidis is also a common finding from dead hedgehogs throughout the country. In this study, we used core genome multilocus sequence typing (cgMLST) to investigate the epidemiology of S. Enteritidis infection. We analyzed 147 isolates collected from animals between 2014 and 2022, as well as two isolates from 2002. All isolates from fox and swine farms and 86 % of those from cattle farms clustered together, suggesting a diffuse and gradual spread of the infection during 2014–2020. In 2021, an outbreak of S. Enteritidis occurred on fox farms, followed by an increase in cases on cattle farms in the fox farming region in 2022. The outbreak in foxes was caused by an endemic strain that had been circulating within animal units before spreading widely in 2021. These findings suggest an endemic S. Enteritidis infection in the fox farming area. The infection is most likely transmitted from infected fox farms to cattle and swine farms via pests, such as rodents and birds. To prevent the spread of infection, better biosecurity measures and improved production hygiene should be implemented in fox farming. Isolates from hedgehogs were genetically distinct from those obtained from other animals. They were highly homogeneous and formed their own cgMLST cluster. All the Finnish isolates, including those from hedgehogs, belonged to ST11 according to classic MLST.