Salmonella enterica serovar Derby isolated from eggs show genomic and phenotypic traits that may be linked to inability to produce human infection.

Salmonella enterica serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to S. Enteritidis from contaminated poultry, we conducted a large survey of commercially available eggs, where we isolated many S. Enteritidis strains but surprisingly also a much larger number (ratio 5:1) of S. Derby strains. At that time, reporting of suspected Salmonella-related human infection was mandatory in the country but no single case of S. Derby infection was detected in that period suggesting that the S. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates as well as fifteen isolates from pork or human infection, that were isolated in Uruguay before and after that period. All sequenced strains had the same sequence type ST40, but phylogenomic analysis showed that they clustered in three different groups. All egg isolates clustered together as a monophyletic group and showed marked differences in gene content with the strains in the other two clusters. Differences included absence of genes involved in acid tolerance, heme-uptake, and type VI secretion system, as well as the absence of a C terminal fragment of SpeF protein. We also identified differences in the mobile genetic element contents, the composition of plasmids, insertion sequences, transposons, and phages between egg isolates and human/pork isolates. Mice challenge experiments showed that while mice infected with human/pork isolates died between 1-7 days p.i., all animals infected with the egg strains survived the challenge. Altogether our results suggest that loss of gene functions, and the absence of plasmids in egg isolates may explain why these S. Derby were not capable of producing human infection despite being the main serovar recovered from eggs countrywide.