Genomic epidemiology of Salmonella Enteritidis human infections in the Netherlands, 2019 to 2023.

Salmonella enterica serotype Enteritidis (SE) is a common foodborne pathogen that can cause human salmonellosis. Identifying closely related cases is essential to control the pathogen through, e.g. outbreak investigation, but it is often challenging due to the low genetic diversity of SE, particularly with traditional typing methods. This study aimed to investigate the population structure of SE genomes collected during routine surveillance in the Netherlands using whole-genome sequencing (WGS), their clustering, temporal distribution and the association between epidemiological and phenotypic antimicrobial resistance (AMR) factors and the persistence of SE clusters. We also investigated the distribution of genotypic AMR markers among these isolates. The study collection comprised 1,669 unique SE isolates from human infections collected from Dutch surveillance between 2019 and 2023, and their relatedness was derived using core-genome multi-locus sequence typing and Hamming distances. Based on the results, the 216 clusters comprised 1,085 sequences, in addition to 584 sequences depicted as singletons. These clusters predominantly fell within three major lineages, of which two were the previously described Global and Atlantic lineages. Of these clusters, approximately a third persisted for more than 1 year during the 5-year study period. However, no statistically significant associations were found between epidemiological factors, such as age, gender and travel history, or phenotypic AMR and the persistence of SE clusters. The most common AMR genetic markers observed were related to antimicrobial classes of (fluor)quinolones, β-lactamases and aminoglycosides. This study provides a better understanding of the genomic epidemiology of SE in the Netherlands based on WGS. Further analysis that includes samples from the food-chain supply, along with higher resolution methods during a post-Coronavirus Disease of 2019 (COVID-19) period, may provide more insights into the possible causes of the persistence of SE clusters.