Global population genomics of Salmonella enterica serotype Napoli, an emerging pathogen with an unusual epidemiologic pattern

We characterised the population structure of Salmonella enterica serotype Napoli ( S. Napoli), an emerging European pathogen. We assembled a collection of 1,320 isolates obtained between 1945 and 2022 from diverse biological sources in Italy, Switzerland, France (regions of known endemicity) and a newly identified endemic area, Spain. Whole-genome analyses linked the rising incidence of S. Napoli to a monophyletic serotype from core genome multilocus typing (cgMLST) superlineage HC2000_1289. The S. Napoli population has considerable genetic diversity, strong spatial structuring, and a very low frequency of antimicrobial resistance determinants. Unlike successful non-typhoidal Salmonella serotypes, for which globalisation has had a homogenising effect, S. Napoli forms at least 15 distinct lineages isolated by geographic distance, each probably subject to local ecological adaptation. This comprehensive description of S. Napoli populations complemented by 12 representative complete genomes provides a valuable resource for future source attribution and surveillance of this serotype.