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An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa.

Original publication

DOI

10.1038/ng.3644

Type

Journal article

Journal

Nat Genet

Publication Date

10/2016

Volume

48

Pages

1211 - 1217

Keywords

Adaptation, Biological, Africa South of the Sahara, Animals, Chickens, Enterocolitis, Epidemics, Female, Genome, Bacterial, Humans, Income, Plasmids, Poultry Diseases, Salmonella Infections, Salmonella enteritidis, Sequence Analysis, DNA