Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

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, whilst in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case-fatality. Whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries reveals the existence of a global epidemic clade and two novel clades of S. Enteritidis that are each geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire and have 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.