Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.
Feasey NA., Hadfield J., Keddy KH., Dallman TJ., Jacobs J., Deng X., Wigley P., Barquist L., Langridge GC., Feltwell T., Harris SR., Mather AE., Fookes M., Aslett M., Msefula C., Kariuki S., Maclennan CA., Onsare RS., Weill F-X., Le Hello S., Smith AM., McClelland M., Desai P., Parry CM., Cheesbrough J., French N., Campos J., Chabalgoity JA., Betancor L., Hopkins KL., Nair S., Humphrey TJ., Lunguya O., Cogan TA., Tapia MD., Sow SO., Tennant SM., Bornstein K., Levine MM., Lacharme-Lora L., Everett DB., Kingsley RA., Parkhill J., Heyderman RS., Dougan G., Gordon MA., Thomson NR.
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.