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; +37 more...Harris, SR; Mather, AE; Fookes, M; Aslett, M; Msefula, C; Kariuki, S; Maclennan, CA; Onsare, RS; Weill, F; 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, NRORCID logo and (2016) Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. Nature genetics, 48 (10). pp. 1211-1217. ISSN 1061-4036 DOI: 10.1038/ng.3644
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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.


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