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

Nicholas A Feasey ; James Hadfield ; Karen H Keddy ; Timothy J Dallman ; Jan Jacobs ; Xiangyu Deng ; Paul Wigley ; Lars Barquist ; Gemma C Langridge ; Theresa Feltwell ; +37 more... Simon R Harris ; Alison E Mather ; Maria Fookes ; Martin Aslett ; Chisomo Msefula ; Samuel Kariuki ; Calman A Maclennan ; Robert S Onsare ; François-Xavier Weill ; Simon Le Hello ; Anthony M Smith ; Michael McClelland ; Prerak Desai ; Christopher M Parry ; John Cheesbrough ; Neil French ; Josefina Campos ; Jose A Chabalgoity ; Laura Betancor ; Katie L Hopkins ; Satheesh Nair ; Tom J Humphrey ; Octavie Lunguya ; Tristan A Cogan ; Milagritos D Tapia ; Samba O Sow ; Sharon M Tennant ; Kristin Bornstein ; Myron M Levine ; Lizeth Lacharme-Lora ; Dean B Everett ; Robert A Kingsley ; Julian Parkhill ; Robert S Heyderman ; Gordon Dougan ; Melita A Gordon ; Nicholas R Thomson ORCID logo ; (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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