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

• Published in: Nature genetics Vol. 48; no. 10; pp. 1211 - 1217
• Main Authors: Feasey, Nicholas A, Hadfield, James, Keddy, Karen H, Dallman, Timothy J, Jacobs, Jan, Deng, Xiangyu, Wigley, Paul, Barquist, Lars, Langridge, Gemma C, Feltwell, Theresa, Harris, Simon R, Mather, Alison E, Fookes, Maria, Aslett, Martin, Msefula, Chisomo, Kariuki, Samuel, Maclennan, Calman A, Onsare, Robert S, Weill, François-Xavier, Le Hello, Simon, Smith, Anthony M, McClelland, Michael, Desai, Prerak, Parry, Christopher M, Cheesbrough, John, French, Neil, Campos, Josefina, Chabalgoity, Jose A, Betancor, Laura, Hopkins, Katie L, Nair, Satheesh, Humphrey, Tom J, Lunguya, Octavie, Cogan, Tristan A, Tapia, Milagritos D, Sow, Samba O, Tennant, Sharon M, Bornstein, Kristin, Levine, Myron M, Lacharme-Lora, Lizeth, Everett, Dean B, Kingsley, Robert A, Parkhill, Julian, Heyderman, Robert S, Dougan, Gordon, Gordon, Melita A, Thomson, Nicholas R
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2016; Nature Publishing Group
• Subjects: 631/208/212; 631/326/325; 692/699/255/1318; Adaptation, Biological; Africa South of the Sahara - epidemiology; Agriculture; Analysis; Animal Genetics and Genomics; Animals; Antimicrobial agents; Biomedicine; Cancer Research; Chickens - microbiology; Data collection; Disease; Diseases; Drug resistance; Eggs; Enterocolitis; Enterocolitis - epidemiology; Enterocolitis - microbiology; Enterocolitis - veterinary; Epidemics; Epidemics - economics; Epidemiology; Female; Gastroenteritis; Gene Function; Genome, Bacterial; Genomes; Genomics; Health aspects; Human Genetics; Humans; Income; Industrial production; Investigations; Life Sciences; Malawi; Medical schools; Microbial drug resistance; Novels; Plasmids; Poultry; Poultry Diseases - microbiology; Salmonella; Salmonella enteritidis; Salmonella enteritidis - classification; Salmonella enteritidis - pathogenicity; Salmonella Infections - economics; Salmonella Infections - epidemiology; Salmonella Infections - microbiology; Salmonella Infections - transmission; Santé publique et épidémiologie; Scholarships & fellowships; Sequence Analysis, DNA; Setting (Literature); South Africa; Sub-Saharan Africa; Surveillance; United Kingdom; South Africa; United Kingdom; Malawi; Sub-Saharan Africa; United Kingdom > UK
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/ng.3644

Nicholas Feasey and colleagues report whole-genome sequence analysis of 675 isolates of Salmonella enterica serovar Enteritidis from 45 countries. They find evidence for a global epidemic clade associated with enterocolitis and two novel clades restricted to distinct regions of Africa and associated with invasive disease. 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.