title: Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.
abstract: 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.
authors.affiliation: Liverpool School of Tropical Medicine, Liverpool, UK.|Wellcome Trust Sanger Institute, Cambridge, UK.|Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Feasey
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: James
authors.initials: J
authors.lastname: Hadfield
authors.affiliation: Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Karen H
authors.initials: KH
authors.lastname: Keddy
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, UK.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Dallman
authors.affiliation: Institute of Tropical Medicine, Antwerp, Belgium.|Department of Microbiology and Immunology, University of Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Jacobs
authors.affiliation: Center for Food Safety, Department of Food Science and Technology, University of Georgia.|Centers for Disease Control and Prevention, Atlanta, USA.
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Deng
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Wigley
authors.affiliation: Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Barquist
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Gemma C
authors.initials: GC
authors.lastname: Langridge
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Theresa
authors.initials: T
authors.lastname: Feltwell
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Alison E
authors.initials: AE
authors.lastname: Mather
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Maria
authors.initials: M
authors.lastname: Fookes
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Aslett
authors.affiliation: Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|University of Malawi, The College of Medicine, Blantyre, Malawi.
authors.forename: Chisomo
authors.initials: C
authors.lastname: Msefula
authors.affiliation: Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
authors.forename: Samuel
authors.initials: S
authors.lastname: Kariuki
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.|Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
authors.forename: Calman A
authors.initials: CA
authors.lastname: Maclennan
authors.affiliation: Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Onsare
authors.affiliation: Institut Pasteur, Paris, France.
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Weill
authors.affiliation: Institut Pasteur, Paris, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Le Hello
authors.affiliation: Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa.
authors.forename: Anthony M
authors.initials: AM
authors.lastname: Smith
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: McClelland
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA.
authors.forename: Prerak
authors.initials: P
authors.lastname: Desai
authors.affiliation: Liverpool School of Tropical Medicine, Liverpool, UK.|London School of Hygiene & Tropical Medicine, London, UK.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Parry
authors.affiliation: Department of Epidemiology and Population Health, University of Liverpool, Liverpool, UK.
authors.forename: John
authors.initials: J
authors.lastname: Cheesbrough
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: Neil
authors.initials: N
authors.lastname: French
authors.affiliation: Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina.
authors.forename: Josefina
authors.initials: J
authors.lastname: Campos
authors.affiliation: Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Uruguay.
authors.forename: Jose A
authors.initials: JA
authors.lastname: Chabalgoity
authors.affiliation: Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Uruguay.
authors.forename: Laura
authors.initials: L
authors.lastname: Betancor
authors.affiliation: Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, Public Health England, Colindale, UK.
authors.forename: Katie L
authors.initials: KL
authors.lastname: Hopkins
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, UK.
authors.forename: Satheesh
authors.initials: S
authors.lastname: Nair
authors.affiliation: Swansea Medical School, Swansea University, Swansea, UK.
authors.forename: Tom J
authors.initials: TJ
authors.lastname: Humphrey
authors.affiliation: National Institute of Biomedical Research, Kinshasa, the Democratic Republic of the Congo.|University Hospital of Kinshasa, Kinshasa, the Democratic Republic of the Congo.
authors.forename: Octavie
authors.initials: O
authors.lastname: Lunguya
authors.affiliation: School of Veterinary Sciences, University of Bristol, Bristol, UK.
authors.forename: Tristan A
authors.initials: TA
authors.lastname: Cogan
authors.affiliation: Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA.
authors.forename: Milagritos D
authors.initials: MD
authors.lastname: Tapia
authors.affiliation: Centre pour le Développement des Vaccins, Bamako, Mali.
authors.forename: Samba O
authors.initials: SO
authors.lastname: Sow
authors.affiliation: Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA.
authors.forename: Sharon M
authors.initials: SM
authors.lastname: Tennant
authors.affiliation: Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Bornstein
authors.affiliation: Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA.
authors.forename: Myron M
authors.initials: MM
authors.lastname: Levine
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: Lizeth
authors.initials: L
authors.lastname: Lacharme-Lora
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: Dean B
authors.initials: DB
authors.lastname: Everett
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.|Institute of Food Research, Colney, Norwich, UK.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Kingsley
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|Division of Infection and Immunity, University College London, London, UK.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Heyderman
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.affiliation: Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: Melita A
authors.initials: MA
authors.lastname: Gordon
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.|London School of Hygiene & Tropical Medicine, London, UK.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
mesh_terms: D000220:Adaptation, Biological; D017954:Africa South of the Sahara / Q000453:epidemiology; D000818:Animals; D002645:Chickens / Q000382:microbiology; D004760:Enterocolitis / Q000453:epidemiology / Q000382:microbiology* / Q000662:veterinary; D058872:Epidemics / Q000191:economics; D005260:Female; D016680:Genome, Bacterial; D006801:Humans; D007182:Income; D010957:Plasmids; D011201:Poultry Diseases / Q000382:microbiology; D012480:Salmonella Infections / Q000191:economics / Q000453:epidemiology / Q000382:microbiology* / Q000635:transmission; D012477:Salmonella enteritidis / Q000145:classification / Q000472:pathogenicity; D017422:Sequence Analysis, DNA