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

Nicholas A Feasey (1, 2, 3) , James Hadfield (2) , Karen H Keddy (4, 5) , Timothy J Dallman (6) , Jan Jacobs (7, 8) , Xiangyu Deng (9) , Paul Wigley (3) , Lars Barquist , Gemma C Langridge (2) , Theresa Feltwell (2) , Simon Harris (2) , Alison E Mather (2) , Maria Fookes (2) , Martin Aslett (2) , Chisomo Msefula , Samuel Kariuki , Calman A Maclennan (2) , Robert S Onsare , François-Xavier Weill (10) , Simon Le Hello (10) , Anthony M Smith (5, 11) , Michael Mcclelland (12) , Prerak Desai (12) , Christopher M Parry (1, 13, 14) , John Cheesbrough , Neil French (3) , Josefina Campos (15) , Jose A Chabalgoity , Laura Betancor , Katie L Hopkins , Satheesh Nair (6) , Tom J Humphrey , Octavie Lunguya (16, 17) , Tristan A Cogan (18) , Milagritos D Tapia (19) , Samba O Sow (20) , Sharon M Tennant (19) , Kristin Bornstein (19) , Myron M Levine (19) , Lizeth Lacharme-Lora (3) , Dean B Everett (3) , Robert A Kingsley (2, 21) , Julian Parkhill (2) , Robert S Heyderman (22) , Gordon Dougan (2) , Melita A Gordon (3) , Nicholas R Thomson (2, 14)

1 LSTM - Liverpool School of Tropical Medicine
2 The Wellcome Trust Sanger Institute [Cambridge]
3 University of Liverpool
4 WITS - University of the Witwatersrand [Johannesburg]
5 NICD - National Institute for Communicable Diseases [Johannesburg]
6 Public Health England [London]
7 KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven
8 ITM - Institute of Tropical Medicine [Antwerp]
9 CDC - Centers for Disease Control and Prevention [Atlanta]
10 CNR-ESS - Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella
11 Plymouth University
12 UC Irvine - University of California [Irvine]
13 LSHTM - London School of Hygiene and Tropical Medicine
14 Nagasaki University
15 ANLIS - Administración Nacional de Laboratorios e Institutos de Salud ‘Carlos Malbran'
16 INRB - Institut National de Recherche Biomédicale [Kinshasa]
17 UNIKIN - University of Kinshasa
18 University of Bristol [Bristol]
19 University of Maryland School of Medicine
20 Centre pour le Développement des Vaccins [Mali]
21 Institute of Food Research [Norwich]
22 UCL - University College of London [London]

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.

Domains: Life Sciences [q-bio]; Santé publique et épidémiologie

Nicholas A Feasey, James Hadfield, Karen H Keddy, Timothy J Dallman, Jan Jacobs, et al.. Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.. Nature Genetics, 2016, 48 (10), pp.1211-7. ⟨10.1038/ng.3644⟩. ⟨pasteur-01421619⟩