title: Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
abstract: Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Elisabeth
authors: E
authors: Njamkepo
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Nizar
authors: N
authors: Fawal
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Alicia
authors: A
authors: Tran-Dien
authors: Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.|Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.|School of Agriculture and Veterinary Science, University of Melbourne, Parkville, Victoria 3010, Australia.
authors: Jane
authors: 0000-0001-9661-5293
authors: J
authors: Hawkey
authors: Centers for Disease Control and Prevention, Escherichia and Shigella Reference Unit, Atlanta, Georgia 30333, USA.
authors: Nancy
authors: N
authors: Strockbine
authors: Public Health England, Gastrointestinal Bacteria Reference Unit, Colindale NW9 5HT, UK.
authors: Claire
authors: C
authors: Jenkins
authors: icddr,b, Enteric and Food Microbiology Laboratory, Dhaka 1212, Bangladesh.
authors: Kaisar A
authors: KA
authors: Talukder
authors: Institut Pasteur de Bangui, BP 923, Bangui, République Centrafricaine.|Institut Pasteur de Dakar, BP 220, Dakar, Senegal.
authors: Raymond
authors: R
authors: Bercion
authors: Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia.
authors: Konstantin
authors: K
authors: Kuleshov
authors: Czech National Collection of Type Cultures (CNCTC), National Institute of Public Health, Prague 10, Czech Republic.
authors: Renáta
authors: R
authors: Kolínská
authors: Public Health England, National Collection of Type Cultures, Porton Down SP4 0JG, UK.
authors: Julie E
authors: JE
authors: Russell
authors: Pasteur Institute of St Petersburg, St Petersburg 197101, Russia.
authors: Lidia
authors: L
authors: Kaftyreva
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Marie
authors: M
authors: Accou-Demartin
authors: Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4041, South Africa.
authors: Andreas
authors: A
authors: Karas
authors: Department of Microbiology, LHUB-ULB, Brussels University Hospitals Laboratory, 1000 Brussels, Belgium.|Environmental Health Research Centre, Public Health School, Université Libre de Bruxelles, 1070 Brussels, Belgium.
authors: Olivier
authors: O
authors: Vandenberg
authors: Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.|Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
authors: Alison E
authors: AE
authors: Mather
authors: Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand.
authors: Carl J
authors: 0000-0002-3676-2811
authors: CJ
authors: Mason
authors: Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
authors: Andrew J
authors: AJ
authors: Page
authors: National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal 700010, India.
authors: Thandavarayan
authors: T
authors: Ramamurthy
authors: Institut Pasteur, Collection de l'Institut Pasteur (CIP), 75724 Paris Cedex 15, France.
authors: Chantal
authors: C
authors: Bizet
authors: Polish Collection of Microorganisms, Institute of Immunology and Experimental Therapy, 53-114 Wroclaw, Poland.
authors: Andrzej
authors: A
authors: Gamian
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Isabelle
authors: I
authors: Carle
authors: Institut Pasteur de Dakar, BP 220, Dakar, Senegal.
authors: Amy Gassama
authors: AG
authors: Sow
authors: Institut Pasteur, Plate-forme Génomique (PF1), 75724 Paris Cedex 15, France.
authors: Christiane
authors: C
authors: Bouchier
authors: Department of Foodborne Infections, Norwegian Institute of Public Health, Nydalen 0403, Oslo, Norway.
authors: Astrid Louise
authors: AL
authors: Wester
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Monique
authors: M
authors: Lejay-Collin
authors: Centre Pasteur du Cameroun, BP 1274, Yaoundé, Cameroon.
authors: Marie-Christine
authors: MC
authors: Fonkoua
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Simon
authors: S
authors: Le Hello
authors: Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, New York 10016, USA.
authors: Martin J
authors: MJ
authors: Blaser
authors: Public Health Agency of Sweden, 17182 Solna, Sweden.
authors: Cecilia
authors: C
authors: Jernberg
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Corinne
authors: C
authors: Ruckly
authors: Biology Department and Infection Control Unit, Bégin Military Hospital, 94160 Saint-Mandé, France.
authors: Audrey
authors: A
authors: Mérens
authors: Epicentre, 75011 Paris, France.
authors: Anne-Laure
authors: AL
authors: Page
authors: Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
authors: Martin
authors: M
authors: Aslett
authors: Institut für Hygiene und Umwelt, 20539 Hamburg, Germany.
authors: Peter
authors: P
authors: Roggentin
authors: Divison of Enteropathogenic Bacteria and Legionella, Robert Koch Institut, 38855 Wernigerode, Germany.
authors: Angelika
authors: A
authors: Fruth
authors: INSERM, IAME, UMR 1137, Univ. Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, 75018 Paris, France.
authors: Erick
authors: E
authors: Denamur
authors: Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA.
authors: Malabi
authors: M
authors: Venkatesan
authors: Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
authors: Hervé
authors: H
authors: Bercovier
authors: Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand.
authors: Ladaporn
authors: L
authors: Bodhidatta
authors: Center of Research and Diagnostics, Centers for Disease Control, Taichung 40855, Taiwan.
authors: Chien-Shun
authors: CS
authors: Chiou
authors: Institut Pasteur, Collection de l'Institut Pasteur (CIP), 75724 Paris Cedex 15, France.
authors: Dominique
authors: D
authors: Clermont
authors: Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie C Darwin, Sapienza Università di Roma, 00185, Roma, Italy.
authors: Bianca
authors: B
authors: Colonna
authors: Pasteur Institute of St Petersburg, St Petersburg 197101, Russia.
authors: Svetlana
authors: S
authors: Egorova
authors: National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal 700010, India.
authors: Gururaja P
authors: GP
authors: Pazhani
authors: Central Laboratories, Ministry of Health, Jerusalem 91342, Israel.
authors: Analia V
authors: AV
authors: Ezernitchi
authors: Institut Pasteur, Genotyping of Pathogens and Public Health Platform, 75724 Paris Cedex 15, France.
authors: Ghislaine
authors: G
authors: Guigon
authors: Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
authors: Simon R
authors: 0000-0003-1512-6194
authors: SR
authors: Harris
authors: Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
authors: Hidemasa
authors: H
authors: Izumiya
authors: Polish Collection of Microorganisms, Institute of Immunology and Experimental Therapy, 53-114 Wroclaw, Poland.
authors: Agnieszka
authors: 0000-0001-7569-8018
authors: A
authors: Korzeniowska-Kowal
authors: Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 00-791 Warsaw, Poland.
authors: Anna
authors: A
authors: Lutyńska
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Malika
authors: M
authors: Gouali
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Francine
authors: F
authors: Grimont
authors: Epicentre, 75011 Paris, France.
authors: Céline
authors: C
authors: Langendorf
authors: National Reference Laboratory for E. coli and Shigella, National Institute of Public Health, Prague 10, Czech Republic.
authors: Monika
authors: M
authors: Marejková
authors: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada.
authors: Lorea A M
authors: LA
authors: Peterson
authors: Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, New York 10016, USA.
authors: Guillermo
authors: G
authors: Perez-Perez
authors: Centre Pasteur du Cameroun, BP 1274, Yaoundé, Cameroon.
authors: Antoinette
authors: A
authors: Ngandjio
authors: Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia.
authors: Alexander
authors: A
authors: Podkolzin
authors: Institut Pasteur, Bioinformatics platform, 75724 Paris Cedex 15, France.
authors: Erika
authors: E
authors: Souche
authors: Pasteur Institute of St Petersburg, St Petersburg 197101, Russia.
authors: Mariia
authors: M
authors: Makarova
authors: Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia.
authors: German A
authors: GA
authors: Shipulin
authors: State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing 102206, China.
authors: Changyun
authors: C
authors: Ye
authors: Czech National Collection of Type Cultures (CNCTC), National Institute of Public Health, Prague 10, Czech Republic.|Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, 500 05, Hradec Kralove, Czech Republic.
authors: Helena
authors: H
authors: Žemličková
authors: Hungarian National Collection of Medical Bacteria, National Center for Epidemiology, H-1097 Budapest, Hungary.
authors: Mária
authors: M
authors: Herpay
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.
authors: Patrick A D
authors: PA
authors: Grimont
authors: Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
authors: Julian
authors: 0000-0002-7069-5958
authors: J
authors: Parkhill
authors: Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 75724 Paris Cedex 15, France.
authors: Philippe
authors: P
authors: Sansonetti
authors: Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.|Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
authors: Kathryn E
authors: 0000-0003-3949-2471
authors: KE
authors: Holt
authors: Institut Pasteur, Genotyping of Pathogens and Public Health Platform, 75724 Paris Cedex 15, France.|Institut Pasteur, Microbial Evolutionary Genomics Unit, 75724 Paris Cedex 15, France.|CNRS, UMR 3525, 75015 Paris, France.
authors: Sylvain
authors: S
authors: Brisse
authors: Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.|London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors: Nicholas R
authors: NR
authors: Thomson
authors: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.|Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
authors: François-Xavier
authors: FX
authors: Weill
mesh_terms: D024881:Drug Resistance, Bacterial; D004405:Dysentery, Bacillary / Q000453:epidemiology* / Q000266:history / Q000382:microbiology*; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D014943:Global Health; D049672:History, 19th Century; D049673:History, 20th Century; D049674:History, 21st Century; D006801:Humans; D017720:Molecular Epidemiology; D058974:Phylogeography; D017422:Sequence Analysis, DNA; D065288:Serogroup; D012762:Shigella dysenteriae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*