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Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Elisabeth Njamkepo 1 Nizar Fawal 1 Alicia Tran-Dien 1 Jane Hawkey Nancy Strockbine Claire Jenkins Kaisar A Talukder Raymond Bercion 2, 3 Konstantin Kuleshov Renáta Kolínská Julie E Russell Lidia Kaftyreva 4 Marie Accou-Demartin 1 Andreas Karas Olivier Vandenberg Alison E Mather Carl J Mason Andrew J Page Anne-Laure Page Thandavarayan Ramamurthy Chantal Bizet 5 Andrzej Gamian Isabelle Carle 1 Amy Gassama Sow 3 Christiane Bouchier 6 Astrid Louise Wester Monique Lejay-Collin 1 Marie-Christine Fonkoua 7 Simon Le Hello 1 Martin Blaser Cecilia Jernberg Corinne Ruckly 1 Audrey Mérens 8 Martin Aslett Peter Roggentin Angelika Fruth Erick Denamur Malabi Venkatesan Hervé Bercovier Ladaporn Bodhidatta Chien-Shun Chiou Dominique Clermont 5 Bianca Colonna 9 Svetlana Egorova 4 Gururaja P Pazhani Analia V Ezernitchi Ghislaine Guigon 10 Simon R Harris Hidemasa Izumiya Agnieszka Korzeniowska-Kowal Anna Lutyńska Malika Gouali 1 Francine Grimont 1 Céline Langendorf Monika Marejková Lorea a M Peterson Guillermo Perez-Perez Antoinette Ngandjio 7 Alexander Podkolzin Erika Souche 11 Mariia Makarova 4 German A Shipulin Changyun Ye Helena Žemličková Mária Herpay Patrick a D Grimont 1 Julian Parkhill 12 Philippe Sansonetti 13, 14 Kathryn E Holt Sylvain Brisse 10, 15 Nicholas R Thomson 12 François-Xavier Weill 1, 12, *
* Corresponding author
1 BPE - Bactéries pathogènes entériques
2 Institut Pasteur de Bangui
3 Institut Pasteur de Dakar
4 Institut Pasteur de Saint-Pétersbourg
5 CIP - Collection de l'Institut Pasteur
6 Génomique (Plate-Forme) - Genomics Platform
7 Centre Pasteur du Cameroun
8 Hôpital d'Instruction des Armées Begin
9 Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti
10 PF8 - Génotypage des Pathogènes et Santé Publique (Plate-forme)
11 C3BI - Centre de Bioinformatique, Biostatistique et Biologie Intégrative
12 The Wellcome Trust Sanger Institute [Cambridge]
13 Pathogénie microbienne moléculaire
14 Chaire Microbiologie et Maladies infectieuses
15 Génomique évolutive des Microbes / Microbial Evolutionary Genomics
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.
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Elisabeth Njamkepo, Nizar Fawal, Alicia Tran-Dien, Jane Hawkey, Nancy Strockbine, et al.. Global phylogeography and evolutionary history of Shigella dysenteriae type 1.. Nature Microbiology, Nature Publishing Group, 2016, 1 (4), pp.16027. ⟨10.1038/NMICROBIOL.2016.27⟩. ⟨pasteur-01422023⟩

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