Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Elisabeth Njamkepo,Martin Aslett,Renáta Kolínská,Jane Hawkey,Kaisar A Talukder,Dominique Clermont,Andreas Karas,Martin J Blaser,Antoinette Ngandjio,Amy Gassama Sow,Cecilia Jernberg,Julie E Russell,Isabelle Carle,Nancy Strockbine,Simon Le Hello,Monique Lejay-Collin,Claire Jenkins,Anna Lutyńska,Astrid Louise Wester,Patrick A D Grimont,Olivier Vandenberg,Erick Denamur,Carl J Mason,Helena Žemličková,Francine Grimont,German A Shipulin,Ghislaine Guigon,Ladaporn Bodhidatta,Simon R Harris,Chien-Shun Chiou,Nicholas R Thomson,Malika Gouali,Audrey Mérens,Sylvain Brisse,Marie Accou-Demartin,Peter Roggentin,Alison E Mather,Angelika Fruth,Chantal Bizet,Andrew J Page,Hidemasa Izumiya,Monika Marejková,Andrzej Gamian,Hervé Bercovier,Christiane Bouchier,Thandavarayan Ramamurthy,Nizar Fawal,Erika Souche,Changyun Ye,Julian Parkhill,Bianca Colonna,Alicia Tran-Dien,Corinne Ruckly,Raymond Bercion,Kathryn E Holt,Céline Langendorf,Gururaja P Pazhani,Egorova Sa ,M Herpay ,Philippe J Sansonetti ,Agnieszka Korzeniowska‐Kowal ,Guillermo I Perez-Perez ,Konstantin V Kuleshov ,Lorea Peterson ,Kaftyreva La ,Anne‐Laure Page ,Malabi M Venkatesan ,Alexander T Podkolzin ,Analía V Ezernitchi ,Marie‐Christine Fonkoua ,François‐Xavier Weill

doi:10.1038/nmicrobiol.2016.27

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.

Highlights

Together with plague, small-pox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries[1]
Our findings show that the global spread of Shigella dysenteriae type 1 (Sd1) predates WWI
We cannot demonstrate causality between the spread of Sd1 and historical events on the basis of the results presented here, but the late 1800s coincided with a period of intense

Summary

Introduction

Small-pox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries[1]. Gyrase gene, gyrA, was acquired seven times in lineage IV Sd1 isolates from South Asia and Africa (Fig. 2) from the 1980s. It was confirmed that all the isolates included belonged to Sd1, by conventional methods and serotyping at the French National Reference Center for E. coli, Shigella and Salmonella, Institut Pasteur, Paris, as previously described[32].

Results

Conclusion