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            <funder>This study was supported by the Institut Pasteur and the Institut Pasteur International Network, the Institut de Veille Sanitaire, the French government’s Investissement d’Avenir programme, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant no. ANR-10-LABX-62-IBEID), the Fondation ‘Le Roch-Les Mousquetaires’, the Canetti family through the Georges, Jacques et Elias Canetti Award 2013, the Wellcome Trust through grant 098051 to the Sanger Institute, the NHMRC of Australia (grant 1061409 to K.E.H), the Victorian Life Sciences Computation Initiative (VLSCI) (grant VR0082) and the Indian Council of Medical Research, New Delhi, India.</funder>
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              <date type="whenSubmitted">2019-03-12 10:03:00</date>
              <date type="whenModified">2026-05-10 03:14:20</date>
              <date type="whenReleased">2019-03-12 11:44:30</date>
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                <title level="j">Nature Microbiology</title>
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                  <publisher>Nature Publishing Group</publisher>
                  <biblScope unit="volume">1</biblScope>
                  <biblScope unit="issue">4</biblScope>
                  <biblScope unit="pp">16027</biblScope>
                  <date type="datePub">2016-03-21</date>
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              <p>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.</p>
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