Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery1,2, spreading efficiently via low-dose fecal-oral transmission3,4. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries but is now emerging as a problem in the developing world, seeming to replace the more diverse Shigella flexneri in areas undergoing economic development and improvements in water quality4,5,6. Classical approaches have shown that S. sonnei is genetically conserved and clonal7. We report here whole-genome sequencing of 132 globally distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and that diversified into several distinct lineages with unique characteristics. Our analysis suggests that the majority of this diversification occurred in Europe and was followed by more recent establishment of local pathogen populations on other continents, predominantly due to the pandemic spread of a single, rapidly evolving, multidrug-resistant lineage.

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We thank M. Levine (University of Maryland School of Medicine) and C. Tang (University of Oxford) for their kind gift of S. sonnei strain 53G. This work was supported by the Wellcome Trust (0689) and a Victorian Life Sciences Computation Initiative (VLSCI) grant (VR0082) on its Peak Computing Facility at the University of Melbourne (an initiative of the Victorian Government, Australia). K.E.H. was supported by a Fellowship from the National Health & Medical Research Council (NHMRC) of Australia (628930); S.B. is supported by an Oak Foundation Fellowship through Oxford University (OAKF9) and by the Li Ka Shing foundation (LG13); F.X.W. was partially funded by the Institut de Veille Sanitaire; J.Y. was supported by a UK Medical Research Council (MRC) grant (G0800173); and D.W.K. was partially supported by grant RTI05-01-01 from the Korean Ministry of Knowledge and Economy (MKE).

Author information


  1. Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia.

    • Kathryn E Holt
  2. The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.

    • Stephen Baker
    •  & Jeremy J Farrar
  3. Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France.

    • François-Xavier Weill
  4. Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.

    • Edward C Holmes
    •  & Andrew Kitchen
  5. Fogarty International Center, US National Institutes of Health, Bethesda, Maryland, USA.

    • Edward C Holmes
  6. Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK.

    • Jun Yu
    •  & Vartul Sangal
  7. Scottish Salmonella, Shigella and Clostridium difficile Reference Laboratory, Stobhill Hospital, Glasgow, UK.

    • Derek J Brown
    •  & John E Coia
  8. Molecular Biology Laboratory, International Vaccine Institute (IVI), Seoul, Republic of Korea.

    • Dong Wook Kim
    • , Seon Young Choi
    •  & Su Hee Kim
  9. Department of Pharmacy, College of Pharmacy, Hanyang University Ansan, Kyeonggi-do, Republic of Korea.

    • Dong Wook Kim
  10. Department of Genetics, Evolution and Bioagents, Biology Institute, Campinas State University (UNICAMP), Campinas, Brazil.

    • Wanderley D da Silveira
  11. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Derek J Pickard
    • , Julian Parkhill
    • , Gordon Dougan
    •  & Nicholas R Thomson


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K.E.H., N.R.T., E.C.H. and A.K. analyzed the data and performed phylogenetic analysis. N.R.T., G.D., J.Y., S.B., J.J.F., K.E.H. and J.P. were involved in the study design. F.-X.W., D.J.B., J.E.C., J.Y., V.S., D.W.K., S.Y.C., S.H.K., W.D.d.S. and D.J.P. were involved in isolate collection, DNA analysis and resistance phenotyping. K.E.H., S.B., N.R.T., G.D., A.K., E.C.H. and F.-X.W. contributed to manuscript writing.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Kathryn E Holt or Nicholas R Thomson.

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    Supplementary Figures 1–6, Supplementary Tables 2 and 3 and Supplementary Note

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    Supplementary Table 1

    Details of Shigella sonnei isolates used in this study.

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