Tracking the establishment of local endemic populations of an emergent enteric pathogen

Kathryn E Holt, Tran Vu Thieu Nga, Duy Pham Thanh, Ha Vinh, Dong Wook Kim, My Phan Vu Tra, James I. Campbell, Nguyen Van Minh Hoang, Nguyen Thanh Vinh, A/Prof Pham Quang Minh, Cao Thu Thuy, Tran Thi Thu Nga, Corinne N Thompson, Tran Thi Ngoc Dung, Nguyen Thi Khanh Nhu, Phat Voong Vinh, Pham Thi Ngoc Tuyet, Hoang Le Phuc, Nguyen Thi Nam Lien, Bui Duc PhuNguyen Thi Thuy Ai, Nguyen Manh Tien, Nguyen Dong, Christopher M. Parry, Tran Tinh M Hien, Jeremy Farrar, Julian Parkhill, Gordon Dougan, Nicholas R Thomson, Stephen Baker

Research output: Contribution to journalArticleResearchpeer-review

96 Citations (Scopus)


Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.

Original languageEnglish
Pages (from-to)17522-17527
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number43
Publication statusPublished - 22 Oct 2013


  • Drug resistance
  • Enteric disease
  • Genomics
  • Phylogeography

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