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 Phu; Nguyen 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

doi:10.1073/pnas.1308632110

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

Microbiology

Research output: Contribution to journal › Article › Research › peer-review

70 Citations (Scopus)

Abstract

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 language	English
Pages (from-to)	17522-17527
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	110
Issue number	43
DOIs	https://doi.org/10.1073/pnas.1308632110
Publication status	Published - 22 Oct 2013

Keywords

Drug resistance
Enteric disease
Genomics
Phylogeography

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10.1073/pnas.1308632110

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Cite this

Holt, K. E., Nga, T. V. T., Thanh, D. P., Vinh, H., Kim, D. W., Tra, M. P. V., Campbell, J. I., Hoang, N. V. M., Vinh, N. T., Quang Minh, AP. P., Thuy, C. T., Nga, T. T. T., Thompson, C. N., Dung, T. T. N., Nhu, N. T. K., Vinh, P. V., Tuyet, P. T. N., Phuc, H. L., Lien, N. T. N., ... Baker, S. (2013). Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proceedings of the National Academy of Sciences of the United States of America, 110(43), 17522-17527. https://doi.org/10.1073/pnas.1308632110

Holt, Kathryn E ; Nga, Tran Vu Thieu ; Thanh, Duy Pham ; Vinh, Ha ; Kim, Dong Wook ; Tra, My Phan Vu ; Campbell, James I. ; Hoang, Nguyen Van Minh ; Vinh, Nguyen Thanh ; Quang Minh, A/Prof Pham ; Thuy, Cao Thu ; Nga, Tran Thi Thu ; Thompson, Corinne N ; Dung, Tran Thi Ngoc ; Nhu, Nguyen Thi Khanh ; Vinh, Phat Voong ; Tuyet, Pham Thi Ngoc ; Phuc, Hoang Le ; Lien, Nguyen Thi Nam ; Phu, Bui Duc ; Ai, Nguyen Thi Thuy ; Tien, Nguyen Manh ; Dong, Nguyen ; Parry, Christopher M. ; Hien, Tran Tinh M ; Farrar, Jeremy ; Parkhill, Julian ; Dougan, Gordon ; Thomson, Nicholas R ; Baker, Stephen. / Tracking the establishment of local endemic populations of an emergent enteric pathogen. In: Proceedings of the National Academy of Sciences of the United States of America. 2013 ; Vol. 110, No. 43. pp. 17522-17527.

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abstract = "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.",

keywords = "Drug resistance, Enteric disease, Genomics, Phylogeography",

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Holt, KE, Nga, TVT, Thanh, DP, Vinh, H, Kim, DW, Tra, MPV, Campbell, JI, Hoang, NVM, Vinh, NT, Quang Minh, APP, Thuy, CT, Nga, TTT, Thompson, CN, Dung, TTN, Nhu, NTK, Vinh, PV, Tuyet, PTN, Phuc, HL, Lien, NTN, Phu, BD, Ai, NTT, Tien, NM, Dong, N, Parry, CM, Hien, TTM, Farrar, J, Parkhill, J, Dougan, G, Thomson, NR & Baker, S 2013, 'Tracking the establishment of local endemic populations of an emergent enteric pathogen', Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 43, pp. 17522-17527. https://doi.org/10.1073/pnas.1308632110

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

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, No. 43, 22.10.2013, p. 17522-17527.

Research output: Contribution to journal › Article › Research › peer-review

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