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

79 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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1073/pnas.1308632110

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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",

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

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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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AU - Thanh, Duy Pham

AU - Vinh, Ha

AU - Kim, Dong Wook

AU - Tra, My Phan Vu

AU - Campbell, James I.

AU - Hoang, Nguyen Van Minh

AU - Vinh, Nguyen Thanh

AU - Quang Minh, A/Prof Pham

AU - Thuy, Cao Thu

AU - Nga, Tran Thi Thu

AU - Thompson, Corinne N

AU - Dung, Tran Thi Ngoc

AU - Nhu, Nguyen Thi Khanh

AU - Vinh, Phat Voong

AU - Tuyet, Pham Thi Ngoc

AU - Phuc, Hoang Le

AU - Lien, Nguyen Thi Nam

AU - Phu, Bui Duc

AU - Ai, Nguyen Thi Thuy

AU - Tien, Nguyen Manh

AU - Dong, Nguyen

AU - Parry, Christopher M.

AU - Hien, Tran Tinh M

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AU - Thomson, Nicholas R

AU - Baker, Stephen

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AB - 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.

KW - Drug resistance

KW - Enteric disease

KW - Genomics

KW - Phylogeography

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DO - 10.1073/pnas.1308632110

M3 - Article

C2 - 24082120

AN - SCOPUS:84886379482

VL - 110

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EP - 17527

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 43

ER -

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

Abstract

Keywords

UN SDGs

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