Genomic epidemiology of artemisinin resistant malaria

被引：216

作者：

Amato, Roberto ^{[1
,2
]}

Miotto, Olivo ^{[1
,2
,3
]}

Woodrow, Charles J. ^{[3
,4
]}

Almagro-Garcia, Jacob ^{[1
,2
]}

Sinha, Ipsita ^{[3
]}

Campino, Susana ^{[1
]}

Mead, Daniel ^{[1
]}

Drury, Eleanor ^{[1
]}

Kekre, Mihir ^{[1
]}

Sanders, Mandy ^{[1
]}

Amambua-Ngwa, Alfred ^{[5
]}

Amaratunga, Chanaki ^{[6
]}

Amenga-Etego, Lucas ^{[7
]}

Andrianaranjaka, Voahangy ^{[8
]}

Apinjoh, Tobias ^{[9
]}

Ashley, Elizabeth ^{[3
]}

Auburn, Sarah ^{[10
,11
]}

Awandare, Gordon A. ^{[12
]}

Baraka, Vito ^{[13
,14
]}

Barry, Alyssa ^{[15
,16
]}

Boni, Maciej F. ^{[4
,17
]}

Borrmann, Steffen ^{[18
,19
]}

Bousema, Teun ^{[20
]}

Branch, Oralee ^{[21
]}

Bull, Peter C. ^{[4
,18
]}

Chotivanich, Kesinee ^{[22
]}

Conway, David J. ^{[5
,20
]}

Craig, Alister ^{[23
]}

Day, Nicholas P. ^{[3
,4
]}

Djimde, Abdoulaye ^{[24
]}

Dolecek, Christiane ^{[4
,25
]}

Dondorp, Arjen M. ^{[3
,4
]}

Drakeley, Chris ^{[20
]}

Duffy, Patrick ^{[6
]}

Echeverry, Diego F. ^{[26
,27
]}

Egwang, Thomas G. ^{[28
]}

Fairhurst, Rick M. ^{[6
]}

Faiz, Md. Abul ^{[29
,30
]}

Fanello, Caterina I. ^{[3
]}

Tran Tinh Hien ^{[4
,7
,25
]}

Hodgson, Abraham

Imwong, Mallika ^{[3
]}

Ishengoma, Deus ^{[13
]}

Lim, Pharath ^{[6
,31
]}

Lon, Chanthap ^{[32
]}

Marfurt, Jutta ^{[10
,11
]}

Marsh, Kevin ^{[18
]}

Mayxay, Mayfong ^{[33
,34
]}

Michon, Pascal ^{[35
]}

Mobegi, Victor ^{[5
,20
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge, England

[2] Wellcome Trust Ctr Human Genet, Ctr Genom & Global Hlth, Oxford, England

[3] Mahidol Univ, Mahidol Oxford Trop Med Res Unit, Bangkok 10700, Thailand

[4] Univ Oxford, Nuffield Dept Med, Ctr Trop Med & Global Hlth, Oxford, England

[5] MRC Unit, Banjul, Gambia

[6] NIAID, NIH, Rockville, MD USA

[7] Navrongo Hlth Res Ctr, Navrongo, Ghana

[8] Inst Pasteur Madagascar, Malaria Res Unit, Antananarivo, Madagascar

[9] Univ Buea, Buea, Cameroon

[10] Menzies Sch Hlth Res, Global & Trop Hlth Div, Darwin, NT, Australia

[11] Charles Darwin Univ, Darwin, NT 0909, Australia

[12] Univ Ghana, Coll Basic & Appl Sci, West African Ctr Cell Biol Infect Pathogens, Legon, Ghana

[13] Natl Inst Med Res, Tanga Ctr, Tanga, Tanzania

[14] Univ Antwerp, Dept Epidemiol, Int Hlth Unit, B-2020 Antwerp, Belgium

[15] Royal Melbourne Hosp, Walter & Eliza Hall Inst Med Res, Div Populat Hlth & Immun, Parkville, Vic 3050, Australia

[16] Univ Melbourne, Dept Med Biol, Carlton, Vic 3053, Australia

[17] Univ Oxford, Ho Chi Minh City, Vietnam

[18] Wellcome Trust Collaborat Res Program, Kenya Med Res Inst, Kilifi, Kenya

[19] Univ Tubingen, Inst Trop Med, Tubingen, Germany

[20] London Sch Hyg & Trop Med, London WC1, England

[21] NYU, Sch Med, New York, NY USA

[22] Mahidol Univ, Fac Trop Med, Bangkok, Thailand

[23] Univ Liverpool, Liverpool Sch Trop Med, Liverpool L3 5QA, Merseyside, England

[24] Univ Bamako, Fac Med, Malaria Res & Training Ctr, Bamako, Mali

[25] Univ Oxford, Clin Res Unit, Ho Chi Minh City, Vietnam

[26] Purdue Univ, Dept Entomol, W Lafayette, IN 47907 USA

[27] CIDEIM, Int Ctr Med Res & Training, Cali, Colombia

[28] Med Biotech Labs, Kampala, Uganda

[29] Malaria Res Grp, Dhaka, Bangladesh

[30] Dev Care Fdn, Dhaka, Bangladesh

[31] Natl Ctr Parasitol Entomol & Malaria Control, Phnom Penh, Cambodia

[32] Armed Forces Res Inst Med Sci, US Army Med Component, Dept Immunol & Med, Bangkok 10400, Thailand

[33] Lao Oxford Mahosot Hosp Wellcome Trust Res Unit, Vientiane, Lao PDR, England

[34] Univ Hlth Sci, Fac Postgrad Studies, Vientiane, Lao PDR, England

[35] Divine Word Univ, Fac Med & Hlth Sci, Madang, Papua N Guinea

[36] Univ Ilorin, Dept Paediat & Child Hlth, Ilorin, Nigeria

[37] Penn State Univ, Dept Biol & Entomol, University Pk, PA 16802 USA

[38] Minist Hlth, Dept Med Res Lower Myanmar, Yangon, Myanmar

[39] Mahidol Univ, Mahido Oxford Trop Med Res Unit, Mae Sot, Thailand

[40] Shoklo Malaria Res Unit, Mae Sot, Thailand

[41] Eijkman Inst Mol Biol, Jakarta, Indonesia

[42] King Fahd Univ Petr & Minerals, Dept Biol, Dhahran, Saudi Arabia

[43] Malawi Liverpool Wellcome Trust Clin Res Programm, Lilongwe, Malawi

[44] Univ Kinshasa, Kinshasa, DEM REP CONGO

[45] Direct Regionale Ouest, Inst Rech Sci Sante, Bobo Dioulasso, Burkina Faso

[46] Shoklo Malaria Res Unit, Bangkok, Thailand

[47] Univ Maryland, Sch Med, Inst Global Hlth, Baltimore, MD 21201 USA

[48] WHO, Global Malaria Programme, CH-1211 Geneva, Switzerland

[49] Univ Nacl Amazonia Peruana, Iquitos, Peru

[50] Univ Dodoma, Dept Biotechnol & Bioinformat, Dodoma, Tanzania

来源：

ELIFE | 2016年 / 5卷

基金：

英国医学研究理事会; 英国惠康基金;

关键词：

MOLECULAR POPULATION-GENETICS; PLASMODIUM-FALCIPARUM; SUBSTITUTION MATRICES; SOFT SWEEPS; ADAPTATION; MUTATIONS; EVOLUTION; SIGNATURES; MECHANISM; PARASITES;

D O I：

10.7554/eLife.08714

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelchl3 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelchl3 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.

引用

页数：29

共 53 条

[1] The kelch repeat superfamily of proteins: propellers of cell function [J].

Adams, J ;

Kelso, R ;

Cooley, L .

TRENDS IN CELL BIOLOGY, 2000, 10 (01) :17-24

[2]

[Anonymous], 2014, WORLD MAL REP 2014

[3] A molecular marker of artemisinin-resistant Plasmodium falciparum malaria [J].

Ariey, Frederic ;

Witkowski, Benoit ;

Amaratunga, Chanaki ;

Beghain, Johann ;

Langlois, Anne-Claire ;

Khim, Nimol ;

Kim, Saorin ;

Duru, Valentine ;

Bouchier, Christiane ;

Ma, Laurence ;

Lim, Pharath ;

Leang, Rithea ;

Duong, Socheat ;

Sreng, Sokunthea ;

Suon, Seila ;

Chuor, Char Meng ;

Bout, Denis Mey ;

Menard, Sandie ;

Rogers, William O. ;

Genton, Blaise ;

Fandeur, Thierry ;

Miotto, Olivo ;

Ringwald, Pascal ;

Le Bras, Jacques ;

Berry, Antoine ;

Barale, Jean-Christophe ;

Fairhurst, Rick M. ;

Benoit-Vical, Franoise ;

Mercereau-Puijalon, Odile ;

Menard, Didier .

NATURE, 2014, 505 (7481) :50-+

[4] Spread of Artemisinin Resistance in Plasmodium falciparum Malaria [J].

Ashley, E. A. ;

Dhorda, M. ;

Fairhurst, R. M. ;

Amaratunga, C. ;

Lim, P. ;

Suon, S. ;

Sreng, S. ;

Anderson, J. M. ;

Mao, S. ;

Sam, B. ;

Sopha, C. ;

Chuor, C. M. ;

Nguon, C. ;

Sovannaroth, S. ;

Pukrittayakamee, S. ;

Jittamala, P. ;

Chotivanich, K. ;

Chutasmit, K. ;

Suchatsoonthorn, C. ;

Runcharoen, R. ;

Hien, T. T. ;

Thuy-Nhien, N. T. ;

Thanh, N. V. ;

Phu, N. H. ;

Htut, Y. ;

Han, K-T. ;

Aye, K. H. ;

Mokuolu, O. A. ;

Olaosebikan, R. R. ;

Folaranmi, O. O. ;

Mayxay, M. ;

Khanthavong, M. ;

Hongvanthong, B. ;

Newton, P. N. ;

Onyamboko, M. A. ;

Fanello, C. I. ;

Tshefu, A. K. ;

Mishra, N. ;

Valecha, N. ;

Phyo, A. P. ;

Nosten, F. ;

Yi, P. ;

Tripura, R. ;

Borrmann, S. ;

Bashraheil, M. ;

Peshu, J. ;

Faiz, M. A. ;

Ghose, A. ;

Hossain, M. A. ;

Samad, R. .

NEW ENGLAND JOURNAL OF MEDICINE, 2014, 371 (05) :411-423

[5] An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing [J].

Auburn, Sarah ;

Campino, Susana ;

Clark, Taane G. ;

Djimde, Abdoulaye A. ;

Zongo, Issaka ;

Pinches, Robert ;

Manske, Magnus ;

Mangano, Valentina ;

Alcock, Daniel ;

Anastasi, Elisa ;

Maslen, Gareth ;

MacInnis, Bronwyn ;

Rockett, Kirk ;

Modiano, David ;

Newbold, Christopher I. ;

Doumbo, Ogobara K. ;

Ouedraogo, Jean Bosco ;

Kwiatkowski, Dominic P. .

PLOS ONE, 2011, 6 (07)

[6] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[7] A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins [J].

Brick, Kevin ;

Pizzi, Elisabetta .

BMC BIOINFORMATICS, 2008, 9 (1)

[8] Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis [J].

Claessens, Antoine ;

Hamilton, William L. ;

Kekre, Mihir ;

Otto, Thomas D. ;

Faizullabhoy, Adnan ;

Rayner, Julian C. ;

Kwiatkowski, Dominic .

PLOS GENETICS, 2014, 10 (12)

[9] Targeting the Cell Stress Response of Plasmodium falciparum to Overcome Artemisinin Resistance [J].

Dogovski, Con ;

Xie, Stanley C. ;

Burgio, Gaetan ;

Bridgford, Jess ;

Mok, Sachel ;

McCaw, James M. ;

Chotivanich, Kesinee ;

Kenny, Shannon ;

Gnaedig, Nina ;

Straimer, Judith ;

Bozdech, Zbynek ;

Fidock, David A. ;

Simpson, Julie A. ;

Dondorp, Arjen M. ;

Foote, Simon ;

Klonis, Nectarios ;

Tilley, Leann .

PLOS BIOLOGY, 2015, 13 (04)

[10] Artemisinin resistance is a clear and present danger [J].

Dondorp, Arjen M. ;

Ringwald, Pascal .

TRENDS IN PARASITOLOGY, 2013, 29 (08) :359-360

← 1 2 3 4 5 6 →