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Behrens HM, Schmidt S, Henshall IG, López-Barona P, Peigney D, Sabitzki R, May J, Maïga-Ascofaré O, Spielmann T. Impact of different mutations on Kelch13 protein levels, ART resistance, and fitness cost in Plasmodium falciparum parasites. mBio 2024:e0198123. [PMID: 38700363 DOI: 10.1128/mbio.01981-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/01/2024] [Indexed: 05/05/2024] Open
Abstract
Reduced susceptibility to ART, the first-line treatment against malaria, is common in South East Asia (SEA). It is associated with point mutations, mostly in kelch13 (k13) but also in other genes, like ubp1. K13 and its compartment neighbors (KICs), including UBP1, are involved in endocytosis of host cell cytosol. We tested 135 mutations in KICs but none conferred ART resistance. Double mutations of k13C580Y with k13R539T or k13C580Y with ubp1R3138H, did also not increase resistance. In contrast, k13C580Y parasites subjected to consecutive RSAs did, but the k13 sequence was not altered. Using isogenic parasites with different k13 mutations, we found correlations between K13 protein amount, resistance, and fitness cost. Titration of K13 and KIC7 indicated that the cellular levels of these proteins determined resistance through the rate of endocytosis. While fitness cost of k13 mutations correlated with ART resistance, ubp1R3138H caused a disproportionately higher fitness cost. IMPORTANCE Parasites with lowered sensitivity to artemisinin-based drugs are becoming widespread. However, even in these "resistant" parasites not all parasites survive treatment. We found that the proportion of surviving parasites correlates with the fitness cost of resistance-inducing mutations which might indicate that the growth disadvantages prevents resistance levels where all parasites survive treatment. We also found that combining two common resistance mutations did not increase resistance levels. However, selection through repeated ART-exposure did, even-though the known resistance genes, including k13, were not further altered, suggesting other causes of increased resistance. We also observed a disproportionally high fitness cost of a resistance mutation in resistance gene ubp1. Such high fitness costs may explain why mutations in ubp1 and other genes functioning in the same pathway as k13 are rare. This highlights that k13 mutations are unique in their ability to cause resistance at a comparably low fitness cost.
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Affiliation(s)
- Hannah M Behrens
- Malaria Cell Biology, Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sabine Schmidt
- Malaria Cell Biology, Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Isabelle G Henshall
- Malaria Cell Biology, Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Patricia López-Barona
- Malaria Cell Biology, Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Domitille Peigney
- Malaria Cell Biology, Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ricarda Sabitzki
- Malaria Cell Biology, Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jürgen May
- Infectious Disease Epidemiology Department, Epidemiology and Diagnostics, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Riems, Hamburg, Germany
| | - Oumou Maïga-Ascofaré
- Infectious Disease Epidemiology Department, Epidemiology and Diagnostics, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Riems, Hamburg, Germany
| | - Tobias Spielmann
- Malaria Cell Biology, Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Abdel Hamid MM, Abdelraheem MH, Acheampong DO, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Aniebo I, Aninagyei E, Ansah F, Ansah PO, Apinjoh T, Arnaldo P, Ashley E, Auburn S, Awandare GA, Ba H, Baraka V, Barry A, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Bouyou-Akotet M, Branch O, Bull PC, Cheah H, Chindavongsa K, Chookajorn T, Chotivanich K, Claessens A, Conway DJ, Corredor V, Courtier E, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Dhorda M, Diakite M, Djimde A, Dolecek C, Dondorp A, Doumbia S, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Enosse SMM, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fleharty M, Forbes M, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Harrison GLA, Healy SA, Hendry JA, Hernandez-Koutoucheva A, Hien TT, Hill CA, Hombhanje F, Hott A, Htut Y, Hussein M, Imwong M, Ishengoma D, Jackson SA, Jacob CG, Jeans J, Johnson KJ, Kamaliddin C, Kamau E, Keatley J, Kochakarn T, Konate DS, Konaté A, Kone A, Kwiatkowski DP, Kyaw MP, Kyle D, Lawniczak M, Lee SK, Lemnge M, Lim P, Lon C, Loua KM, Mandara CI, Marfurt J, Marsh K, Maude RJ, Mayxay M, Maïga-Ascofaré O, Miotto O, Mita T, Mobegi V, Mohamed AO, Mokuolu OA, Montgomery J, Morang’a CM, Mueller I, Murie K, Newton PN, Ngo Duc T, Nguyen T, Nguyen TN, Nguyen Thi Kim T, Nguyen Van H, Noedl H, Nosten F, Noviyanti R, Ntui VNN, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Oyibo WA, Pearson R, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Quang HH, Randrianarivelojosia M, Rayner JC, Ringwald P, Rosanas-Urgell A, Rovira-Vallbona E, Ruano-Rubio V, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Sissoko MS, Smith C, Su XZ, Sutherland C, Takala-Harrison S, Talman A, Tavul L, Thanh NV, Thathy V, Thu AM, Toure M, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Whitton G, Yavo W, van der Pluijm RW. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Res 2023; 8:22. [PMID: 36864926 PMCID: PMC9971654 DOI: 10.12688/wellcomeopenres.18681.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.
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Affiliation(s)
| | | | - Mohamed Hassan Abdelraheem
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Nuclear Applications In Biological Sciences, Sudan Atomic Energy Commission, Khartoum, Sudan
| | - Desmond Omane Acheampong
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Ambroise Ahouidi
- Health Research Epidemiological Surveillance and Training Institute (IRESSEF), Université Cheikh Anta Diop, Dakar, Senegal
| | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | - Tim Anderson
- Texas Biomedical Research Institute, San Antonio, USA
| | | | | | - Enoch Aninagyei
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health & Allied Sciences, Ho, Ghana
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Patrick O Ansah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | | | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Maputo, Mozambique
| | - Elizabeth Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Nuffield Department of Medicine, University of Oxford, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- Department of Epidemiology, International Health Unit, Universiteit Antwerpen, Antwerp, Belgium
| | - Alyssa Barry
- Walter and Eliza Hall Institute, Melbourne, Australia
- Deakin University, Geelong, Australia
- Burnet Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F Boni
- Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marielle Bouyou-Akotet
- Department of Parasitology-Mycology, Université des Sciences de la Santé, Libreville, Gabon
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Huch Cheah
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | | | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David J Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- WorldWide Antimalarial Resistance Network – Asia Regional Centre, Bangkok, Thailand
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Seydou Doumbia
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Diego F Echeverry
- Departamento de Microbiología, Universidad del Valle, Cali, Colombia
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia
| | | | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Caterina A Fanello
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Mark Fleharty
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | | | - Mark Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Sara Anne Healy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason A Hendry
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Tran Tinh Hien
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, USA
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Madang, Papua New Guinea
| | | | - Ye Htut
- Department of Medical Research, Yangon, Myanmar
| | - Mazza Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Deus Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | | | | | - Claire Kamaliddin
- Institute of Research for Development (IRD), Paris, France
- The University of Calgary, Calgary, Canada
| | - Edwin Kamau
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Drissa S Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Aminatou Kone
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Myat P Kyaw
- Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar
- University of Public Health, Yangon, Myanmar
| | - Dennis Kyle
- University of South Florida, Tampa, USA
- University of Georgia, Athens, USA
| | | | - Samuel K Lee
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | - Martha Lemnge
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Kovana M Loua
- University Gamal Abdel Nasser of Conakry, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Celine I Mandara
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Jutta Marfurt
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Richard James Maude
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Harvard TH Chan School of Public Health, Harvard University, Boston, USA
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford University, Oxford, UK
| | | | - Victor Mobegi
- Department of Biochemistry and Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | | | - Olugbenga A Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jaqui Montgomery
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
- World Mosquito Program, Monash University, Melbourne, Australia
| | - Collins Misita Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | | | - Paul N Newton
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Thang Ngo Duc
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | | | - Thuy-Nhien Nguyen
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | | | - Hong Nguyen Van
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
- Medical University of Vienna, Vienna, Austria
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dhahran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya
- Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- Wellcome Sanger Institute, Hinxton, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria
- Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | | | | | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung P Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Ric N Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Huynh Hong Quang
- Institute of Malariology, Parasitology, and Entomology (IMPE) Quy Nhon, Ministry of Health, Quy Nhon, Vietnam
| | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Medicine, Uniformed Services University, Bethesda, MD, USA
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | - Mahamadou S. Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Arthur Talman
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ngo Viet Thanh
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aung Myint Thu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Mahamoudou Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Yale School of Medicine, New Haven, CT, USA
| | - Thomas E Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason Wendler
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Seattle Children’s Hospital, Seattle, USA
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire
- Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
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Bassat Q, Maïga-Ascofaré O, May J, Clain J, Mombo-Ngoma G, Groger M, Adegnika AA, Agobé JCD, Djimde A, Mischlinger J, Ramharter M. Challenges in the clinical development pathway for triple and multiple drug combinations in the treatment of uncomplicated falciparum malaria. Malar J 2022; 21:61. [PMID: 35193586 PMCID: PMC8864855 DOI: 10.1186/s12936-022-04079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/06/2022] [Indexed: 11/23/2022] Open
Abstract
The addition of a third anti-malarial drug matching the pharmacokinetic characteristics of the slowly eliminated partner drug in artemisinin-based combination therapy (ACT) has been proposed as new therapeutic paradigm for the treatment of uncomplicated falciparum malaria. These triple artemisinin-based combination therapy (TACT) should in theory more effectively prevent the development and spread of multidrug resistance than current ACT. Several clinical trials evaluating TACT—or other multidrug anti-malarial combination therapy (MDACT)—have been reported and more are underway. From a regulatory perspective, these clinical development programmes face a strategic dilemma: pivotal clinical trials evaluating TACT are designed to test for non-inferiority of efficacy compared to standard ACT as primary endpoint. While meeting the endpoint of non-inferior efficacy, TACT are consistently associated with a slightly higher frequency of adverse drug reactions than currently used ACT. Moreover, the prevention of the selection of specific drug resistance—one of the main reasons for TACT development—is beyond the scope of even large-scale clinical trials. This raises important questions: if equal efficacy is combined with poorer tolerability, how can then the actual benefit of these drug combinations be demonstrated? How should clinical development plans be conceived to provide objective evidence for or against an improved management of patients and effective prevention of anti-malarial drug resistance by TACT? What are the objective criteria to ultimately convince regulators to approve these new products? In this Opinion paper, the authors discuss the challenges for the clinical development of triple and multidrug anti-malarial combination therapies and the hard choices that need to be taken in the further clinical evaluation and future implementation of this new treatment paradigm.
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Affiliation(s)
- Quique Bassat
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ICREA, Passeig de Lluís Companys 23, 08010, Barcelona, Spain.,Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Barcelona, Spain.,Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Oumou Maïga-Ascofaré
- Kumasi Center for Collaborative Research, Kumasi, Ghana.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Jerôme Clain
- Université de Paris, Centre National de Référence du Paludisme, Hôpital Bichat- Claude Bernard, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Ghyslain Mombo-Ngoma
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany.,Centre de Recherches de Lambaréné, Lambaréné, Gabon
| | - Mirjam Groger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Ayôla A Adegnika
- Centre de Recherches de Lambaréné, Lambaréné, Gabon.,Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Abdoulaye Djimde
- Malaria Research and Training Centre (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Johannes Mischlinger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. .,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany. .,Centre de Recherches de Lambaréné, Lambaréné, Gabon.
| | | |
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4
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441 DOI: 10.12688/wellcomeopenres.16168.1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
| |
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5
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441.2 DOI: 10.12688/wellcomeopenres.16168.2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
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6
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Amambua-Ngwa A, Amenga-Etego L, Kamau E, Amato R, Ghansah A, Golassa L, Randrianarivelojosia M, Ishengoma D, Apinjoh T, Maïga-Ascofaré O, Andagalu B, Yavo W, Bouyou-Akotet M, Kolapo O, Mane K, Worwui A, Jeffries D, Simpson V, D'Alessandro U, Kwiatkowski D, Djimde AA. Major subpopulations of Plasmodium falciparum in sub-Saharan Africa. Science 2020; 365:813-816. [PMID: 31439796 DOI: 10.1126/science.aav5427] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/05/2019] [Indexed: 01/04/2023]
Abstract
Understanding genomic variation and population structure of Plasmodium falciparum across Africa is necessary to sustain progress toward malaria elimination. Genome clustering of 2263 P. falciparum isolates from 24 malaria-endemic settings in 15 African countries identified major western, central, and eastern ancestries, plus a highly divergent Ethiopian population. Ancestry aligned to these regional blocs, overlapping with both the parasite's origin and with historical human migration. The parasite populations are interbred and shared genomic haplotypes, especially across drug resistance loci, which showed the strongest recent identity-by-descent between populations. A recent signature of selection on chromosome 12 with candidate resistance loci against artemisinin derivatives was evident in Ghana and Malawi. Such selection and the emerging substructure may affect treatment-based intervention strategies against P. falciparum malaria.
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Affiliation(s)
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Edwin Kamau
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya.,Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research (NMIMR), Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Deus Ishengoma
- National Institute for Medical Research (NIMR), Tanga, Tanzania
| | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | - William Yavo
- Unite des Sciences Pharmaceutiques et Biologiques, University Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | | | - Oyebola Kolapo
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia.,Department of Zoology, University of Lagos, Lagos, Nigeria
| | - Karim Mane
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - Vikki Simpson
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Dominic Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Abdoulaye A Djimde
- Wellcome Sanger Institute, Hinxton, UK. .,Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
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7
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Otienoburu SD, Maïga-Ascofaré O, Schramm B, Jullien V, Jones JJ, Zolia YM, Houzé P, Ashley EA, Kiechel JR, Guérin PJ, Le Bras J, Houzé S. Selection of Plasmodium falciparum pfcrt and pfmdr1 polymorphisms after treatment with artesunate-amodiaquine fixed dose combination or artemether-lumefantrine in Liberia. Malar J 2016; 15:452. [PMID: 27596849 PMCID: PMC5011943 DOI: 10.1186/s12936-016-1503-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 08/26/2016] [Indexed: 12/22/2022] Open
Abstract
Background Plasmodium falciparum uncomplicated malaria can successfully be treated with an artemisinin-based combination therapy (ACT). However resistance is spreading to the different ACT compounds; the artemisinin derivative and the partner drug. Studies of P. falciparum polymorphisms associated with drug resistance can provide a useful tool to track resistance and guide treatment policy as well as an in-depth understanding of the development and spread of resistance. Methods The role of P. falciparum molecular markers in selection of reinfections was assessed in an efficacy trial comparing artesunate–amodiaquine fixed-dose combination with artemether–lumefantrine to treat malaria in Nimba County, Liberia 2008–2009. P. falciparum polymorphisms in pfcrt 76, pfmdr1 86, 184 and 1246, and pfmrp1 876 and 1466 were analysed by PCR-RFLP and pyrosequencing. Results High baseline prevalence of pfmdr1 1246Y was found in Nimba county (38 %). Pfmdr1 1246Y and pfmdr1 86+184+1246 haplotypes NYY and YYY were selected in reinfections in the artesunate–amodiaquine arm and pfcrt K76, pfmdr1 N86 and pfmdr1 haplotype NFD were selected in artemether–lumefantrine reinfections. Parasites harbouring pfmdr1 1246Y could reinfect earlier after treatment with artesunate–amodiaquine and parasites carrying pfmdr1 N86 could reinfect at higher lumefantrine concentrations in patients treated with artemether–lumefantrine. Conclusions Although treatment is highly efficacious, selection of molecular markers in reinfections could indicate a decreased sensitivity or tolerance of parasites to the current treatments and the baseline prevalence of molecular markers should be closely monitored. Since individual drug levels and the day of reinfection were demonstrated to be key determinants for selection of reinfections, this data needs to be collected and taken into account for accurate evaluation of molecular markers for anti-malarial treatments. The protocols for the clinical trial was registered with Current Controlled Trials, under the Identifier Number ISRCTN51688713 on 9 October 2008
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Affiliation(s)
- Sabina Dahlström Otienoburu
- Institut de Médecine et d'Epidémiologie Appliquée, Bichat-C. Bernard Hospital, Paris, France. .,WorldWide Antimalarial Resistance Network, Oxford, UK. .,Johnson C. Smith University, Charlotte, NC, 28216, USA.
| | - Oumou Maïga-Ascofaré
- Institut de Médecine et d'Epidémiologie Appliquée, Bichat-C. Bernard Hospital, Paris, France.,Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | | | - Vincent Jullien
- INSERM U1129, Service de Pharmacologie, Hôpital Européen Georges Pompidou, Université Paris Descartes, 75015, Paris, France
| | - Joel J Jones
- National Malaria Control Programme, Ministry of Health and Social Welfare, Monrovia, Liberia
| | - Yah M Zolia
- National Malaria Control Programme, Ministry of Health and Social Welfare, Monrovia, Liberia
| | - Pascal Houzé
- AP-HP, Saint-Louis Hospital Biochemistry Laboratory, Paris, France
| | - Elizabeth A Ashley
- Epicentre, 75012, Paris, France.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Philippe J Guérin
- WorldWide Antimalarial Resistance Network, Oxford, UK.,Epicentre, 75012, Paris, France.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Jacques Le Bras
- Institut de Médecine et d'Epidémiologie Appliquée, Bichat-C. Bernard Hospital, Paris, France.,IRD UMR216, Paris-Descartes University, Paris, France.,Parasitology Laboratory-French National Malaria Reference Centre, AP-HP, Bichat-C. Bernard Hospital, Paris, France
| | - Sandrine Houzé
- IRD UMR216, Paris-Descartes University, Paris, France.,Parasitology Laboratory-French National Malaria Reference Centre, AP-HP, Bichat-C. Bernard Hospital, Paris, France
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8
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Maïga-Ascofaré O, May J. Is the A578S Single-Nucleotide Polymorphism in K13-propeller a Marker of Emerging Resistance to Artemisinin Among Plasmodium falciparum in Africa? J Infect Dis 2015; 213:165-6. [PMID: 26268852 DOI: 10.1093/infdis/jiv414] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/30/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Jürgen May
- Benhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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9
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Maïga-Ascofaré O, Rakotozandrindrainy R, Girmann M, Hahn A, Randriamampionona N, Poppert S, May J, Schwarz NG. Molecular epidemiology and seroprevalence in asymptomatic Plasmodium falciparum infections of Malagasy pregnant women in the highlands. Malar J 2015; 14:188. [PMID: 25935753 PMCID: PMC4432997 DOI: 10.1186/s12936-015-0704-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/22/2015] [Indexed: 11/29/2022] Open
Abstract
Background Malaria epidemiology in Madagascar is classified into four different areas, ranging from unstable seasonal transmission in the highlands to hyperendemic perennial transmission areas in the costal level. Most malaria studies in Madagascar are focused on symptomatic children. However, because of the low transmission in some areas with correspondingly low level of semi-immunity, adults are also at risk, in particular pregnant women. The objective of this study was to gain information on the genetic epidemiology of malarial infections in pregnant women in order to provide information for malaria control and elimination programmes in Madagascar. Methods Between May and August 2010, we carried out cross-sectional surveys targeting healthy pregnant women in six locations, three in the coastal area and three in the highlands at 850–1300 m. 1244 blood samples were screened for anti-Plasmodium falciparum antibodies by immunofluorescence test and for malarial infection by realtime-PCR. The prevalence of chloroquine and sulphadoxine-pyrimethamine resistance markers was also determined in all Plasmodium falciparum samples by PCR-RFLP as well as the multiplicity of infection through genotyping six neutral microsatellites. Results In the highlands, 67.4% of the women presented antibodies against Plasmodium falciparum and 9.2% were carrying parasites, at the coast 95.6% and 14.8%, respectively. In the mean, 1.2 clones were detected in infected pregnant woman in the highlands and 1.5 at the coast. A higher level of monoclonal infections was found in the highlands (85.4%) compared to the coast (61.8%). Resistance markers for sulphadoxine-pyrimethamine were present only in two sites. Conclusion Immunity is triggered in Malagasy highland populations when they are infected with malaria parasites, but these populations could also serve as a reservoir for epidemics. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0704-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Mirko Girmann
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | - Andreas Hahn
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | | | | | - Jürgen May
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
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10
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Ghansah A, Amenga-Etego L, Amambua-Ngwa A, Andagalu B, Apinjoh T, Bouyou-Akotet M, Cornelius V, Golassa L, Andrianaranjaka VH, Ishengoma D, Johnson K, Kamau E, Maïga-Ascofaré O, Mumba D, Tindana P, Tshefu-Kitoto A, Randrianarivelojosia M, William Y, Kwiatkowski DP, Djimde AA. Monitoring parasite diversity for malaria elimination in sub-Saharan Africa. Science 2014; 345:1297-8. [PMID: 25214619 DOI: 10.1126/science.1259423] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The African continent continues to bear the greatest burden of malaria and the greatest diversity of parasites, mosquito vectors, and human victims. The evolutionary plasticity of malaria parasites and their vectors is a major obstacle to eliminating the disease. Of current concern is the recently reported emergence of resistance to the front-line drug, artemisinin, in South-East Asia in Plasmodium falciparum, which calls for preemptive surveillance of the African parasite population for genetic markers of emerging drug resistance. Here we describe the Plasmodium Diversity Network Africa (PDNA), which has been established across 11 countries in sub-Saharan Africa to ensure that African scientists are enabled to work together and to play a key role in the global effort for tracking and responding to this public health threat.
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Affiliation(s)
- Anita Ghansah
- Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | | | | | - Ben Andagalu
- KEMRI/United States Army Medical Research Unit-Kenya, Kisumu, Nairobi, Kenya
| | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Marielle Bouyou-Akotet
- Department of Parasitology Mycology, Faculty of Medicine, Université des Sciences de la Sante, Libreville, Gabon
| | - Victoria Cornelius
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University and Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Deus Ishengoma
- National Institute for Medical Research, Tanga, Tanzania
| | - Kimberly Johnson
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Edwin Kamau
- KEMRI/United States Army Medical Research Unit-Kenya, Kisumu, Nairobi, Kenya
| | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre (MRTC), Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali. Bernhard Nocht Institute for Tropical Medicine in Hamburg, Germany
| | - Dieudonne Mumba
- Institut National de Recherche Biomédicale, Ecole de Santé Publique/Faculté de Médecine/Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | - Antoinette Tshefu-Kitoto
- Institut National de Recherche Biomédicale, Ecole de Santé Publique/Faculté de Médecine/Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | - Yavo William
- Malaria Research and Control Center, National Institute of Public Health, Abidjan, Ivory Coast
| | - Dominic P Kwiatkowski
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK. Wellcome Trust Sanger Institute, Hinxton, UK
| | - Abdoulaye A Djimde
- Malaria Research and Training Centre (MRTC), Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali. Wellcome Trust Sanger Institute, Hinxton, UK.
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11
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Maïga-Ascofaré O, Le Bras J, Mazmouz R, Renard E, Falcão S, Broussier E, Bustos D, Randrianarivelojosia M, Omar SA, Aubouy A, Lepère JF, Jean-François V, Djimdé AA, Clain J. Adaptive differentiation of Plasmodium falciparum populations inferred from single-nucleotide polymorphisms (SNPs) conferring drug resistance and from neutral SNPs. J Infect Dis 2010; 202:1095-103. [PMID: 20726766 DOI: 10.1086/656142] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Theoretical and experimental data support the geographic differentiation strategy as a valuable tool for detecting loci under selection. In the context of Plasmodium falciparum malaria, few populations have been studied, with limited genomic coverage. METHODS We examined geographic differentiation in P. falciparum populations on the basis of 12 single-nucleotide polymorphisms (SNPs) in 4 genes encoding drug resistance determinants, 5 SNPs in 2 genes encoding antigens, and a set of 17 putatively neutral SNPs dispersed on 13 chromosomes. We sampled 326 parasite isolates representing 7 P. falciparum populations from regions with varied levels of malaria transmission (Gabon, Kenya, Madagascar, Mali, Mayotte, Haiti, and the Philippines). RESULTS Frequencies of drug resistance alleles varied considerably among populations (mean F(ST), 0.52). In contrast, allele frequencies varied significantly less for antigenic and neutral SNPs (mean F(ST), 0.16 and 0.24, respectively). This contrasting pattern was more pronounced when only the African populations were considered. Signature of selection was detected for most of the resistant SNPs but not for the antigenic SNPs. CONCLUSION These data further validate the utility of geographic differentiation for identifying loci under strong positive selection, such as drug resistance loci. This study also provides frequencies of molecular makers of resistance in some overlooked populations.
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Affiliation(s)
- Oumou Maïga-Ascofaré
- Unité Mixte de Recherche 216, Institut de Recherche pour le Développement, Mère et Enfant Face aux Infections Tropicales, Université Paris Descartes, Paris, France
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