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Cabrera-Sosa L, Safarpour M, Kattenberg JH, Ramirez R, Vinetz J, Rosanas-Urgell A, Gamboa D, Delgado-Ratto C. Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.611954. [PMID: 39314390 PMCID: PMC11418992 DOI: 10.1101/2024.09.09.611954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He ) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST ) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends ( He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.
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Chen YA, Vickers EN, Aranda-Diaz A, Murphy M, Gerlovina I, Rerolle F, Dantzer E, Hongvanthong B, Chang HH, Lover AA, Hathaway NJ, Bennett A, Greenhouse B. Genomic epidemiology demonstrates spatially clustered, local transmission of Plasmodium falciparum in forest-going populations in southern Lao PDR. PLoS Pathog 2024; 20:e1012194. [PMID: 39312594 PMCID: PMC11449315 DOI: 10.1371/journal.ppat.1012194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 10/03/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
While there has been significant progress in controlling falciparum malaria in the Lao People's Democratic Republic (PDR), sporadic cases persist in southern provinces where the extent and patterns of transmission remain largely unknown. To assess parasite transmission in this area, 53 Plasmodium falciparum (Pf) positive cases detected through active test and treat campaigns from December 2017 to November 2018 were sequenced, targeting 204 highly polymorphic amplicons. Two R packages, MOIRE and Dcifer, were applied to assess the multiplicity of infections (MOI), effective MOI (eMOI), within-host parasite relatedness, and between-host parasite relatedness ([Formula: see text]). Genomic data were integrated with survey data to characterize the temporal and spatial structures of identified clusters. The positive cases were mainly captured during the focal test and treat campaign conducted in 2018, and in the Pathoomphone area, which had the highest test positivity and forest activity. About 30% of the cases were polyclonal infections, with over half of theses (63%) showing within-host relatedness greater than 0.6, suggesting that cotransmission rather than superinfection was primarily responsible for maintaining polyclonality. A large majority of cases (81%) were infected by parasites genetically linked to one or more other cases. We identified five genetically distinct clusters in forest fringe villages within the Pathoomphone district, characterized by a high degree of genetic relatedness between parasites (mean [Formula: see text] = 0.8). Four smaller clusters of 2-3 cases linked Moonlapamok and Pathoomphone districts, with an average [Formula: see text] of 0.6, suggesting cross-district transmission. Most of the clustered cases occurred within 20 km and 2 months of each other, consistent with focal transmission. Transmission clusters identified in this study confirm the role of ongoing focal parasite transmission occurring within the forest or forest-fringe in the highly mobile population.
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Affiliation(s)
- Ying-An Chen
- EPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
- Institute of Bioinformatics and Structural Biology, College of Life Science and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Eric Neubauer Vickers
- EPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Andres Aranda-Diaz
- EPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Maxwell Murphy
- EPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Inna Gerlovina
- EPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Francois Rerolle
- Malaria Elimination Initiative, The Global Health Group, University of California, San Francisco, San Francisco, California, United States of America
| | - Emily Dantzer
- Malaria Elimination Initiative, The Global Health Group, University of California, San Francisco, San Francisco, California, United States of America
| | - Bouasy Hongvanthong
- Center for Malariology, Parasitology and Entomology, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Hsiao-Han Chang
- Institute of Bioinformatics and Structural Biology, College of Life Science and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Andrew A Lover
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Nicholas J Hathaway
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Adam Bennett
- Malaria Elimination Initiative, The Global Health Group, University of California, San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
- PATH, Seattle, Washington, United States of America
| | - Bryan Greenhouse
- EPPIcenter Research Program, Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
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Rosenthal PJ, Asua V, Bailey JA, Conrad MD, Ishengoma DS, Kamya MR, Rasmussen C, Tadesse FG, Uwimana A, Fidock DA. The emergence of artemisinin partial resistance in Africa: how do we respond? THE LANCET. INFECTIOUS DISEASES 2024; 24:e591-e600. [PMID: 38552654 DOI: 10.1016/s1473-3099(24)00141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 04/21/2024]
Abstract
Malaria remains one of the most important infectious diseases in the world, with the greatest burden in sub-Saharan Africa, primarily from Plasmodium falciparum infection. The treatment and control of malaria is challenged by resistance to most available drugs, but partial resistance to artemisinins (ART-R), the most important class for the treatment of malaria, was until recently confined to southeast Asia. This situation has changed, with the emergence of ART-R in multiple countries in eastern Africa. ART-R is mediated primarily by single point mutations in the P falciparum kelch13 protein, with several mutations present in African parasites that are now validated resistance mediators based on clinical and laboratory criteria. Major priorities at present are the expansion of genomic surveillance for ART-R mutations across the continent, more frequent testing of the efficacies of artemisinin-based regimens against uncomplicated and severe malaria in trials, more regular assessment of ex-vivo antimalarial drug susceptibilities, consideration of changes in treatment policy to deter the spread of ART-R, and accelerated development of new antimalarial regimens to overcome the impacts of ART-R. The emergence of ART-R in Africa is an urgent concern, and it is essential that we increase efforts to characterise its spread and mitigate its impact.
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Affiliation(s)
- Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, CA, USA.
| | - Victor Asua
- Infectious Diseases Research Collaboration, Kampala, Uganda; University of Tübingen, Tübingen, Germany
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Departments of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Melissa D Conrad
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; School of Public Health, Harvard University, Boston, MA, USA
| | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda; Department of Medicine, Makerere University, Kampala, Uganda
| | | | - Fitsum G Tadesse
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia; London School of Hygiene and Tropical Medicine, London, UK
| | - Aline Uwimana
- Rwanda Biomedical Center, Kigali, Rwanda; Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - David A Fidock
- Department of Microbiology and Immunology and Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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Kane J, Li X, Kumar S, Button-Simons KA, Vendrely Brenneman KM, Dahlhoff H, Sievert MAC, Checkley LA, Shoue DA, Singh PP, Abatiyow BA, Haile MT, Nair S, Reyes A, Tripura R, Peto TJ, Lek D, Mukherjee A, Kappe SHI, Dhorda M, Nkhoma SC, Cheeseman IH, Vaughan AM, Anderson TJC, Ferdig MT. A Plasmodium falciparum genetic cross reveals the contributions of pfcrt and plasmepsin II/III to piperaquine drug resistance. mBio 2024; 15:e0080524. [PMID: 38912775 PMCID: PMC11253641 DOI: 10.1128/mbio.00805-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Piperaquine (PPQ) is widely used in combination with dihydroartemisinin as a first-line treatment against malaria. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multidrug-resistant KEL1/PLA1 lineage isolate (KH004) and a drug-susceptible Malawian parasite (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and multiple copies of pm2/3. We recovered 104 unique recombinant parasites and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3. We performed a detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes with these progenies, including PPQ survival assay, area under the dose response curve, and a limited point IC50. We find that inheritance of the KH004 pfcrt allele is required for reduced PPQ sensitivity, whereas copy number variation in pm2/3 further decreases susceptibility but does not confer resistance in the absence of additional mutations in pfcrt. A deep investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background to a range of PPQ-related traits. Additionally, we find that the resistance phenotype associated with parasites inheriting the G367C substitution in pfcrt is consistent with previously validated PPQ resistance mutations in this transporter.IMPORTANCEResistance to piperaquine, used in combination with dihydroartemisinin, has emerged in Cambodia and threatens to spread to other malaria-endemic regions. Understanding the causal mutations of drug resistance and their impact on parasite fitness is critical for surveillance and intervention and can also reveal new avenues to limiting the evolution and spread of drug resistance. An experimental genetic cross is a powerful tool for pinpointing the genetic determinants of key drug resistance and fitness phenotypes and has the distinct advantage of quantifying the effects of naturally evolved genetic variation. Our study was strengthened since the full range of copies of KH004 pm2/3 was inherited among the progeny clones, allowing us to directly test the role of the pm2/3 copy number on resistance-related phenotypes in the context of a unique pfcrt allele. Our multigene model suggests an important role for both loci in the evolution of this multidrug-resistant parasite lineage.
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Affiliation(s)
- John Kane
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Katrina A. Button-Simons
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Katelyn M. Vendrely Brenneman
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Haley Dahlhoff
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Mackenzie A. C. Sievert
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lisa A. Checkley
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Douglas A. Shoue
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Puspendra P. Singh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ann Reyes
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Rupam Tripura
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, United Kingdom
| | - Thomas J. Peto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, United Kingdom
| | - Dysoley Lek
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
- School of Public Health, National Institute of Public Health, Phnom Penh, Cambodia
| | - Angana Mukherjee
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, USA
| | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, United Kingdom
| | - Standwell C. Nkhoma
- BEI Resources, American Type Culture Collection (ATCC), Manassas, Virginia, USA
| | - Ian H. Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Timothy J. C. Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Michael T. Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
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5
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Rosenthal PJ, Asua V, Conrad MD. Emergence, transmission dynamics and mechanisms of artemisinin partial resistance in malaria parasites in Africa. Nat Rev Microbiol 2024; 22:373-384. [PMID: 38321292 DOI: 10.1038/s41579-024-01008-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2024] [Indexed: 02/08/2024]
Abstract
Malaria, mostly due to Plasmodium falciparum infection in Africa, remains one of the most important infectious diseases in the world. Standard treatment for uncomplicated P. falciparum malaria is artemisinin-based combination therapy (ACT), which includes a rapid-acting artemisinin derivative plus a longer-acting partner drug, and standard therapy for severe P. falciparum malaria is intravenous artesunate. The efficacy of artemisinins and ACT has been threatened by the emergence of artemisinin partial resistance in Southeast Asia, mediated principally by mutations in the P. falciparum Kelch 13 (K13) protein. High ACT treatment failure rates have occurred when resistance to partner drugs is also seen. Recently, artemisinin partial resistance has emerged in Rwanda, Uganda and the Horn of Africa, with independent emergences of different K13 mutants in each region. In this Review, we summarize our current knowledge of artemisinin partial resistance and focus on the emergence of resistance in Africa, including its epidemiology, transmission dynamics and mechanisms. At present, the clinical impact of emerging resistance in Africa is unclear and most available evidence suggests that the efficacies of leading ACTs remain excellent, but there is an urgent need to better appreciate the extent of the problem and its consequences for the treatment and control of malaria.
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Affiliation(s)
| | - Victor Asua
- Infectious Diseases Research Collaboration, Kampala, Uganda
- University of Tübingen, Tübingen, Germany
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Rotejanaprasert C, Malaphone V, Mayxay M, Chindavongsa K, Banouvong V, Khamlome B, Vilay P, Vanisavaeth V, Maude RJ. Malaria epidemiology, surveillance and response for elimination in Lao PDR. Infect Dis Poverty 2024; 13:35. [PMID: 38783374 PMCID: PMC11112833 DOI: 10.1186/s40249-024-01202-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Lao PDR has made significant progress in malaria control. The National Strategic Plans outline ambitious targets, aiming for the elimination of Plasmodium falciparum and P. vivax malaria from all northern provinces by 2025 and national elimination by 2030. This article presents an overview of malaria epidemiology, surveillance, and response systems in Lao PDR, emphasizing experiences and achievements in transmission reduction. METHODS Data on surveillance, monitoring and evaluation systems, human resources, infrastructure, and community malaria knowledge during 2010-2020 were systematically gathered from the national program and relevant documents. The collected information was synthesized, and discussions on challenges and future prospects were provided. RESULTS Malaria control and elimination activities in Lao PDR were implemented at various levels, with a focus on health facility catchment areas. There has been significant progress in reducing malaria transmission throughout the country. Targeted interventions, such as case management, vector control, and community engagement, using stratification of control interventions by catchment areas have contributed to the decline in malaria cases. In elimination areas, active surveillance strategies, including case and foci investigation, are implemented to identify and stop transmission. The surveillance system has facilitated timely detection and response to malaria cases, enabling these targeted interventions in higher-risk areas. CONCLUSIONS The malaria surveillance and response system in Lao PDR has played a crucial role in reducing transmission and advancing the country towards elimination. Challenges such as importation, drug resistance, and sustaining support require ongoing efforts. Further strengthening surveillance, improving access to services, and addressing transmission determinants are key areas of focus to achieve malaria elimination and enhance population health in Lao PDR.
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Affiliation(s)
- Chawarat Rotejanaprasert
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Vilayvone Malaphone
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Institute of Research and Education Development, University of Health Sciences, Ministry of Health, Vientiane, Laos
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Virasack Banouvong
- Center of Malariology, Parasitology, and Entomology, Vientiane, Lao PDR, Laos
| | - Boualam Khamlome
- Center of Malariology, Parasitology, and Entomology, Vientiane, Lao PDR, Laos
| | - Phoutnalong Vilay
- Center of Malariology, Parasitology, and Entomology, Vientiane, Lao PDR, Laos
| | | | - Richard J Maude
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Open University, Milton Keynes, UK
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7
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Girgis ST, Adika E, Nenyewodey FE, Senoo Jnr DK, Ngoi JM, Bandoh K, Lorenz O, van de Steeg G, Harrott AJR, Nsoh S, Judge K, Pearson RD, Almagro-Garcia J, Saiid S, Atampah S, Amoako EK, Morang'a CM, Asoala V, Adjei ES, Burden W, Roberts-Sengier W, Drury E, Pierce ML, Gonçalves S, Awandare GA, Kwiatkowski DP, Amenga-Etego LN, Hamilton WL. Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana. Nat Microbiol 2023; 8:2365-2377. [PMID: 37996707 PMCID: PMC10686832 DOI: 10.1038/s41564-023-01516-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/06/2023] [Indexed: 11/25/2023]
Abstract
Malaria results in over 600,000 deaths annually, with the highest burden of deaths in young children living in sub-Saharan Africa. Molecular surveillance can provide important information for malaria control policies, including detection of antimalarial drug resistance. However, genome sequencing capacity in malaria-endemic countries is limited. We designed and implemented an end-to-end workflow to detect Plasmodium falciparum antimalarial resistance markers and diversity in the vaccine target circumsporozoite protein (csp) using nanopore sequencing in Ghana. We analysed 196 clinical samples and showed that our method is rapid, robust, accurate and straightforward to implement. Importantly, our method could be applied to dried blood spot samples, which are readily collected in endemic settings. We report that P. falciparum parasites in Ghana are mostly susceptible to chloroquine, with persistent sulfadoxine-pyrimethamine resistance and no evidence of artemisinin resistance. Multiple single nucleotide polymorphisms were identified in csp, but their significance is uncertain. Our study demonstrates the feasibility of nanopore sequencing for malaria genomic surveillance in endemic countries.
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Affiliation(s)
- Sophia T Girgis
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Edem Adika
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Felix E Nenyewodey
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Dodzi K Senoo Jnr
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Joyce M Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Kukua Bandoh
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Oliver Lorenz
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Guus van de Steeg
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Sebastian Nsoh
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Kim Judge
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Samirah Saiid
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Solomon Atampah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Enock K Amoako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Victor Asoala
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Elrmion S Adjei
- Ledzokuku Krowor Municipal Assembly (LEKMA) Hospital, Accra, Ghana
| | - William Burden
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Eleanor Drury
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Megan L Pierce
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sónia Gonçalves
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | | | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.
| | - William L Hamilton
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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8
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Cao VAT, Nguyen TQ, Le Quyen D, Boon WPC, Moors EHM, Dondorp AM, de Haan F, Amaratunga C. Exploring the feasibility of introducing triple artemisinin-based combination therapy in the malaria treatment policy in Vietnam. Malar J 2023; 22:326. [PMID: 37898749 PMCID: PMC10613363 DOI: 10.1186/s12936-023-04763-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/22/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND This study investigates the processes regarding changing malaria treatment policies in Vietnam. Moreover, it explores the feasibility of introducing triple artemisinin-based combination therapy (TACT) in Vietnam to support the national malaria control and elimination plan. METHODS Data were collected via 12 in-depth interviews with key stakeholders, combined with a review of policy documents. RESULTS TACT is considered as a useful backup strategy in case future treatment failures with current artemisinin-based combination therapy (ACT) would occur. Moreover, TACT is also considered as a promising strategy to prevent the re-establishment of malaria. However, regulatory procedures and implementation timelines for TACT were expected to be lengthy. Therefore, strategies to engage national decision-makers, regulators, and suppliers should be initiated soon, stipulating the benefits of TACT deployment. In Vietnam, a procedure to apply for an import permit without registration that has previously been applied to the introduction of artesunate-pyronaridine was proposed to accelerate the introduction of TACT. Global-level support through the World Health Organization recommendations and prequalification were considered critical for supporting the introduction of TACT in Vietnam. CONCLUSIONS Appropriate approach strategies and early stakeholder engagement will be needed to accelerate the introduction of TACT in Vietnam.
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Affiliation(s)
- Van Anh Thi Cao
- The University of North Carolina Project Office, Hanoi, Vietnam.
| | - Thieu Quang Nguyen
- National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | | | - Wouter P C Boon
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands
| | - Ellen H M Moors
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands
| | - Arjen M Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Freek de Haan
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands
| | - Chanaki Amaratunga
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Fola AA, Feleke SM, Mohammed H, Brhane BG, Hennelly CM, Assefa A, Crudal RM, Reichert E, Juliano JJ, Cunningham J, Mamo H, Solomon H, Tasew G, Petros B, Parr JB, Bailey JA. Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia. Nat Microbiol 2023; 8:1911-1919. [PMID: 37640962 PMCID: PMC10522486 DOI: 10.1038/s41564-023-01461-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/26/2023] [Indexed: 08/31/2023]
Abstract
Diagnosis and treatment of Plasmodium falciparum infections are required for effective malaria control and are pre-requisites for malaria elimination efforts; hence we need to monitor emergence, evolution and spread of drug- and diagnostics-resistant parasites. We deep sequenced key drug-resistance mutations and 1,832 SNPs in the parasite genomes of 609 malaria cases collected during a diagnostic-resistance surveillance study in Ethiopia. We found that 8.0% (95% CI 7.0-9.0) of malaria cases were caused by P. falciparum carrying the candidate artemisinin partial-resistance kelch13 (K13) 622I mutation, which was less common in diagnostic-resistant parasites mediated by histidine-rich proteins 2 and 3 (pfhrp2/3) deletions than in wild-type parasites (P = 0.03). Identity-by-descent analyses showed that K13 622I parasites were significantly more related to each other than to wild type (P < 0.001), consistent with recent expansion and spread of this mutation. Pfhrp2/3-deleted parasites were also highly related, with evidence of clonal transmissions at the district level. Of concern, 8.2% of K13 622I parasites also carried the pfhrp2/3 deletions. Close monitoring of the spread of combined drug- and diagnostic-resistant parasites is needed.
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Affiliation(s)
- Abebe A Fola
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | | | | | | | - Christopher M Hennelly
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca M Crudal
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Emily Reichert
- Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Geremew Tasew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jonathan B Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.
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10
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Guissou RM, Amaratunga C, de Haan F, Tou F, Cheah PY, Yerbanga RS, Moors EHM, Dhorda M, Tindana P, Boon WPC, Dondorp AM, Ouédraogo JB. The impact of anti-malarial markets on artemisinin resistance: perspectives from Burkina Faso. Malar J 2023; 22:269. [PMID: 37705004 PMCID: PMC10498571 DOI: 10.1186/s12936-023-04705-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Widespread artemisinin resistance in Africa could be catastrophic when drawing parallels with the failure of chloroquine in the 1970s and 1980s. This article explores the role of anti-malarial market characteristics in the emergence and spread of arteminisin resistance in African countries, drawing on perspectives from Burkina Faso. METHODS Data were collected through in-depth interviews and focus group discussions. A representative sample of national policy makers, regulators, public and private sector wholesalers, retailers, clinicians, nurses, and community members were purposively sampled. Additional information was also sought via review of policy publications and grey literature on anti-malarial policies and deployment practices in Burkina Faso. RESULTS Thirty seven in-depth interviews and 6 focus group discussions were conducted. The study reveals that the current operational mode of anti-malarial drug markets in Burkina Faso promotes arteminisin resistance emergence and spread. The factors are mainly related to the artemisinin-based combination therapy (ACT) supply chain, to ACT quality, ACT prescription monitoring and to ACT access and misuse by patients. CONCLUSION Study findings highlight the urgent requirement to reform current characteristics of the anti-malarial drug market in order to delay the emergence and spread of artemisinin resistance in Burkina Faso. Four recommendations for public policy emerged during data analysis: (1) Address the suboptimal prescription of anti-malarial drugs, (2) Apply laws that prohibit the sale of anti-malarials without prescription, (3) Restrict the availability of street drugs, (4) Sensitize the population on the value of compliance regarding correct acquisition and intake of anti-malarials. Funding systems for anti-malarial drugs in terms of availability and accessibility must also be stabilized.
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Affiliation(s)
- Rosemonde M Guissou
- Institut de Recherche en Sciences de la Sante, Centre National de la Recherche Scientifique et Technologique, Ouagadougou, Burkina Faso.
| | - Chanaki Amaratunga
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Freek de Haan
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands
| | - Fatoumata Tou
- Institut des Sciences et Techniques, Bobo-Dioulasso, Burkina Faso
| | - Phaik Yeong Cheah
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - R Serge Yerbanga
- Institut de Recherche en Sciences de la Sante, Centre National de la Recherche Scientifique et Technologique, Ouagadougou, Burkina Faso
- Institut des Sciences et Techniques, Bobo-Dioulasso, Burkina Faso
| | - Ellen H M Moors
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands
| | - Mehul Dhorda
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paulina Tindana
- School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Wouter P C Boon
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands
| | - Arjen M Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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11
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Meena P, Jha V. Environmental Change, Changing Biodiversity, and Infections-Lessons for Kidney Health Community. Kidney Int Rep 2023; 8:1714-1729. [PMID: 37705916 PMCID: PMC10496083 DOI: 10.1016/j.ekir.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 09/15/2023] Open
Abstract
There is a direct and accelerating connection between ongoing environmental change, the unprecedented decline in biodiversity, and the increase in infectious disease epidemiology worldwide. Rising global temperatures are threatening the biodiversity that underpins the richness and diversity of flora and fauna species in our ecosystem. Anthropogenic activities such as burning fossil fuels, deforestation, rapid urbanization, and expanding population are the primary drivers of environmental change resulting in biodiversity collapse. Climate change is influencing the emergence, prevalence, and transmission of infectious diseases both directly and through its impact on biodiversity. The environment is gradually becoming more suitable for infectious diseases by affecting a variety of pathogens, hosts, and vectors and by favoring transmission rates in many parts of the world that were until recently free of these infections. The acute effects of these zoonotic, vector and waterborne diseases are well known; however, evidence is emerging about their role in the development of chronic kidney disease. The pathways linking environmental change and biodiversity loss to infections impacting kidney health are diverse and complex. Climate change and biodiversity loss disproportionately affect the vulnerable and limit their ability to access healthcare. The kidney health community needs to contribute to the issue of environmental change and biodiversity loss through multisectoral action alongside government, policymakers, advocates, businesses, and the general population. We describe various aspects of the environmental change effects on the transmission and emergence of infectious diseases particularly focusing on its potential impact on kidney health. We also discuss the adaptive and mitigation measures and the gaps in research and policy action.
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Affiliation(s)
- Priti Meena
- Department of Nephrology, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Vivekanand Jha
- George Institute for Global Health, UNSW, New Delhi, India
- Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, India
- School of Public Health, Imperial College, London, UK
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12
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Barry AE. Malaria outbreak in Laos caused by formerly rare artemisinin resistant strains of Plasmodium falciparum. THE LANCET INFECTIOUS DISEASES 2022; 23:513-514. [PMID: 36462527 DOI: 10.1016/s1473-3099(22)00761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Alyssa E Barry
- Institute for Mental and Physical Health and Clinical Translation and School of Medicine, Deakin University, Geelong, VIC 3220, Australia; Burnet Institute, Melbourne, VIC, Australia.
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