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Milong Melong CS, Peloewetse E, Russo G, Tamgue O, Tchoumbougnang F, Paganotti GM. An overview of artemisinin-resistant malaria and associated Pfk13 gene mutations in Central Africa. Parasitol Res 2024; 123:277. [PMID: 39023630 DOI: 10.1007/s00436-024-08301-2] [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: 04/02/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Malaria caused by Plasmodium falciparum is one of the deadliest and most common tropical infectious diseases. However, the emergence of artemisinin drug resistance associated with the parasite's Pfk13 gene, threatens the public health of individual countries as well as current efforts to reduce malaria burdens globally. It is of concern that artemisinin-resistant parasites may be selected or have already emerged in Africa. This narrative review aims to evaluate the published evidence concerning validated, candidate, and novel Pfk13 polymorphisms in ten Central African countries. Results show that four validated non-synonymous polymorphisms (M476I, R539T, P553L, and P574L), directly associated with a delayed therapy response, have been reported in the region. Also, two Pfk13 polymorphisms associated to artemisinin resistance but not validated (C469F and P527H) have been reported. Furthermore, several non-validated mutations have been observed in Central Africa, and one allele A578S, is commonly found in different countries, although additional molecular and biochemical studies are needed to investigate whether those mutations alter artemisinin effects. This information is discussed in the context of biochemical and genetic aspects of Pfk13, and related to the regional malaria epidemiology of Central African countries.
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Affiliation(s)
- Charlotte Sabine Milong Melong
- Department of Biochemistry, Faculty of Sciences, University of Douala, P.O. Box 24157, Douala, Cameroon
- Botswana-University of Pennsylvania Partnership, P.O. Box 45498, Gaborone, Riverwalk, Botswana
| | - Elias Peloewetse
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Private Bag, 0022, Gaborone, UB, Botswana
| | - Gianluca Russo
- Department of Public Health and Infectious Diseases, Faculty of Pharmacy and Medicine, Sapienza University of Rome, P.Le Aldo Moro 5, 00185, Rome, Italy
| | - Ousman Tamgue
- Department of Biochemistry, Faculty of Sciences, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Francois Tchoumbougnang
- Department of Processing and Quality Control of Aquatic Products, Institute of Fisheries and Aquatic Sciences, University of Douala, P.O. Box 7236, Douala, Cameroon
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, P.O. Box 45498, Gaborone, Riverwalk, Botswana.
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, 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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Popkin-Hall ZR, Niaré K, Crudale R, Simkin A, Fola AA, Sanchez JF, Pannebaker DL, Giesbrecht DJ, Kim IE, Aydemir Ö, Bailey JA, Valdivia HO, Juliano JJ. High-Throughput Genotyping of Plasmodium vivax in the Peruvian Amazon via Molecular Inversion Probes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.27.24309599. [PMID: 38978652 PMCID: PMC11230302 DOI: 10.1101/2024.06.27.24309599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Plasmodium vivax transmission occurs throughout the tropics and is an emerging threat in areas of Plasmodium falciparum decline, causing relapse infections that complicate treatment and control. Targeted sequencing for P. falciparum has been widely deployed to detect population structure and the geographic spread of antimalarial and diagnostic resistance. However, there are fewer such tools for P. vivax . Leveraging global variation data, we designed four molecular inversion probe (MIP) genotyping panels targeting geographically differentiating SNPs, neutral SNPs, putative antimalarial resistance genes, and vaccine candidate genes. We deployed these MIP panels on 866 infections from the Peruvian Amazon and identified transmission networks with clonality (IBD>0.99), copy number variation in Pvdbp and multiple Pvrbps , fixation of putative antimalarial resistance, and balancing selection in 13 vaccine candidate genes. Our MIP panels are the broadest genotyping panel currently available and are poised for successful deployment in other regions of P. vivax transmission.
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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; 15:e0198123. [PMID: 38700363 PMCID: PMC11237660 DOI: 10.1128/mbio.01981-23] [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: 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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Ciubotariu II, Broyles BK, Xie S, Thimmapuram J, Mwenda MC, Mambwe B, Mulube C, Matoba J, Schue JL, Moss WJ, Bridges DJ, He Q, Carpi G. Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.11.24307175. [PMID: 38766239 PMCID: PMC11100930 DOI: 10.1101/2024.05.11.24307175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background A highly effective vaccine for malaria remains an elusive target, at least in part due to the under-appreciated natural parasite variation. This study aimed to investigate genetic and structural variation, and immune selection of leading malaria vaccine candidates across the Plasmodium falciparum's life cycle. Methods We analyzed 325 P. falciparum whole genome sequences from Zambia, in addition to 791 genomes from five other African countries available in the MalariaGEN Pf3k Rdatabase. Ten vaccine antigens spanning three life-history stages were examined for genetic and structural variations, using population genetics measures, haplotype network analysis, and 3D structure selection analysis. Findings Among the ten antigens analyzed, only three in the transmission-blocking vaccine category display P. falciparum 3D7 as the dominant haplotype. The antigens AMA1, CSP, MSP119 and CelTOS, are much more diverse than the other antigens, and their epitope regions are under moderate to strong balancing selection. In contrast, Rh5, a blood stage antigen, displays low diversity yet slightly stronger immune selection in the merozoite-blocking epitope region. Except for CelTOS, the transmission-blocking antigens Pfs25, Pfs48/45, Pfs230, Pfs47, and Pfs28 exhibit minimal diversity and no immune selection in epitopes that induce strain-transcending antibodies, suggesting potential effectiveness of 3D7-based vaccines in blocking transmission. Interpretations These findings offer valuable insights into the selection of optimal vaccine candidates against P. falciparum. Based on our results, we recommend prioritizing conserved merozoite antigens and transmission-blocking antigens. Combining these antigens in multi-stage approaches may be particularly promising for malaria vaccine development initiatives. Funding Purdue Department of Biological Sciences; Puskas Memorial Fellowship; National Institute of Allergy and Infectious Diseases (U19AI089680).
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Affiliation(s)
- Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Bradley K. Broyles
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Mulenga C. Mwenda
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | | | - Jessica L. Schue
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - William J. Moss
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana, USA
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Wang T, Shen H, Xu B, Yang W, Chen S, Chen J. Genome Analysis of Plasmodium falciparum: A Preliminary Observation - Sierra Leone, 2022-2023. China CDC Wkly 2024; 6:368-373. [PMID: 38737823 PMCID: PMC11082561 DOI: 10.46234/ccdcw2024.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/21/2024] [Indexed: 05/14/2024] Open
Abstract
What is already known about this topic? Sierra Leone, with a gross domestic product (GDP) per capita below $300 and significant poverty, ranks among the world's least developed countries (LDCs). Despite its modest population of 8.6 million, the nation reports approximately 2.6 million malaria cases annually. Previously, there has been no reporting on the malaria genome data from this country. What is added by this report? In this study, we present the first reported whole-genome sequence analysis of 19 high parasite-density Plasmodium falciparum isolates from Sierra Leone, providing insights into the genomic epidemiology of this high-prevalence area. We found a high degree of relatedness among infections and substantial genetic diversity, consistent with the gradual reduction in overall case numbers. Moreover, our whole-genome analysis revealed that, beyond drug-resistance genes, gene families related to blood cell invasion, immune evasion, and others are undergoing directional selection. This suggests that the population in Sierra Leone has developed a relatively strong acquired immunity. What are the implications for public health practice? The genomic data not only facilitate the creation of single nucleotide polymorphism barcodes for case tracking but also enable the analysis of evolving transmission dynamics and selection pressures. Additionally, the samples from Sierra Leone exhibited higher selective pressures on resistance genes compared to those from Asia, a trend not commonly observed in other African samples. This suggests that less stringent healthcare systems and inconsistent treatment strategies can subject parasites to increased drug pressure, thereby accelerating the development of resistant strains.
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Affiliation(s)
- Tianyu Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Haimo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Wanxuan Yang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou City, Zhejiang Province, China
| | - Shenbo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Junhu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou City, Zhejiang Province, China
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Hainan Tropical Diseases Research Center (Hainan Sub-Center, Chinese Center for Tropical Diseases Research), Haikou City, Hainan Province, China
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Zupko RJ, Servadio JL, Nguyen TD, Tran TNA, Tran KT, Somé AF, Boni MF. Role of seasonal importation and genetic drift on selection for drug-resistant genotypes of Plasmodium falciparum in high-transmission settings. J R Soc Interface 2024; 21:20230619. [PMID: 38442861 PMCID: PMC10914515 DOI: 10.1098/rsif.2023.0619] [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: 10/23/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Historically Plasmodium falciparum has followed a pattern of drug resistance first appearing in low-transmission settings before spreading to high-transmission settings. Several features of low-transmission regions are hypothesized as explanations: higher chance of symptoms and treatment seeking, better treatment access, less within-host competition among clones and lower rates of recombination. Here, we test whether importation of drug-resistant parasites is more likely to lead to successful emergence and establishment in low-transmission or high-transmission periods of the same epidemiological setting, using a spatial, individual-based stochastic model of malaria and drug-resistance evolution calibrated for Burkina Faso. Upon controlling for the timing of importation of drug-resistant genotypes and examination of key model variables, we found that drug-resistant genotypes imported during the low-transmission season were (i) more susceptible to stochastic extinction due to the action of genetic drift, and (ii) more likely to lead to establishment of drug resistance when parasites are able to survive early stochastic loss due to drift. This implies that rare importation events are more likely to lead to establishment if they occur during a high-transmission season, but that constant importation (e.g. neighbouring countries with high levels of resistance) may produce a greater risk during low-transmission periods.
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Affiliation(s)
- Robert J. Zupko
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph L. Servadio
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Tran Dang Nguyen
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Kien Trung Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Anyirékun Fabrice Somé
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l'Ouest, Bobo Dioulasso, Burkina Faso
| | - Maciej F. Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Matrevi SA, Adams T, Tandoh KZ, Opoku-Agyeman P, Bruku S, Ennuson NA, Apau-Danso PK, Fiagbedzi E, Avornyo M, Myers CJ, Futagbi J, Hagan OC, Abuaku B, Koram KA, Awandare G, Quashie NB, Duah-Quashie NO. Putative molecular markers of Plasmodium falciparum resistance to antimalarial drugs in malaria parasites from Ghana. FRONTIERS IN EPIDEMIOLOGY 2024; 4:1279835. [PMID: 38456076 PMCID: PMC10910922 DOI: 10.3389/fepid.2024.1279835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
Introduction Antimalarial drugs including artemisinin-based combination therapy (ACT) regimens and sulphadoxine-pyrimethamine (SP) are used in Ghana for malaria therapeutics and prophylaxis respectively. The genetic basis of Plasmodium falciparum development of drug resistance involves single nucleotide polymorphisms in genes encoding proteins for multiple cellular and metabolic processes. The prevalence of single nucleotide polymorphisms in nine P. falciparum genes linked to ACT and SP resistance in the malaria parasite population was determined. Methods Archived filter paper blood blot samples from patients aged 9 years and below with uncomplicated malaria reporting at 10 sentinel sites located in three ecological zones for the Malaria Therapeutic Efficacy Studies were used. The samples used were collected from 2007-2018 malaria transmission seasons and mutations in the genes were detected using PCR and Sanger sequencing. Results In all 1,142 samples were used for the study. For falcipain-2 gene (pffp2), Sanger sequencing was successful for 872 samples and were further analysed. The prevalence of the mutants was 45% (392/872) with pffp2 markers V51I and S59F occurring in 15.0% (128/872) and 3.0% (26/872) of the samples respectively. Prevalence of other P. falciparum gene mutations: coronin (pfcoronin) was 44.8% (37/90); cysteine desulfurase (pfnfs) was 73.9% (68/92); apicoplast ribosomal protein S10 (pfarps10) was 36.8% (35/95); ferredoxin (pffd) was 8.8% (8/91); multidrug resistance protein-1 (pfmrp1) was 95.2.0% (80/84); multidrug resistance protein-2 (pfmrp2) was 91.4% (32/35); dihydrofolate reductase (pfdhfr) was 99.0% (84/85); dihydropteroate synthase (pfdhps) was 72% (68/95). Discussion The observation of numerous mutations in these genes of interest in the Ghanaian isolates, some of which have been implicated in delayed parasite clearance is of great interest. The presence of these genotypes may account for the decline in the efficacies of ACT regimens being used to treat uncomplicated malaria in the country. The need for continuous monitoring of these genetic markers to give first-hand information on parasite susceptibility to antimalarial drugs to inform policy makers and stakeholders in malaria elimination in the country is further discussed.
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Affiliation(s)
- Sena Adzoa Matrevi
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Tryphena Adams
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Kwesi Zandoh Tandoh
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Philip Opoku-Agyeman
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Selassie Bruku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nana Aba Ennuson
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Paa Kwesi Apau-Danso
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Emmanuel Fiagbedzi
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Mary Avornyo
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Charles James Myers
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Joy Futagbi
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Oheneba Charles Hagan
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Benjamin Abuaku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Kwadwo Ansah Koram
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Gordon Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Neils Ben Quashie
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Nancy Odurowah Duah-Quashie
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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9
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de Cesare M, Mwenda M, Jeffreys AE, Chirwa J, Drakeley C, Schneider K, Mambwe B, Glanz K, Ntalla C, Carrasquilla M, Portugal S, Verity RJ, Bailey JA, Ghinai I, Busby GB, Hamainza B, Hawela M, Bridges DJ, Hendry JA. Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing. Nat Commun 2024; 15:1413. [PMID: 38360754 PMCID: PMC10869361 DOI: 10.1038/s41467-024-45688-z] [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: 03/06/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3-4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.
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Affiliation(s)
- Mariateresa de Cesare
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | | | - Anna E Jeffreys
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Jacob Chirwa
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | | | | | | | - Karolina Glanz
- Max Planck Institute for Infection Biology, Berlin, Germany
| | | | | | | | | | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Isaac Ghinai
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - George B Busby
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Busiku Hamainza
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | - Moonga Hawela
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | | | - Jason A Hendry
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK.
- Max Planck Institute for Infection Biology, Berlin, Germany.
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10
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Gnondjui AA, Toure OA, Ako BA, Koui TS, Assohoun SE, Gbessi EA, N'Guessan LT, Tuo K, Beourou S, Assi SB, Yapo FA, Sanogo I, Jambou R. In vitro delayed response to dihydroartemisinin of malaria parasites infecting sickle cell erythocytes. Malar J 2024; 23:9. [PMID: 38178227 PMCID: PMC10768257 DOI: 10.1186/s12936-023-04819-5] [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: 05/23/2023] [Accepted: 12/09/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Decreased efficacy of artemisinin-based combination therapy (ACT) for Plasmodium falciparum malaria has been previously reported in patients with sickle cell disease (SCD). The main purpose of this study was to investigate the in vitro susceptibility of isolates to dihydro-artemisinin (DHA) to provide a hypothesis to explain this treatment failure. METHODS Isolates were collected from patients attending health centres in Abidjan with uncomplicated P. falciparum malaria. The haemoglobin type has been identified and in vitro drug sensitivity tests were conducted with the ring stage assay and maturation inhibition assay. RESULTS 134 isolates were obtained. Parasitaemia and haemoglobin levels at inclusion were lower in patients with haemoglobin HbSS and HbSC than in patients with normal HbAA. After ex vivo RSA and drug inhibition assays, the lowest rate of parasitic growth was found with isolates from HbAS red cells. Conversely, a significantly higher survival rate of parasites ranging from 15 to 34% were observed in isolates from HbSS. Isolates with in vitro reduced DHA sensitivity correlate with lower RBC count and haematocrit and higher parasitaemia at inclusion compared to those with isolates with normal DHA sensitivity. However, this decrease of in vitro sensitivity to DHA was not associated with Kelch 13-Propeller gene polymorphism. CONCLUSION This study highlights an in vitro decreased sensitivity to DHA, for isolates collected from HbSS patients, not related to the Pfkelch13 gene mutations. These results are in line with recent studies pointing out the role of the redox context in the efficacy of the drug. Indeed, SCD red cells harbour a highly different ionic and redox context in comparison with normal red cells. This study offers new insights into the understanding of artemisinin selective pressure on the malaria parasite in the context of haemoglobinopathies in Africa.
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Affiliation(s)
- Albert A Gnondjui
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
- Laboratoire Biologie et Santé, Université Felix Houphouët Boigny, Abidjan, Côte d'Ivoire
| | - Offianan A Toure
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Berenger A Ako
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Tossea S Koui
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
- Laboratoire Biologie et Santé, Université Felix Houphouët Boigny, Abidjan, Côte d'Ivoire
| | - Stanislas E Assohoun
- Laboratoire de Mécanique et Informatique, Université Felix Houphouët BoignyCôte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Eric A Gbessi
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
- Laboratoire Biologie et Santé, Université Felix Houphouët Boigny, Abidjan, Côte d'Ivoire
| | - Landry T N'Guessan
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Karim Tuo
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Sylvain Beourou
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Serge-Brice Assi
- Institut Pierre Richet/Programme National de Lutte contre le Paludisme, Bouaké, Côte d'Ivoire
| | - Francis A Yapo
- Laboratoire Biologie et Santé, Université Felix Houphouët Boigny, Abidjan, Côte d'Ivoire
| | | | - Ronan Jambou
- Unité de Paludologie, Institut Pasteur Côte d'Ivoire, 01 BP 490, Abidjan 01, Côte d'Ivoire.
- Global Health Department, Institut Pasteur Paris, 25 rue du Dr Roux, 75015, Paris, France.
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11
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Dieng CC, Morrison V, Donu D, Cui L, Amoah L, Afrane Y, Lo E. Distribution of Plasmodium falciparum K13 gene polymorphisms across transmission settings in Ghana. BMC Infect Dis 2023; 23:801. [PMID: 37974079 PMCID: PMC10652499 DOI: 10.1186/s12879-023-08812-w] [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: 12/14/2022] [Accepted: 11/12/2023] [Indexed: 11/19/2023] Open
Abstract
Malaria is a significant global health concern, with a majority of cases in Sub-Saharan African nations. Numerous antimalarial drugs have been developed to counter the rampant prevalence of Plasmodium falciparum malaria. Artemisinin-based Combination Therapy (ACT) has served as the primary treatment of uncomplicated malaria in Ghana since 2005. However, a growing concern has emerged due to the escalating reports of ACT resistance, particularly in Southeast Asia, and its encroachment into Africa. Specifically, mutations in the Kelch propeller domain on chromosome 13 (Pfk13) have been linked to ACT resistance. Yet, our understanding of mutation prevalence in Africa remains largely uncharted. In this study, we compared Pfk13 sequences obtained from 172 P. falciparum samples across three ecological and transmission zones in Ghana. We identified 27 non-synonymous mutations among these sequences, of which two of the mutations, C580Y (found in two samples from the central region) and Y493H (found in one sample from the north), had previously been validated for their association with artemisinin resistance, a phenomenon widespread in Southeast Asia. The Pfk13 gene diversity was most pronounced in the northern savannah than the central forest and south coastal regions, where transmission rates are lower. The observed mutations were not significantly associated with geographical regions, suggesting a frequent spread of mutations across the country. The ongoing global surveillance of artemisinin resistance remains pivotal, and our findings provides insights into the potential spread of resistant parasites in West Africa. Furthermore, the identification of novel codon mutations in this study raises their potential association to ACT resistance, warranting further investigation through in vitro assays to ascertain their functional significance.
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Affiliation(s)
- Cheikh Cambel Dieng
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA.
| | - Victoria Morrison
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Dickson Donu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Liwang Cui
- Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Linda Amoah
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West Africa Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Yaw Afrane
- Department of Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Eugenia Lo
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA.
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12
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Mok S, Yeo T, Hong D, Shears MJ, Ross LS, Ward KE, Dhingra SK, Kanai M, Bridgford JL, Tripathi AK, Mlambo G, Burkhard AY, Ansbro MR, Fairhurst KJ, Gil-Iturbe E, Park H, Rozenberg FD, Kim J, Mancia F, Fairhurst RM, Quick M, Uhlemann AC, Sinnis P, Fidock DA. Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness. SCIENCE ADVANCES 2023; 9:eadi2364. [PMID: 37939186 PMCID: PMC10631731 DOI: 10.1126/sciadv.adi2364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Drug-resistant Plasmodium falciparum parasites have swept across Southeast Asia and now threaten Africa. By implementing a P. falciparum genetic cross using humanized mice, we report the identification of key determinants of resistance to artemisinin (ART) and piperaquine (PPQ) in the dominant Asian KEL1/PLA1 lineage. We mapped k13 as the central mediator of ART resistance in vitro and identified secondary markers. Applying bulk segregant analysis, quantitative trait loci mapping using 34 recombinant haplotypes, and gene editing, our data reveal an epistatic interaction between mutant PfCRT and multicopy plasmepsins 2/3 in mediating high-grade PPQ resistance. Susceptibility and parasite fitness assays implicate PPQ as a driver of selection for KEL1/PLA1 parasites. Mutant PfCRT enhanced susceptibility to lumefantrine, the first-line partner drug in Africa, highlighting a potential benefit of opposing selective pressures with this drug and PPQ. We also identified that the ABCI3 transporter can operate in concert with PfCRT and plasmepsins 2/3 in mediating multigenic resistance to antimalarial agents.
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Affiliation(s)
- Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Davin Hong
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Melanie J. Shears
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Leila S. Ross
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kurt E. Ward
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Satish K. Dhingra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mariko Kanai
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Jessica L. Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Abhai K. Tripathi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Godfree Mlambo
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Y. Burkhard
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan R. Ansbro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Kate J. Fairhurst
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Felix D. Rozenberg
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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13
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Zupko RJ, Servadio JL, Nguyen TD, Tran TNA, Tran KT, Somé AF, Boni MF. Role of Seasonal Importation and Random Genetic Drift on Selection for Drug-Resistant Genotypes of Plasmodium falciparum in High Transmission Settings. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563204. [PMID: 37961194 PMCID: PMC10634683 DOI: 10.1101/2023.10.20.563204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Historically Plasmodium falciparum has followed a pattern of drug resistance first appearing in low transmission settings before spreading to high transmission settings. Several features of low-transmission regions are hypothesized as explanations: higher chance of symptoms and treatment seeking, better treatment access, less within-host competition among clones, and lower rates of recombination. Here, we test whether importation of drug-resistant parasites is more likely to lead to successful emergence and establishment in low-transmission or high-transmission periods of the same epidemiological setting, using a spatial, individual-based stochastic model of malaria and drug-resistance evolution calibrated for Burkina Faso. Upon controlling for the timing of importation of drug-resistant genotypes and examination of key model variables, we found that drug-resistant genotypes imported during the low transmission season were, (1) more susceptible to stochastic extinction due to the action of random genetic drift, and (2) more likely to lead to establishment of drug resistance when parasites are able to survive early stochastic loss due to drift. This implies that rare importation events are more likely to lead to establishment if they occur during a high-transmission season, but that constant importation (e.g., neighboring countries with high levels of resistance) may produce a greater risk during low-transmission periods.
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Affiliation(s)
- Robert J. Zupko
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Joseph L. Servadio
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Tran Dang Nguyen
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kien Trung Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Anyirékun Fabrice Somé
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo Dioulasso, Burkina Faso
| | - Maciej F. Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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14
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Kane J, Li X, Kumar S, Button-Simons KA, Brenneman KMV, Dahlhoff H, Sievert MA, Checkley LA, Shoue DA, Singh PP, Abatiyow BA, Haile MT, Nair S, Reyes A, Tripura R, Peto T, Lek D, Kappe SH, 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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543862. [PMID: 37745488 PMCID: PMC10515748 DOI: 10.1101/2023.06.06.543862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Piperaquine (PPQ) is widely used in combination with dihydroartemisinin (DHA) as a first-line treatment against malaria parasites. 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 multi-drug resistant KEL1/PLA1 lineage isolate (KH004) and a drug susceptible parasite isolated in Malawi (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 four copies of pm2/3. We recovered 104 unique recombinant progeny and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3 for detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes, including PPQ survival assay (PSA), area under the dose-response curve (AUC), and a limited point IC50 (LP-IC50). We find that inheritance of the KH004 pfcrt allele is required for PPQ resistance, whereas copy number variation in pm2/3 further enhances resistance but does not confer resistance in the absence of PPQ-R-associated mutations in pfcrt. Deeper 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 and confirm the critical role of the PfCRT G367C substitution in PPQ resistance.
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Affiliation(s)
- John Kane
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Katrina A. Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Haley Dahlhoff
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Mackenzie A.C. Sievert
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Lisa A. Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Puspendra P. Singh
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ann Reyes
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 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, UK
| | - Tom 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, UK
| | - 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
| | - Stefan H.I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 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, UK
| | - Standwell C Nkhoma
- BEI Resources, American Type Culture Collection (ATCC), Manassas, VA, USA
| | - Ian H. Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Timothy J. C. Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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15
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Sharma S, Ali ME. How do the mutations in PfK13 protein promote anti-malarial drug resistance? J Biomol Struct Dyn 2023; 41:7329-7338. [PMID: 36153000 DOI: 10.1080/07391102.2022.2120539] [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: 03/03/2022] [Accepted: 08/27/2022] [Indexed: 10/14/2022]
Abstract
Plasmodium falciparum develops resistance to artemisinin upon exposure to the anti-malarial drug. Various mutations in the Plasmodium falciparum Kelch13 (PfK13) protein such as Y493H, R539T, I543T and C580Y have been associated with anti-malarial drug resistance. These mutations impede the regular ubiquitination process that eventually invokes drug resistance. However, the relationship between the mutation and the mechanism of drug resistance has not yet been fully elucidated. The comparative protein dynamics are studied by performing the classical molecular dynamics (MD) simulations and subsequent analysis of the trajectories adopting root-mean-square fluctuations, the secondary-structure predictions and the dynamical cross-correlation matrix analysis tools. Here, we observed that the mutations in the Kelch-domain do not have any structural impact on the mutated site; however, it significantly alters the overall dynamics of the protein. The loop-region of the BTB-domain especially for Y493H and C580Y mutants is found to have the enhanced dynamical fluctuations. The enhanced fluctuations in the BTB-domain could affect the protein-protein (PfK13-Cullin) binding interactions in the ubiquitination process and eventually lead to anti-malarial drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shikha Sharma
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab, India
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16
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Rovira-Vallbona E, Kattenberg JH, Hong NV, Guetens P, Imamura H, Monsieurs P, Chiheb D, Erhart A, Phuc BQ, Xa NX, Rosanas-Urgell A. Molecular surveillance of Plasmodium falciparum drug-resistance markers in Vietnam using multiplex amplicon sequencing (2000-2016). Sci Rep 2023; 13:13948. [PMID: 37626131 PMCID: PMC10457381 DOI: 10.1038/s41598-023-40935-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Emergence and spread of Plasmodium falciparum resistance to artemisinin-based combination therapies (ACT) is a major challenge for Greater Mekong Subregion countries in their goal to eliminate malaria by 2030. Tools to efficiently monitor drug resistance beyond resource-demanding therapeutic efficacy studies are necessary. A custom multiplex amplicon sequencing assay based on Illumina technology was designed to target the marker of partial resistance to artemisinin (K13), five candidate modulators of artemisinin resistance, the marker of resistance to chloroquine (crt), and four neutral microsatellite loci. The assay was used to genotype 635 P. falciparum-positive blood samples collected across seven provinces of Vietnam and one of Cambodia between 2000 and 2016. Markers of resistance to artemisinin partner-drugs piperaquine (copy number of plasmepsin-2) and mefloquine (copy number of multidrug-resistance 1) were determined by qPCR. Parasite population structure was further assessed using a 101-SNP barcode. Validated mutations of artemisinin partial resistance in K13 were found in 48.1% of samples, first detection was in 2000, and by 2015 prevalence overcame > 50% in Central Highlands and Binh Phuoc province. K13-C580Y variant became predominant country-wide, quickly replacing an outbreak of K13-I543T in Central Highlands. Mutations in candidate artemisinin resistance modulator genes paralleled the trends of K13 mutants, whereas resistance to piperaquine and mefloquine remained low (≈ 10%) by 2015-2016. Genomic tools applied to malaria surveillance generate comprehensive information on dynamics of drug resistance and population structure and reflect drug efficacy profiles from in vivo studies.
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Affiliation(s)
- Eduard Rovira-Vallbona
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
- ISGlobal, Hospital Clínic/Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
| | | | - Nguyen Van Hong
- National Institute of Malariology, Parasitology and Entomology, Hanoi, 10200, Vietnam
| | - Pieter Guetens
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
- Vrije Universiteit Brussel, Campus Jette, 1090, Brussels, Belgium
- UZ Brussel, Centre for Medical Genetics, 1090, Brussels, Belgium
| | - Pieter Monsieurs
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Driss Chiheb
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Annette Erhart
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Bui Quang Phuc
- National Institute of Malariology, Parasitology and Entomology, Hanoi, 10200, Vietnam
| | - Nguyen Xuan Xa
- National Institute of Malariology, Parasitology and Entomology, Hanoi, 10200, Vietnam
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium.
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17
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Shukla N, Tang WK, Coelho CH, Long CA, Healy SA, Sagara I, Miura K, Duffy PE, Tolia NH. A human antibody epitope map of the malaria vaccine antigen Pfs25. NPJ Vaccines 2023; 8:108. [PMID: 37542029 PMCID: PMC10403551 DOI: 10.1038/s41541-023-00712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/12/2023] [Indexed: 08/06/2023] Open
Abstract
Pfs25 is a leading antigen for a malaria transmission-blocking vaccine and shows moderate transmission-blocking activity and induction of rapidly decreasing antibody titers in clinical trials. A comprehensive definition of all transmission-reducing epitopes of Pfs25 will inform structure-guided design to enhance Pfs25-based vaccines, leading to potent transmission-blocking activity. Here, we compiled a detailed human antibody epitope map comprising epitope binning data and structures of multiple human monoclonal antibodies, including three new crystal structures of Pfs25 in complex with transmission-reducing antibodies from Malian volunteers immunized with Pfs25 conjugated to EPA and adjuvanted with AS01. These structures revealed additional epitopes in Pfs25 capable of reducing transmission and expanded this characterization to malaria-exposed humans. This work informs immunogen design to focus the antibody response to transmission-reducing epitopes of Pfs25, enabling development of more potent transmission-blocking vaccines for malaria.
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Affiliation(s)
- Niharika Shukla
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Wai Kwan Tang
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Camila H Coelho
- Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carole A Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Sara A Healy
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Issaka Sagara
- Malaria Research and Training Center, University of Sciences, Techniques, and Technology, Bamako, Mali
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Patrick E Duffy
- Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Niraj H Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA.
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18
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Holzschuh A, Lerch A, Gerlovina I, Fakih BS, Al-Mafazy AWH, Reaves EJ, Ali A, Abbas F, Ali MH, Ali MA, Hetzel MW, Yukich J, Koepfli C. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania. Nat Commun 2023; 14:3699. [PMID: 37349311 PMCID: PMC10287761 DOI: 10.1038/s41467-023-39417-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 samples from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA
| | - Inna Gerlovina
- EPPIcenter Research Program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bakar S Fakih
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | | | - Erik J Reaves
- U.S. Centers for Disease Control and Prevention, President's Malaria Initiative, Dar es Salaam, United Republic of Tanzania
| | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Faiza Abbas
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Haji Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Ali Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Joshua Yukich
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
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19
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da Silva C, Boene S, Datta D, Rovira-Vallbona E, Aranda-Díaz A, Cisteró P, Hathaway N, Tessema S, Chidimatembue A, Matambisso G, Nhama A, Macete E, Pujol A, Nhamussua L, Galatas B, Guinovart C, Enosse S, De Carvalho E, Rogier E, Plucinski MM, Colborn J, Zulliger R, Saifodine A, Alonso PL, Candrinho B, Greenhouse B, Aide P, Saute F, Mayor A. Targeted and whole-genome sequencing reveal a north-south divide in P. falciparum drug resistance markers and genetic structure in Mozambique. Commun Biol 2023; 6:619. [PMID: 37291425 PMCID: PMC10250372 DOI: 10.1038/s42003-023-04997-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Mozambique is one of the four African countries which account for over half of all malaria deaths worldwide, yet little is known about the parasite genetic structure in that country. We performed P. falciparum amplicon and whole genome sequencing on 2251 malaria-infected blood samples collected in 2015 and 2018 in seven provinces of Mozambique to genotype antimalarial resistance markers and interrogate parasite population structure using genome-wide microhaplotyes. Here we show that the only resistance-associated markers observed at frequencies above 5% were pfmdr1-184F (59%), pfdhfr-51I/59 R/108 N (99%) and pfdhps-437G/540E (89%). The frequency of pfdhfr/pfdhps quintuple mutants associated with sulfadoxine-pyrimethamine resistance increased from 80% in 2015 to 89% in 2018 (p < 0.001), with a lower expected heterozygosity and higher relatedness of microhaplotypes surrounding pfdhps mutants than wild-type parasites suggestive of recent selection. pfdhfr/pfdhps quintuple mutants also increased from 72% in the north to 95% in the south (2018; p < 0.001). This resistance gradient was accompanied by a concentration of mutations at pfdhps-436 (17%) in the north, a south-to-north increase in the genetic complexity of P. falciparum infections (p = 0.001) and a microhaplotype signature of regional differentiation. The parasite population structure identified here offers insights to guide antimalarial interventions and epidemiological surveys.
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Affiliation(s)
- Clemente da Silva
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Simone Boene
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Debayan Datta
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Andrés Aranda-Díaz
- EPPIcenter Research Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Pau Cisteró
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Sofonias Tessema
- EPPIcenter Research Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Glória Matambisso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Abel Nhama
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Eusebio Macete
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Arnau Pujol
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Lidia Nhamussua
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Beatriz Galatas
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Sónia Enosse
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Eva De Carvalho
- World Health Organization, WHO Country Office Maputo, Maputo, Mozambique
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mateusz M Plucinski
- United States President's Malaria Initiative, Malaria Branch, Division of Parasitic Diseases and Malaria, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James Colborn
- Clinton Health Access Initiative, Maputo, Mozambique
| | - Rose Zulliger
- U.S. President's Malaria Initiative, USAID, Washington, DC, USA
| | | | - Pedro L Alonso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Hospital Clinic-Universitat de Barcelona, Barcelona, Spain
| | - Baltazar Candrinho
- National Malaria Control Programme, Ministry of Health, Maputo, Mozambique
| | - Bryan Greenhouse
- EPPIcenter Research Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique.
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20
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Mok S, Yeo T, Hong D, Shears MJ, Ross LS, Ward KE, Dhingra SK, Kanai M, Bridgford JL, Tripathi AK, Mlambo G, Burkhard AY, Fairhurst KJ, Gil-Iturbe E, Park H, Rozenberg FD, Kim J, Mancia F, Quick M, Uhlemann AC, Sinnis P, Fidock DA. Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543338. [PMID: 37398288 PMCID: PMC10312498 DOI: 10.1101/2023.06.02.543338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Drug-resistant Plasmodium falciparum parasites have swept across Southeast Asia and now threaten Africa. By implementing a P. falciparum genetic cross using humanized mice, we report the identification of key determinants of resistance to artemisinin (ART) and piperaquine (PPQ) in the dominant Asian KEL1/PLA1 lineage. We mapped k13 as the central mediator of ART resistance and identified secondary markers. Applying bulk segregant analysis, quantitative trait loci mapping and gene editing, our data reveal an epistatic interaction between mutant PfCRT and multicopy plasmepsins 2/3 in mediating high-grade PPQ resistance. Susceptibility and parasite fitness assays implicate PPQ as a driver of selection for KEL1/PLA1 parasites. Mutant PfCRT enhanced susceptibility to lumefantrine, the first-line partner drug in Africa, highlighting a potential benefit of opposing selective pressures with this drug and PPQ. We also identified that the ABCI3 transporter can operate in concert with PfCRT and plasmepsins 2/3 in mediating multigenic resistance to antimalarial agents.
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Affiliation(s)
- Sachel Mok
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
| | - Davin Hong
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Melanie J. Shears
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Leila S. Ross
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
| | - Kurt E. Ward
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
| | - Satish K. Dhingra
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
| | - Mariko Kanai
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
| | - Jessica L. Bridgford
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
| | - Abhai K. Tripathi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Godfree Mlambo
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Anna Y. Burkhard
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
| | - Kate J. Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Felix D. Rozenberg
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - David A. Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY
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21
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Wasakul V, Disratthakit A, Mayxay M, Chindavongsa K, Sengsavath V, Thuy-Nhien N, Pearson RD, Phalivong S, Xayvanghang S, Maude RJ, Gonçalves S, Day NP, Newton PN, Ashley EA, Kwiatkowski DP, Dondorp AM, Miotto O. Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis. THE LANCET. INFECTIOUS DISEASES 2023; 23:568-577. [PMID: 36462526 PMCID: PMC10914674 DOI: 10.1016/s1473-3099(22)00697-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND Malaria outbreaks are important public health concerns that can cause resurgence in endemic regions approaching elimination. We investigated a Plasmodium falciparum outbreak in Attapeu Province, Laos, during the 2020-21 malaria season, using genomic epidemiology methods to elucidate parasite population dynamics and identify its causes. METHODS In this genetic analysis, 2164 P falciparum dried blood spot samples were collected from southern Laos between Jan 1, 2017, and April 1, 2021, which included 249 collected during the Attapeu outbreak between April 1, 2020, and April 1, 2021, by routine surveillance. Genetic barcodes obtained from these samples were used to investigate epidemiological changes underpinning the outbreak, estimate population diversity, and analyse population structure. Whole-genome sequencing data from additional historical samples were used to reconstruct the ancestry of outbreak strains using identity-by-descent analyses. FINDINGS The outbreak parasite populations were characterised by unprecedented loss of genetic diversity, primarily caused by rapid clonal expansion of a multidrug-resistant strain (LAA1) carrying the kelch13 Arg539Thr (R539T) mutation. LAA1 replaced kelch13 Cys580Tyr (C580Y) mutants resistant to dihydroartemisinin-piperaquine (KEL1/PLA1) as the dominant strain. LAA1 inherited 58·8% of its genome from a strain circulating in Cambodia in 2008. A secondary outbreak strain (LAA2) carried the kelch13 C580Y allele, and a genome that is essentially identical to a Cambodian parasite from 2009. A third, low-frequency strain (LAA7) was a recombinant of KEL1/PLA1 with a kelch13 R539T mutant. INTERPRETATION These results strongly suggest that the outbreak was driven by a selective sweep, possibly associated with multidrug-resistant phenotypes of the outbreak strains. Established resistant populations can circulate at low frequencies for years before suddenly overwhelming dominant strains when the conditions for selection become favourable-eg, when front-line therapies change. Genetic surveillance can support elimination by characterising key properties of outbreaks such as population diversity, drug resistance marker prevalence, and the origins of outbreak strains. FUNDING Bill & Melinda Gates Foundation; The Global Fund to Fight AIDS, Tuberculosis and Malaria; Wellcome Trust. TRANSLATION For the Lao translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Varanya Wasakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Areeya Disratthakit
- 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, Oxford University, Oxford, UK
| | | | | | - Nguyen Thuy-Nhien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | | | - Sonexay Phalivong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Saiamphone Xayvanghang
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, 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, Oxford University, Oxford, UK; Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Nicholas P Day
- 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, Oxford University, Oxford, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Elizabeth A Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, UK
| | | | - 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, Oxford University, Oxford, UK
| | - Olivo Miotto
- 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, Oxford University, Oxford, UK; Wellcome Sanger Institute, Hinxton, UK.
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22
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Maniga JN, Samuel M, John O, Rael M, Muchiri JN, Bwogo P, Martin O, Sankarapandian V, Wilberforce M, Albert O, Onkoba SK, Adebayo IA, Adeyemo RO, Akinola SA. Novel Plasmodium falciparum k13 gene polymorphisms from Kisii County, Kenya during an era of artemisinin-based combination therapy deployment. Malar J 2023; 22:87. [PMID: 36894982 PMCID: PMC9996564 DOI: 10.1186/s12936-023-04517-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Currently, chemotherapy stands out as the major malaria intervention strategy, however, anti-malarial resistance may hamper global elimination programs. Artemisinin-based combination therapy (ACT) stands as the drug of choice for the treatment of Plasmodium falciparum malaria. Plasmodium falciparum kelch13 gene mutations are associated with artemisinin resistance. Thus, this study was aimed at evaluating the circulation of P. falciparum k13 gene polymorphisms from Kisii County, Kenya during an era of ACT deployment. METHODS Participants suspected to have malaria were recruited. Plasmodium falciparum was confirmed using the microscopy method. Malaria-positive patients were treated with artemether-lumefantrine (AL). Blood from participants who tested positive for parasites after day 3 was kept on filter papers. DNA was extracted using chelex-suspension method. A nested polymerase chain reaction (PCR) was conducted and the second-round products were sequenced using the Sanger method. Sequenced products were analysed using DNAsp 5.10.01 software and then blasted on the NCBI for k13 propeller gene sequence identity using the Basic Local Alignment Search Tool (BLAST). To assess the selection pressure in P. falciparum parasite population, Tajima' D statistic and Fu & Li's D test in DnaSP software 5.10.01 was used. RESULTS Out of 275 enrolled participants, 231 completed the follow-up schedule. 13 (5.6%) had parasites on day 28 hence characterized for recrudescence. Out of the 13 samples suspected of recrudescence, 5 (38%) samples were positively amplified as P. falciparum, with polymorphisms in the k13-propeller gene detected. Polymorphisms detected in this study includes R539T, N458T, R561H, N431S and A671V, respectively. The sequences have been deposited in NCBI with bio-project number PRJNA885380 and accession numbers SAMN31087434, SAMN31087433, SAMN31087432, SAMN31087431 and SAMN31087430 respectively. CONCLUSIONS WHO validated polymorphisms in the k13-propeller gene previously reported to be associated with ACT resistance were not detected in the P. falciparum isolates from Kisii County, Kenya. However, some previously reported un-validated k13 resistant single nucleotide polymorphisms were reported in this study but with limited occurrences. The study has also reported new SNPs. More studies need to be carried out in the entire country to understand the association of reported mutations if any, with ACT resistance.
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Affiliation(s)
- Josephat Nyabayo Maniga
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda.
| | | | - Odda John
- School of Pharmacy, Kampala International University Western Campus, Bushenyi, Uganda.,Department of Pharmacology and Therapeutics, Makerere University, Kampala, Uganda.,Department of Pharmacology and Toxicology, School of Medicine, King Caesor University, Kampala, Uganda
| | - Masai Rael
- Department of Biological Sciences, Kisii University, Kisii, Kenya
| | | | - Pacifica Bwogo
- Department of Biological Sciences, Kisii University, Kisii, Kenya
| | - Odoki Martin
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda.,Department of Medical Microbiology and Immunology, School of Medicine, King Ceasor University, Kampala, Uganda.,Department of Applied Sciences, School of Sciences, Nkumba University, Entebbe, Uganda
| | - Vidya Sankarapandian
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda
| | - Mfitundinda Wilberforce
- School of Pharmacy, Kampala International University Western Campus, Bushenyi, Uganda.,Department of Pharmacology and Toxicology, School of Medicine, King Caesor University, Kampala, Uganda
| | - Ochweri Albert
- School of Pharmacy, Kampala International University Western Campus, Bushenyi, Uganda
| | - Sarah Kemuma Onkoba
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda
| | - Ismail Abiola Adebayo
- Department of Medical Biochemistry, Molecular Biology and Genetics, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Butare, Rwanda
| | - Rasheed Omotayo Adeyemo
- Department of Medical Microbiology and Parasitology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Butare, Rwanda
| | - Saheed Adekunle Akinola
- Department of Medical Microbiology and Parasitology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Butare, Rwanda
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Ahorhorlu SY, Quashie NB, Jensen RW, Kudzi W, Nartey ET, Duah-Quashie NO, Zoiku F, Dzudzor B, Wang CW, Hansson H, Alifrangis M, Adjei GO. Assessment of artemisinin tolerance in Plasmodium falciparum clinical isolates in children with uncomplicated malaria in Ghana. Malar J 2023; 22:58. [PMID: 36803541 PMCID: PMC9938975 DOI: 10.1186/s12936-023-04482-w] [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: 11/22/2022] [Accepted: 02/04/2023] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Artemisinin-based combination therapy (ACT) is the first-line treatment for uncomplicated malaria in Ghana. Artemisinin (ART) tolerance in Plasmodium falciparum has arisen in Southeast Asia and recently, in parts of East Africa. This is ascribed to the survival of ring-stage parasites post treatment. The present study sought to assess and characterize correlates of potential ART tolerance based on post-treatment parasite clearance, ex vivo and in vitro drug sensitivity, and molecular markers of drug resistance in P. falciparum isolates from children with uncomplicated malaria in Ghana. METHODS Six months to fourteen years old children presenting with acute uncomplicated malaria (n = 115) were enrolled in two hospitals and a Health Centre in Ghana's Greater Accra region and treated with artemether-lumefantrine (AL) according to body weight. Pre- and post-treatment parasitaemia (day 0 and day 3) was confirmed by microscopy. The ex vivo ring-stage survival assay (RSA) was used to detect percent ring survival while the 72 h SYBR Green I assay was used to measure the 50% inhibition concentration (IC50s) of ART and its derivatives and partner drugs. Genetic markers of drug tolerance /resistance were evaluated using selective whole genome sequencing. RESULTS Of the total of 115 participants, 85 were successfully followed up on day 3 post-treatment and 2/85 (2.4%) had parasitaemia. The IC50 values of ART, artesunate (AS), artemether (AM), dihydroartemisinin (DHA), amodiaquine (AQ), and lumefantrine (LUM) were not indicative of drug tolerance. However, 7/90 (7.8%) pre-treatment isolates had > 10% ring survival rates against DHA. Of the four isolates (2 RSA positive and 2 RSA negative) with high genomic coverage, P. falciparum (Pf) kelch 13 K188* and Pfcoronin V424I mutations were only present in the two RSA positive isolates with > 10% ring survival rates. CONCLUSIONS The observed low proportion of participants with day-3 post-treatment parasitaemia is consistent with rapid ART clearance. However, the increased rates of survival observed in the ex vivo RSA against DHA, maybe a pointer of an early start of ART tolerance. Furthermore, the role of two novel mutations in PfK13 and Pfcoronin genes, harboured by the two RSA positive isolates that had high ring survival in the present study, remains to be elucidated.
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Affiliation(s)
- Samuel Yao Ahorhorlu
- grid.8652.90000 0004 1937 1485Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana, P.O. Box 4236, Accra, Ghana ,grid.8652.90000 0004 1937 1485West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Neils Ben Quashie
- grid.8652.90000 0004 1937 1485Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana, P.O. Box 4236, Accra, Ghana ,grid.8652.90000 0004 1937 1485West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Rasmus Weisel Jensen
- grid.5254.60000 0001 0674 042XCentre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark ,grid.475435.4Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - William Kudzi
- grid.8652.90000 0004 1937 1485Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana, P.O. Box 4236, Accra, Ghana
| | - Edmund Tetteh Nartey
- grid.8652.90000 0004 1937 1485Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana, P.O. Box 4236, Accra, Ghana
| | - Nancy Odurowah Duah-Quashie
- grid.462644.60000 0004 0452 2500Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana ,grid.8652.90000 0004 1937 1485West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Felix Zoiku
- grid.462644.60000 0004 0452 2500Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Bartholomew Dzudzor
- grid.8652.90000 0004 1937 1485Department of Medical Biochemistry, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Christian William Wang
- grid.5254.60000 0001 0674 042XCentre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark ,grid.475435.4Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Helle Hansson
- grid.5254.60000 0001 0674 042XCentre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark ,grid.475435.4Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Michael Alifrangis
- grid.5254.60000 0001 0674 042XCentre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark ,grid.475435.4Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - George Obeng Adjei
- Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana, P.O. Box 4236, Accra, Ghana.
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24
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Niaré K, Chege T, Rosenkranz M, Mwai K, Saßmannshausen Z, Odera D, Nyamako L, Tuju J, Alfred T, Waitumbi JN, Ogutu B, Sirima SB, Awandare G, Kouriba B, Rayner JC, Osier FHA. Characterization of a novel Plasmodium falciparum merozoite surface antigen and potential vaccine target. Front Immunol 2023; 14:1156806. [PMID: 37122725 PMCID: PMC10140549 DOI: 10.3389/fimmu.2023.1156806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Detailed analyses of genetic diversity, antigenic variability, protein localization and immunological responses are vital for the prioritization of novel malaria vaccine candidates. Comprehensive approaches to determine the most appropriate antigen variants needed to provide broad protection are challenging and consequently rarely undertaken. Methods Here, we characterized PF3D7_1136200, which we named Asparagine-Rich Merozoite Antigen (ARMA) based on the analysis of its sequence, localization and immunogenicity. We analyzed IgG and IgM responses against the common variants of ARMA in independent prospective cohort studies in Burkina Faso (N = 228), Kenya (N = 252) and Mali (N = 195) using a custom microarray, Div-KILCHIP. Results We found a marked population structure between parasites from Africa and Asia. African isolates shared 34 common haplotypes, including a dominant pair although the overall selection pressure was directional (Tajima's D = -2.57; Fu and Li's F = -9.69; P < 0.02). ARMA was localized to the merozoite surface, IgG antibodies induced Fc-mediated degranulation of natural killer cells and strongly inhibited parasite growth in vitro. We found profound serological diversity, but IgG and IgM responses were highly correlated and a hierarchical clustering analysis identified only three major serogroups. Protective IgG and IgM antibodies appeared to target both cross-reactive and distinct epitopes across variants. However, combinations of IgG and IgM antibodies against selected variants were associated with complete protection against clinical episodes of malaria. Discussion Our systematic strategy exploits genomic data to deduce the handful of antigen variants with the strongest potential to induce broad protection and may be broadly applicable to other complex pathogens for which effective vaccines remain elusive.
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Affiliation(s)
- Karamoko Niaré
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
- 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
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
- *Correspondence: Karamoko Niaré, ; Faith H. A. Osier,
| | - Timothy Chege
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
| | - Micha Rosenkranz
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kennedy Mwai
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
- Epidemiology and Biostatistics Division, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Zoe Saßmannshausen
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Odera
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Lydia Nyamako
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
| | - James Tuju
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
| | - Tiono Alfred
- Public Health Department, Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso
| | - John N. Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate-Africa/Kenya Medical Research Institute, Kisumu, Kenya
| | - Bernhards Ogutu
- Kenya Medical Research Institute, Centre for Clinical Research, Nairobi, Kenya
| | | | - Gordon Awandare
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Bourema Kouriba
- 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
- Centre d’Infectiologie Charles Mérieux-Mali, Bamako, Mali
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Faith H. A. Osier
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
- *Correspondence: Karamoko Niaré, ; Faith H. A. Osier,
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25
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Ring-stage growth arrest: Metabolic basis of artemisinin tolerance in Plasmodium falciparum. iScience 2022; 26:105725. [PMID: 36579133 PMCID: PMC9791339 DOI: 10.1016/j.isci.2022.105725] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 12/09/2022] Open
Abstract
The emergence and spread of artemisinin-tolerant malaria parasites threatens malaria control programmes worldwide. Mutations in the propeller domain of the Kelch13 protein confer Plasmodium falciparum artemisinin resistance (ART-R). ART-R is linked to the reduced susceptibility of temporary growth-arrested ring-stage parasites, but the metabolic mechanisms remain elusive. We generated two PfKelch13 mutant lines via CRISPR-Cas9 gene editing which displayed a reduced susceptibility accompanied by an extended ring stage. The metabolome of ART-induced ring-stage growth arrest parasites carrying PfKelch13 mutations showed significant alterations in the tricarboxylic acid (TCA) cycle, glycolysis, and amino acids metabolism, pointing to altered energy and porphyrin metabolism with metabolic plasticity. The critical role of these pathways was further confirmed by altering metabolic flow or through chemical inhibition. Our findings uncover that the growth arrestment associated with ART-R is potentially attributed to the adaptative metabolic plasticity, indicating that the defined metabolic remodeling turns out to be the trigger for ART-R.
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Egwu CO, Aloke C, Chukwu J, Agwu A, Alum E, Tsamesidis I, Aja PM, Offor CE, Obasi NA. A world free of malaria: It is time for Africa to actively champion and take leadership of elimination and eradication strategies. Afr Health Sci 2022; 22:627-640. [PMID: 37092107 PMCID: PMC10117514 DOI: 10.4314/ahs.v22i4.68] [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] [Indexed: 03/06/2023] Open
Abstract
The global burden of malaria seems unabated. Africa carries the greatest burden accounting for over 95% of the annual cases of malaria. For the vision of a world free of malaria by Global Technical Strategy to be achieved, Africa must take up the stakeholder's role. It is therefore imperative that Africa rises up to the challenge of malaria and champion the fight against it. The fight against malaria may just be a futile or mere academic venture if Africans are not directly and fully involved. This work reviews the roles playable by Africans in order to curb the malaria in Africa and the world at large.
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Affiliation(s)
- Chinedu Ogbonnia Egwu
- Medical Biochemistry Department, College of Medicine, Alex-Ekwueme Federal University Ndufu-Alike Ikwo, P.M.B. 1010 Ebonyi State, Nigeria
| | - Chinyere Aloke
- Medical Biochemistry Department, College of Medicine, Alex-Ekwueme Federal University Ndufu-Alike Ikwo, P.M.B. 1010 Ebonyi State, Nigeria
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
| | - Jennifer Chukwu
- World Health Organization, United Nations House Plot 617/618 Central Area District PMB 2861 Abuja, Nigeria
| | - Anthony Agwu
- Biochemistry Department, Ebonyi State University Abakaliki, P.M.B. 053 Ebonyi State Nigeria
| | - Esther Alum
- Biochemistry Department, Ebonyi State University Abakaliki, P.M.B. 053 Ebonyi State Nigeria
| | - Ioannis Tsamesidis
- Department of Prosthodontics, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki 54124 Greece
| | - Patrick M Aja
- Biochemistry Department, Ebonyi State University Abakaliki, P.M.B. 053 Ebonyi State Nigeria
| | - Christian E Offor
- Biochemistry Department, Ebonyi State University Abakaliki, P.M.B. 053 Ebonyi State Nigeria
| | - Nwogo Ajuka Obasi
- Medical Biochemistry Department, College of Medicine, Alex-Ekwueme Federal University Ndufu-Alike Ikwo, P.M.B. 1010 Ebonyi State, Nigeria
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27
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Stabler TC, Dwivedi A, Shrestha B, Joshi S, Schindler T, Ouattara A, García GA, Daubenberger C, Silva JC. Gene Coverage Count and Classification (GC 3): a locus sequence coverage assessment tool using short-read whole genome sequencing data, and its application to identify and classify histidine-rich protein 2 and 3 deletions in Plasmodium falciparum. Malar J 2022; 21:357. [PMID: 36447234 PMCID: PMC9706933 DOI: 10.1186/s12936-022-04376-3] [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: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The ability of malaria rapid diagnostic tests (RDTs) to effectively detect active infections is being compromised by the presence of malaria strains with genomic deletions at the hrp2 and hrp3 loci, encoding the antigens most commonly targeted in diagnostics for Plasmodium falciparum detection. The presence of such deletions can be determined in publically available P. falciparum whole genome sequencing (WGS) datasets. A computational approach was developed and validated, termed Gene Coverage Count and Classification (GC3), to analyse genome-wide sequence coverage data and provide informative outputs to assess presence and coverage profile of a target locus in WGS data. GC3 was applied to detect deletions at hrp2 and hrp3 (hrp2/3) and flanking genes in different geographic regions and across time points. METHODS GC3 uses Python and R scripts to extract locus read coverage metrics from mapped WGS data according to user-defined parameters and generates relevant tables and figures. GC3 was tested using WGS data for laboratory reference strains with known hrp2/3 genotypes, and its results compared to those of a hrp2/3-specific qPCR assay. Samples with at least 25% of coding region positions with zero coverage were classified as having a deletion. Publicly available sequence data was analysed and compared with published deletion frequency estimates. RESULTS GC3 results matched the expected coverage of known laboratory reference strains. Agreement between GC3 and a hrp2/3-specific qPCR assay reported for 19/19 (100%) hrp2 deletions and 18/19 (94.7%) hrp3 deletions. Among Cambodian (n = 127) and Brazilian (n = 20) WGS datasets, which had not been previously analysed for hrp2/3 deletions, GC3 identified hrp2 deletions in three and four samples, and hrp3 deletions in 10 and 15 samples, respectively. Plots of hrp2/3 coding regions, grouped by year of sample collection, showed a decrease in median standardized coverage among Malawian samples (n = 150) suggesting the importance of a careful, properly controlled follow up to determine if an increase in frequency of deletions has occurred between 2007-2008 and 2014-2015. Among Malian (n = 90) samples, median standardized coverage was lower in 2002 than 2010, indicating widespread deletions present at the gene locus in 2002. CONCLUSIONS The GC3 tool accurately classified hrp2/3 deletions and provided informative tables and figures to analyse targeted gene coverage. GC3 is an appropriate tool when performing preliminary and exploratory assessment of locus coverage data.
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Affiliation(s)
- Thomas C Stabler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Biraj Shrestha
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sudhaunshu Joshi
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tobias Schindler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
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Structural analysis of Plasmodium falciparum ookinete surface antigen Pfs28 relevant for malaria vaccine design. Sci Rep 2022; 12:19556. [PMID: 36379968 PMCID: PMC9664031 DOI: 10.1038/s41598-022-24054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Pfs28 is a Plasmodium falciparum malaria transmission-blocking vaccine candidate that is anchored to the parasite surface through a C-terminal glycosylphosphatidylinositol (GPI) moiety, and plays a role in parasite survival in the mosquito midgut. Pfs28 contains epidermal growth factor (EGF)-like domains and is part of a family of sexual stage malaria proteins that includes the related vaccine antigen Pfs25. The lack of structural definition of Pfs28 and the immune response to this candidate has limited further malaria vaccine development for this antigen. Here, we present the crystal structure of Pfs28, examine its conservation with P. vivax Pvs28, and evaluate the cross-reactivity of Pfs28 to antibodies that recognize Pfs25. Pfs28 is comprised of four EGF-like domains stabilized by ten disulfide bridges with an overall architecture that highly resembles Pfs25. Despite the high sequence and structural similarity between these antigens, no cross reactivity of Pfs28 to anti-Pfs25 monoclonal antibodies could be demonstrated.
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Mensah BA, Akyea-Bobi NE, Ghansah A. Genomic approaches for monitoring transmission dynamics of malaria: A case for malaria molecular surveillance in Sub-Saharan Africa. FRONTIERS IN EPIDEMIOLOGY 2022; 2:939291. [PMID: 38455324 PMCID: PMC10911004 DOI: 10.3389/fepid.2022.939291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/10/2022] [Indexed: 03/09/2024]
Abstract
Transmission dynamics is an important indicator for malaria control and elimination. As we move closer to eliminating malaria in Sub-Saharan Africa (sSA), transmission indices with higher resolution (genomic approaches) will complement our current measurements of transmission. Most of the present programmatic knowledge of malaria transmission patterns are derived from assessments of epidemiologic and clinical data, such as case counts, parasitological estimates of parasite prevalence, and Entomological Inoculation Rates (EIR). However, to eliminate malaria from endemic areas, we need to track changes in the parasite population and how they will impact transmission. This is made possible through the evolving field of genomics and genetics, as well as the development of tools for more in-depth studies on the diversity of parasites and the complexity of infections, among other topics. If malaria elimination is to be achieved globally, country-specific elimination activities should be supported by parasite genomic data from regularly collected blood samples for diagnosis, surveillance and possibly from other programmatic interventions. This presents a unique opportunity to track the spread of malaria parasites and shed additional light on intervention efficacy. In this review, various genetic techniques are highlighted along with their significance for an enhanced understanding of transmission patterns in distinct topological settings throughout Sub-Saharan Africa. The importance of these methods and their limitations in malaria surveillance to guide control and elimination strategies, are explored.
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Affiliation(s)
- Benedicta A. Mensah
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nukunu E. Akyea-Bobi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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30
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Cui L, Sattabongkot J, Aung PL, Brashear A, Cao Y, Kaewkungwal J, Khamsiriwatchara A, Kyaw MP, Lawpoolsri S, Menezes L, Miao J, Nguitragool W, Parker D, Phuanukoonnon S, Roobsoong W, Siddiqui F, Soe MT, Sriwichai P, Yang Z, Zhao Y, Zhong D. Multidisciplinary Investigations of Sustained Malaria Transmission in the Greater Mekong Subregion. Am J Trop Med Hyg 2022; 107:138-151. [PMID: 36228909 DOI: 10.4269/ajtmh.21-1267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/28/2022] [Indexed: 11/07/2022] Open
Abstract
In the course of malaria elimination in the Greater Mekong Subregion (GMS), malaria epidemiology has experienced drastic spatiotemporal changes with residual transmission concentrated along international borders and the rising predominance of Plasmodium vivax. The emergence of Plasmodium falciparum parasites resistant to artemisinin and partner drugs renders artemisinin-based combination therapies less effective while the potential spread of multidrug-resistant parasites elicits concern. Vector behavioral changes and insecticide resistance have reduced the effectiveness of core vector control measures. In recognition of these problems, the Southeast Asian International Center of Excellence for Malaria Research (ICEMR) has been conducting multidisciplinary research to determine how human migration, antimalarial drug resistance, vector behavior, and insecticide resistance sustain malaria transmission at international borders. These efforts allow us to comprehensively understand the ecology of border malaria transmission and develop population genomics tools to identify and track parasite introduction. In addition to employing in vivo, in vitro, and molecular approaches to monitor the emergence and spread of drug-resistant parasites, we also use genomic and genetic methods to reveal novel mechanisms of antimalarial drug resistance of parasites. We also use omics and population genetics approaches to study insecticide resistance in malaria vectors and identify changes in mosquito community structure, vectorial potential, and seasonal dynamics. Collectively, the scientific findings from the ICEMR research activities offer a systematic view of the factors sustaining residual malaria transmission and identify potential solutions to these problems to accelerate malaria elimination in the GMS.
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Affiliation(s)
- Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | | | | | - Awtum Brashear
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Yaming Cao
- Department of Immunology, China Medical University, Shenyang, China
| | | | | | | | | | - Lynette Menezes
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Wang Nguitragool
- Mahidol Vivax Research Unit, Mahidol University, Bangkok, Thailand
| | - Daniel Parker
- Department of Epidemiology, University of California at Irvine, Irvine, California
| | | | | | - Faiza Siddiqui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Myat Thu Soe
- Myanmar Health Network Organization, Yangon, Myanmar
| | - Patchara Sriwichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yan Zhao
- Department of Immunology, China Medical University, Shenyang, China
| | - Daibin Zhong
- Program in Public Health, University of California at Irvine, Irvine, California
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31
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Molecular Epidemiology of Drug Resistance Genes in Plasmodium falciparum Isolates Imported from Nigeria between 2016 and 2020: Continued Emergence of Fully Resistant
Pfdhfr
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Pfdhps
Alleles. Microbiol Spectr 2022; 10:e0052822. [PMID: 36106887 PMCID: PMC9604097 DOI: 10.1128/spectrum.00528-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Malaria poses public health threats worldwide. Nigeria accounted for the highest numbers of cases (26.8%) and deaths (31.9%) among countries where malaria is endemic in 2020. Currently, monitoring molecular markers in imported malaria cases provides an efficient means to screen for emerging drug resistance in countries where malaria is endemic, particularly in those where field surveillance is challenging. Here, we investigated 165 Plasmodium falciparum infections imported from Nigeria to Zhejiang Province, China, between 2016 and 2020. Multiple molecular markers in k13, Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps were detected. The prevalences and patterns of mutations were analyzed. Polymorphism of k13 was limited to 5 of 156 (3.21%) isolates. The wild-type CVMNK allele of Pfcrt became predominant (65.36%) compared with the triple mutation CVIET. A low frequency (4.73%) of double mutations (N86Y and Y184F) in Pfmdr1 was observed. The dominant haplotypes of Pfdhfr and Pfdhps were IRNDI (92.41%) and ISGKAA (36.84%), respectively. The newly discovered mutant I431V was identified in 21.71% of isolates. A “fully resistant” combination of Pfdhfr-Pfdhps, IRN-GE, was found in eight (5.67%) samples, which was hardly seen in Nigeria. The current study demonstrated a high frequency of wild-type Pfcrt. Limited polymorphism of Pfmdr1 but a high prevalence of Pfdhfr and Pfdhps mutations was illustrated. Our data so far serve as comprehensive surveillance of molecular markers of the k13, Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps genes. Based on our findings, it has become crucial to evaluate the impact of the emerging fully resistant type of Pfdhfr-Pfdhps as well as its combination with I431V on the efficacy of sulfadoxine-pyrimethamine (SP) in Nigeria. IMPORTANCE Monitoring the current resistance to antimalarial drugs is critical to enable timely action to prevent its spread and limit its impact. The high prevalence of wild-type Pfcrt found in our study is an optimistic signal to reevaluate chloroquine (CQ) sensitivity in Nigeria, which is cost-effective and once played a crucial role in the fight against malaria. Based on the continued emergence of fully resistant Pfdhfr-Pfdhps alleles illustrated in the current investigation, actions are needed in Nigeria, such as national systemic surveillance to monitor their updated epidemiology as well as assessments of their influence on SP efficacy to minimize any public health impact. These findings urge a response to the threat of drug resistance to facilitate appropriate drug policies in the study area.
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32
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Thiam LG, Mangou K, Ba A, Mbengue A, Bei AK. Leveraging genome editing to functionally evaluate Plasmodium diversity. Trends Parasitol 2022; 38:558-571. [PMID: 35469746 DOI: 10.1016/j.pt.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022]
Abstract
The ambitious goal of malaria elimination requires an in-depth understanding of the parasite's biology to counter the growing threat of antimalarial resistance and immune evasion. Timely assessment of the functional impact of antigenic diversity in the early stages of vaccine development will be critical for achieving the goal of malaria control, elimination, and ultimately eradication. Recent advances in targeted genome editing enabled the functional validation of resistance-associated markers in Plasmodium falciparum, the deadliest malaria-causing pathogen and strain-specific immune neutralization. This review explores recent advances made in leveraging genome editing to aid the functional evaluation of Plasmodium diversity and highlights how these techniques can assist in prioritizing both therapeutic and vaccine candidates.
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Affiliation(s)
- Laty Gaye Thiam
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Khadidiatou Mangou
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Aboubacar Ba
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Alassane Mbengue
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amy K Bei
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
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33
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Cutts JC, O'Flaherty K, Zaloumis SG, Ashley EA, Chan JA, Onyamboko MA, Fanello C, Dondorp AM, Day NP, Phyo AP, Dhorda M, Imwong M, Fairhurst RM, Lim P, Amaratunga C, Pukrittayakamee S, Hien TT, Htut Y, Mayxay M, Abdul Faiz M, Takashima E, Tsuboi T, Beeson JG, Nosten F, Simpson JA, White NJ, Fowkes FJI. Comparison of antibody responses and parasite clearance in artemisinin therapeutic efficacy studies in Democratic Republic of Congo and Asia. J Infect Dis 2022; 226:324-331. [PMID: 35703955 PMCID: PMC9400417 DOI: 10.1093/infdis/jiac232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Understanding the effect of immunity on Plasmodium falciparum clearance is essential for interpreting therapeutic efficacy studies designed to monitor emergence of artemisinin drug resistance. In low-transmission areas of Southeast Asia, where resistance has emerged, P. falciparum antibodies confound parasite clearance measures. However, variation in naturally acquired antibodies across Asian and sub-Saharan African epidemiological contexts and their impact on parasite clearance re yet to be quantified. Methods In an artemisinin therapeutic efficacy study, antibodies to 12 pre-erythrocytic and erythrocytic P. falciparum antigens were measured in 118 children with uncomplicated P. falciparum malaria in the Democratic Republic of Congo (DRC) and compared with responses in patients from Asian sites, described elsewhere. Results Parasite clearance half-life was shorter in DRC patients (median, 2 hours) compared with most Asian sites (median, 2–7 hours), but P. falciparum antibody levels and seroprevalences were similar. There was no evidence for an association between antibody seropositivity and parasite clearance half-life (mean difference between seronegative and seropositive, −0.14 to +0.40 hour) in DRC patients. Conclusions In DRC, where artemisinin remains highly effective, the substantially shorter parasite clearance time compared with Asia was not explained by differences in the P. falciparum antibody responses studied.
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Affiliation(s)
- Julia C Cutts
- Burnet Institute, Melbourne, Victoria 3004, Australia.,Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | | | - Sophie G Zaloumis
- Centre for Epidemiology and Biostatistics, Melbourne, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom.,Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Jo Anne Chan
- Burnet Institute, Melbourne, Victoria 3004, Australia.,Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.,Department of Immunology, Monash University, Melbourne Australia
| | - Marie A Onyamboko
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Caterina Fanello
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom.,Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Nicholas P Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | | | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom.,Worldwide Antimalarial Resistance Network, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Pharath Lim
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Chanaki Amaratunga
- Worldwide Antimalarial Resistance Network, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | | | - Tran Tinh Hien
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Ye Htut
- Department of Medical Research, Yangon, Myanmar
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom.,Institute of Research and Education Development, University of Health Sciences, Vientiane, Lao PDR.,Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - M Abdul Faiz
- Malaria Research Group & Dev Care Foundation, Chittagong, Bangladesh
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - James G Beeson
- Burnet Institute, Melbourne, Victoria 3004, Australia.,Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.,Department of Immunology, Monash University, Melbourne Australia
| | - Francois Nosten
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom.,Shoklo Malaria Research Unit, Mae Sot, Thailand
| | - Julie A Simpson
- Centre for Epidemiology and Biostatistics, Melbourne, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Freya J I Fowkes
- Burnet Institute, Melbourne, Victoria 3004, Australia.,Centre for Epidemiology and Biostatistics, Melbourne, School of Population and Global Health, The University of Melbourne, Melbourne, Australia.,Department of Infectious Diseases and Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Australia
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34
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Matrevi SA, Tandoh KZ, Bruku S, Opoku-Agyeman P, Adams T, Ennuson NA, Asare B, Hagan OCK, Abuaku B, Koram KA, Fox A, Quashie NB, Letizia AG, Duah-Quashie NO. Novel pfk13 polymorphisms in Plasmodium falciparum population in Ghana. Sci Rep 2022; 12:7797. [PMID: 35551239 PMCID: PMC9098865 DOI: 10.1038/s41598-022-11790-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/29/2022] [Indexed: 01/22/2023] Open
Abstract
The molecular determinants of Plasmodium falciparum artemisinin resistance are the single nucleotide polymorphisms in the parasite’s kelch propeller domain, pfk13. Validated and candidate markers are under surveillance in malaria endemic countries using artemisinin-based combination therapy. However, pfk13 mutations which may confer parasite artemisinin resistance in Africa remains elusive. It has therefore become imperative to report all observed pfk13 gene polymorphisms in malaria therapeutic efficacy studies for functional characterization. We herein report all novel pfk13 mutations observed only in the Ghanaian parasite population. In all, 977 archived samples from children aged 12 years and below with uncomplicated malaria from 2007 to 2017 were used. PCR/Sanger sequencing analysis revealed 78% (763/977) of the samples analyzed were wild type (WT) for pfk13 gene. Of the 214 (22%) mutants, 78 were novel mutations observed only in Ghana. The novel SNPs include R404G, P413H, N458D/H/I, C473W/S, R529I, M579T/Y, C580R/V, D584L, N585H/I, Q661G/L. Some of the mutations were sites and ecological zones specific. There was low nucleotide diversity and purifying selection at the pfk13 locus in Ghanaian parasite population. With increasing drug pressure and its consequent parasite resistance, documenting these mutations as baseline data is crucial for future molecular surveillance of P. falciparum resistance to artemisinin in Ghana.
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Affiliation(s)
- Sena Adzoa Matrevi
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Kwesi Zandoh Tandoh
- West Africa Centre for Cell Biology and Infectious Pathogens, Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Selassie Bruku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Philip Opoku-Agyeman
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Tryphena Adams
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Nana Aba Ennuson
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Bright Asare
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Oheneba Charles Kofi Hagan
- West Africa Centre for Cell Biology and Infectious Pathogens, Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Benjamin Abuaku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Kwadwo Ansah Koram
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Ann Fox
- United States Naval Medical Research Unit 3, Ghana Laboratory, Accra, Ghana
| | - Neils Ben Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Andrew G Letizia
- United States Naval Medical Research Unit 3, Ghana Laboratory, Accra, Ghana
| | - Nancy Odurowah Duah-Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
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35
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Rawat M, Kanyal A, Choubey D, Deshmukh B, Malhotra R, Mamatharani DV, Rao AG, Karmodiya K. Identification of Co-Existing Mutations and Gene Expression Trends Associated With K13-Mediated Artemisinin Resistance in Plasmodium falciparum. Front Genet 2022; 13:824483. [PMID: 35464842 PMCID: PMC9019836 DOI: 10.3389/fgene.2022.824483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum infects millions and kills thousands of people annually the world over. With the emergence of artemisinin and/or multidrug resistant strains of the pathogen, it has become even more challenging to control and eliminate the disease. Multiomics studies of the parasite have started to provide a glimpse into the confounding genetics and mechanisms of artemisinin resistance and identified mutations in Kelch13 (K13) as a molecular marker of resistance. Over the years, thousands of genomes and transcriptomes of artemisinin-resistant/sensitive isolates have been documented, supplementing the search for new genes/pathways to target artemisinin-resistant isolates. This meta-analysis seeks to recap the genetic landscape and the transcriptional deregulation that demarcate artemisinin resistance in the field. To explore the genetic territory of artemisinin resistance, we use genomic single-nucleotide polymorphism (SNP) datasets from 2,517 isolates from 15 countries from the MalariaGEN Network (The Pf3K project, pilot data release 4, 2015) to dissect the prevalence, geographical distribution, and co-existing patterns of genetic markers associated with/enabling artemisinin resistance. We have identified several mutations which co-exist with the established markers of artemisinin resistance. Interestingly, K13-resistant parasites harbor α-ß hydrolase and putative HECT domain-containing protein genes with the maximum number of SNPs. We have also explored the multiple, publicly available transcriptomic datasets to identify genes from key biological pathways whose consistent deregulation may be contributing to the biology of resistant parasites. Surprisingly, glycolytic and pentose phosphate pathways were consistently downregulated in artemisinin-resistant parasites. Thus, this meta-analysis highlights the genetic and transcriptomic features of resistant parasites to propel further exploratory studies in the community to tackle artemisinin resistance.
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Affiliation(s)
- Mukul Rawat
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Deepak Choubey
- Life Science Research Unit, Persistent Systems Limited, Pune, India
| | - Bhagyashree Deshmukh
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Rashim Malhotra
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - D V Mamatharani
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Anjani Gopal Rao
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
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36
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Marwa K, Kapesa A, Baraka V, Konje E, Kidenya B, Mukonzo J, Kamugisha E, Swedberg G. Therapeutic efficacy of artemether-lumefantrine, artesunate-amodiaquine and dihydroartemisinin-piperaquine in the treatment of uncomplicated Plasmodium falciparum malaria in Sub-Saharan Africa: A systematic review and meta-analysis. PLoS One 2022; 17:e0264339. [PMID: 35271592 PMCID: PMC8912261 DOI: 10.1371/journal.pone.0264339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 02/08/2022] [Indexed: 12/04/2022] Open
Abstract
Background Sub-Saharan Africa has the highest burden of malaria in the world. Artemisinin-based combination therapies (ACTs) have been the cornerstone in the efforts to reduce the global burden of malaria. In the effort to facilitate early detection of resistance for artemisinin derivatives and partner drugs, WHO recommends monitoring of ACT’s efficacy in the malaria endemic countries. The present systematic meta-analysis study summarises the evidence of therapeutic efficacy of the commonly used artemisinin-based combinations for the treatment of uncomplicated P. falciparum malaria in Sub-Saharan Africa after more than a decade since the introduction of the drugs. Methods Fifty two studies carried out from 2010 to 2020 on the efficacy of artemether-lumefantrine or dihydro-artemisinin piperaquine or artesunate amodiaquine in patients with uncomplicated P. falciparum malaria in Sub-Saharan Africa were searched for using the Google Scholar, Cochrane Central Register of controlled trials (CENTRAL), PubMed, Medline, LILACS, and EMBASE online data bases. Data was extracted by two independent reviewers. Random analysis effect was performed in STATA 13. Heterogeneity was established using I2 statistics. Results Based on per protocol analysis, unadjusted cure rates in malaria infected patients treated with artemether-lumefantrine (ALU), artesunate-amodiaquine (ASAQ) and dihydroartemisinin-piperaquine (DHP) were 89%, 94% and 91% respectively. However, the cure rates after PCR correction were 98% for ALU, 99% for ASAQ and 99% for DHP. Conclusion The present meta-analysis reports the overall high malaria treatment success for artemether-lumefantrine, artesunate-amodiaquine and dihydroartemisinin-piperaquine above the WHO threshold value in Sub-Saharan Africa.
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Affiliation(s)
- Karol Marwa
- Department of Pharmacology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
- * E-mail: ,
| | - Anthony Kapesa
- Department of Community Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Vito Baraka
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Evelyne Konje
- Department of Epidemiology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Benson Kidenya
- Department of Biochemistry, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Jackson Mukonzo
- Department of Pharmacology and Therapeutics, Makerere University, Kampala, Uganda
| | - Erasmus Kamugisha
- Department of Biochemistry, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Gote Swedberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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37
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LaVerriere E, Schwabl P, Carrasquilla M, Taylor AR, Johnson ZM, Shieh M, Panchal R, Straub TJ, Kuzma R, Watson S, Buckee CO, Andrade CM, Portugal S, Crompton PD, Traore B, Rayner JC, Corredor V, James K, Cox H, Early AM, MacInnis BL, Neafsey DE. Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study. Mol Ecol Resour 2022; 22:2285-2303. [PMID: 35437908 DOI: 10.1111/1755-0998.13622] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, and shows strong potential for genomic epidemiology of infectious disease. AmpSeq data from infectious microbes can inform disease control in multiple ways, including measuring drug resistance marker prevalence, distinguishing imported from local cases, and determining the effectiveness of therapeutics. We describe the design and comparative evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites: a four-locus panel ('4CAST') composed of highly diverse antigens, and a 129-locus panel ('AMPLseq') composed of drug resistance markers, highly diverse loci for inferring relatedness, and a locus to detect Plasmodium vivax co-infection. We explore the performance of each panel in various public health use cases with in silico simulations as well as empirical experiments. The 4CAST panel appears highly suitable for evaluating the number of distinct parasite strains within samples (complexity of infection), showing strong performance across a wide range of parasitemia levels without a DNA pre-amplification step. For relatedness inference, the larger AMPLseq panel performs similarly to two existing panels of comparable size, despite differences in the data and approach used for designing each panel. Finally, we describe an R package (paneljudge) that facilitates the design and comparative evaluation of genetic panels for relatedness estimation, and we provide general guidance on the design and implementation of AmpSeq panels for genomic epidemiology of infectious disease.
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Affiliation(s)
- Emily LaVerriere
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manuela Carrasquilla
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zachary M Johnson
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Meg Shieh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruchit Panchal
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy J Straub
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca Kuzma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean Watson
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caroline O Buckee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carolina M Andrade
- Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Silvia Portugal
- Max Planck Institute for Infection Biology, Berlin, Germany.,Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, BP 1805, Point G, Bamako, Mali
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Kashana James
- Guyana National Malaria Control Program, Ministry of Health, 0592, Georgetown, Guyana
| | - Horace Cox
- Guyana Vector Control Services, Ministry of Health, 0592, Georgetown, Guyana
| | - Angela M Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Brenneman KV, Li X, Kumar S, Delgado E, Checkley LA, Shoue DA, Reyes A, Abatiyow BA, Haile MT, Tripura R, Peto T, Lek D, Button-Simons KA, Kappe SH, Dhorda M, Nosten F, Nkhoma SC, Cheeseman IH, Vaughan AM, Ferdig MT, Anderson TJ. Optimizing bulk segregant analysis of drug resistance using Plasmodium falciparum genetic crosses conducted in humanized mice. iScience 2022; 25:104095. [PMID: 35372813 PMCID: PMC8971943 DOI: 10.1016/j.isci.2022.104095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 01/15/2023] Open
Abstract
Classical malaria parasite genetic crosses involve isolation, genotyping, and phenotyping of progeny parasites, which is time consuming and laborious. We tested a rapid alternative approach-bulk segregant analysis (BSA)-that utilizes sequencing of bulk progeny populations with and without drug selection for rapid identification of drug resistance loci. We used dihydroartemisinin (DHA) selection in two genetic crosses and investigated how synchronization, cryopreservation, and the drug selection regimen impacted BSA success. We detected a robust quantitative trait locus (QTL) at kelch13 in both crosses but did not detect QTLs at four other candidate loci. QTLs were detected using synchronized, but not unsynchronized progeny pools, consistent with the stage-specific action of DHA. We also successfully applied BSA to cryopreserved progeny pools, expanding the utility of this approach. We conclude that BSA provides a powerful approach for investigating the genetic architecture of drug resistance in Plasmodium falciparum.
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Affiliation(s)
- Katelyn Vendrely Brenneman
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Elizabeth Delgado
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Lisa A. Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Ann Reyes
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, 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, UK
| | - Tom 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, UK
| | - 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
| | - Katrina A. Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stefan H.I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 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, UK
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Ian H. Cheeseman
- Program in Host Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Corresponding author
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- Corresponding author
| | - Tim J.C. Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
- Corresponding author
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Adam I, Alam MS, Alemu S, Amaratunga C, Amato R, Andrianaranjaka V, Anstey NM, Aseffa A, Ashley E, Assefa A, Auburn S, Barber BE, Barry A, Batista Pereira D, Cao J, Chau NH, Chotivanich K, Chu C, Dondorp AM, Drury E, Echeverry DF, Erko B, Espino F, Fairhurst R, Faiz A, Fernanda Villegas M, Gao Q, Golassa L, Goncalves S, Grigg MJ, Hamedi Y, Hien TT, Htut Y, Johnson KJ, Karunaweera N, Khan W, Krudsood S, Kwiatkowski DP, Lacerda M, Ley B, Lim P, Liu Y, Llanos-Cuentas A, Lon C, Lopera-Mesa T, Marfurt J, Michon P, Miotto O, Mohammed R, Mueller I, Namaik-larp C, Newton PN, Nguyen TN, Nosten F, Noviyanti R, Pava Z, Pearson RD, Petros B, Phyo AP, Price RN, Pukrittayakamee S, Rahim AG, Randrianarivelojosia M, Rayner JC, Rumaseb A, Siegel SV, Simpson VJ, Thriemer K, Tobon-Castano A, Trimarsanto H, Urbano Ferreira M, Vélez ID, Wangchuk S, Wellems TE, White NJ, William T, Yasnot MF, Yilma D. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples. Wellcome Open Res 2022; 7:136. [PMID: 35651694 PMCID: PMC9127374 DOI: 10.12688/wellcomeopenres.17795.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 01/13/2023] Open
Abstract
This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
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Affiliation(s)
| | - Ishag Adam
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Sisay Alemu
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia,Addis Ababa University, Addis Ababa, Ethiopia,MilliporeSigma (Bioreliance), Rockville, USA
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | | | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Abraham Aseffa
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
| | - Elizabeth Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Bridget E Barber
- Menzies School of Health Research, Darwin, Australia,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Alyssa Barry
- Walter and Eliza Hall Institute, Parkville, Australia,Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia
| | | | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Nguyen Hoang Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Cindy Chu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Arjen M. Dondorp
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Diego F. Echeverry
- Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia
| | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fe Espino
- Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
| | | | | | | | - Qi Gao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Matthew J Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Yaghoob Hamedi
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Ye Htut
- Department of Medical Research, Yangon, Myanmar
| | | | - Nadira Karunaweera
- University of Colombo, Colombo, Sri Lanka,School of Public Health, Harvard University, Boston, USA
| | - Wasif Khan
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | | | | | - Marcus Lacerda
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil,Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
| | - Benedikt Ley
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Parsons Corporation, Walter Reed Army Institute of Research (WRAIR), Silver Spring, USA
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | | | - Chanthap Lon
- National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Rezika Mohammed
- Department of Internal Medicine, University of Gondar, Gondar, Ethiopia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Parkville, Australia
| | | | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thuy-Nhien Nguyen
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Zuleima Pava
- Centro Internacionale de Entrenamiento e Investigaciones Medicas, Cali, Colombia
| | | | | | - Aung P Phyo
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Awab Ghulam Rahim
- Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Jalalabad, Afghanistan
| | - 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
| | - Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | | | - Kamala Thriemer
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | | | - Marcelo Urbano Ferreira
- Universidade de São Paulo, São Paulo, Brazil,Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal
| | | | - Sonam Wangchuk
- Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Thomas E Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Nicholas J White
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Timothy William
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia,Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Maria F Yasnot
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, Colombia
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Ye R, Zhang Y, Zhang D. Evaluations of candidate markers of dihydroartemisinin-piperaquine resistance in Plasmodium falciparum isolates from the China-Myanmar, Thailand-Myanmar, and Thailand-Cambodia borders. Parasit Vectors 2022; 15:130. [PMID: 35413937 PMCID: PMC9004172 DOI: 10.1186/s13071-022-05239-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background The fast-declining clinical efficacy of dihydroartemisinin-piperaquine (DHA-PPQ) in Cambodia is a warning of the underlying westward dissemination of piperaquine resistance in the Greater Mekong Subregion (GMS). Mutations in the Plasmodium falciparum Kelch 13-propeller (PfK13) and the P. falciparum chloroquine resistance transporter (PfCRT), as well as plasmepsin 2/3 gene amplification, have been discovered as molecular markers for predicting DHA-PPQ treatment failure. Determining whether these genetic variations of P. falciparum are linked to DHA-PPQ resistance is critical, especially along the China–Myanmar (CM) border, where PPQ has been utilized for decades. Methods A total of 173 P. falciparum samples of dried blood spots (DBS) were collected along the CM border between 2007 and 2010, the Thailand–Cambodia (TC) border between 2009 and 2013, and the Thailand–Myanmar (TM) border between 2012 and 2014. PCR and sequencing were used to identified PfCRT mutations, while qPCR was used to determine the copy number of plasmepsin 2/3. The prevalence of DHA-PPQ resistance in three locations was investigated using data paired with K13 mutations. Results Three fragments of the pfcrt gene were amplified for all 173 samples, and seven SNPs were identified (M74I, N75E/D, K76T, H97L, I218F, A220S, I356L). No new PfCRT mutations conferring resistance to PPQ (T93S, H97Y, F145I, M343L, and G353V) were discovered, except for one mutant I218F identified in the TM border (2.27%, 1/44). Additionally, mutant H97L was found in the TC, TM, and CM borders at 3.57% (1/28), 6.82% (3/44), and 1% (1/101), respectively. A substantial K13 C580Y variant prevalence was found in the TC and TM border, accounting for 64.29% (18/28) and 43.18% (19/44), respectively, while only 1% (1/101) was found in the CM border. The K13 F446I variant was only identified and found to reach a high level (28.71%, 29/101) in the CM border. Furthermore, 10.71% (3/28) of TC isolates and 2.27% (1/44) of TM isolates carried more than one copy of plasmepsin 2/3 and K13 C580Y variant, while no plasmepsin 2/3 amplification was identified in the CM isolates. Conclusions Compared with the P. falciparum samples collected from the TC and TM borders, fewer parasites carried plasmepsin 2/3 amplification and novel PfCRT variants, while more parasites carried predominant K13 mutations at position F446I, in the CM border. Clear evidence of DHA-PPQ resistance associated with candidate markers was not found in this border region suggesting a further evaluation of these markers and continuous surveillance is warranted. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05239-1.
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Affiliation(s)
- Run Ye
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, People's Republic of China
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, People's Republic of China.
| | - Dongmei Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, People's Republic of China.
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Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance. Malar J 2022; 21:88. [PMID: 35292038 PMCID: PMC8922754 DOI: 10.1186/s12936-022-04122-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/07/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood samples can be collected as whole blood and stored at - 20 °C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Despite the wide use of either method, systematic comparisons of how the method of blood sample preservation affects the limit of detection (LOD) of molecular diagnosis and the proportion of DNA recovered for downstream applications are lacking. METHODS Extractions based on spin columns, magnetic beads, Tween-Chelex, and direct PCR without prior extraction were compared for whole blood and dried blood spots (DBS) using dilution series of Plasmodium falciparum culture samples. Extracted DNA was quantified by qPCR and droplet digital PCR (ddPCR). RESULTS DNA recovery was 5- to 10-fold higher for whole blood compared to DBS, resulting in a 2- to 3-fold lower LOD for both extraction methods compared to DBS. For whole blood, a magnetic bead-based method resulted in a DNA recovery rate of 88-98% when extracting from whole blood compared to 17-33% for a spin-column based method. For extractions from DBS, the magnetic bead-based method resulted in 8-20% DNA recovery, while the spin-column based method resulted in only 2% DNA recovery. The Tween-Chelex method was superior to other methods with 15-21% DNA recovery, and even more sensitive than extractions from whole blood samples. The direct PCR method was found to have the lowest LOD overall for both, whole blood and DBS. CONCLUSIONS Pronounced differences in LOD and DNA yield need to be considered when comparing prevalence estimates based on molecular methods and when selecting sampling protocols for other molecular surveillance applications.
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42
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Thieu NQ, Chinh VD, Van Hanh T, Van Dung N, Takagi H, Annoura T, Kawai S, Masuda G, Van Tuan N, Hung VV, Nakazawa S, Culleton R, Binh NTH, Maeno Y. Reduction in Plasmodium falciparum Pfk13 and pfg377 allele diversity through time in southern Vietnam. Trop Med Health 2022; 50:19. [PMID: 35232492 PMCID: PMC8887123 DOI: 10.1186/s41182-022-00409-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/20/2022] [Indexed: 11/24/2022] Open
Abstract
Background Plasmodium falciparum has acquired resistance to artemisinin in Southeast Asia, with mutations in the P. falciparum Kelch-13 (Pfk13) gene associated with the resistance phenotype. The widespread use of Artemisinin-based combination therapy (ACT)s in Southeast Asia has led to the selection and spread of parasites carrying mutations in Pfk13. We characterised the allele diversity of Pfk13 and pfg377, an artemisinin-resistance neutral polymorphic gene, in parasite DNA extracted human blood from in southern Vietnam in 2003, 2012, 2015 and 2018. Method This study was conducted in Bu Gia Map commune, Binh Phuoc province, Vietnam, from May 2018 to January 2019. Twenty-four samples from 2018 to 2019, 30 from 2003, 24 from 2012 and 32 from 2015 were analysed. Malaria-infected human blood was collected by finger-prick and used for molecular analysis. A nested-PCR targeting the small subunit ribosomal RNA gene was used for Plasmodium species identification, followed by amplification and nucleotide sequencing of Pfk13 and region 3 of pfg377. Archived blood samples collected in the same region in 2012 and 2015 were also analysed as above for comparison. Results The genetic diversity of Pfk13 and pfg377 was lower in 2018–2019 compared to 2012 and 2015. The number of distinct Pfk13 mutants decreased from three in 2012 and 2015, P553L, V568G and C580Y, to one, C580Y in 2018–2019. In 2018–2019, the frequency of C580Y mutant strains was 71% (17/24 isolates). All samples were wild type in 2003. In 2012 and 2015, there were single-strain infections as well as co-infections with two mutant strains or with mutant and wild strains, whereas there were no co-infections in 2018. pfg377 allele diversity decreased from five alleles in 2012 to two alleles in 2018–2019. Conclusion The genetic diversity of P. falciparum was reduced at the two genetic loci surveyed in this study, Pfk13 and pfg377. In the case of the former gene, we observed an increase in the prevalence of parasites carrying the C580Y gene, known to confer reduced susceptibility to ACTs. The reduction in the diversity of pfg377 may be linked to the clonal expansion of parasite strains carrying the C580Y mutation, leading to an overall reduction in parasite genetic diversity across the population. Supplementary Information The online version contains supplementary material available at 10.1186/s41182-022-00409-4.
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Coppée R, Mama A, Sarrasin V, Kamaliddin C, Adoux L, Palazzo L, Ndam NT, Letourneur F, Ariey F, Houzé S, Clain J. 5WBF: a low-cost and straightforward whole blood filtration method suitable for whole-genome sequencing of Plasmodium falciparum clinical isolates. Malar J 2022; 21:51. [PMID: 35172825 PMCID: PMC8848818 DOI: 10.1186/s12936-022-04073-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background Whole-genome sequencing (WGS) is becoming increasingly helpful to assist malaria control programmes. A major drawback of this approach is the large amount of human DNA compared to parasite DNA extracted from unprocessed whole blood. As red blood cells (RBCs) have a diameter of about 7–8 µm and exhibit some deformability, it was hypothesized that cheap and commercially available 5 µm filters might retain leukocytes but much less of Plasmodium falciparum-infected RBCs. This study aimed to test the hypothesis that such a filtration method, named 5WBF (for 5 µm Whole Blood Filtration), may provide highly enriched parasite material suitable for P. falciparum WGS. Methods Whole blood was collected from five patients experiencing a P. falciparum malaria episode (ring-stage parasitaemia range: 0.04–5.5%) and from mock samples obtained by mixing synchronized, ring-stage cultured P. falciparum 3D7 parasites with uninfected human whole blood (final parasitaemia range: 0.02–1.1%). These whole blood samples (50 to 400 µL) were diluted in RPMI 1640 medium or PBS 1× buffer and filtered with a syringe connected to a 5 µm commercial filter. DNA was extracted from 5WBF-treated and unfiltered counterpart blood samples using a commercial kit. The 5WBF method was evaluated on the ratios of parasite:human DNA assessed by qPCR and by sequencing depth and percentages of coverage from WGS data (Illumina NextSeq 500). As a comparison, the popular selective whole-genome amplification (sWGA) method, which does not rely on blood filtration, was applied to the unfiltered counterpart blood samples. Results After applying 5WBF, qPCR indicated an average of twofold loss in the amount of parasite template DNA (Pf ARN18S gene) and from 4096- to 65,536-fold loss of human template DNA (human β actin gene). WGS analyses revealed that > 95% of the parasite nuclear and organellar genomes were all covered at ≥ 10× depth for all samples tested. In sWGA counterparts, the organellar genomes were poorly covered and from 47.7 to 82.1% of the nuclear genome was covered at ≥ 10× depth depending on parasitaemia. Sequence reads were homogeneously distributed across gene sequences for 5WBF-treated samples (n = 5460 genes; mean coverage: 91×; median coverage: 93×; 5th percentile: 70×; 95th percentile: 103×), allowing the identification of gene copy number variations such as for gch1. This later analysis was not possible for sWGA-treated samples, as a much more heterogeneous distribution of reads across gene sequences was observed (mean coverage: 80×; median coverage: 51×; 5th percentile: 7×; 95th percentile: 245×). Conclusions The novel 5WBF leucodepletion method is simple to implement and based on commercially available, standardized 5 µm filters which cost from 1.0 to 1.7€ per unit depending on suppliers. 5WBF permits extensive genome-wide analysis of P. falciparum ring-stage isolates from minute amounts of whole blood even with parasitaemias as low as 0.02%. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04073-1.
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Affiliation(s)
- Romain Coppée
- Université de Paris, IRD, MERIT, 75006, Paris, France. .,Université de Paris, Infection Modelisation Antimicrobial Evolution (IAME), Inserm UMR1137, 75018, Paris, France.
| | - Atikatou Mama
- Université de Paris, IRD, MERIT, 75006, Paris, France
| | - Véronique Sarrasin
- Université de Paris, IRD, MERIT, 75006, Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France
| | - Claire Kamaliddin
- Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France.,Cumming School of Medicine, Pathology and Laboratory Medicine, The University of Calgary, Calgary, AB, Canada
| | - Lucie Adoux
- Cochin Institute, INSERM U1016, UMR CNRS 8104, Genomic Platform, 75014, Paris, France
| | | | | | - Franck Letourneur
- Cochin Institute, INSERM U1016, UMR CNRS 8104, Genomic Platform, 75014, Paris, France
| | - Frédéric Ariey
- Université de Paris, INSERM 1016, Service de Parasitologie-Mycologie Hôpital Cochin, 75014, Paris, France
| | - Sandrine Houzé
- Université de Paris, IRD, MERIT, 75006, Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France
| | - Jérôme Clain
- Université de Paris, IRD, MERIT, 75006, Paris, France. .,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France.
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Berzosa P, Molina de la Fuente I, Ta-Tang TH, González V, García L, Rodríguez-Galet A, Díaz-Regañón R, Galán R, Cerrada-Gálvez L, Ncogo P, Riloha M, Benito A. Temporal evolution of the resistance genotypes of Plasmodium falciparum in isolates from Equatorial Guinea during 20 years (1999 to 2019). Malar J 2021; 20:463. [PMID: 34906159 PMCID: PMC8670137 DOI: 10.1186/s12936-021-04000-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
Background Malaria is one of the deadliest diseases in the world, particularly in Africa. As such, resistance to anti-malarial drugs is one of the most important problems in terms of global malaria control. This study assesses the evolution of the different resistance markers over time and the possible influence of interventions and treatment changes that have been made in Equatorial Guinea. Methods A total of 1223 biological samples obtained in the period 1999 to 2019 were included in the study. Screening for mutations in the pfdhfr, pfdhps, pfmdr1, and pfcrt genes was carried out by nested PCR and restriction-fragment length polymorphisms (RFLPs), and the study of pfk13 genes was carried out by nested PCR, followed by sequencing to determine the presence of mutations. Results The partially and fully resistant haplotypes (pfdhfr + pfdhps) were found to increase over time. Moreover, in 2019, the fully resistant haplotype was found to be increasing, although its super-resistant counterpart remains much less prevalent. A continued decline in pfmdr1 and pfcrt gene mutations over time was also found. The number of mutations detected in pfk13 has increased since 2008, when artemisinin-based combination therapy (ACT) were first introduced, with more mutations being observed in 2019, with two synonymous and five non-synonymous mutations being detected, although these are not related to resistance to ACT. In addition, the non-synonymous A578S mutation, which is the most frequent on the African continent, was detected in 2013, although not in the following years. Conclusions Withdrawal of the use of chloroquine (CQ) as a treatment in Equatorial Guinea has been shown to be effective over time, as wild-type parasite populations outnumber mutant populations. The upward trend observed in sulfadoxine-pyrimethamine (SP) resistance markers suggest its misuse, either alone or in combination with artesunate (AS) or amodiaquine (AQ), in some areas of the country, as was found in a previous study conducted by this group, which allows selective pressure from SP to continue. Single nucleotide polymorphisms (SNPs) 540E and 581G do not exceed the limit of 50 and 10%, respectively, thus meaning that SP is still effective as an intermittent preventive treatment (IPT) in this country. As for the pfk13 gene, no mutations have been detected in relation to resistance to ACT. However, in 2019 there is a greater accumulation of non-synonymous mutations compared to years prior to 2008. Graphical Abstract ![]()
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Affiliation(s)
- Pedro Berzosa
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain.
| | - Irene Molina de la Fuente
- Department of Biomedicine and Biotechnology, University of Alcalá and National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
| | - Thuy-Huong Ta-Tang
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
| | - Vicenta González
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
| | - Luz García
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
| | - Ana Rodríguez-Galet
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain.,HIV Molecular Epidemiology Laboratory, Ramón y Cajal-IRyCIS Hospital, Madrid, Spain
| | - Ramón Díaz-Regañón
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
| | - Rosario Galán
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
| | - Laura Cerrada-Gálvez
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
| | - Policarpo Ncogo
- State Foundation, Health, Childhood and Social Welfare FSP, Madrid, Spain
| | - Matilde Riloha
- Ministry of Health and Social Welfare-Malaria National Programme of Equatorial Guinea, Malabo, Equatorial Guinea
| | - Agustin Benito
- National Centre of Tropical Medicine-Institute of Health Carlos III, Madrid, Spain
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Doolan DL. Malaria research in Australia: looking through the lens of the past towards the future. Int J Parasitol 2021; 51:1255-1263. [PMID: 34780720 DOI: 10.1016/j.ijpara.2021.11.005] [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: 10/29/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
Malaria remains a global health priority, with substantial resources devoted to control and intervention since the causative parasite was first identified in 1880. Major advances have been made in discovery and translational research activities aimed at prevention, treatment and control. Laboratory-based, clinical, and field-based studies have complemented public health approaches. Australian scientists have played important roles, developing and applying innovative approaches, novel research tools and cutting-edge technologies in animal and human models of disease, as well as in disease-endemic settings. This article will provide an insight into 50 years of Australian efforts to discover mechanisms and targets of immunity and pathogenesis; develop new diagnostics, drugs, vaccines, and therapeutics; and assess new public health interventions and control measures in malaria-endemic settings.
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Affiliation(s)
- Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns QLD 4878, Australia.
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46
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Lee WC, Russell B, Lee B, Chu CS, Phyo AP, Sriprawat K, Lau YL, Nosten F, Rénia L. Plasmodium falciparum rosetting protects schizonts against artemisinin. EBioMedicine 2021; 73:103680. [PMID: 34749300 PMCID: PMC8586750 DOI: 10.1016/j.ebiom.2021.103680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/04/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
Background Artemisinin (ART) resistance in Plasmodium falciparum is thought to occur during the early stage of the parasite's erythrocytic cycle. Here, we identify a novel factor associated with the late stage parasite development that contributes to ART resistance. Methods Rosetting rates of clinical isolates pre- and post- brief (one hour) exposure to artesunate (AS, an ART derivative) were evaluated. The effects of AS-mediated rosetting on the post-AS-exposed parasite's replication and survival, as well as the extent of protection by AS-mediated rosetting on different parasite stages were investigated. The rosetting ligands, mechanisms, and gene mutations involved were studied. Findings Brief AS exposure stimulated rosetting, with AS-resistant isolates forming more rosettes in a more rapid manner. AS-mediated rosetting enabled infected erythrocytes (IRBC) to withstand AS exposure for several hours and protected the IRBC from phagocytosis. When their rosetting ability was blocked experimentally, the post-AS exposure survival advantage by the AS-resistant parasites was abrogated. Deletions in two genes coding for PfEMP1 exon 2 (PF3D7_0200300 and PF3D7_0223300) were found to be associated with AS-mediated rosetting, and these mutations were significantly selected through time in the parasite population under study, along with the K13 mutations, a molecular marker of ART-resistance. Interpretation Rapid ART parasite clearance is driven by the direct oxidative damages on IRBC by ART and the phagocytic destruction of the damaged IRBC. Rosetting serves as a rapid ‘buying time’ strategy that allows more parasites to complete schizont maturation, reinvasion and subsequent development into the intrinsically less ART-susceptible ring stage. Funding A*STAR, NMRC-OF-YIRG, HRC e-ASIA, Wellcome.
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Affiliation(s)
- Wenn-Chyau Lee
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore; Singapore Immunology Network (SIgN), A*STAR, Singapore.
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
| | - Bernett Lee
- Singapore Immunology Network (SIgN), A*STAR, Singapore
| | - Cindy S Chu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Laurent Rénia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore; Singapore Immunology Network (SIgN), A*STAR, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
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47
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Zhao H, Pi L, Zhao L, Qin Y, Zeng W, Xiang Z, Yang Q, Pan M, Li X, Zou C, Chen X, Zhao W, Lu Y, Wu Y, Duan M, Wang X, Li X, Mazier D, Huang Y, Yang Z. First Detection in West Africa of a Mutation That May Contribute to Artemisinin Resistance Plasmodium falciparum. Front Genet 2021; 12:701750. [PMID: 34691144 PMCID: PMC8531651 DOI: 10.3389/fgene.2021.701750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Background: The spread of drug resistance has seriously impacted the effective treatment of infection with the malaria parasite, Plasmodium falciparum. Continuous monitoring of molecular marker polymorphisms associated with drug resistance in parasites is essential for malaria control and elimination efforts. Our study describes mutations observed in the resistance genes Pfkelch13, Pfcrt, and Pfmdr1 in imported malaria and identifies additional potential drug resistance-associated molecular markers. Methods: Chinese patients infected in Africa with P. falciparum were treated with intravenous (IV) injections of artesunate 240–360 mg for 3–5 days while hospitalized and treated with oral dihydroartemisinin-piperaquine (DHP) for 3 days after hospital discharge. Blood samples were collected and PCR sequencing performed on genes Pfkelch13, Pfcrt, and Pfmdr1 from all isolates. Results: We analyzed a total of 225 patients from Guangxi, China with P. falciparum malaria acquired in Africa between 2016 and 2018. All patients were cured completely after treatment. The F446I mutation of the Pfkelch13 gene was detected for the first time from samples of West African P. falciparum, with a frequency of 1.0%. Five haplotypes of Pfcrt that encode residues 72–76 were found, with the wild-type CVMNK sequence predominating (80.8% of samples), suggesting that the parasites might be chloroquine sensitive. For Pfmdr1, N86Y (13.1%) and Y184F (58.8%) were the most prevalent, suggesting that artemether-lumefantrine may not, in general, be a suitable treatment for the group. Conclusions: For the first time, this study detected the F446I mutation of the Pfkelch13 gene from Africa parasites that lacked clinical evidence of resistance. This study provides the latest data for molecular marker surveillance related to antimalarial drug resistance genes Pfkelch13, Pfcrt, and Pfmdr1 imported from Africa, in Guangxi, China from Chinese migrate workers. Clinical Trial Registration: ChiCTROPC17013106.
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Affiliation(s)
- Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Liang Pi
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Luyi Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yucheng Qin
- Shanglin County People's Hospital, Guangxi, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Qi Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Maohua Pan
- Shanglin County People's Hospital, Guangxi, China
| | - Xinxin Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Chunyan Zou
- Guangxi Zhuang Autonomous Region People's Hospital, Nanning, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Wei Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yuxin Lu
- Shanglin County People's Hospital, Guangxi, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming, China
| | - Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Dominique Mazier
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, CIMI, Paris, France
| | - Yaming Huang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China.,Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
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Mairet-Khedim M, Nsango S, Ngou C, Menard S, Roesch C, Khim N, Srun S, Iriart X, Lanot T, Otam L, Abega F, Ayong L, Morlais I, Gandia P, Witkowski B, Berry A. Efficacy of dihydroartemisinin/piperaquine in patients with non-complicated Plasmodium falciparum malaria in Yaoundé, Cameroon. J Antimicrob Chemother 2021; 76:3037-3044. [PMID: 34453535 DOI: 10.1093/jac/dkab281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Dihydroartemisinin/piperaquine is increasingly used for the treatment of uncomplicated Plasmodium falciparum malaria in Africa. The efficacy of this combination in Cameroon is poorly documented, while resistance to dihydroartemisinin/piperaquine readily spreads in Southeast Asia. OBJECTIVES This study evaluated the clinical efficacy of dihydroartemisinin/piperaquine in Cameroon, as well as the molecular profile and phenotypic susceptibility of collected isolates to dihydroartemisinin and piperaquine. PATIENTS AND METHODS Dihydroartemisinin/piperaquine efficacy in 42 days was followed-up for 138 patients presenting non-complicated falciparum malaria. Piperaquine concentration was determined at day 7 for 124 patients. kelch13 gene polymorphisms (n = 150) and plasmepsin2 gene amplification (n = 148) were determined as molecular markers of resistance to dihydroartemisinin and piperaquine, respectively. Parasite susceptibility to dihydroartemisinin and piperaquine was determined using validated in vitro survival assays. RESULTS The efficacy of dihydroartemisinin/piperaquine treatment was 100% after PCR correction. The reinfections were not associated with a variation of piperaquine concentration at day 7. Ninety-six percent (144/150) of the samples presented a WT allele of the kelch13 gene. Two percent (3/150) presented the non-synonymous mutation A578S, which is not associated with resistance to dihydroartemisinin. No duplication of the plasmepsin2 gene was observed (0/148). All the samples tested in vitro by survival assays (n = 87) were susceptible to dihydroartemisinin and piperaquine. CONCLUSIONS Dihydroartemisinin/piperaquine has demonstrated excellent therapeutic efficacy with no evidence of emerging artemisinin or piperaquine resistance in Yaoundé, Cameroon. This observation suggests that dihydroartemisinin/piperaquine could be a sustainable therapeutic solution for P. falciparum malaria if implemented in areas previously free of artemisinin- and piperaquine-resistant parasites, unlike Southeast Asia.
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Affiliation(s)
- Mélissa Mairet-Khedim
- Malaria Translational Research Unit, Pasteur International Unit, Pasteur International Network, Phnom Penh, Cambodia and Paris, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France.,Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris 15, France
| | - Sandrine Nsango
- Department of Biological Sciences, Faculté de Médecine et des Sciences Pharmaceutiques, Université de Douala, Douala, Cameroon.,Malaria Research Unit, Centre Pasteur du Cameroon, Yaoundé, Cameroon
| | - Christelle Ngou
- Malaria Research Unit, Centre Pasteur du Cameroon, Yaoundé, Cameroon.,MIVEGEC, IRD, CNRS, Univ. Montpellier, Montpellier, France
| | - Sandie Menard
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France
| | - Camille Roesch
- Malaria Translational Research Unit, Pasteur International Unit, Pasteur International Network, Phnom Penh, Cambodia and Paris, France.,Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Nimol Khim
- Malaria Translational Research Unit, Pasteur International Unit, Pasteur International Network, Phnom Penh, Cambodia and Paris, France.,Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sreynet Srun
- Malaria Translational Research Unit, Pasteur International Unit, Pasteur International Network, Phnom Penh, Cambodia and Paris, France.,Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Xavier Iriart
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France.,Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Toulouse F-31300, France
| | - Thomas Lanot
- Laboratoire de Pharmacocinétique et Toxicologie, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Toulouse F-31300, France
| | - Laure Otam
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France.,Département des Sciences Biomédicales, Faculté des Sciences, Université de Ngaoundéré, Ngaoundéré, Cameroon
| | | | - Lawrence Ayong
- Malaria Research Unit, Centre Pasteur du Cameroon, Yaoundé, Cameroon
| | | | - Peggy Gandia
- Laboratoire de Pharmacocinétique et Toxicologie, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Toulouse F-31300, France.,INTHERES, Université de Toulouse, INRA, ENVT, BP 87614, 31076 Toulouse Cedex 3, France
| | - Benoit Witkowski
- Malaria Translational Research Unit, Pasteur International Unit, Pasteur International Network, Phnom Penh, Cambodia and Paris, France.,Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Antoine Berry
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France.,Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Toulouse F-31300, France
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Mutation in Plasmodium falciparum BTB/POZ domain of K13 protein confers artemisinin resistance. Antimicrob Agents Chemother 2021; 66:e0132021. [PMID: 34606334 PMCID: PMC8765297 DOI: 10.1128/aac.01320-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Partial artemisinin resistance, defined in patients as a delayed parasite clearance following artemisinin-based treatment, is conferred by non-synonymous mutations in the Kelch beta-propeller domain of the Plasmodium falciparum k13 (pfk13) gene. Here, we carried out in vitro selection over a one-year period on a West African P. falciparum strain isolated from Kolle (Mali) under a dose-escalating artemisinin regimen. After 18 cycles of sequential drug pressure, the selected parasites exhibited enhanced survival to dihydroartemisinin in the ring-stage survival assay (RSA0-3h = 9.2%). Sanger and whole-genome sequence analyses identified the PfK13 P413A mutation, localized in the BTB/POZ domain, upstream of the propeller domain. This mutation was sufficient to confer in vitro artemisinin resistance when introduced into the PfK13 coding sequence of the parasite strain Dd2 by CRISPR/Cas9 gene editing. These results together with structural studies of the protein demonstrate that the propeller domain is not the sole in vitro mediator of PfK13-mediated artemisinin resistance, and highlight the importance of monitoring for mutations throughout PfK13.
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50
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Serrano D, Santos-Reis A, Silva C, Dias A, Dias B, Toscano C, Conceição C, Baptista-Fernandes T, Nogueira F. Imported Malaria in Portugal: Prevalence of Polymorphisms in the Anti-Malarial Drug Resistance Genes pfmdr1 and pfk13. Microorganisms 2021; 9:microorganisms9102045. [PMID: 34683365 PMCID: PMC8538333 DOI: 10.3390/microorganisms9102045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 02/04/2023] Open
Abstract
Malaria is one of the ‘big three’ killer infectious diseases, alongside tuberculosis and HIV. In non-endemic areas, malaria may occur in travelers who have recently been to or visited endemic regions. The number of imported malaria cases in Portugal has increased in recent years, mostly due to the close relationship with the community of Portuguese language countries. Samples were collected from malaria-infected patients attending Centro Hospitalar Lisboa Ocidental (CHLO) or the outpatient clinic of Instituto de Higiene e Medicina Tropical (IHMT-NOVA) between March 2014 and May 2021. Molecular characterization of Plasmodium falciparum pfk13 and pfmdr1 genes was performed. We analyzed 232 imported malaria cases. The majority (68.53%) of the patients came from Angola and only three patients travelled to a non-African country; one to Brazil and two to Indonesia. P. falciparum was diagnosed in 81.47% of the cases, P. malariae in 7.33%, P. ovale 6.47% and 1.72% carried P. vivax. No mutations were detected in pfk13. Regarding pfmdr1, the wild-type haplotype (N86/Y184/D1246) was also the most prevalent (64.71%) and N86/184F/D1246 was detected in 26.47% of the cases. The typical imported malaria case was middle-aged male, traveling from Angola, infected with P. falciparum carrying wild type pfmdr1 and pfk13. Our study highlights the need for constant surveillance of malaria parasites imported into Portugal as an important pillar of public health.
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Affiliation(s)
- Debora Serrano
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT-NOVA), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (D.S.); (A.S.-R.); (C.S.); (B.D.); (C.C.)
| | - Ana Santos-Reis
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT-NOVA), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (D.S.); (A.S.-R.); (C.S.); (B.D.); (C.C.)
| | - Clemente Silva
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT-NOVA), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (D.S.); (A.S.-R.); (C.S.); (B.D.); (C.C.)
| | - Ana Dias
- Laboratório de Microbiologia Clínica e Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar Lisboa Ocidental (CHLO), Rua da Junqueira 126, 1349-019 Lisboa, Portugal; (A.D.); (C.T.); (T.B.-F.)
| | - Brigite Dias
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT-NOVA), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (D.S.); (A.S.-R.); (C.S.); (B.D.); (C.C.)
| | - Cristina Toscano
- Laboratório de Microbiologia Clínica e Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar Lisboa Ocidental (CHLO), Rua da Junqueira 126, 1349-019 Lisboa, Portugal; (A.D.); (C.T.); (T.B.-F.)
| | - Cláudia Conceição
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT-NOVA), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (D.S.); (A.S.-R.); (C.S.); (B.D.); (C.C.)
| | - Teresa Baptista-Fernandes
- Laboratório de Microbiologia Clínica e Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar Lisboa Ocidental (CHLO), Rua da Junqueira 126, 1349-019 Lisboa, Portugal; (A.D.); (C.T.); (T.B.-F.)
| | - Fatima Nogueira
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT-NOVA), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (D.S.); (A.S.-R.); (C.S.); (B.D.); (C.C.)
- Correspondence: ; Tel.: +351-213652600
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