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Guo B, Takala-Harrison S, O’Connor TD. Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592538. [PMID: 38746392 PMCID: PMC11092787 DOI: 10.1101/2024.05.04.592538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Genomic surveillance is crucial for identifying at-risk populations for targeted malaria control and elimination. Identity-by-descent (IBD) is being used in Plasmodium population genomics to estimate genetic relatedness, effective population size ( N e ) , population structure, and positive selection. However, a comprehensive evaluation of IBD segment detection tools is lacking for species with high rates of recombination. Here, we employ genetic simulations reflecting P. falciparum's high recombination rate and decreasing N e to benchmark IBD callers, including probabilistic (hmmIBD, isoRelate), identity-by-state-based (hap-IBD, phased IBD) and others (Refined IBD), using genealogy-based true IBD and downstream inference of population characteristics. Our findings reveal that low marker density per genetic unit, related to high recombination rates relative to mutation rates, significantly affects the quality of detected IBD segments. Most IBD callers suffer from high false negative rates, which can be improved with parameter optimization. Optimized parameters allow for more accurate capture of selection signals and population structure, but hmmIBD is unique in providing less biased estimates of N e . Empirical data subsampled from the MalariaGEN Pf7 database, representing different transmission settings, confirmed these patterns. We conclude that the detection of IBD in high-recombining species requires context-specific evaluation and parameter optimization and recommend that hmmIBD be used for quality-sensitive analysis, such as estimation of N e in these species.
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Affiliation(s)
- Bing Guo
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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2
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [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: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
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3
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Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum. Nat Commun 2024; 15:2499. [PMID: 38509066 PMCID: PMC10954658 DOI: 10.1038/s41467-024-46659-0] [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: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates. We demonstrate that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discover that the removal of IBD peak regions partially restores the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness and extent of inbreeding. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
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Affiliation(s)
- Bing Guo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michele D Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mariusz Wojnarski
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Brian A Vesely
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - 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
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisbon, Portugal
| | - Norman C Waters
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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Kattenberg JH, Monsieurs P, De Meyer J, De Meulenaere K, Sauve E, de Oliveira TC, Ferreira MU, Gamboa D, Rosanas‐Urgell A. Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America. Ecol Evol 2024; 14:e11103. [PMID: 38529021 PMCID: PMC10961478 DOI: 10.1002/ece3.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility - crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.
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Affiliation(s)
| | - Pieter Monsieurs
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Julie De Meyer
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Present address:
Integrated Molecular Plant physiology Research (IMPRES) and Plants and Ecosystems (PLECO), Department of BiologyUniversity of AntwerpAntwerpBelgium
| | | | - Erin Sauve
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Thaís C. de Oliveira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical MedicineNova University of LisbonLisbonPortugal
| | - Dionicia Gamboa
- Instituto de Medicina Tropical “Alexander von Humboldt”Universidad Peruana Cayetano HerediaLimaPeru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e IngenieríaUniversidad Peruana Cayetano HerediaLimaPeru
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5
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Holzschuh A, Ewnetu Y, Carlier L, Lerch A, Gerlovina I, Baker SC, Yewhalaw D, Haileselassie W, Berhane N, Lemma W, Koepfli C. Plasmodium falciparum transmission in the highlands of Ethiopia is driven by closely related and clonal parasites. Mol Ecol 2024; 33:e17292. [PMID: 38339833 DOI: 10.1111/mec.17292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/28/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Malaria cases are frequently recorded in the Ethiopian highlands even at altitudes above 2000 m. The epidemiology of malaria in the Ethiopian highlands, and, in particular, the role of importation by human migration from the highly endemic lowlands is not well understood. We sequenced 187 Plasmodium falciparum samples from two sites in the Ethiopian highlands, Gondar (n = 159) and Ziway (n = 28), using a multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug resistance loci. Here, we characterize the parasite population structure and genetic relatedness. We identify moderate parasite diversity (mean HE : 0.54) and low infection complexity (74.9% monoclonal). A significant percentage of infections share microhaplotypes, even across transmission seasons and sites, indicating persistent local transmission. We identify multiple clusters of clonal or near-clonal infections, highlighting high genetic relatedness. Only 6.3% of individuals diagnosed with P. falciparum reported recent travel. Yet, in clonal or near-clonal clusters, infections of travellers were frequently observed first in time, suggesting that parasites may have been imported and then transmitted locally. 31.1% of infections are pfhrp2-deleted and 84.4% pfhrp3-deleted, and 28.7% have pfhrp2/3 double deletions. Parasites with pfhrp2/3 deletions and wild-type parasites are genetically distinct. Mutations associated with resistance to sulphadoxine-pyrimethamine or suggested to reduce sensitivity to lumefantrine are observed at near-fixation. In conclusion, genomic data corroborate local transmission and the importance of intensified control in the Ethiopian highlands.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yalemwork Ewnetu
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Lise Carlier
- Trinity Centre for Global Health, Trinity College Dublin, Dublin, Ireland
- Noul Inc., Seoul, Republic of Korea
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Inna Gerlovina
- Department of Medicine, Division of HIV, ID and Global Medicine, EPPIcenter Research Program, University of California, San Francisco, California, USA
| | - Sarah Cate Baker
- Trinity Centre for Global Health, Trinity College Dublin, Dublin, Ireland
| | - Delenasaw Yewhalaw
- Tropical and Infectious Disease Research Center, Jimma University, Jimma, Ethiopia
| | | | - Nega Berhane
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Wossenseged Lemma
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
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6
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
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7
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Holzschuh A, Lerch A, Fakih BS, Aliy SM, Ali MH, Ali MA, Bruzzese DJ, Yukich J, Hetzel MW, Koepfli C. Using a mobile nanopore sequencing lab for end-to-end genomic surveillance of Plasmodium falciparum: A feasibility study. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0002743. [PMID: 38300956 PMCID: PMC10833559 DOI: 10.1371/journal.pgph.0002743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
Genomic epidemiology holds promise for malaria control and elimination efforts, for example by informing on Plasmodium falciparum genetic diversity and prevalence of mutations conferring anti-malarial drug resistance. Limited sequencing infrastructure in many malaria-endemic areas prevents the rapid generation of genomic data. To address these issues, we developed and validated assays for P. falciparum nanopore sequencing in endemic sites using a mobile laboratory, targeting key antimalarial drug resistance markers and microhaplotypes. Using two multiplexed PCR reactions, we amplified six highly polymorphic microhaplotypes and ten drug resistance markers. We developed a bioinformatics workflow that allows genotyping of polyclonal malaria infections, including minority clones. We validated the panels on mock dried blood spot (DBS) and rapid diagnostic test (RDT) samples and archived DBS, demonstrating even, high read coverage across amplicons (range: 580x to 3,212x median coverage), high haplotype calling accuracy, and the ability to explore within-sample diversity of polyclonal infections. We field-tested the feasibility of rapid genotyping in Zanzibar in close collaboration with the local malaria elimination program using DBS and routinely collected RDTs as sample inputs. Our assay identified haplotypes known to confer resistance to known antimalarials in the dhfr, dhps and mdr1 genes, but no evidence of artemisinin partial resistance. Most infections (60%) were polyclonal, with high microhaplotype diversity (median HE = 0.94). In conclusion, our assays generated actionable data within a few days, and we identified current challenges for implementing nanopore sequencing in endemic countries to accelerate malaria control and elimination.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - 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
| | - Safia Mohammed Aliy
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Mohamed Haji Ali
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Mohamed Ali Ali
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Daniel J. Bruzzese
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Joshua Yukich
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, United States of America
| | - Manuel W. Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
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Casanova D, Baptista V, Costa M, Freitas B, Pereira MDNI, Calçada C, Mota P, Kythrich O, Pereira MHJS, Osório NS, Veiga MI. Artemisinin resistance-associated gene mutations in Plasmodium falciparum: A case study of severe malaria from Mozambique. Travel Med Infect Dis 2024; 57:102684. [PMID: 38159875 DOI: 10.1016/j.tmaid.2023.102684] [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: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The effectiveness of artemisinin-based combination therapies (ACT) in treating Plasmodium falciparum, is vital for global malaria control efforts, particularly in sub-Saharan Africa. The examination of imported cases from endemic areas holds implications for malaria chemotherapy on a global scale. METHOD A 45-year-old male presented with high fever, dry cough, diarrhoea and generalized muscle pain, following a two-week trip to Mozambique. P. falciparum infection with hiperparasitemia was confirmed and the patient was treated initially with quinine and doxycycline, then intravenous artesunate. To assess drug susceptibility, ex vivo half-maximal inhibitory concentration assays were conducted, and the isolated P. falciparum genome was deep sequenced. RESULTS The clinical isolate exhibited elevated ex vivo half-maximal inhibitory concentration values to dihydroartemisinin, lumefantrine, mefloquine and piperaquine. Genomic analysis identified a I416V mutation in the P. falciparum Kelch13 (PF3D7_1343700) gene, and several mutations at the Kelch13 interaction candidate genes, pfkics (PF3D7_0813000, PF3D7_1138700, PF3D7_1246300), including the ubiquitin carboxyl-terminal hydrolase 1, pfubp1 (PF3D7_0104300). Mutations at the drug transporters and genes linked to next-generation antimalarial drug resistance were also present. CONCLUSIONS This case highlights the emergence of P. falciparum strains carrying mutations in artemisinin resistance-associated genes in Mozambique, couple with a reduction in ex vivo susceptibility to ACT drugs. Continuous surveillance of mutations linked to drug resistance and regular monitoring of drug susceptibility are imperative to anticipate the spread of potential resistant strains emerging in Mozambique and to maintain effective malaria control strategies.
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Affiliation(s)
- Daniela Casanova
- Internal Medicine Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Vitória Baptista
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal; Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, University of Minho, Campus de Azurém, 4800-058, Guimarães, Portugal
| | - Magda Costa
- Internal Medicine Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Bruno Freitas
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Maria das Neves Imaculada Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Carla Calçada
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Paula Mota
- Clinical Pathology Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Olena Kythrich
- Clinical Pathology Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | | | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Maria Isabel Veiga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal; Clinical Academic Center-Braga (2CA-Braga), 4710-243, Braga, Portugal.
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9
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Adegbite G, Edeki S, Isewon I, Emmanuel J, Dokunmu T, Rotimi S, Oyelade J, Adebiyi E. Mathematical modeling of malaria transmission dynamics in humans with mobility and control states. Infect Dis Model 2023; 8:1015-1031. [PMID: 37649792 PMCID: PMC10463202 DOI: 10.1016/j.idm.2023.08.005] [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: 04/27/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
Malaria importation is one of the hypothetical drivers of malaria transmission dynamics across the globe. Several studies on malaria importation focused on the effect of the use of conventional malaria control strategies as approved by the World Health Organization (WHO) on malaria transmission dynamics but did not capture the effect of the use of traditional malaria control strategies by vigilant humans. In order to handle the aforementioned situation, a novel system of Ordinary Differential Equations (ODEs) was developed comprising the human and the malaria vector compartments. Analysis of the system was carried out to assess its quantitative properties. The novel computational algorithm used to solve the developed system of ODEs was implemented and benchmarked with the existing Runge-Kutta numerical solution method. Furthermore, simulations of different vigilant conditions useful to control malaria were carried out. The novel system of malaria models was well-posed and epidemiologically meaningful based on its quantitative properties. The novel algorithm performed relatively better in terms of model simulation accuracy than Runge-Kutta. At the best model-fit condition of 98% vigilance to the use of conventional and traditional malaria control strategies, this study revealed that malaria importation has a persistent impact on malaria transmission dynamics. In lieu of this, this study opined that total vigilance to the use of the WHO-approved and traditional malaria management tools would be the most effective control strategy against malaria importation.
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Affiliation(s)
- Gbenga Adegbite
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Sunday Edeki
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Mathematics, Covenant University, Ota, Nigeria
| | - Itunuoluwa Isewon
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communications-African Centre of Excellence, Covenant University, Ota, Ogun State, Nigeria
| | - Jerry Emmanuel
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communications-African Centre of Excellence, Covenant University, Ota, Ogun State, Nigeria
| | - Titilope Dokunmu
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communications-African Centre of Excellence, Covenant University, Ota, Ogun State, Nigeria
| | - Solomon Rotimi
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communications-African Centre of Excellence, Covenant University, Ota, Ogun State, Nigeria
| | - Jelili Oyelade
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communications-African Centre of Excellence, Covenant University, Ota, Ogun State, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communications-African Centre of Excellence, Covenant University, Ota, Ogun State, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Girgis ST, Adika E, Nenyewodey FE, Senoo Jnr DK, Ngoi JM, Bandoh K, Lorenz O, van de Steeg G, Harrott AJR, Nsoh S, Judge K, Pearson RD, Almagro-Garcia J, Saiid S, Atampah S, Amoako EK, Morang'a CM, Asoala V, Adjei ES, Burden W, Roberts-Sengier W, Drury E, Pierce ML, Gonçalves S, Awandare GA, Kwiatkowski DP, Amenga-Etego LN, Hamilton WL. Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana. Nat Microbiol 2023; 8:2365-2377. [PMID: 37996707 PMCID: PMC10686832 DOI: 10.1038/s41564-023-01516-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/06/2023] [Indexed: 11/25/2023]
Abstract
Malaria results in over 600,000 deaths annually, with the highest burden of deaths in young children living in sub-Saharan Africa. Molecular surveillance can provide important information for malaria control policies, including detection of antimalarial drug resistance. However, genome sequencing capacity in malaria-endemic countries is limited. We designed and implemented an end-to-end workflow to detect Plasmodium falciparum antimalarial resistance markers and diversity in the vaccine target circumsporozoite protein (csp) using nanopore sequencing in Ghana. We analysed 196 clinical samples and showed that our method is rapid, robust, accurate and straightforward to implement. Importantly, our method could be applied to dried blood spot samples, which are readily collected in endemic settings. We report that P. falciparum parasites in Ghana are mostly susceptible to chloroquine, with persistent sulfadoxine-pyrimethamine resistance and no evidence of artemisinin resistance. Multiple single nucleotide polymorphisms were identified in csp, but their significance is uncertain. Our study demonstrates the feasibility of nanopore sequencing for malaria genomic surveillance in endemic countries.
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Affiliation(s)
- Sophia T Girgis
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Edem Adika
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Felix E Nenyewodey
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Dodzi K Senoo Jnr
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Joyce M Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Kukua Bandoh
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Oliver Lorenz
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Guus van de Steeg
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Sebastian Nsoh
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Kim Judge
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Samirah Saiid
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Solomon Atampah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Enock K Amoako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Victor Asoala
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Elrmion S Adjei
- Ledzokuku Krowor Municipal Assembly (LEKMA) Hospital, Accra, Ghana
| | - William Burden
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Eleanor Drury
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Megan L Pierce
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sónia Gonçalves
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | | | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.
| | - William L Hamilton
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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11
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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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12
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Coonahan E, Gage H, Chen D, Noormahomed EV, Buene TP, Mendes de Sousa I, Akrami K, Chambal L, Schooley RT, Winzeler EA, Cowell AN. Whole-genome surveillance identifies markers of Plasmodium falciparum drug resistance and novel genomic regions under selection in Mozambique. mBio 2023; 14:e0176823. [PMID: 37750720 PMCID: PMC10653802 DOI: 10.1128/mbio.01768-23] [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: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Malaria is a devastating disease caused by Plasmodium parasites. The evolution of parasite drug resistance continues to hamper progress toward malaria elimination, and despite extensive efforts to control malaria, it remains a leading cause of death in Mozambique and other countries in the region. The development of successful vaccines and identification of molecular markers to track drug efficacy are essential for managing the disease burden. We present an analysis of the parasite genome in Mozambique, a country with one of the highest malaria burdens globally and limited available genomic data, revealing current selection pressure. We contribute additional evidence to limited prior studies supporting the effectiveness of SWGA in producing reliable genomic data from complex clinical samples. Our results provide the identity of genomic loci that may be associated with current antimalarial drug use, including artemisinin and lumefantrine, and reveal selection pressure predicted to compromise the efficacy of current vaccine candidates.
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Affiliation(s)
- Erin Coonahan
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Hunter Gage
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Daisy Chen
- Department of Pediatrics, University of California San Diego (UCSD), La Jolla, California, USA
| | - Emilia Virginia Noormahomed
- School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Microbiology, Parasitology Laboratory, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
| | - Titos Paulo Buene
- Department of Microbiology, Parasitology Laboratory, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
| | - Irina Mendes de Sousa
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
- Biological Sciences Department, Faculty of Sciences, Eduardo Mondlane University, Maputo, Mozambique
| | - Kevan Akrami
- School of Medicine, University of California San Diego, La Jolla, California, USA
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Lucia Chambal
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
- Department of Internal Medicine, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Maputo Central Hospital, Maputo, Mozambique
| | - Robert T. Schooley
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, University of California San Diego (UCSD), La Jolla, California, USA
| | - Annie N. Cowell
- School of Medicine, University of California San Diego, La Jolla, California, USA
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13
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Siqueira-Neto JL, Wicht KJ, Chibale K, Burrows JN, Fidock DA, Winzeler EA. Antimalarial drug discovery: progress and approaches. Nat Rev Drug Discov 2023; 22:807-826. [PMID: 37652975 PMCID: PMC10543600 DOI: 10.1038/s41573-023-00772-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 09/02/2023]
Abstract
Recent antimalarial drug discovery has been a race to produce new medicines that overcome emerging drug resistance, whilst considering safety and improving dosing convenience. Discovery efforts have yielded a variety of new molecules, many with novel modes of action, and the most advanced are in late-stage clinical development. These discoveries have led to a deeper understanding of how antimalarial drugs act, the identification of a new generation of drug targets, and multiple structure-based chemistry initiatives. The limited pool of funding means it is vital to prioritize new drug candidates. They should exhibit high potency, a low propensity for resistance, a pharmacokinetic profile that favours infrequent dosing, low cost, preclinical results that demonstrate safety and tolerability in women and infants, and preferably the ability to block Plasmodium transmission to Anopheles mosquito vectors. In this Review, we describe the approaches that have been successful, progress in preclinical and clinical development, and existing challenges. We illustrate how antimalarial drug discovery can serve as a model for drug discovery in diseases of poverty.
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Affiliation(s)
| | - Kathryn J Wicht
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Kelly Chibale
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | | | - David A Fidock
- Department of Microbiology and Immunology and Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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14
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Plaza DF, Zerebinski J, Broumou I, Lautenbach MJ, Ngasala B, Sundling C, Färnert A. A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing. CELL REPORTS METHODS 2023; 3:100574. [PMID: 37751696 PMCID: PMC10545912 DOI: 10.1016/j.crmeth.2023.100574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 06/18/2023] [Accepted: 08/07/2023] [Indexed: 09/28/2023]
Abstract
Many vaccine candidate proteins in the malaria parasite Plasmodium falciparum are under strong immunological pressure and confer antigenic diversity. We present a sequencing and data analysis platform for the genomic surveillance of the insertion or deletion (indel)-rich antigens merozoite surface protein 1 (MSP1), MSP2, glutamate-rich protein (GLURP), and CSP from P. falciparum using long-read circular consensus sequencing (CCS) in multiclonal malaria isolates. Our platform uses 40 PCR primers per gene to asymmetrically barcode and identify multiclonal infections in pools of up to 384 samples. With msp2, we validated the method using 235 mock infections combining 10 synthetic variants at different concentrations and infection complexities. We applied this strategy to P. falciparum isolates from a longitudinal cohort in Tanzania. Finally, we constructed an analysis pipeline that streamlines the processing and interpretation of epidemiological and antigenic diversity data from demultiplexed FASTQ files. This platform can be easily adapted to other polymorphic antigens of interest in Plasmodium or any other human pathogen.
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Affiliation(s)
- David Fernando Plaza
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden.
| | - Julia Zerebinski
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Ioanna Broumou
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Maximilian Julius Lautenbach
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar es Salaam 57RF+V8, Tanzania
| | - Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden
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15
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Liu R, Liu T, Dan T, Yang S, Li Y, Luo B, Zhuang Y, Fan X, Zhang X, Cai H, Teng Y. AIDMAN: An AI-based object detection system for malaria diagnosis from smartphone thin-blood-smear images. PATTERNS (NEW YORK, N.Y.) 2023; 4:100806. [PMID: 37720337 PMCID: PMC10499858 DOI: 10.1016/j.patter.2023.100806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/02/2023] [Accepted: 07/07/2023] [Indexed: 09/19/2023]
Abstract
Malaria is a significant public health concern, with ∼95% of cases occurring in Africa, but accurate and timely diagnosis is problematic in remote and low-income areas. Here, we developed an artificial intelligence-based object detection system for malaria diagnosis (AIDMAN). In this system, the YOLOv5 model is used to detect cells in a thin blood smear. An attentional aligner model (AAM) is then applied for cellular classification that consists of multi-scale features, a local context aligner, and multi-scale attention. Finally, a convolutional neural network classifier is applied for diagnosis using blood-smear images, reducing interference caused by false positive cells. The results demonstrate that AIDMAN handles interference well, with a diagnostic accuracy of 98.62% for cells and 97% for blood-smear images. The prospective clinical validation accuracy of 98.44% is comparable to that of microscopists. AIDMAN shows clinically acceptable detection of malaria parasites and could aid malaria diagnosis, especially in areas lacking experienced parasitologists and equipment.
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Affiliation(s)
- Ruicun Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Tuoyu Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Tingting Dan
- School of Computer Science and Engineering, South China University of Technology, Guangzhou 510600, China
| | - Shan Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yanbing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Boyu Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yingtan Zhuang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xinyue Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xianchao Zhang
- Key Laboratory of Medical Electronics and Digital Health of Zhejiang Province, Jiaxing University, Jiaxing 314001, China
- Engineering Research Center of Intelligent Human Health Situation Awareness of Zhejiang Province, Jiaxing University, Jiaxing 314001, China
| | - Hongmin Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou 510600, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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16
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Wu PC, Lee YQ, Möller M, Storry JR, Olsson ML. Elucidation of the low-expressing erythroid CR1 phenotype by bioinformatic mining of the GATA1-driven blood-group regulome. Nat Commun 2023; 14:5001. [PMID: 37591894 PMCID: PMC10435571 DOI: 10.1038/s41467-023-40708-w] [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: 11/21/2022] [Accepted: 08/08/2023] [Indexed: 08/19/2023] Open
Abstract
Genetic determinants underlying most human blood groups are now clarified but variation in expression levels remains largely unexplored. By developing a bioinformatics pipeline analyzing GATA1/Chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets, we identify 193 potential regulatory sites in 33 blood-group genes. As proof-of-concept, we aimed to delineate the low-expressing complement receptor 1 (CR1) Helgeson phenotype on erythrocytes, which is correlated with several diseases and protects against severe malaria. We demonstrate that two candidate CR1 enhancer motifs in intron 4 bind GATA1 and drive transcription. Both are functionally abolished by naturally-occurring SNVs. Erythrocyte CR1-mRNA and CR1 levels correlate dose-dependently with genotype of one SNV (rs11117991) in two healthy donor cohorts. Haplotype analysis of rs11117991 with previously proposed markers for Helgeson shows high linkage disequilibrium in Europeans but explains the poor prediction reported for Africans. These data resolve the longstanding debate on the genetic basis of inherited low CR1 and form a systematic starting point to investigate the blood group regulome.
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Affiliation(s)
- Ping Chun Wu
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Yan Quan Lee
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Mattias Möller
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Jill R Storry
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Martin L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden.
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17
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Gwarinda HB, Tessema SK, Raman J, Greenhouse B, Birkholtz LM. Population structure and genetic connectivity of Plasmodium falciparum in pre-elimination settings of Southern Africa. FRONTIERS IN EPIDEMIOLOGY 2023; 3:1227071. [PMID: 38455947 PMCID: PMC10910941 DOI: 10.3389/fepid.2023.1227071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/17/2023] [Indexed: 03/09/2024]
Abstract
To accelerate malaria elimination in the Southern African region by 2030, it is essential to prevent cross-border malaria transmission. However, countries within the region are highly interconnected due to human migration that aids in the movement of the parasite across geographical borders. It is therefore important to better understand Plasmodium falciparum transmission dynamics in the region, and identify major parasite source and sink populations, as well as cross-border blocks of high parasite connectivity. We performed a meta-analysis using collated parasite allelic data generated by microsatellite genotyping of malaria parasites from Namibia, Eswatini, South Africa, and Mozambique (N = 5,314). The overall number of unique alleles was significantly higher (P ≤ 0.01) in Namibia (mean A = 17.3 ± 1.46) compared to South Africa (mean A = 12.2 ± 1.22) and Eswatini (mean A = 13.3 ± 1.27, P ≤ 0.05), whilst the level of heterozygosity was not significantly different between countries. The proportion of polyclonal infections was highest for Namibia (77%), and lowest for Mozambique (64%). A was significant population structure was detected between parasites from the four countries, and patterns of gene flow showed that Mozambique was the major source area and Eswatini the major sink area of parasites between the countries. This study showed strong signals of parasite population structure and genetic connectivity between malaria parasite populations across national borders. This calls for strengthening the harmonization of malaria control and elimination efforts between countries in the southern African region. This data also proves its potential utility as an additional surveillance tool for malaria surveillance on both a national and regional level for the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance as countries work towards malaria elimination.
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Affiliation(s)
- Hazel B. Gwarinda
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Sofonias K. Tessema
- EppiCenter, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Jaishree Raman
- Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research (ARMMOR), Centre for Emerging Zoonotic and Parasitic Diseases, A Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, Wits Research Institute for Malaria, University of Witwatersrand, Johannesburg, South Africa
| | - Bryan Greenhouse
- EppiCenter, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Lyn-Marié Birkholtz
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
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18
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Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong Positive Selection Biases Identity-By-Descent-Based Inferences of Recent Demography and Population Structure in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549114. [PMID: 37502843 PMCID: PMC10370022 DOI: 10.1101/2023.07.14.549114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD). Yet, strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we utilized simulations, a true IBD inference algorithm, and empirical datasets from different malaria transmission settings to investigate the extent of such bias and explore potential correction strategies. We analyzed whole genome sequence data generated from 640 new and 4,026 publicly available Plasmodium falciparum clinical isolates. Our findings demonstrated that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discovered that the removal of IBD peak regions partially restored the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
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Affiliation(s)
- Bing Guo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michele D Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mariusz Wojnarski
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Brian A Vesely
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Norman C Waters
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
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19
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Niaré K, Greenhouse B, Bailey JA. An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis. Malar J 2023; 22:207. [PMID: 37420214 DOI: 10.1186/s12936-023-04632-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here a falciparum variant calling pipeline based on GATK version 4 (GATK4) was optimized and applied to 6626 public Illumina WGS samples. METHODS Control WGS and accurate PacBio assemblies of 10 laboratory strains were leveraged to optimize parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs. From these controls, a high-quality training dataset was generated to recalibrate the raw variant data. RESULTS On current high-quality samples (read length = 250 bp, insert size = 405-524 bp), the optimized pipeline shows improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). Its sensitivity on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. The resulting combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. Finally, increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection. CONCLUSIONS Overall, this study provides an optimized falciparum GATK4 pipeline resource for variant calling which should help improve genomic studies of malaria.
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Affiliation(s)
- Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
| | - Bryan Greenhouse
- EPPIcenter Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
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20
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Amambua-Ngwa A, Button-Simons KA, Li X, Kumar S, Brenneman KV, Ferrari M, Checkley LA, Haile MT, Shoue DA, McDew-White M, Tindall SM, Reyes A, Delgado E, Dalhoff H, Larbalestier JK, Amato R, Pearson RD, Taylor AB, Nosten FH, D'Alessandro U, Kwiatkowski D, Cheeseman IH, Kappe SHI, Avery SV, Conway DJ, Vaughan AM, Ferdig MT, Anderson TJC. Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1. Nat Microbiol 2023; 8:1213-1226. [PMID: 37169919 PMCID: PMC10322710 DOI: 10.1038/s41564-023-01377-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/29/2023] [Indexed: 05/13/2023]
Abstract
Malaria parasites break down host haemoglobin into peptides and amino acids in the digestive vacuole for export to the parasite cytoplasm for growth: interrupting this process is central to the mode of action of several antimalarial drugs. Mutations in the chloroquine (CQ) resistance transporter, pfcrt, located in the digestive vacuole membrane, confer CQ resistance in Plasmodium falciparum, and typically also affect parasite fitness. However, the role of other parasite loci in the evolution of CQ resistance is unclear. Here we use a combination of population genomics, genetic crosses and gene editing to demonstrate that a second vacuolar transporter plays a key role in both resistance and compensatory evolution. Longitudinal genomic analyses of the Gambian parasites revealed temporal signatures of selection on a putative amino acid transporter (pfaat1) variant S258L, which increased from 0% to 97% in frequency between 1984 and 2014 in parallel with the pfcrt1 K76T variant. Parasite genetic crosses then identified a chromosome 6 quantitative trait locus containing pfaat1 that is selected by CQ treatment. Gene editing demonstrated that pfaat1 S258L potentiates CQ resistance but at a cost of reduced fitness, while pfaat1 F313S, a common southeast Asian polymorphism, reduces CQ resistance while restoring fitness. Our analyses reveal hidden complexity in CQ resistance evolution, suggesting that pfaat1 may underlie regional differences in the dynamics of resistance evolution, and modulate parasite resistance or fitness by manipulating the balance between both amino acid and drug transport.
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Affiliation(s)
- Alfred Amambua-Ngwa
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Katrina A Button-Simons
- 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
| | - Katelyn Vendrely Brenneman
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Marco Ferrari
- Disease Intervention and Prevention Program, 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
| | - Meseret T Haile
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Douglas A Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Marina McDew-White
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sarah M Tindall
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ann Reyes
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Elizabeth Delgado
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Haley Dalhoff
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - James K Larbalestier
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Alexander B Taylor
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, Antonio, TX, USA
| | - François H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Umberto D'Alessandro
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | - Ian H Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 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
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - David J Conway
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - 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.
| | - Michael T Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Timothy J C Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
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21
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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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22
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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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23
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Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023; 14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.
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Affiliation(s)
- Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Courage Adobor
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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24
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Dieng CC, Ford CT, Lerch A, Doniou D, Vegesna K, Janies D, Cui L, Amoah L, Afrane Y, Lo E. Genetic variations of Plasmodium falciparum circumsporozoite protein and the impact on interactions with human immunoproteins and malaria vaccine efficacy. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105418. [PMID: 36841398 DOI: 10.1016/j.meegid.2023.105418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
In October 2021, the world's first malaria vaccine RTS,S was endorsed by WHO for broad use in children, despite its low efficacy. This study examined polyclonal infections and the associations of parasite genetic variations with binding affinity to human leukocyte antigen (HLA). Multiplicity of infection was determined by amplicon deep sequencing of PfMSP1. Genetic variations in PfCSP were examined across 88 samples from Ghana and analyzed together with 1655 PfCSP sequences from other African and non-African isolates. Binding interactions of PfCSP peptide variants and HLA were predicted using NetChop and HADDOCK. High polyclonality was detected among infections, with each infection harboring multiple non-3D7 PfCSP variants. Twenty-seven PfCSP haplotypes were detected in the Ghanaian samples, and they broadly represented PfCSP diversity across Africa. The number of genetic differences between 3D7 and non-3D7 PfCSP variants does not influence binding to HLA. However, CSP peptide length after proteolytic degradation significantly affects its molecular weight and binding affinity to HLA. Despite the high diversity of HLA, the majority of the HLAI and II alleles interacted/bound with all Ghana CSP peptides. Multiple non-3D7 strains among P. falciparum infections could impact the effectiveness of RTS,S. Longer peptides of the Th2R/Th3R CSP regions should be considered in future versions of RTS,S.
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Affiliation(s)
- Cheikh Cambel Dieng
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Colby T Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Anita Lerch
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Dickson Doniou
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Kovidh Vegesna
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Liwang Cui
- Department of Internal Medicine, 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 Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, NC, USA.
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Niaré K, Greenhouse B, Bailey JA. An Optimized GATK4 Pipeline for Plasmodium falciparum Whole Genome Sequencing Variant Calling and Analysis. RESEARCH SQUARE 2023:rs.3.rs-2561857. [PMID: 36824880 PMCID: PMC9949269 DOI: 10.21203/rs.3.rs-2561857/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here we optimized a falciparum variant calling pipeline based on GATK version 4 (GATK4) and applied it to 6,626 public Illumina WGS samples. Methods We optimized parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs leveraging control WGS and accurate PacBio assemblies of 10 laboratory strains. From these controls we generated a high-quality training dataset to recalibrate the raw variant data. Results On current high-quality samples (read length = 250bp, insert size = 405 - 524 bp ), we show improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). The sensitivity of our pipeline on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. We further show that using the combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. We finally demonstrate that increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection. Conclusions Overall, we provide an optimized GATK4 pipeline and resource for falciparum variant calling which should help improve genomic studies of malaria.
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Tan MH, Shim H, Chan YB, Day KP. Unravelling var complexity: Relationship between DBLα types and var genes in Plasmodium falciparum. FRONTIERS IN PARASITOLOGY 2023; 1. [PMID: 36998722 PMCID: PMC10060044 DOI: 10.3389/fpara.2022.1006341] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The enormous diversity and complexity of var genes that diversify rapidly by recombination has led to the exclusion of assembly of these genes from major genome initiatives (e.g., Pf6). A scalable solution in epidemiological surveillance of var genes is to use a small ‘tag’ region encoding the immunogenic DBLα domain as a marker to estimate var diversity. As var genes diversify by recombination, it is not clear the extent to which the same tag can appear in multiple var genes. This relationship between marker and gene has not been investigated in natural populations. Analyses of in vitro recombination within and between var genes have suggested that this relationship would not be exclusive. Using a dataset of publicly-available assembled var sequences, we test this hypothesis by studying DBLα-var relationships for four study sites in four countries: Pursat (Cambodia) and Mae Sot (Thailand), representing low malaria transmission, and Navrongo (Ghana) and Chikwawa (Malawi), representing high malaria transmission. In all study sites, DBLα-var relationships were shown to be predominantly 1-to-1, followed by a second largest proportion of 1-to-2 DBLα-var relationships. This finding indicates that DBLα tags can be used to estimate not just DBLα diversity but var gene diversity when applied in a local endemic area. Epidemiological applications of this result are discussed.
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Affiliation(s)
- Mun Hua Tan
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Melbourne, VIC, Australia
| | - Heejung Shim
- School of Mathematics and Statistics/Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Yao-ban Chan
- School of Mathematics and Statistics/Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Karen P. Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Melbourne, VIC, Australia
- CORRESPONDENCE Karen P. Day,
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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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Tavares W, Morais J, Martins JF, Scalsky RJ, Stabler TC, Medeiros MM, Fortes FJ, Arez AP, Silva JC. Malaria in Angola: recent progress, challenges and future opportunities using parasite demography studies. Malar J 2022; 21:396. [PMID: 36577996 PMCID: PMC9795141 DOI: 10.1186/s12936-022-04424-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Over the past two decades, a considerable expansion of malaria interventions has occurred at the national level in Angola, together with cross-border initiatives and regional efforts in southern Africa. Currently, Angola aims to consolidate malaria control and to accelerate the transition from control to pre-elimination, along with other country members of the Elimination 8 initiative. However, the tremendous heterogeneity in malaria prevalence among Angolan provinces, as well as internal population movements and migration across borders, represent major challenges for the Angolan National Malaria Control Programme. This review aims to contribute to the understanding of factors underlying the complex malaria situation in Angola and to encourage future research studies on transmission dynamics and population structure of Plasmodium falciparum, important areas to complement host epidemiological information and to help reenergize the goal of malaria elimination in the country.
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Affiliation(s)
- Wilson Tavares
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Joana Morais
- Instituto Nacional de Investigação Em Saúde, INIS, Luanda, Angola
| | - José F. Martins
- Programa Nacional de Controlo da Malária, PNCM, Luanda, Angola
| | - Ryan J. Scalsky
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Thomas C. Stabler
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, Basel, Switzerland
| | - Márcia M. Medeiros
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Filomeno J. Fortes
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Ana Paula Arez
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Joana C. Silva
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA ,grid.411024.20000 0001 2175 4264Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
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Plasmodium malariae structure and genetic diversity in sub-Saharan Africa determined from microsatellite variants and linked SNPs in orthologues of antimalarial resistance genes. Sci Rep 2022; 12:21881. [PMID: 36536036 PMCID: PMC9761029 DOI: 10.1038/s41598-022-26625-w] [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: 08/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Plasmodium malariae, a neglected human malaria parasite, contributes up to 10% of malaria infections in sub-Saharan Africa (sSA). Though P. malariae infection is considered clinically benign, it presents mostly as coinfections with the dominant P. falciparum. Completion of its reference genome has paved the way to further understand its biology and interactions with the human host, including responses to antimalarial interventions. We characterized 75 P. malariae isolates from seven endemic countries in sSA using highly divergent microsatellites. The P. malariae infections were highly diverse and five subpopulations from three ancestries (independent of origin of isolates) were determined. Sequences of 11 orthologous antimalarial resistance genes, identified low frequency single nucleotide polymorphisms (SNPs), strong linkage disequilibrium between loci that may be due to antimalarial drug selection. At least three sub-populations were detectable from a subset of denoised SNP data from mostly the mitochondrial cytochrome b coding region. This evidence of diversity and selection calls for including P. malariae in malaria genomic surveillance towards improved tools and strategies for malaria elimination.
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Tadele G, Jaiteh FK, Oboh M, Oriero E, Dugassa S, Amambua-Ngwa A, Golassa L. Low genetic diversity of Plasmodium falciparum merozoite surface protein 1 and 2 and multiplicity of infections in western Ethiopia following effective malaria interventions. Malar J 2022; 21:383. [PMID: 36522733 PMCID: PMC9753253 DOI: 10.1186/s12936-022-04394-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Genetic diversity of malaria parasites can inform the intensity of transmission and poses a major threat to malaria control and elimination interventions. Characterization of the genetic diversity would provide essential information about the ongoing control efforts. This study aimed to explore allelic polymorphism of merozoite surface protein 1 (msp1) and merozoite surface protein 2 (msp2) to determine the genetic diversity and multiplicity of Plasmodium falciparum infections circulating in high and low transmission sites in western Ethiopia. METHODS Parasite genomic DNA was extracted from a total of 225 dried blood spots collected from confirmed uncomplicated P. falciparum malaria-infected patients in western Ethiopia. Of these, 72.4% (163/225) and 27.6% (62/225) of the samples were collected in high and low transmission areas, respectively. Polymorphic msp1 and msp2 genes were used to explore the genetic diversity and multiplicity of falciparum malaria infections. Genotyping of msp1 was successful in 86.5% (141/163) and 88.7% (55/62) samples collected from high and low transmission areas, respectively. Genotyping of msp2 was carried out among 85.3% (139/163) and 96.8% (60/62) of the samples collected in high and low transmission sites, respectively. Plasmodium falciparum msp1 and msp2 genes were amplified by nested PCR and the PCR products were analysed by QIAxcel ScreenGel Software. A P-value of less or equal to 0.05 was considered significant. RESULTS High prevalence of falciparum malaria was identified in children less than 15 years as compared with those ≥ 15 years old (AOR = 2.438, P = 0.005). The three allelic families of msp1 (K1, MAD20, and RO33) and the two allelic families of msp2 (FC27 and 3D7), were observed in samples collected in high and low transmission areas. However, MAD 20 and FC 27 alleles were the predominant allelic families in both settings. Plasmodium falciparum isolates circulating in western Ethiopia had low genetic diversity and mean MOI. No difference in mean MOI between high transmission sites (mean MOI 1.104) compared with low transmission area (mean MOI 1.08) (p > 0.05). The expected heterozygosity of msp1 was slightly higher in isolates collected from high transmission sites (He = 0.17) than in those isolates from low transmission (He = 0.12). However, the heterozygosity of msp2 was not different in both settings (Pfmsp2: 0.04 in high transmission; pfmsp2: 0.03 in low transmission). CONCLUSION Plasmodium falciparum from clinical malaria cases in western Ethiopia has low genetic diversity and multiplicity of infection irrespective of the intensity of transmission at the site of sampling. These may be signaling the effectiveness of malaria control strategies in Ethiopia; although further studies are required to determine how specific intervention strategies and other parameters that drive the pattern.
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Affiliation(s)
- Geletta Tadele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Fatou K Jaiteh
- Medical Research Council Unit the Gambia, London School of Hygiene and Tropical Medicine, Serrekunda, The Gambia
| | - Mary Oboh
- Medical Research Council Unit the Gambia, London School of Hygiene and Tropical Medicine, Serrekunda, The Gambia
| | - Eniyou Oriero
- Medical Research Council Unit the Gambia, London School of Hygiene and Tropical Medicine, Serrekunda, The Gambia
| | - Sisay Dugassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit the Gambia, London School of Hygiene and Tropical Medicine, Serrekunda, The Gambia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
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Carrasquilla M, Early AM, Taylor AR, Knudson Ospina A, Echeverry DF, Anderson TJC, Mancilla E, Aponte S, Cárdenas P, Buckee CO, Rayner JC, Sáenz FE, Neafsey DE, Corredor V. Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis. PLoS Pathog 2022; 18:e1010993. [PMID: 36542676 PMCID: PMC9815574 DOI: 10.1371/journal.ppat.1010993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/05/2023] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P. falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring less genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to changes in drug regime. Using newly sequenced whole genomes, we measure relatedness between 166 parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore past selection events in the region. Two genes associated with chloroquine resistance, crt and aat1, show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci (dhps, mdr1, and dhfr). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in small populations, as will occur in any region nearing malaria elimination.
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Affiliation(s)
- Manuela Carrasquilla
- Department of Immunology and Infectious Diseases, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Angela M. Early
- Department of Immunology and Infectious Diseases, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Aimee R. Taylor
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Angélica Knudson Ospina
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Diego F. Echeverry
- Departamento de Microbiología, Facultad de Salud, Universidad del Valle, Cali, Colombia
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Timothy J. C. Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institution, San Antonio, Texas, United States of America
| | - Elvira Mancilla
- Secretaría Departamental de Salud del Cauca, Popayán, Colombia
| | - Samanda Aponte
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Julian C. Rayner
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Fabián E. Sáenz
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Daniel E. Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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Mbye H, Mane K, Diop MF, Demba MA, Bojang F, Mohammed NI, Jeffries D, Quashie NB, D'Alessandro U, Amambua-Ngwa A. Plasmodium falciparum merozoite invasion ligands, linked antimalarial resistance loci and ex vivo responses to antimalarials in The Gambia. J Antimicrob Chemother 2022; 77:2946-2955. [PMID: 35904009 PMCID: PMC9616547 DOI: 10.1093/jac/dkac244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/23/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Artemether/lumefantrine is the most commonly used artemisinin-based combination treatment (ACT) for malaria in sub-Saharan Africa. Drug resistance to ACT components is a major threat to malaria elimination efforts. Therefore, rigorous monitoring of drug efficacy is required for adequate management of malaria and to sustain the effectiveness of ACTs. OBJECTIVES This study identified and described genomic loci that correlate with differences in ex vivo responses of natural Plasmodium falciparum isolates from The Gambia to antimalarial drugs. METHODS Natural P. falciparum isolates from The Gambia were assayed for IC50 responses to four antimalarial drugs (artemether, dihydroartemisinin, amodiaquine and lumefantrine). Genome-wide SNPs from 56 of these P. falciparum isolates were applied to mixed-model regression and network analyses to determine linked loci correlating with drug responses. Genomic regions of shared haplotypes and positive selection within and between Gambian and Cambodian P. falciparum isolates were mapped by identity-by-descent (IBD) analysis of 209 genomes. RESULTS SNPs in 71 genes, mostly involved in stress and drug resistance mechanisms correlated with drug responses. Additionally, erythrocyte invasion and permeability loci, including merozoite surface proteins (Pfdblmsp, Pfsurfin), and high-molecular-weight rhoptry protein 2 (Pfrhops2) were correlated with responses to multiple drugs. Haplotypes of pfdblmsp2 and known drug resistance loci (pfaat1, pfcrt and pfdhfr) from The Gambia showed high IBD with those from Cambodia, indicating co-ancestry, with significant linkage disequilibrium between their alleles. CONCLUSIONS Multiple linked genic loci correlating with drug response phenotypes suggest a genomic backbone may be under selection by antimalarials. This calls for further analysis of molecular pathways to drug resistance in African P. falciparum.
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Affiliation(s)
- Haddijatou Mbye
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Karim Mane
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Mouhamadou Fadel Diop
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Martha Anita Demba
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Fatoumata Bojang
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - David Jeffries
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Umberto D'Alessandro
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Alfred Amambua-Ngwa
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
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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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Assogba BS, Sillah S, Opondo KO, Cham ST, Camara MM, Jadama L, Camara L, Ndiaye A, Wathuo M, Jawara M, Diabaté A, Achan J, D'Alessandro U. Anopheles gambiae s.l. swarms trapping as a complementary tool against residual malaria transmission in eastern Gambia. Sci Rep 2022; 12:17057. [PMID: 36224312 PMCID: PMC9556655 DOI: 10.1038/s41598-022-21577-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/29/2022] [Indexed: 12/30/2022] Open
Abstract
Malaria remains a major health problem and vector control is an essential approach to decrease its burden, although it is threatened by insecticide resistance. New approaches for vector control are needed. The females of Anopheles gambiae s.l. mate once in their life and in the swarms formed by males. Trapping swarms of Anopheles gambiae s.l. males is a potential new intervention for vector control, alternative to the use of insecticides, as it would disrupt mating . The proof-of-concept pilot study aiming at investigating swarm trapping as a potential vector control intervention, was carried out in 6 villages as in eastern Gambia. Swarms of Anopheles gambiae s.l. were identified and their size, height, and duration determined during the baseline year. Swarm trapping by local volunteers was implemented the following transmission season in 4 villages while the other 2 villages were taken as controls. Entomological outcomes were monitored by Human Landing Catches and Pyrethrum Spray Catches. A cross-sectional survey to determine malaria prevalence was carried out at the peak of the malaria transmission season for two consecutive years. At baseline, 23 swarming sites of Anopheles gambiae s.l. were identified. Before the intervention, mean indoor resting density per house and malaria prevalence were similar between control and intervention villages. Following the intervention, Anopheles gambiae s.l. indoor resting density was 44% lower in intervention than in control villages (adj IRR: 0.0.56; 95% CI 0.47-0.68); the odds of malaria infections were 68% lower in intervention than in control villages (OR: 0.32; 95% CI 0.11-0.97). Swarm trapping seems to be a promising, community-based vector control intervention that could reduce malaria prevalence by reducing vector density. Such results should be further investigated and confirmed by larger cluster-randomized trials.
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Affiliation(s)
- Benoît Sessinou Assogba
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
| | - Salimina Sillah
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Kevin O Opondo
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Sheikh Tijan Cham
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Muhammed M Camara
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Lamin Jadama
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Lamin Camara
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Assane Ndiaye
- Laboratoire d'Ecologie Vectorielle et Parasitaire, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Miriam Wathuo
- Statistic and Bioinformatic Department, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Musa Jawara
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Abdoulaye Diabaté
- Institut de Recherche en Science de la Santé/Centre Muraz, BP 545, Bobo-Dioulasso, Burkina Faso
| | - Jane Achan
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Umberto D'Alessandro
- Disease Control and Elimination Theme, Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
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Coulibaly A, Diop MF, Kone A, Dara A, Ouattara A, Mulder N, Miotto O, Diakite M, Djimde A, Amambua-Ngwa A. Genome-wide SNP analysis of Plasmodium falciparum shows differentiation at drug-resistance-associated loci among malaria transmission settings in southern Mali. Front Genet 2022; 13:943445. [PMID: 36267403 PMCID: PMC9576839 DOI: 10.3389/fgene.2022.943445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/26/2022] [Indexed: 11/15/2022] Open
Abstract
Plasmodium falciparum malaria cases in Africa represent over 90% of the global burden with Mali being amongst the 11 highest burden countries that account for 70% of this annual incidence. The persistence of P. falciparum despite massive global interventions is because of its genetic diversity that drives its ability to adapt to environmental changes, develop resistance to drugs, and evade the host immune system. Knowledge on P. falciparum genetic diversity across populations and intervention landscape is thus critical for the implementation of new strategies to eliminate malaria. This study assessed genetic variation with 12,177 high-quality SNPs from 830 Malian P. falciparum isolates collected between 2007 and 2017 from seven locations. The complexity of infections remained high, varied between sites, and showed a trend toward overall decreasing complexity over the decade. Though there was no significant substructure, allele frequencies varied geographically, partly driven by temporal variance in sampling, particularly for drug resistance and antigen loci. Thirty-two mutations in known drug resistance markers (pfcrt, pfdhps, pfdhfr, pfmdr1, pfmdr2, and pfk13) attained a frequency of at least 2% in the populations. SNPs within and around the major markers of resistance to quinolines (pfmdr1 and pfcrt) and antifolates (pfdhfr and pfdhps) varied temporally and geographically, with strong linkage disequilibrium and signatures of directional selection in the genome. These geo-temporal populations also differentiated at alleles in immune-related loci, including, protein E140, pfsurfin8, pfclag8, and pfceltos, as well as pftrap, which showed signatures of haplotype differentiation between populations. Several regions across the genomes, including five known drug resistance loci, showed signatures of differential positive selection. These results suggest that drugs and immune pressure are dominant selective forces against P. falciparum in Mali, but their effect on the parasite genome varies temporally and spatially. Interventions interacting with these genomic variants need to be routinely evaluated as malaria elimination strategies are implemented.
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Affiliation(s)
- Aoua Coulibaly
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako, Mali
- Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Mouhamadou Fadel Diop
- Disease Control and Elimination, Medical Research Council Unit The Gambia at LSHTM, Banjul, Gambia
| | - Aminatou Kone
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Antoine Dara
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Amed Ouattara
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako, Mali
- University of Maryland Baltimore, Baltimore, MD, United States
| | - Nicola Mulder
- Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Olivo Miotto
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Mahamadou Diakite
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimde
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Alfred Amambua-Ngwa
- Disease Control and Elimination, Medical Research Council Unit The Gambia at LSHTM, Banjul, Gambia
- *Correspondence: Alfred Amambua-Ngwa,
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36
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Atuh NI, Anong DN, Jerome FC, Oriero E, Mohammed NI, D’Alessandro U, Amambua-Ngwa A. High genetic complexity but low relatedness in Plasmodium falciparum infections from Western Savannah Highlands and coastal equatorial Lowlands of Cameroon. Pathog Glob Health 2022; 116:428-437. [PMID: 34308788 PMCID: PMC9518281 DOI: 10.1080/20477724.2021.1953686] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To determine the diversity and connectivity of infections in Northwestern and Southwestern Cameroon, 232 Plasmodium falciparum infections, collected in 2018 from the Ndop Health District (NHD) in the western savannah highlands in the Northwest and the Limbe Health District (LHD) in the coastal lowland forests in the Southwest of Cameroon were genotyped for nine neutral microsatellite markers. Overall infection complexity and genetic diversity was significantly (p < 0.05) lower in NHD than LHD, (Mean MOI = 2.45 vs. 2.97; Fws = 0.42 vs. 0.47; Mean He = 0.84 vs. 0.89, respectively). Multi-locus linkage disequilibrium was generally low but significantly higher in the NHD than LHD population (mean ISA= 0.376 vs 0.093). Consequently, highly related pairs of isolates were observed in NHD (mean IBS = 0.086) compared to those from the LHD (mean IBS = 0.059). Infections from the two regions were mostly unrelated (mean IBS = 0.059), though the overall genetic differentiation across the geographical range was low. Indices of differentiation between the populations were however significant (overall pairwise Fst = 0.048, Jost's D = 0.133, p < 0.01). Despite the high human migration across the 270km separating the study sites, these results suggest significant restrictions to gene flow against contiguous geospatial transmission of malaria in west Cameroon. Clonal infections in the highland sites could be driven by lower levels of malaria prevalence and seasonal transmission. How these differences in genetic diversity and complexity affect responses to interventions such as drugs will require further investigations from broader community sampling.
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Affiliation(s)
- Ngoh Ines Atuh
- Department of Biomedical Science, Faculty of Health Science, University of Buea, Buea, Cameroon
- Disease Control and Elimination, Medical Research Council Unit the Gambia at LSHTM. Banjul, The Gambia
| | - Damian Nota Anong
- Department of Microbiology & Parasitology, Faculty of Science, University of Buea, Molyko Buea, Cameroon
| | - Fru-Cho Jerome
- Department of Biomedical Science, Faculty of Health Science, University of Buea, Buea, Cameroon
| | - Eniyou Oriero
- Disease Control and Elimination, Medical Research Council Unit the Gambia at LSHTM. Banjul, The Gambia
| | - Nuredin Ibrahim Mohammed
- Disease Control and Elimination, Medical Research Council Unit the Gambia at LSHTM. Banjul, The Gambia
| | - Umberto D’Alessandro
- Department of Microbiology & Parasitology, Faculty of Science, University of Buea, Molyko Buea, Cameroon
| | - Alfred Amambua-Ngwa
- Disease Control and Elimination, Medical Research Council Unit the Gambia at LSHTM. Banjul, The Gambia
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Carpi G, Gorenstein L, Harkins TT, Samadi M, Vats P. A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study. Brief Bioinform 2022; 23:6658853. [PMID: 35945154 PMCID: PMC9487672 DOI: 10.1093/bib/bbac314] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/03/2022] [Accepted: 07/12/2022] [Indexed: 11/15/2022] Open
Abstract
As recently demonstrated by the COVID-19 pandemic, large-scale pathogen genomic data are crucial to characterize transmission patterns of human infectious diseases. Yet, current methods to process raw sequence data into analysis-ready variants remain slow to scale, hampering rapid surveillance efforts and epidemiological investigations for disease control. Here, we introduce an accelerated, scalable, reproducible, and cost-effective framework for pathogen genomic variant identification and present an evaluation of its performance and accuracy across benchmark datasets of Plasmodium falciparum malaria genomes. We demonstrate superior performance of the GPU framework relative to standard pipelines with mean execution time and computational costs reduced by 27× and 4.6×, respectively, while delivering 99.9% accuracy at enhanced reproducibility.
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Affiliation(s)
- Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lev Gorenstein
- Rosen Center for Advanced Computing, Purdue University, West Lafayette IN, USA
| | | | | | - Pankaj Vats
- NVIDIA, 2788 San Tomas, Santa Clara, CA, USA
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Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey J, Ishengoma DS. Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa. Front Cell Infect Microbiol 2022; 12:757844. [PMID: 35909968 PMCID: PMC9326448 DOI: 10.3389/fcimb.2022.757844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - David J. Giesbrecht
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | | | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Bronwyn MacInnis
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute, Boston, MA, United States
| | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Jane A. Cunningham
- Global Malaria Programme, World Health Organization, Headquarters, Geneva, Switzerland
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jonathan J. Juliano
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey A. Bailey
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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Genetic Diversity and Phylogenetic Relatedness of Plasmodium ovale curtisi and Plasmodium ovale wallikeri in sub-Saharan Africa. Microorganisms 2022; 10:microorganisms10061147. [PMID: 35744665 PMCID: PMC9227610 DOI: 10.3390/microorganisms10061147] [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: 05/05/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 12/14/2022] Open
Abstract
P. ovale was until recently thought to be a single unique species. However, the deployment of more sensitive tools has led to increased diagnostic sensitivity, including new evidence supporting the presence of two sympatric species: P. ovale curtisi (Poc) and P. ovale wallikeri (Pow). The increased reports and evolution of P. ovale subspecies are concerning for sub-Saharan Africa where the greatest burden of malaria is borne. Employing published sequence data, we set out to decipher the genetic diversity and phylogenetic relatedness of P. ovale curtisi and P. ovale wallikeri using the tryptophan-rich protein and small subunit ribosomal RNA genes from Gabon, Senegal, Ethiopia and Kenya. Higher number of segregating sites were recorded in Poc isolates from Gabon than from Ethiopia, with a similar trend in the number of haplotypes. With regards to Pow, the number of segregating sites and haplotypes from Ethiopia were higher than from those in Gabon. Poc from Kenya, had higher segregating sites (20), and haplotypes (4) than isolates from Senegal (8 and 3 respectively), while nucleotide from Senegal were more diverse (θw = 0.02159; π = 0.02159) than those from Kenya (θw = 0.01452; π = 0.01583). Phylogenetic tree construction reveal two large clades with Poc from Gabon and Ethiopia, and distinct Gabonese and Ethiopian clades on opposite ends. A similar observation was recorded for the phylogeny of Poc isolates from Kenya and Senegal. With such results, there is a high potential that ovale malaria control measures deployed in one country may be effective in the other since parasite from both countries show some degree of relatedness. How this translates to malaria control efforts throughout the continent would be next step deserving more studies.
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Van Bortel W, Van den Poel B, Hermans G, Vanden Driessche M, Molzahn H, Deblauwe I, De Wolf K, Schneider A, Van Hul N, Müller R, Wilmaerts L, Gombeer S, Smitz N, Kattenberg JH, Monsieurs P, Rosanas-Urgell A, Van Esbroeck M, Bottieau E, Maniewski-Kelner U, Rebolledo J. Two fatal autochthonous cases of airport malaria, Belgium, 2020. EURO SURVEILLANCE : BULLETIN EUROPEEN SUR LES MALADIES TRANSMISSIBLES = EUROPEAN COMMUNICABLE DISEASE BULLETIN 2022; 27. [PMID: 35451360 PMCID: PMC9027149 DOI: 10.2807/1560-7917.es.2022.27.16.2100724] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report an outbreak investigation of two fatal cases of autochthonous Plasmodium falciparum malaria that occurred in Belgium in September 2020. Various hypotheses of the potential source of infection were investigated. The most likely route of transmission was through an infectious exotic Anopheles mosquito that was imported via the international airport of Brussels or the military airport Melsbroek and infected the cases who lived at 5 km from the airports. Based on genomic analysis of the parasites collected from the two cases, the most likely origin of the Plasmodium was Gabon or Cameroon. Further, the parasites collected from the two Belgian patients were identical by descent, which supports the assumption that the two infections originated from the bite of the same mosquito, during interrupted feeding. Although airport malaria remains a rare event, it has significant implications, particularly for the patient, as delayed or missed diagnosis of the cause of illness often results in complications and mortality. Therefore, to prevent such severe or fatal outcomes, we suggest a number of public health actions including increased awareness among health practitioners, especially those working in the vicinity of airports, and increased surveillance of exotic mosquito species at airports.
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Affiliation(s)
- Wim Van Bortel
- Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium.,Outbreak Research Team, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bea Van den Poel
- Clinical Laboratory, Jan Portaels General Hospital, Vilvoorde, Belgium
| | - Greet Hermans
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Helmut Molzahn
- Intensive Care Unit, Jan Portaels General Hospital, Vilvoorde, Belgium
| | - Isra Deblauwe
- Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Katrien De Wolf
- Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anna Schneider
- Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nick Van Hul
- Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ruth Müller
- Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Wilmaerts
- Veterinary Service, Military Hospital Queen Astrid, Brussels, Belgium
| | - Sophie Gombeer
- Royal Belgian Institute of Natural Sciences, Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo), Brussels, Belgium
| | - Nathalie Smitz
- Royal Museum for Central Africa, Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo), Tervuren, Belgium
| | - Johanna Helena Kattenberg
- Unit of Malariology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Monsieurs
- Unit of Malariology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Unit of Malariology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ula Maniewski-Kelner
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Javiera Rebolledo
- Department of epidemiology and infectious diseases, Sciensano, Brussels, Belgium
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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Rosenthal PJ, Björkman A, Dhorda M, Djimde A, Dondorp AM, Gaye O, Guerin PJ, Juma E, Kwiatkowski DP, Merson L, Ntoumi F, Price RN, Raman J, Roos DS, ter Kuile F, Tinto H, Tomko SS, White NJ, Barnes KI. Cooperation in Countering Artemisinin Resistance in Africa: Learning from COVID-19. Am J Trop Med Hyg 2022; 106:tpmd220148. [PMID: 35413688 PMCID: PMC9209939 DOI: 10.4269/ajtmh.22-0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/05/2022] [Indexed: 01/13/2023] Open
Affiliation(s)
| | - Anders Björkman
- Malaria Group, University of Karolinska Institutet, Stockholm, Sweden
| | - Mehul Dhorda
- Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies, Bamako, Mali
| | - Arjen M. Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Oumar Gaye
- Department of Medical Parasitology, Faculty of Medicine, Pharmacy and Dentistry, L’Université Cheikh Anta Diop, Dakar, Senegal
| | - Philippe J. Guerin
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- WorldWide Antimalarial Resistance Network and Infectious Diseases Data Observatory, Oxford University, Oxford, United Kingdom
| | - Elizabeth Juma
- World Health Organization African Regional Office, Accra, Ghana
| | | | - Laura Merson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- WorldWide Antimalarial Resistance Network and Infectious Diseases Data Observatory, Oxford University, Oxford, United Kingdom
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Ric N. Price
- Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- WorldWide Antimalarial Resistance Network and Infectious Diseases Data Observatory, Oxford University, Oxford, United Kingdom
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Jaishree Raman
- South African National Institute for Communicable Diseases, Johannesburg, South Africa
- Wits Research Institute for Malaria, School of Pathology, University of Witwatersrand, Johannesburg, South Africa
| | - David S. Roos
- University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feiko ter Kuile
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Halidou Tinto
- Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | | | | | - Karen I. Barnes
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
- WorldWide Antimalarial Resistance Network, Pharmacology Scientific Module, Department of Medicine, University of Cape Town, Cape Town, South Africa
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43
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Coppée R, Bailly J, Sarrasin V, Vianou B, Zinsou BE, Mazars E, Georges H, Hamane S, Lavergne RA, Dannaoui E, Balikagala B, Fukuda N, Odongo-Aginya EI, Mita T, Houzé S, Clain J. Circulation of an artemisinin-resistant malaria lineage in a traveller returning from East Africa to France. Clin Infect Dis 2022; 75:1242-1244. [PMID: 35213688 DOI: 10.1093/cid/ciac162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
A returned traveller to Uganda presented with a Plasmodium falciparum kelch13 A675V mutant infection that exhibited delayed clearance under artesunate therapy. Parasites were genetically related to recently reported Ugandan artemisinin-resistant A675V parasites. Adequate malaria prevention measures and clinical and genotypic surveillance are important tools to avoid and track artemisinin resistance.
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Affiliation(s)
- Romain Coppée
- Université de Paris, IRD, MERIT, F-75006 Paris, France
| | - Justine Bailly
- Université de Paris, IRD, MERIT, F-75006 Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Véronique Sarrasin
- Université de Paris, IRD, MERIT, F-75006 Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Bertin Vianou
- Institut de Recherche Clinique du Bénin, Cotonou, Bénin
| | | | - Edith Mazars
- Laboratoire de microbiologie, Pôle de Biologie-hygiène, Centre Hospitalier de Valenciennes, F-59322 Valenciennes, France
| | - Hugues Georges
- Service de Réanimation Médicale et Maladies Infectieuses, Hôpital Chatiliez, F-59200 Tourcoing, France
| | - Samia Hamane
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis Lariboisière Fernand-Widal, F-75010 Paris, France
| | - Rose-Anne Lavergne
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, Centre Hospitalier Universitaire de Nantes, F-44093 Nantes, France
| | - Eric Dannaoui
- Laboratoire de Parasitologie-Mycologie, AP-HP, Département de Microbiologie, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Betty Balikagala
- Department of Tropical Medicine and Parasitology, School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Naoyuki Fukuda
- Department of Tropical Medicine and Parasitology, School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | | | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Sandrine Houzé
- Université de Paris, IRD, MERIT, F-75006 Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Jérôme Clain
- Université de Paris, IRD, MERIT, F-75006 Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
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44
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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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45
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Omedo I, Bartilol B, Kimani D, Gonçalves S, Drury E, Rono MK, Abdi AI, Almagro-Garcia J, Amato R, Pearson RD, Ochola-Oyier LI, Kwiatkowski D, Bejon P. Spatio-temporal distribution of antimalarial drug resistant gene mutations in a Plasmodium falciparum parasite population from Kilifi, Kenya: A 25-year retrospective study. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17656.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Antimalarial drug resistance is a major obstacle to sustainable malaria control. Here we use amplicon sequencing to describe molecular markers of drug resistance in Plasmodium falciparum parasites from Kilifi county in the coastal region of Kenya over a 25-year period. Methods: We performed P. falciparum amplicon sequencing on 1162 malaria-infected blood samples collected between 1994 and 2018 to identify markers of antimalarial drug resistance in the Pfcrt, Pfdhfr, Pfdhps, Pfmdr1, Pfexo, Pfkelch13, plasmepsin 2/3, Pfarps10, Pffd, and Pfmdr2 genes. We further interrogated parasite population structure using a genetic barcode of 101 drug resistance-unrelated single nucleotide polymorphisms (SNPs) distributed across the genomes of 1245 P. falciparum parasites. Results: Two major changes occurred in the parasite population over the 25 years studied. In 1994, approximately 75% of parasites carried the marker of chloroquine resistance, CVIET. This increased to 100% in 1999 and then declined steadily, reaching 6.7% in 2018. Conversely, the quintuple mutation form of sulfadoxine-pyrimethamine resistance increased from 16.7% in 1994 to 83.6% in 2018. Several non-synonymous mutations were identified in the Kelch13 gene, although none of them are currently associated with artemisinin resistance. We observed a temporal increase in the Pfmdr1 NFD haplotype associated with lumefantrine resistance, but observed no evidence of piperaquine resistance. SNPs in other parts of the genome showed no significant temporal changes despite the marked changes in drug resistance loci over this period. Conclusions: We identified substantial changes in molecular markers of P. falciparum drug resistance over 25 years in coastal Kenya, but no associated changes in the parasite population structure.
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46
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Voinson M, Nunn CL, Goldberg A. Primate malarias as a model for cross-species parasite transmission. eLife 2022; 11:e69628. [PMID: 35086643 PMCID: PMC8798051 DOI: 10.7554/elife.69628] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 01/14/2022] [Indexed: 12/16/2022] Open
Abstract
Parasites regularly switch into new host species, representing a disease burden and conservation risk to the hosts. The distribution of these parasites also gives insight into characteristics of ecological networks and genetic mechanisms of host-parasite interactions. Some parasites are shared across many species, whereas others tend to be restricted to hosts from a single species. Understanding the mechanisms producing this distribution of host specificity can enable more effective interventions and potentially identify genetic targets for vaccines or therapies. As ecological connections between human and local animal populations increase, the risk to human and wildlife health from novel parasites also increases. Which of these parasites will fizzle out and which have the potential to become widespread in humans? We consider the case of primate malarias, caused by Plasmodium parasites, to investigate the interacting ecological and evolutionary mechanisms that put human and nonhuman primates at risk for infection. Plasmodium host switching from nonhuman primates to humans led to ancient introductions of the most common malaria-causing agents in humans today, and new parasite switching is a growing threat, especially in Asia and South America. Based on a wild host-Plasmodium occurrence database, we highlight geographic areas of concern and potential areas to target further sampling. We also discuss methodological developments that will facilitate clinical and field-based interventions to improve human and wildlife health based on this eco-evolutionary perspective.
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Affiliation(s)
- Marina Voinson
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke Global Health, Duke UniversityDurhamUnited States
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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47
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022; 18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
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Affiliation(s)
- Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Anthony Kocoski
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail:
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48
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Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM, Macharia AW, Hubbart C, Jeffreys AE, Rowlands K, Nguyen T, Gonçalves S, Ariani CV, Stalker J, Pearson RD, Amato R, Drury E, Sirugo G, d'Alessandro U, Bojang KA, Marsh K, Peshu N, Saelens JW, Diakité M, Taylor SM, Conway DJ, Williams TN, Rockett KA, Kwiatkowski DP. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature 2021; 602:106-111. [PMID: 34883497 PMCID: PMC8810385 DOI: 10.1038/s41586-021-04288-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations. A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.
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Affiliation(s)
- Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Muminatou Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Edward Francis Small Teaching Hospital (formerly Royal Victoria Teaching Hospital), Independence Drive, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Thuy Nguyen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Jim Stalker
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA
| | | | | | - Giorgio Sirugo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Umberto d'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kalifa A Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford, UK
| | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - David J Conway
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial College, London, London, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
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49
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Ndiaye YD, Hartl DL, McGregor D, Badiane A, Fall FB, Daniels RF, Wirth DF, Ndiaye D, Volkman SK. Genetic surveillance for monitoring the impact of drug use on Plasmodium falciparum populations. Int J Parasitol Drugs Drug Resist 2021; 17:12-22. [PMID: 34333350 PMCID: PMC8342550 DOI: 10.1016/j.ijpddr.2021.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022]
Abstract
The use of antimalarial drugs is an effective strategy in the fight against malaria. However, selection of drug resistant parasites is a constant threat to the continued use of this approach. Antimalarial drugs are used not only to treat infections but also as part of population-level strategies to reduce malaria transmission toward elimination. While there is strong evidence that the ongoing use of antimalarial drugs increases the risk of the emergence and spread of drug-resistant parasites, it is less clear how population-level use of drug-based interventions like seasonal malaria chemoprevention (SMC) or mass drug administration (MDA) may contribute to drug resistance or loss of drug efficacy. Critical to sustained use of drug-based strategies for reducing the burden of malaria is the surveillance of population-level signals related to transmission reduction and resistance selection. Here we focus on Plasmodium falciparum and discuss the genetic signatures of a parasite population that are correlated with changes in transmission and related to drug pressure and resistance as a result of drug use. We review the evidence for MDA and SMC contributing to malaria burden reduction and drug resistance selection and examine the use and impact of these interventions in Senegal. Throughout we consider best strategies for ongoing surveillance of both population and resistance signals in the context of different parasite population parameters. Finally, we propose a roadmap for ongoing surveillance during population-level drug-based interventions to reduce the global malaria burden.
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Affiliation(s)
| | | | - David McGregor
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | | | - Fatou Ba Fall
- Programme National de Lutte Contre le Paludisme, Senegal.
| | - Rachel F Daniels
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA.
| | - Dyann F Wirth
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA.
| | | | - Sarah K Volkman
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA; Simmons University, Boston, MA, USA.
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50
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Comparative Analysis of Plasmodium falciparum Genotyping via SNP Detection, Microsatellite Profiling, and Whole-Genome Sequencing. Antimicrob Agents Chemother 2021; 66:e0116321. [PMID: 34694871 PMCID: PMC8765236 DOI: 10.1128/aac.01163-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Research efforts to combat antimalarial drug resistance rely on quick, robust, and sensitive methods to genetically characterize Plasmodium falciparum parasites. We developed a single-nucleotide polymorphism (SNP)-based genotyping method that can assess 33 drug resistance-conferring SNPs in dhfr, dhps, pfmdr1, pfcrt, and k13 in nine PCRs, performed directly from P. falciparum cultures or infected blood. We also optimized multiplexed fragment analysis and gel electrophoresis-based microsatellite typing methods using a set of five markers that can distinguish 12 laboratory strains of diverse geographical and temporal origin. We demonstrate how these methods can be applied to screen for the multidrug-resistant KEL1/PLA1/PfPailin (KelPP) lineage that has been sweeping across the Greater Mekong Subregion, verify parasite in vitro SNP-editing, identify novel recombinant genetic cross progeny, or cluster strains to infer their geographical origins. Results were compared with Illumina-based whole-genome sequence analysis that provides the most detailed sequence information but is cost-prohibitive. These adaptable, simple, and inexpensive methods can be easily implemented into routine genotyping of P. falciparum parasites in both laboratory and field settings.
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