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Iglhaut C, Pečerska J, Gil M, Anisimova M. Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels. Mol Biol Evol 2024; 41:msae109. [PMID: 38842253 PMCID: PMC11221656 DOI: 10.1093/molbev/msae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.
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Affiliation(s)
- Clara Iglhaut
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Faculty of Mathematics and Science, University of Zurich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jūlija Pečerska
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Manuel Gil
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Anisimova
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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2
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Kane J, Li X, Kumar S, Button-Simons KA, Vendrely Brenneman KM, Dahlhoff H, Sievert MAC, Checkley LA, Shoue DA, Singh PP, Abatiyow BA, Haile MT, Nair S, Reyes A, Tripura R, Peto TJ, Lek D, Mukherjee A, Kappe SHI, Dhorda M, Nkhoma SC, Cheeseman IH, Vaughan AM, Anderson TJC, Ferdig MT. A Plasmodium falciparum genetic cross reveals the contributions of pfcrt and plasmepsin II/III to piperaquine drug resistance. mBio 2024:e0080524. [PMID: 38912775 DOI: 10.1128/mbio.00805-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Piperaquine (PPQ) is widely used in combination with dihydroartemisinin as a first-line treatment against malaria. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multidrug-resistant KEL1/PLA1 lineage isolate (KH004) and a drug-susceptible Malawian parasite (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and multiple copies of pm2/3. We recovered 104 unique recombinant parasites and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3. We performed a detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes with these progenies, including PPQ survival assay, area under the dose response curve, and a limited point IC50. We find that inheritance of the KH004 pfcrt allele is required for reduced PPQ sensitivity, whereas copy number variation in pm2/3 further decreases susceptibility but does not confer resistance in the absence of additional mutations in pfcrt. A deep investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background to a range of PPQ-related traits. Additionally, we find that the resistance phenotype associated with parasites inheriting the G367C substitution in pfcrt is consistent with previously validated PPQ resistance mutations in this transporter.IMPORTANCEResistance to piperaquine, used in combination with dihydroartemisinin, has emerged in Cambodia and threatens to spread to other malaria-endemic regions. Understanding the causal mutations of drug resistance and their impact on parasite fitness is critical for surveillance and intervention and can also reveal new avenues to limiting the evolution and spread of drug resistance. An experimental genetic cross is a powerful tool for pinpointing the genetic determinants of key drug resistance and fitness phenotypes and has the distinct advantage of quantifying the effects of naturally evolved genetic variation. Our study was strengthened since the full range of copies of KH004 pm2/3 was inherited among the progeny clones, allowing us to directly test the role of the pm2/3 copy number on resistance-related phenotypes in the context of a unique pfcrt allele. Our multigene model suggests an important role for both loci in the evolution of this multidrug-resistant parasite lineage.
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Affiliation(s)
- John Kane
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Katrina A Button-Simons
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Katelyn M Vendrely Brenneman
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Haley Dahlhoff
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Mackenzie A C Sievert
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lisa A Checkley
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Douglas A Shoue
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Puspendra P Singh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Biley A Abatiyow
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Meseret T Haile
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ann Reyes
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Rupam Tripura
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, United Kingdom
| | - Thomas J Peto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, United Kingdom
| | - Dysoley Lek
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
- School of Public Health, National Institute of Public Health, Phnom Penh, Cambodia
| | - Angana Mukherjee
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, USA
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, United Kingdom
| | - Standwell C Nkhoma
- BEI Resources, American Type Culture Collection (ATCC), Manassas, Virginia, USA
| | - Ian H Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ashley M Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Timothy J C Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Michael T Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
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3
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Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. PLoS Pathog 2024; 20:e1012013. [PMID: 38870266 PMCID: PMC11206942 DOI: 10.1371/journal.ppat.1012013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/26/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. In low transmission settings, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. We performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016-2021). We characterized the relatedness between each pair of monoclonal infections (n = 1,409) through estimation of identity-by-descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 multi-isolate clones (mean IBD ≥ 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD ≥ 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally observed 61 nonsynonymous substitutions that increased markedly in frequency over the study period as well as a novel pfk13 mutation (G718S). However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions, given that clones carrying drug resistance polymorphisms do not demonstrate enhanced persistence or higher abundance than clones carrying polymorphisms of comparable frequency that are unrelated to resistance. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation.
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Affiliation(s)
- Mathieu Vanhove
- 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
| | - Philipp Schwabl
- 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
| | - Margaret Laws
- 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
| | - Frank Anthony
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Célia Florimond
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Luana Mathieu
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Kashana James
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Cheyenne Knox
- 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
| | - Narine Singh
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Caroline O. Buckee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Lise Musset
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Horace Cox
- National Malaria Program, Ministry of Health, Georgetown, Guyana
- Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago
| | - Reza Niles-Robin
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - 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
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Markwalter CF, Lapp Z, Abel L, Kimachas E, Omollo E, Freedman E, Chepkwony T, Amunga M, McCormick T, Bérubé S, Mangeni JN, Wesolowski A, Obala AA, Taylor SM, Prudhomme O'Meara W. Plasmodium falciparum infection in humans and mosquitoes influence natural Anopheline biting behavior and transmission. Nat Commun 2024; 15:4626. [PMID: 38816383 PMCID: PMC11139876 DOI: 10.1038/s41467-024-49080-9] [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: 02/20/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
The human infectious reservoir of Plasmodium falciparum is governed by transmission efficiency during vector-human contact and mosquito biting preferences. Understanding biting bias in a natural setting can help target interventions to interrupt transmission. In a 15-month cohort in western Kenya, we detected P. falciparum in indoor-resting Anopheles and human blood samples by qPCR and matched mosquito bloodmeals to cohort participants using short-tandem repeat genotyping. Using risk factor analyses and discrete choice models, we assessed mosquito biting behavior with respect to parasite transmission. Biting was highly unequal; 20% of people received 86% of bites. Biting rates were higher on males (biting rate ratio (BRR): 1.68; CI: 1.28-2.19), children 5-15 years (BRR: 1.49; CI: 1.13-1.98), and P. falciparum-infected individuals (BRR: 1.25; CI: 1.01-1.55). In aggregate, P. falciparum-infected school-age (5-15 years) boys accounted for 50% of bites potentially leading to onward transmission and had an entomological inoculation rate 6.4x higher than any other group. Additionally, infectious mosquitoes were nearly 3x more likely than non-infectious mosquitoes to bite P. falciparum-infected individuals (relative risk ratio 2.76, 95% CI 1.65-4.61). Thus, persistent P. falciparum transmission was characterized by disproportionate onward transmission from school-age boys and by the preference of infected mosquitoes to feed upon infected people.
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Affiliation(s)
| | - Zena Lapp
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Emmah Kimachas
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | | | - Elizabeth Freedman
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Tabitha Chepkwony
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Mark Amunga
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Tyler McCormick
- Departments of Statistics & Sociology, University of Washington, Seattle, WA, USA
| | - Sophie Bérubé
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Judith N Mangeni
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew A Obala
- School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Steve M Taylor
- Duke Global Health Institute, Duke University, Durham, NC, USA.
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.
| | - Wendy Prudhomme O'Meara
- Duke Global Health Institute, Duke University, Durham, NC, USA.
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.
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5
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Pastusiak A, Reddy MR, Chen X, Hoyer I, Dorman J, Gebhardt ME, Carpi G, Norris DE, Pipas JM, Jackson EK. A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes. Commun Biol 2024; 7:667. [PMID: 38816486 PMCID: PMC11139907 DOI: 10.1038/s42003-024-06337-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
The Anopheles gambiae 1000 Genomes (Ag1000G) Consortium previously utilized deep sequencing methods to catalogue genetic diversity across African An. gambiae populations. We analyzed the complete datasets of 1142 individually sequenced mosquitoes through Microsoft Premonition's Bayesian mixture model based (BMM) metagenomics pipeline. All specimens were confirmed as either An. gambiae sensu stricto (s.s.) or An. coluzzii with a high degree of confidence ( > 98% identity to reference). Homo sapiens DNA was identified in all specimens indicating contamination may have occurred either at the time of specimen collection, preparation and/or sequencing. We found evidence of vertebrate hosts in 162 specimens. 59 specimens contained validated Plasmodium falciparum reads. Human hepatitis B and primate erythroparvovirus-1 viral sequences were identified in fifteen and three mosquito specimens, respectively. 478 of the 1,142 specimens were found to contain bacterial reads and bacteriophage-related contigs were detected in 27 specimens. This analysis demonstrates the capacity of metagenomic approaches to elucidate important vector-host-pathogen interactions of epidemiological significance.
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Affiliation(s)
| | - Michael R Reddy
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA.
| | - Xiaoji Chen
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
| | - Isaiah Hoyer
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Mary E Gebhardt
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Douglas E Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ethan K Jackson
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
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Ciubotariu II, Broyles BK, Xie S, Thimmapuram J, Mwenda MC, Mambwe B, Mulube C, Matoba J, Schue JL, Moss WJ, Bridges DJ, He Q, Carpi G. Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.11.24307175. [PMID: 38766239 PMCID: PMC11100930 DOI: 10.1101/2024.05.11.24307175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background A highly effective vaccine for malaria remains an elusive target, at least in part due to the under-appreciated natural parasite variation. This study aimed to investigate genetic and structural variation, and immune selection of leading malaria vaccine candidates across the Plasmodium falciparum's life cycle. Methods We analyzed 325 P. falciparum whole genome sequences from Zambia, in addition to 791 genomes from five other African countries available in the MalariaGEN Pf3k Rdatabase. Ten vaccine antigens spanning three life-history stages were examined for genetic and structural variations, using population genetics measures, haplotype network analysis, and 3D structure selection analysis. Findings Among the ten antigens analyzed, only three in the transmission-blocking vaccine category display P. falciparum 3D7 as the dominant haplotype. The antigens AMA1, CSP, MSP119 and CelTOS, are much more diverse than the other antigens, and their epitope regions are under moderate to strong balancing selection. In contrast, Rh5, a blood stage antigen, displays low diversity yet slightly stronger immune selection in the merozoite-blocking epitope region. Except for CelTOS, the transmission-blocking antigens Pfs25, Pfs48/45, Pfs230, Pfs47, and Pfs28 exhibit minimal diversity and no immune selection in epitopes that induce strain-transcending antibodies, suggesting potential effectiveness of 3D7-based vaccines in blocking transmission. Interpretations These findings offer valuable insights into the selection of optimal vaccine candidates against P. falciparum. Based on our results, we recommend prioritizing conserved merozoite antigens and transmission-blocking antigens. Combining these antigens in multi-stage approaches may be particularly promising for malaria vaccine development initiatives. Funding Purdue Department of Biological Sciences; Puskas Memorial Fellowship; National Institute of Allergy and Infectious Diseases (U19AI089680).
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Affiliation(s)
- Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Bradley K. Broyles
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Mulenga C. Mwenda
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | | | - Jessica L. Schue
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - William J. Moss
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana, USA
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7
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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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8
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Dogga SK, Rop JC, Cudini J, Farr E, Dara A, Ouologuem D, Djimdé AA, Talman AM, Lawniczak MKN. A single cell atlas of sexual development in Plasmodium falciparum. Science 2024; 384:eadj4088. [PMID: 38696552 DOI: 10.1126/science.adj4088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/14/2024] [Indexed: 05/04/2024]
Abstract
The developmental decision made by malaria parasites to become sexual underlies all malaria transmission. Here, we describe a rich atlas of short- and long-read single-cell transcriptomes of over 37,000 Plasmodium falciparum cells across intraerythrocytic asexual and sexual development. We used the atlas to explore transcriptional modules and exon usage along sexual development and expanded it to include malaria parasites collected from four Malian individuals naturally infected with multiple P. falciparum strains. We investigated genotypic and transcriptional heterogeneity within and among these wild strains at the single-cell level, finding differential expression between different strains even within the same host. These data are a key addition to the Malaria Cell Atlas interactive data resource, enabling a deeper understanding of the biology and diversity of transmission stages.
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Affiliation(s)
| | - Jesse C Rop
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Elias Farr
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Institute for Computational Biomedicine, University of Heidelberg, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany
| | - Antoine Dara
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Dinkorma Ouologuem
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Abdoulaye A Djimdé
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Arthur M Talman
- MIVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
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9
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Wang T, Shen H, Xu B, Yang W, Chen S, Chen J. Genome Analysis of Plasmodium falciparum: A Preliminary Observation - Sierra Leone, 2022-2023. China CDC Wkly 2024; 6:368-373. [PMID: 38737823 PMCID: PMC11082561 DOI: 10.46234/ccdcw2024.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/21/2024] [Indexed: 05/14/2024] Open
Abstract
What is already known about this topic? Sierra Leone, with a gross domestic product (GDP) per capita below $300 and significant poverty, ranks among the world's least developed countries (LDCs). Despite its modest population of 8.6 million, the nation reports approximately 2.6 million malaria cases annually. Previously, there has been no reporting on the malaria genome data from this country. What is added by this report? In this study, we present the first reported whole-genome sequence analysis of 19 high parasite-density Plasmodium falciparum isolates from Sierra Leone, providing insights into the genomic epidemiology of this high-prevalence area. We found a high degree of relatedness among infections and substantial genetic diversity, consistent with the gradual reduction in overall case numbers. Moreover, our whole-genome analysis revealed that, beyond drug-resistance genes, gene families related to blood cell invasion, immune evasion, and others are undergoing directional selection. This suggests that the population in Sierra Leone has developed a relatively strong acquired immunity. What are the implications for public health practice? The genomic data not only facilitate the creation of single nucleotide polymorphism barcodes for case tracking but also enable the analysis of evolving transmission dynamics and selection pressures. Additionally, the samples from Sierra Leone exhibited higher selective pressures on resistance genes compared to those from Asia, a trend not commonly observed in other African samples. This suggests that less stringent healthcare systems and inconsistent treatment strategies can subject parasites to increased drug pressure, thereby accelerating the development of resistant strains.
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Affiliation(s)
- Tianyu Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Haimo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Wanxuan Yang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou City, Zhejiang Province, China
| | - Shenbo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
| | - Junhu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Centre for International Research on Tropical Diseases, Shanghai, China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou City, Zhejiang Province, China
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Hainan Tropical Diseases Research Center (Hainan Sub-Center, Chinese Center for Tropical Diseases Research), Haikou City, Hainan Province, China
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10
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Letcher B, Maciuca S, Iqbal Z. Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum. PLoS Biol 2024; 22:e3002507. [PMID: 38451924 PMCID: PMC10919680 DOI: 10.1371/journal.pbio.3002507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/19/2024] [Indexed: 03/09/2024] Open
Abstract
While the malaria parasite Plasmodium falciparum has low average genome-wide diversity levels, likely due to its recent introduction from a gorilla-infecting ancestor (approximately 10,000 to 50,000 years ago), some genes display extremely high diversity levels. In particular, certain proteins expressed on the surface of human red blood cell-infecting merozoites (merozoite surface proteins (MSPs)) possess exactly 2 deeply diverged lineages that have seemingly not recombined. While of considerable interest, the evolutionary origin of this phenomenon remains unknown. In this study, we analysed the genetic diversity of 2 of the most variable MSPs, DBLMSP and DBLMSP2, which are paralogs (descended from an ancestral duplication). Despite thousands of available Illumina WGS datasets from malaria-endemic countries, diversity in these genes has been hard to characterise as reads containing highly diverged alleles completely fail to align to the reference genome. To solve this, we developed a pipeline leveraging genome graphs, enabling us to genotype them at high accuracy and completeness. Using our newly- resolved sequences, we found that both genes exhibit 2 deeply diverged lineages in a specific protein domain (DBL) and that one of the 2 lineages is shared across the genes. We identified clear evidence of nonallelic gene conversion between the 2 genes as the likely mechanism behind sharing, leading us to propose that gene conversion between diverged paralogs, and not recombination suppression, can generate this surprising genealogy; a model that is furthermore consistent with high diversity levels in these 2 genes despite the strong historical P. falciparum transmission bottleneck.
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Affiliation(s)
- Brice Letcher
- EMBL-EBI, Hinxton, United Kingdom
- Laboratory of Biology and Modelling of the Cell, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
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11
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Florimond C, de Laval F, Early AM, Sauthier S, Lazrek Y, Pelleau S, Monteiro WM, Agranier M, Taudon N, Morin F, Magris M, Lacerda MVG, Viana GMR, Herrera S, Adhin MR, Ferreira MU, Woodrow CJ, Awab GR, Cox H, Ade MP, Mosnier E, Djossou F, Neafsey DE, Ringwald P, Musset L. Impact of piperaquine resistance in Plasmodium falciparum on malaria treatment effectiveness in The Guianas: a descriptive epidemiological study. THE LANCET. INFECTIOUS DISEASES 2024; 24:161-171. [PMID: 37858325 PMCID: PMC10808503 DOI: 10.1016/s1473-3099(23)00502-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/17/2023] [Accepted: 08/01/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Plasmodium falciparum is an apicomplexan parasite responsible for lethal cases of malaria. According to WHO recommendations, P falciparum cases are treated with artemisinin-based combination therapy including dihydroartemisinin-piperaquine. However, the emergence of resistant parasites against dihydroartemisinin-piperaquine was reported in southeast Asia in 2008 and, a few years later, suspected in South America. METHODS To characterise resistance emergence, a treatment efficacy study was performed on the reported patients infected with P falciparum and treated with dihydroartemisinin-piperaquine in French Guiana (n=6, 2016-18). Contemporary isolates collected in French Guiana were genotyped for P falciparum chloroquine resistance transporter (pfCRT; n=845) and pfpm2 and pfpm3 copy number (n=231), phenotyped using the in vitro piperaquine survival assay (n=86), and analysed through genomic studies (n=50). Additional samples from five Amazonian countries and one outside the region were genotyped (n=1440). FINDINGS In field isolates, 40 (47%) of 86 (95% CI 35·9-57·1) were resistant to piperaquine in vitro; these phenotypes were more associated with pfCRTC350R (ie, Cys350Arg) and pfpm2 and pfpm3 amplifications (Dunn test, p<0·001). Those markers were also associated with dihydroartemisinin-piperaquine treatment failure (n=3 [50%] of 6). A high prevalence of piperaquine resistance markers was observed in Suriname in 19 (83%) of 35 isolates and in Guyana in 579 (73%) of 791 isolates. The pfCRTC350R mutation emerged before pfpm2 and pfpm3 amplification in a temporal sequence different from southeast Asia, and in the absence of artemisinin partial resistance, suggesting a geographically distinctive epistatic relationship between these genetic markers. INTERPRETATION The high prevalence of piperaquine resistance markers in parasite populations of the Guianas, and the risk of associated therapeutic failures calls for caution on dihydroartemisinin-piperaquine use in the region. Furthermore, greater attention should be given to potential differences in genotype to phenotype mapping across genetically distinct parasite populations from different continents. FUNDING Pan American Health Organization and WHO, French Ministry for Research, European Commission, Santé publique France, Agence Nationale de la Recherche, Fundação de Amparo à Pesquisa do Estado do Amazonas, Ministry of Health of Brazil, Oswaldo Cruz Foundation, and National Institutes of Health. TRANSLATIONS For the French and Portuguese translations of the abstract see Supplementary Materials section.
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Affiliation(s)
- Celia Florimond
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Franck de Laval
- Service de Santé des Armées (SSA), Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France; Sciences Economiques Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM), Aix Marseille University, INSERM, IRD, Marseille, France
| | - Angela M Early
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA; Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Swaélie Sauthier
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Yassamine Lazrek
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Stéphane Pelleau
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana; Infectious Diseases Epidemiology and Analytics Unit, Department of Global Health, Institut Pasteur, Université Paris Cité, Paris, France
| | - Wuelton M Monteiro
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil; Escola de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Maxime Agranier
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Nicolas Taudon
- Unité de développements analytiques et bioanalyse, Institut de recherche biomédicale des armées, Brétigny-sur-Orge, France
| | - François Morin
- Service de Santé des Armées (SSA), Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France
| | - Magda Magris
- Amazonic Center for Research and Control of Tropical Diseases "Simón Bolívar", Puerto Ayacucho, Venezuela
| | - Marcus V G Lacerda
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil; Instituto Leônidas & Maria Deane, Fiocruz, Manaus, Brazil
| | - Giselle M R Viana
- Laboratory of Basic Research in Malaria, Evandro Chagas Institute, Brazil Ministry of Health, Ananindeua, Brazil
| | - Sócrates Herrera
- Malaria Vaccine and Drug Development Center, Cali, Colombia; Caucaseco Scientific Research Center, Cali, Colombia
| | - Malti R Adhin
- Department of Biochemistry Kernkampweg 5, Faculty of Medical Sciences, Anton de Kom Universiteit van Suriname, Paramaribo, Suriname
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | - Charles J Woodrow
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ghulam R Awab
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Ministry of Public Health, Kabul, Afghanistan
| | - Horace Cox
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Maria-Paz Ade
- Department of Communicable Diseases and Environmental Determinants of Health, Pan American Health Organization/World Health Organization, Washington DC, USA
| | - Emilie Mosnier
- Sciences Economiques Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM), Aix Marseille University, INSERM, IRD, Marseille, France
| | - Félix Djossou
- Infectious and Tropical Diseases Unit, Cayenne General Hospital, Cayenne, French Guiana
| | - Daniel E Neafsey
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA; Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Pascal Ringwald
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Lise Musset
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana.
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12
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Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578156. [PMID: 38352461 PMCID: PMC10862847 DOI: 10.1101/2024.01.31.578156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission settings where most mosquitoes become infected with only a single parasite clone, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. To investigate whether this clonality was potentially associated with the persistence and spatial spread of the mutation, we performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016-2021). We characterized the relatedness between each pair of monoclonal infections (n=1,409) through estimation of identity by descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 clones (mean IBD ≥ 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD ≥ 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally report polymorphisms exhibiting evidence of selection for drug resistance or other phenotypes and reported a novel pfk13 mutation (G718S) as well as 61 nonsynonymous substitutions that increased markedly in frequency. However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation.
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Affiliation(s)
- Mathieu Vanhove
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Angela M Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Margaret Laws
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Frank Anthony
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Célia Florimond
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Luana Mathieu
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Kashana James
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Cheyenne Knox
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Narine Singh
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Caroline O Buckee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lise Musset
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Horace Cox
- National Malaria Program, Ministry of Health, Georgetown, Guyana
- Caribbean Public Health Agency, Trinidad and Tobago
| | - Reza Niles-Robin
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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13
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Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MCS, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nat Commun 2024; 15:937. [PMID: 38297033 PMCID: PMC10831071 DOI: 10.1038/s41467-024-45224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Craig J Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, VIC, Australia
| | - Riley D Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kate J Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Dana M Klug
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Peter J Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Luiz C Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - David A Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 4HN, UK
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Matthew H Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK.
- Structural Genomics Consortium, University College London, London, WC1N 1AX, UK.
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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14
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De Meulenaere K, Cuypers WL, Gauglitz JM, Guetens P, Rosanas-Urgell A, Laukens K, Cuypers B. Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling. mBio 2024; 15:e0196723. [PMID: 38054750 PMCID: PMC10790762 DOI: 10.1128/mbio.01967-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Malaria is caused by parasites of the genus Plasmodium, and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich Plasmodium DNA. We used the Oxford Nanopore Technologies' adaptive sampling feature to circumvent this problem and enrich Plasmodium reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches Plasmodium reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.
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Affiliation(s)
- Katlijn De Meulenaere
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wim L. Cuypers
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
| | - Julia M. Gauglitz
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
| | - Pieter Guetens
- Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kris Laukens
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
| | - Bart Cuypers
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
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15
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Srivastava SK, Parker C, O'Brien CN, Tucker MS, Thompson PC, Rosenthal BM, Dubey JP, Khan A, Jenkins MC. Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella. Sci Rep 2023; 13:22802. [PMID: 38129566 PMCID: PMC10739835 DOI: 10.1038/s41598-023-50117-0] [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: 08/30/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, "ERR296879") share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development.
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Affiliation(s)
- Subodh K Srivastava
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Carolyn Parker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Celia N O'Brien
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Matthew S Tucker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Peter C Thompson
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Benjamin M Rosenthal
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Jitender P Dubey
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Asis Khan
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Mark C Jenkins
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
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16
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Liu S, Ebel ER, Luniewski A, Zulawinska J, Simpson ML, Kim J, Ene N, Braukmann TWA, Congdon M, Santos W, Yeh E, Guler JL. Direct long read visualization reveals metabolic interplay between two antimalarial drug targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528367. [PMID: 36824743 PMCID: PMC9948948 DOI: 10.1101/2023.02.13.528367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Increases in the copy number of large genomic regions, termed genome amplification, are an important adaptive strategy for malaria parasites. Numerous amplifications across the Plasmodium falciparum genome contribute directly to drug resistance or impact the fitness of this protozoan parasite. During the characterization of parasite lines with amplifications of the dihydroorotate dehydrogenase (DHODH) gene, we detected increased copies of an additional genomic region that encompassed 3 genes (~5 kb) including GTP cyclohydrolase I (GCH1 amplicon). While this gene is reported to increase the fitness of antifolate resistant parasites, GCH1 amplicons had not previously been implicated in any other antimalarial resistance context. Here, we further explored the association between GCH1 and DHODH copy number. Using long read sequencing and single read visualization, we directly observed a higher number of tandem GCH1 amplicons in parasites with increased DHODH copies (up to 9 amplicons) compared to parental parasites (3 amplicons). While all GCH1 amplicons shared a consistent structure, expansions arose in 2-unit steps (from 3 to 5 to 7, etc copies). Adaptive evolution of DHODH and GCH1 loci was further bolstered when we evaluated prior selection experiments; DHODH amplification was only successful in parasite lines with pre-existing GCH1 amplicons. These observations, combined with the direct connection between metabolic pathways that contain these enzymes, lead us to propose that the GCH1 locus is beneficial for the fitness of parasites exposed to DHODH inhibitors. This finding highlights the importance of studying variation within individual parasite genomes as well as biochemical connections of drug targets as novel antimalarials move towards clinical approval.
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Affiliation(s)
- Shiwei Liu
- University of Virginia, Department of Biology, Charlottesville, VA, USA
- Current affiliation: Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emily R. Ebel
- Stanford, Departments of Pediatrics and Microbiology & Immunology, Stanford, CA, USA
| | | | - Julia Zulawinska
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Jane Kim
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | - Nnenna Ene
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Molly Congdon
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Webster Santos
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Ellen Yeh
- Stanford University, Departments of Pathology and Microbiology & Immunology, Stanford, CA, USA
| | - Jennifer L. Guler
- University of Virginia, Department of Biology, Charlottesville, VA, USA
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17
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Schaffner SF, Badiane A, Khorgade A, Ndiop M, Gomis J, Wong W, Ndiaye YD, Diedhiou Y, Thwing J, Seck MC, Early A, Sy M, Deme A, Diallo MA, Sy N, Sene A, Ndiaye T, Sow D, Dieye B, Ndiaye IM, Gaye A, Ndiaye A, Battle KE, Proctor JL, Bever C, Fall FB, Diallo I, Gaye S, Sene D, Hartl DL, Wirth DF, MacInnis B, Ndiaye D, Volkman SK. Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal. Nat Commun 2023; 14:7268. [PMID: 37949851 PMCID: PMC10638404 DOI: 10.1038/s41467-023-43087-4] [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: 06/13/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in 2019; it provides a baseline for analyzing parasite genetic metrics as they vary over time and geographic space. The study's goal was to identify genetic metrics that were informative about transmission intensity and other aspects of transmission dynamics, focusing on measures of genetic relatedness between parasites. We found the best genetic proxy for local malaria incidence to be the proportion of polygenomic infections (those with multiple genetically distinct parasites), although this relationship broke down at low incidence. The proportion of related parasites was less correlated with incidence while local genetic diversity was uninformative. The type of relatedness could discriminate local transmission patterns: two nearby areas had similarly high fractions of relatives, but one was dominated by clones and the other by outcrossed relatives. Throughout Senegal, 58% of related parasites belonged to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci and at one novel locus, reflective of ongoing selection pressure.
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Affiliation(s)
- Stephen F Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Aida Badiane
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Akanksha Khorgade
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Medoune Ndiop
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yaye Die Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Julie Thwing
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mame Cheikh Seck
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Angela Early
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Mouhamad Sy
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Awa Deme
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mamadou Alpha Diallo
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic, Thies, Senegal
| | - Aita Sene
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Tolla Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Djiby Sow
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Baba Dieye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amy Gaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Aliou Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Katherine E Battle
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Caitlin Bever
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Fatou Ba Fall
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Ibrahima Diallo
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Seynabou Gaye
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Doudou Sene
- Programme National de Lutte Contre le Paludisme (PNLP), Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Bronwyn MacInnis
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Daouda Ndiaye
- Centre International de recherche, de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Sarah K Volkman
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA.
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18
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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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19
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Kane J, Li X, Kumar S, Button-Simons KA, Brenneman KMV, Dahlhoff H, Sievert MA, Checkley LA, Shoue DA, Singh PP, Abatiyow BA, Haile MT, Nair S, Reyes A, Tripura R, Peto T, Lek D, Kappe SH, Dhorda M, Nkhoma SC, Cheeseman IH, Vaughan AM, Anderson TJC, Ferdig MT. A Plasmodium falciparum genetic cross reveals the contributions of pfcrt and plasmepsin II/III to piperaquine drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543862. [PMID: 37745488 PMCID: PMC10515748 DOI: 10.1101/2023.06.06.543862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Piperaquine (PPQ) is widely used in combination with dihydroartemisinin (DHA) as a first-line treatment against malaria parasites. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multi-drug resistant KEL1/PLA1 lineage isolate (KH004) and a drug susceptible parasite isolated in Malawi (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and four copies of pm2/3. We recovered 104 unique recombinant progeny and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3 for detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes, including PPQ survival assay (PSA), area under the dose-response curve (AUC), and a limited point IC50 (LP-IC50). We find that inheritance of the KH004 pfcrt allele is required for PPQ resistance, whereas copy number variation in pm2/3 further enhances resistance but does not confer resistance in the absence of PPQ-R-associated mutations in pfcrt. Deeper investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background, to a range of PPQ-related traits and confirm the critical role of the PfCRT G367C substitution in PPQ resistance.
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Affiliation(s)
- John Kane
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Katrina A. Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Haley Dahlhoff
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Mackenzie A.C. Sievert
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Lisa A. Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Puspendra P. Singh
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ann Reyes
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Rupam Tripura
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Tom Peto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Dysoley Lek
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
- School of Public Health, National Institute of Public Health, Phnom Penh, Cambodia
| | - Stefan H.I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Standwell C Nkhoma
- BEI Resources, American Type Culture Collection (ATCC), Manassas, VA, USA
| | - Ian H. Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Timothy J. C. Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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20
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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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21
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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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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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Schaffner SF, Badiane A, Khorgade A, Ndiop M, Gomis J, Wong W, Ndiaye YD, Diedhiou Y, Thwing J, Seck MC, Early A, Sy M, Deme A, Diallo MA, Sy N, Sene A, Ndiaye T, Sow D, Dieye B, Ndiaye IM, Gaye A, Ndiaye A, Battle KE, Proctor JL, Bever C, Fall FB, Diallo I, Gaye S, Sene D, Hartl DL, Wirth DF, MacInnis B, Ndiaye D, Volkman SK. Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.11.23288401. [PMID: 37131838 PMCID: PMC10153316 DOI: 10.1101/2023.04.11.23288401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Parasite genetic surveillance has the potential to play an important role in malaria control. We describe here an analysis of data from the first year of an ongoing, nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal, intended to provide actionable information for malaria control efforts. Looking for a good proxy for local malaria incidence, we found that the best predictor was the proportion of polygenomic infections (those with multiple genetically distinct parasites), although that relationship broke down in very low incidence settings (r = 0.77 overall). The proportion of closely related parasites in a site was more weakly correlated ( r = -0.44) with incidence while the local genetic diversity was uninformative. Study of related parasites indicated their potential for discriminating local transmission patterns: two nearby study areas had similarly high fractions of relatives, but one area was dominated by clones and the other by outcrossed relatives. Throughout the country, 58% of related parasites proved to belong to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci as well as at one novel locus, reflective of ongoing selection pressure.
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25
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Kümpornsin K, Kochakarn T, Yeo T, Okombo J, Luth MR, Hoshizaki J, Rawat M, Pearson RD, Schindler KA, Mok S, Park H, Uhlemann AC, Jana GP, Maity BC, Laleu B, Chenu E, Duffy J, Moliner Cubel S, Franco V, Gomez-Lorenzo MG, Gamo FJ, Winzeler EA, Fidock DA, Chookajorn T, Lee MCS. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum. Nat Commun 2023; 14:3059. [PMID: 37244916 DOI: 10.1038/s41467-023-38774-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/12/2023] [Indexed: 05/29/2023] Open
Abstract
In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5-8 fold elevation in the mutation rate, with an increase of 13-28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an "irresistible" compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this "mutator" parasite can be leveraged to drive P. falciparum resistome discovery.
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Affiliation(s)
- Krittikorn Kümpornsin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, USA
| | - Theerarat Kochakarn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Mukul Rawat
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, 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
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, 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
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Benoît Laleu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - Elodie Chenu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | | | - Virginia Franco
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | | | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 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, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Thanat Chookajorn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
- Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK.
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26
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Girard C, Zwicker D, Mercier R. The regulation of meiotic crossover distribution: a coarse solution to a century-old mystery? Biochem Soc Trans 2023:233030. [PMID: 37145037 DOI: 10.1042/bst20221329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Meiotic crossovers, which are exchanges of genetic material between homologous chromosomes, are more evenly and distantly spaced along chromosomes than expected by chance. This is because the occurrence of one crossover reduces the likelihood of nearby crossover events - a conserved and intriguing phenomenon called crossover interference. Although crossover interference was first described over a century ago, the mechanism allowing coordination of the fate of potential crossover sites half a chromosome away remains elusive. In this review, we discuss the recently published evidence supporting a new model for crossover patterning, coined the coarsening model, and point out the missing pieces that are still needed to complete this fascinating puzzle.
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Affiliation(s)
- Chloe Girard
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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27
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Bohmer MJ, Wang J, Istvan ES, Luth MR, Collins JE, Huttlin EL, Wang L, Mittal N, Hao M, Kwiatkowski NP, Gygi SP, Chakrabarti R, Deng X, Goldberg DE, Winzeler EA, Gray NS, Chakrabarti D. Human Polo-like Kinase Inhibitors as Antiplasmodials. ACS Infect Dis 2023; 9:1004-1021. [PMID: 36919909 PMCID: PMC10106425 DOI: 10.1021/acsinfecdis.3c00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Protein kinases have proven to be a very productive class of therapeutic targets, and over 90 inhibitors are currently in clinical use primarily for the treatment of cancer. Repurposing these inhibitors as antimalarials could provide an accelerated path to drug development. In this study, we identified BI-2536, a known potent human polo-like kinase 1 inhibitor, with low nanomolar antiplasmodial activity. Screening of additional PLK1 inhibitors revealed further antiplasmodial candidates despite the lack of an obvious orthologue of PLKs in Plasmodium. A subset of these inhibitors was profiled for their in vitro killing profile, and commonalities between the killing rate and inhibition of nuclear replication were noted. A kinase panel screen identified PfNEK3 as a shared target of these PLK1 inhibitors; however, phosphoproteome analysis confirmed distinct signaling pathways were disrupted by two structurally distinct inhibitors, suggesting PfNEK3 may not be the sole target. Genomic analysis of BI-2536-resistant parasites revealed mutations in genes associated with the starvation-induced stress response, suggesting BI-2536 may also inhibit an aminoacyl-tRNA synthetase.
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Affiliation(s)
- Monica J Bohmer
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biolo gy, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Jennifer E Collins
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lushun Wang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mingfeng Hao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biolo gy, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Nicholas P Kwiatkowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biolo gy, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ratna Chakrabarti
- Division of Cancer Research, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Xianming Deng
- School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
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28
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Dans MG, Piirainen H, Nguyen W, Khurana S, Mehra S, Razook Z, Geoghegan ND, Dawson AT, Das S, Parkyn Schneider M, Jonsdottir TK, Gabriela M, Gancheva MR, Tonkin CJ, Mollard V, Goodman CD, McFadden GI, Wilson DW, Rogers KL, Barry AE, Crabb BS, de Koning-Ward TF, Sleebs BE, Kursula I, Gilson PR. Sulfonylpiperazine compounds prevent Plasmodium falciparum invasion of red blood cells through interference with actin-1/profilin dynamics. PLoS Biol 2023; 21:e3002066. [PMID: 37053271 PMCID: PMC10128974 DOI: 10.1371/journal.pbio.3002066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/25/2023] [Accepted: 03/06/2023] [Indexed: 04/15/2023] Open
Abstract
With emerging resistance to frontline treatments, it is vital that new antimalarial drugs are identified to target Plasmodium falciparum. We have recently described a compound, MMV020291, as a specific inhibitor of red blood cell (RBC) invasion, and have generated analogues with improved potency. Here, we generated resistance to MMV020291 and performed whole genome sequencing of 3 MMV020291-resistant populations. This revealed 3 nonsynonymous single nucleotide polymorphisms in 2 genes; 2 in profilin (N154Y, K124N) and a third one in actin-1 (M356L). Using CRISPR-Cas9, we engineered these mutations into wild-type parasites, which rendered them resistant to MMV020291. We demonstrate that MMV020291 reduces actin polymerisation that is required by the merozoite stage parasites to invade RBCs. Additionally, the series inhibits the actin-1-dependent process of apicoplast segregation, leading to a delayed death phenotype. In vitro cosedimentation experiments using recombinant P. falciparum proteins indicate that potent MMV020291 analogues disrupt the formation of filamentous actin in the presence of profilin. Altogether, this study identifies the first compound series interfering with the actin-1/profilin interaction in P. falciparum and paves the way for future antimalarial development against the highly dynamic process of actin polymerisation.
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Affiliation(s)
- Madeline G Dans
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Henni Piirainen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - William Nguyen
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Sachin Khurana
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Somya Mehra
- Burnet Institute, Melbourne, Victoria, Australia
| | - Zahra Razook
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | | | | | - Sujaan Das
- Ludwig Maximilian University, Faculty of Veterinary Medicine, Munich, Germany
| | | | - Thorey K Jonsdottir
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Mikha Gabriela
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | - Maria R Gancheva
- Research Centre for Infectious Diseases, The University of Adelaide, Adelaide, Australia
| | | | - Vanessa Mollard
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Geoffrey I McFadden
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Danny W Wilson
- Research Centre for Infectious Diseases, The University of Adelaide, Adelaide, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Alyssa E Barry
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | - Brendan S Crabb
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Tania F de Koning-Ward
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | - Brad E Sleebs
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Inari Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Paul R Gilson
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
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29
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Honma H, Takahashi N, Arisue N, Sugishita T. Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T). Microb Genom 2023; 9. [PMID: 37083479 DOI: 10.1099/mgen.0.001003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Malarial parasites exhibit extensive genomic plasticity, which induces the antigen diversification and the development of antimalarial drug resistance. Only a few studies have examined the genome maintenance mechanisms of parasites. The study aimed at elucidating the impact of a mutation in a DNA mismatch repair gene on genome stability by maintaining the mutant and wild-type parasites through serial in vitro cultures for approximately 400 days and analysing the subsequent spontaneous mutations. A P513T mutant of the DNA mismatch repair protein PfMSH2-1 from Plasmodium falciparum 3D7 was created. The mutation did not influence the base substitution rate but significantly increased the insertion/deletion (indel) mutation rate in short tandem repeats (STRs) and minisatellite loci. STR mutability was affected by allele size, genomic category and certain repeat motifs. In the mutants, significant telomere healing and homologous recombination at chromosomal ends caused extensive gene loss and generation of chimeric genes, resulting in large-scale chromosomal alteration. Additionally, the mutant showed increased tolerance to N-methyl-N'-nitro-N-nitrosoguanidine, suggesting that PfMSH2-1 was involved in recognizing DNA methylation damage. This work provides valuable insights into the role of PfMSH2-1 in genome stability and demonstrates that the genomic destabilization caused by its dysfunction may lead to antigen diversification.
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Affiliation(s)
- Hajime Honma
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Nobuyuki Takahashi
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Nobuko Arisue
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Tomohiko Sugishita
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
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30
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Siegel SV, Amato R, Trimarsanto H, Sutanto E, Kleinecke M, Murie K, Whitton G, Taylor AR, Watson JA, Imwong M, Assefa A, Rahim AG, Chau NH, Hien TT, Green JA, Koh G, White NJ, Day N, Kwiatkowski DP, Rayner JC, Price RN, Auburn S. Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.13.23287179. [PMID: 36993192 PMCID: PMC10055443 DOI: 10.1101/2023.03.13.23287179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Challenges in understanding the origin of recurrent Plasmodium vivax infections constrains the surveillance of antimalarial efficacy and transmission of this neglected parasite. Recurrent infections within an individual may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or new inoculations (reinfection). Molecular inference of familial relatedness (identity-by-descent or IBD) based on whole genome sequence data, together with analysis of the intervals between parasitaemic episodes ("time-to-event" analysis), can help resolve the probable origin of recurrences. Whole genome sequencing of predominantly low-density P. vivax infections is challenging, so an accurate and scalable genotyping method to determine the origins of recurrent parasitaemia would be of significant benefit. We have developed a P. vivax genome-wide informatics pipeline to select specific microhaplotype panels that can capture IBD within small, amplifiable segments of the genome. Using a global set of 615 P. vivax genomes, we derived a panel of 100 microhaplotypes, each comprising 3-10 high frequency SNPs within <200 bp sequence windows. This panel exhibits high diversity in regions of the Asia-Pacific, Latin America and the horn of Africa (median HE = 0.70-0.81) and it captured 89% (273/307) of the polyclonal infections detected with genome-wide datasets. Using data simulations, we demonstrate lower error in estimating pairwise IBD using microhaplotypes, relative to traditional biallelic SNP barcodes. Our panel exhibited high accuracy in predicting the country of origin (median Matthew's correlation coefficient >0.9 in 90% countries tested) and it also captured local infection outbreak and bottlenecking events. The informatics pipeline is available open-source and yields microhaplotypes that can be readily transferred to high-throughput amplicon sequencing assays for surveillance in malaria-endemic regions.
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Affiliation(s)
- Sasha V. Siegel
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Hidayat Trimarsanto
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta 10430, Indonesia
| | - Edwin Sutanto
- Exeins Health Initiative, Jakarta Selatan 12870, Indonesia
| | - Mariana Kleinecke
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Kathryn Murie
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Aimee R. Taylor
- Institut Pasteur, University de Paris, Infectious Disease Epidemiology and Analytics Unit, Paris, France
| | - James A. Watson
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Awab Ghulam Rahim
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Afghanistan
| | - Nguyen Hoang Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | | | | | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Nicholas Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Ric N. Price
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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31
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Nguyen W, Dans MG, Currie I, Awalt JK, Bailey BL, Lumb C, Ngo A, Favuzza P, Palandri J, Ramesh S, Penington J, Jarman KE, Mukherjee P, Chakraborty A, Maier AG, van Dooren GG, Papenfuss T, Wittlin S, Churchyard A, Baum J, Winzeler EA, Baud D, Brand S, Jackson PF, Cowman AF, Sleebs BE. 7- N-Substituted-3-oxadiazole Quinolones with Potent Antimalarial Activity Target the Cytochrome bc1 Complex. ACS Infect Dis 2023; 9:668-691. [PMID: 36853190 PMCID: PMC10012268 DOI: 10.1021/acsinfecdis.2c00607] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The development of new antimalarials is required because of the threat of resistance to current antimalarial therapies. To discover new antimalarial chemotypes, we screened the Janssen Jumpstarter library against the P. falciparum asexual parasite and identified the 7-N-substituted-3-oxadiazole quinolone hit class. We established the structure-activity relationship and optimized the antimalarial potency. The optimized analog WJM228 (17) showed robust metabolic stability in vitro, although the aqueous solubility was limited. Forward genetic resistance studies uncovered that WJM228 targets the Qo site of cytochrome b (cyt b), an important component of the mitochondrial electron transport chain (ETC) that is essential for pyrimidine biosynthesis and an established antimalarial target. Profiling against drug-resistant parasites confirmed that WJM228 confers resistance to the Qo site but not Qi site mutations, and in a biosensor assay, it was shown to impact the ETC via inhibition of cyt b. Consistent with other cyt b targeted antimalarials, WJM228 prevented pre-erythrocytic parasite and male gamete development and reduced asexual parasitemia in a P. berghei mouse model of malaria. Correcting the limited aqueous solubility and the high susceptibility to cyt b Qo site resistant parasites found in the clinic will be major obstacles in the future development of the 3-oxadiazole quinolone antimalarial class.
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Affiliation(s)
- William Nguyen
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Madeline G Dans
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Iain Currie
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Jon Kyle Awalt
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Brodie L Bailey
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Chris Lumb
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Anna Ngo
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Paola Favuzza
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Josephine Palandri
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Saishyam Ramesh
- Research School of Biology, The Australian National University, Canberra 2600, Australia
| | - Jocelyn Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Kate E Jarman
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | | | | | - Alexander G Maier
- Research School of Biology, The Australian National University, Canberra 2600, Australia
| | - Giel G van Dooren
- Research School of Biology, The Australian National University, Canberra 2600, Australia
| | - Tony Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, South Kensington, SW7 2AZ U.K
| | - Jake Baum
- Department of Life Sciences, Imperial College London, South Kensington, SW7 2AZ U.K.,School of Biomedical Sciences, University of New South Wales, Sydney 2031, Australia
| | - Elizabeth A Winzeler
- School of Medicine, University of California San Diego, 9500 Gilman Drive 0760, La Jolla, California 92093, United States
| | - Delphine Baud
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Stephen Brand
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Paul F Jackson
- Global Public Health, Janssen R&D LLC, La Jolla, California 92121, United States
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Brad E Sleebs
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
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32
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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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33
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Ibrahim A, Manko E, Dombrowski JG, Campos M, Benavente ED, Nolder D, Sutherland CJ, Nosten F, Fernandez D, Vélez-Tobón G, Castaño AT, Aguiar ACC, Pereira DB, da Silva Santos S, Suarez-Mutis M, Di Santi SM, Regina de Souza Baptista A, Dantas Machado RL, Marinho CR, Clark TG, Campino S. Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America. LANCET REGIONAL HEALTH. AMERICAS 2023; 18:100420. [PMID: 36844008 PMCID: PMC9950661 DOI: 10.1016/j.lana.2022.100420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 01/03/2023]
Abstract
Background Brazil is a unique and understudied setting for malaria, with complex foci of transmission associated with human and environmental conditions. An understanding of the population genomic diversity of P. vivax parasites across Brazil can support malaria control strategies. Methods Through whole genome sequencing of P. vivax isolates across 7 Brazilian states, we use population genomic approaches to compare genetic diversity within country (n = 123), continent (6 countries, n = 315) and globally (26 countries, n = 885). Findings We confirm that South American isolates are distinct, have more ancestral populations than the other global regions, with differentiating mutations in genes under selective pressure linked to antimalarial drugs (pvmdr1, pvdhfr-ts) and mosquito vectors (pvcrmp3, pvP45/48, pvP47). We demonstrate Brazil as a distinct parasite population, with signals of selection including ABC transporter (PvABCI3) and PHIST exported proteins. Interpretation Brazil has a complex population structure, with evidence of P. simium infections and Amazonian parasites separating into multiple clusters. Overall, our work provides the first Brazil-wide analysis of P. vivax population structure and identifies important mutations, which can inform future research and control measures. Funding AI is funded by an MRC LiD PhD studentship. TGC is funded by the Medical Research Council (Grant no. MR/M01360X/1, MR/N010469/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1). SC is funded by Medical Research Council UK grants (MR/M01360X/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1) and Bloomsbury SET (ref. CCF17-7779). FN is funded by The Shloklo Malaria Research Unit - part of the Mahidol Oxford Research Unit, supported by the Wellcome Trust (Grant no. 220211). ARSB is funded by São Paulo Research Foundation - FAPESP (Grant no. 2002/09546-1). RLDM is funded by Brazilian National Council for Scientific and Technological Development - CNPq (Grant no. 302353/2003-8 and 471605/2011-5); CRFM is funded by FAPESP (Grant no. 2020/06747-4) and CNPq (Grant no. 302917/2019-5 and 408636/2018-1); JGD is funded by FAPESP fellowships (2016/13465-0 and 2019/12068-5) and CNPq (Grant no. 409216/2018-6).
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Affiliation(s)
- Amy Ibrahim
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Emilia Manko
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Jamille G. Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Mónica Campos
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Debbie Nolder
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Colin J. Sutherland
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research
Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak,
Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of
Clinical Medicine Research Building, University of Oxford Old Road Campus,
Oxford, UK
| | - Diana Fernandez
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | - Gabriel Vélez-Tobón
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | | | | | | | - Simone da Silva Santos
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | - Martha Suarez-Mutis
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | | | - Andrea Regina de Souza Baptista
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Ricardo Luiz Dantas Machado
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Claudio R.F. Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Taane G. Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Faculty of Epidemiology & Population Health, London School of Hygiene
& Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
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34
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Quansah E, Chen Y, Yang S, Wang J, Sun D, Zhao Y, Chen M, Yu L, Zhang C. CRISPR-Cas13 in malaria parasite: Diagnosis and prospective gene function identification. Front Microbiol 2023; 14:1076947. [PMID: 36760507 PMCID: PMC9905151 DOI: 10.3389/fmicb.2023.1076947] [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: 10/24/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
Malaria caused by Plasmodium is still a serious public health problem. Genomic editing is essential to understand parasite biology, elucidate mechanical pathways, uncover gene functions, identify novel therapeutic targets, and develop clinical diagnostic tools. Recent advances have seen the development of genomic diagnostic technologies and the emergence of genetic manipulation toolbox comprising a host of several systems for editing the genome of Plasmodium at the DNA, RNA, and protein level. Genomic manipulation at the RNA level is critical as it allows for the functional characterization of several transcripts. Of notice, some developed artificial RNA genome editing tools hinge on the endogenous RNA interference system of Plasmodium. However, Plasmodium lacks a robust RNAi machinery, hampering the progress of these editing tools. CRISPR-Cas13, which belongs to the VI type of the CRISPR system, can specifically bind and cut RNA under the guidance of crRNA, with no or minimal permanent genetic scar on genes. This review summarizes CRISPR-Cas13 system from its discovery, classification, principle of action, and diagnostic platforms. Further, it discusses the application prospects of Cas13-based systems in Plasmodium and highlights its advantages and drawbacks.
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Affiliation(s)
- Elvis Quansah
- Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yihuan Chen
- The Second Clinical Medical College, Anhui Medical University, Hefei, China
| | - Shijie Yang
- The Second Clinical Medical College, Anhui Medical University, Hefei, China
| | - Junyan Wang
- The Second Clinical Medical College, Anhui Medical University, Hefei, China
| | - Danhong Sun
- The Second Clinical Medical College, Anhui Medical University, Hefei, China
| | - Yangxi Zhao
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Ming Chen
- The Second Clinical Medical College, Anhui Medical University, Hefei, China
| | - Li Yu
- Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China,*Correspondence: Li Yu, ✉
| | - Chao Zhang
- Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China,Chao Zhang, ✉
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Kucharski M, Wirjanata G, Nayak S, Boentoro J, Dziekan JM, Assisi C, van der Pluijm RW, Miotto O, Mok S, Dondorp AM, Bozdech Z. Short tandem repeat polymorphism in the promoter region of cyclophilin 19B drives its transcriptional upregulation and contributes to drug resistance in the malaria parasite Plasmodium falciparum. PLoS Pathog 2023; 19:e1011118. [PMID: 36696458 PMCID: PMC9901795 DOI: 10.1371/journal.ppat.1011118] [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: 08/26/2022] [Revised: 02/06/2023] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Resistance of the human malaria parasites, Plasmodium falciparum, to artemisinins is now fully established in Southeast Asia and is gradually emerging in Sub-Saharan Africa. Although nonsynonymous SNPs in the pfk13 Kelch-repeat propeller (KREP) domain are clearly associated with artemisinin resistance, their functional relevance requires cooperation with other genetic factors/alterations of the P. falciparum genome, collectively referred to as genetic background. Here we provide experimental evidence that P. falciparum cyclophilin 19B (PfCYP19B) may represent one putative factor in this genetic background, contributing to artemisinin resistance via its increased expression. We show that overexpression of PfCYP19B in vitro drives limited but significant resistance to not only artemisinin but also piperaquine, an important partner drug in artemisinin-based combination therapies. We showed that PfCYP19B acts as a negative regulator of the integrated stress response (ISR) pathway by modulating levels of phosphorylated eIF2α (eIF2α-P). Curiously, artemisinin and piperaquine affect eIF2α-P in an inverse direction that in both cases can be modulated by PfCYP19B towards resistance. Here we also provide evidence that the upregulation of PfCYP19B in the drug-resistant parasites appears to be maintained by a short tandem repeat (SRT) sequence polymorphism in the gene's promoter region. These results support a model that artemisinin (and other drugs) resistance mechanisms are complex genetic traits being contributed to by altered expression of multiple genes driven by genetic polymorphism at their promoter regions.
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Affiliation(s)
- Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sourav Nayak
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Christina Assisi
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Rob W. van der Pluijm
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sachel Mok
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Arjen M. Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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Abdel Hamid MM, Abdelraheem MH, Acheampong DO, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Aniebo I, Aninagyei E, Ansah F, Ansah PO, Apinjoh T, Arnaldo P, Ashley E, Auburn S, Awandare GA, Ba H, Baraka V, Barry A, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Bouyou-Akotet M, Branch O, Bull PC, Cheah H, Chindavongsa K, Chookajorn T, Chotivanich K, Claessens A, Conway DJ, Corredor V, Courtier E, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Dhorda M, Diakite M, Djimde A, Dolecek C, Dondorp A, Doumbia S, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Enosse SMM, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fleharty M, Forbes M, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Harrison GLA, Healy SA, Hendry JA, Hernandez-Koutoucheva A, Hien TT, Hill CA, Hombhanje F, Hott A, Htut Y, Hussein M, Imwong M, Ishengoma D, Jackson SA, Jacob CG, Jeans J, Johnson KJ, Kamaliddin C, Kamau E, Keatley J, Kochakarn T, Konate DS, Konaté A, Kone A, Kwiatkowski DP, Kyaw MP, Kyle D, Lawniczak M, Lee SK, Lemnge M, Lim P, Lon C, Loua KM, Mandara CI, Marfurt J, Marsh K, Maude RJ, Mayxay M, Maïga-Ascofaré O, Miotto O, Mita T, Mobegi V, Mohamed AO, Mokuolu OA, Montgomery J, Morang’a CM, Mueller I, Murie K, Newton PN, Ngo Duc T, Nguyen T, Nguyen TN, Nguyen Thi Kim T, Nguyen Van H, Noedl H, Nosten F, Noviyanti R, Ntui VNN, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Oyibo WA, Pearson R, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Quang HH, Randrianarivelojosia M, Rayner JC, Ringwald P, Rosanas-Urgell A, Rovira-Vallbona E, Ruano-Rubio V, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Sissoko MS, Smith C, Su XZ, Sutherland C, Takala-Harrison S, Talman A, Tavul L, Thanh NV, Thathy V, Thu AM, Toure M, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Whitton G, Yavo W, van der Pluijm RW. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Res 2023; 8:22. [PMID: 36864926 PMCID: PMC9971654 DOI: 10.12688/wellcomeopenres.18681.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.
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Affiliation(s)
| | | | - Mohamed Hassan Abdelraheem
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Nuclear Applications In Biological Sciences, Sudan Atomic Energy Commission, Khartoum, Sudan
| | - Desmond Omane Acheampong
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Ambroise Ahouidi
- Health Research Epidemiological Surveillance and Training Institute (IRESSEF), Université Cheikh Anta Diop, Dakar, Senegal
| | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | - Tim Anderson
- Texas Biomedical Research Institute, San Antonio, USA
| | | | | | - Enoch Aninagyei
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health & Allied Sciences, Ho, Ghana
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Patrick O Ansah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | | | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Maputo, Mozambique
| | - Elizabeth Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Nuffield Department of Medicine, University of Oxford, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- Department of Epidemiology, International Health Unit, Universiteit Antwerpen, Antwerp, Belgium
| | - Alyssa Barry
- Walter and Eliza Hall Institute, Melbourne, Australia
- Deakin University, Geelong, Australia
- Burnet Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F Boni
- Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marielle Bouyou-Akotet
- Department of Parasitology-Mycology, Université des Sciences de la Santé, Libreville, Gabon
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Huch Cheah
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | | | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David J Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- WorldWide Antimalarial Resistance Network – Asia Regional Centre, Bangkok, Thailand
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Seydou Doumbia
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Diego F Echeverry
- Departamento de Microbiología, Universidad del Valle, Cali, Colombia
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia
| | | | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Caterina A Fanello
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Mark Fleharty
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | | | - Mark Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Sara Anne Healy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason A Hendry
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Tran Tinh Hien
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, USA
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Madang, Papua New Guinea
| | | | - Ye Htut
- Department of Medical Research, Yangon, Myanmar
| | - Mazza Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Deus Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | | | | | - Claire Kamaliddin
- Institute of Research for Development (IRD), Paris, France
- The University of Calgary, Calgary, Canada
| | - Edwin Kamau
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Drissa S Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Aminatou Kone
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Myat P Kyaw
- Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar
- University of Public Health, Yangon, Myanmar
| | - Dennis Kyle
- University of South Florida, Tampa, USA
- University of Georgia, Athens, USA
| | | | - Samuel K Lee
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | - Martha Lemnge
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Kovana M Loua
- University Gamal Abdel Nasser of Conakry, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Celine I Mandara
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Jutta Marfurt
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Richard James Maude
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Harvard TH Chan School of Public Health, Harvard University, Boston, USA
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford University, Oxford, UK
| | | | - Victor Mobegi
- Department of Biochemistry and Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | | | - Olugbenga A Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jaqui Montgomery
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
- World Mosquito Program, Monash University, Melbourne, Australia
| | - Collins Misita Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | | | - Paul N Newton
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Thang Ngo Duc
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | | | - Thuy-Nhien Nguyen
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | | | - Hong Nguyen Van
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
- Medical University of Vienna, Vienna, Austria
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dhahran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya
- Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- Wellcome Sanger Institute, Hinxton, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria
- Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | | | | | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung P Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Ric N Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Huynh Hong Quang
- Institute of Malariology, Parasitology, and Entomology (IMPE) Quy Nhon, Ministry of Health, Quy Nhon, Vietnam
| | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Medicine, Uniformed Services University, Bethesda, MD, USA
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | - Mahamadou S. Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Arthur Talman
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ngo Viet Thanh
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aung Myint Thu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Mahamoudou Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Yale School of Medicine, New Haven, CT, USA
| | - Thomas E Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason Wendler
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Seattle Children’s Hospital, Seattle, USA
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire
- Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
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Measurably recombining malaria parasites. Trends Parasitol 2023; 39:17-25. [PMID: 36435688 PMCID: PMC9893849 DOI: 10.1016/j.pt.2022.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022]
Abstract
Genomic epidemiology has guided research and policy for various viral pathogens and there has been a parallel effort towards using genomic epidemiology to combat diseases that are caused by eukaryotic pathogens, such as the malaria parasite. However, the central concept of viral genomic epidemiology, namely that of measurably mutating pathogens, does not apply easily to sexually recombining parasites. Here we introduce the related but different concept of measurably recombining malaria parasites to promote convergence around a unifying theoretical framework for malaria genomic epidemiology. Akin to viral phylodynamics, we anticipate that an inferential framework developed around recombination will help guide practical research and thus realize the full public health potential of genomic epidemiology for malaria parasites and other sexually recombining pathogens.
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Deelder W, Manko E, Phelan JE, Campino S, Palla L, Clark TG. Geographical classification of malaria parasites through applying machine learning to whole genome sequence data. Sci Rep 2022; 12:21150. [PMID: 36476815 PMCID: PMC9729610 DOI: 10.1038/s41598-022-25568-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Malaria, caused by Plasmodium parasites, is a major global health challenge. Whole genome sequencing (WGS) of Plasmodium falciparum and Plasmodium vivax genomes is providing insights into parasite genetic diversity, transmission patterns, and can inform decision making for clinical and surveillance purposes. Advances in sequencing technologies are helping to generate timely and big genomic datasets, with the prospect of applying Artificial Intelligence analytical techniques (e.g., machine learning) to support programmatic malaria control and elimination. Here, we assess the potential of applying deep learning convolutional neural network approaches to predict the geographic origin of infections (continents, countries, GPS locations) using WGS data of P. falciparum (n = 5957; 27 countries) and P. vivax (n = 659; 13 countries) isolates. Using identified high-quality genome-wide single nucleotide polymorphisms (SNPs) (P. falciparum: 750 k, P. vivax: 588 k), an analysis of population structure and ancestry revealed clustering at the country-level. When predicting locations for both species, classification (compared to regression) methods had the lowest distance errors, and > 90% accuracy at a country level. Our work demonstrates the utility of machine learning approaches for geo-classification of malaria parasites. With timelier WGS data generation across more malaria-affected regions, the performance of machine learning approaches for geo-classification will improve, thereby supporting disease control activities.
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Affiliation(s)
- Wouter Deelder
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Dalberg Advisors, 7 Rue de Chantepoulet, 1201, Geneva, Switzerland
| | - Emilia Manko
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jody E Phelan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Susana Campino
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Luigi Palla
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, Rome, Italy
| | - Taane G Clark
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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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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Zheng S, Xu P, Wu Z, Zhang H, Li D, Liu S, Liu B, Ren J, Chen H, Huang M. Genetic structure and domestication footprints of the tusk, coat color, and ear morphology in East Chinese pigs. J Genet Genomics 2022; 49:1053-1063. [PMID: 35413463 DOI: 10.1016/j.jgg.2022.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/29/2022]
Abstract
The domestication and artificial selection of wild boars have led to dramatic morphological and behavioral changes, especially in East Chinese (ECN) pigs. Here, we provide insights into the population structure and current genetic diversity of representative ECN pig breeds. We identify a 500-kb region containing six tooth development-relevant genes with almost completely different haplotypes between ECN pigs and Chinese wild boars or European domestic pigs. Notably, the c.195A>G missense mutation in exon 2 of AMBN may cause alterations in its protein structure associated with tusk degradation in ECN pigs. In addition, ESR1 may play an important role in the reproductive performance of ECN pigs. A major haplotype of the large lop ear-related MSRB3 gene and eight alleles in the deafness-related GRM7 gene may affect ear morphology and hearing in ECN pigs. Interestingly, we find that the two-end black (TEB) coat color in Jinhua pigs is most likely caused by EDNRB with genetic mechanisms different from other Chinese TEB pigs. This study identifies key loci that may be artificially selected in Chinese native pigs related to the tusk, coat color, and ear morphology, thus providing new insights into the genetic mechanisms of domesticated pigs.
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Affiliation(s)
- Sumei Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Pan Xu
- School of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, China
| | - Zhongping Wu
- Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, China
| | - Hui Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Desen Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Shaojuan Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Bingbing Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jun Ren
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hao Chen
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, Jiangxi 330013, China.
| | - Min Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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Opute AO, Akinkunmi JA, Funsho AO, Obaniyi AK, Anifowoshe AT. Genetic diversity of Plasmodium falciparum isolates in Nigeria. A review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00340-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The complexity of infection in malaria-endemic areas is exacerbated by the presence of genetically diverse Plasmodium falciparum strains. There is a risk that more virulent or drug-resistant versions of the disease may arise. Therefore, we reviewed most reported molecular markers that have been detailed to date in Nigeria.
Main body of the abstract
In this review, we have summarized the genetic diversity of P. falciparum in Nigeria using the two well-reported genes (msp1 and msp2) as genetic diversity biomarkers. The review includes the findings obtained from research conducted in all major geopolitical regions of the country. We found that MSP-2 infection complexity is generally moderate to high in the North-central region. However, in the South-West, there were several regions where the multiplicity of infection (MOI) was either low or extremely high.
Conclusion
Understanding how Nigeria's malaria situation fits into various reports on P. falciparum genetic variation can improve treatment and immunization options. This review will be helpful for future treatment strategies that would be tailored to the specific needs of Nigeria's malaria-endemic populations.
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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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Declines in prevalence alter the optimal level of sexual investment for the malaria parasite Plasmodium falciparum. Proc Natl Acad Sci U S A 2022; 119:e2122165119. [PMID: 35867831 PMCID: PMC9335338 DOI: 10.1073/pnas.2122165119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Like most human pathogens, the malaria parasite Plasmodium falciparum experiences strong selection pressure from public health interventions such as drug treatment. While most commonly studied in the context of drug targets and related pathways, parasite adaptation to control measures likely extends to phenotypes beyond drug resistance. Here, we use modeling to explore how control measures can reduce levels of within-host competition between P. falciparum genotypes and favor higher rates of sexual investment. We validate these predictions with longitudinally sampled genomic data from French Guiana during a period of malaria decline and find that the most strongly selected genes are enriched for transcription factors involved in commitment to and development of the parasite’s sexual gametocyte form. Successful infectious disease interventions can result in large reductions in parasite prevalence. Such demographic change has fitness implications for individual parasites and may shift the parasite’s optimal life history strategy. Here, we explore whether declining infection rates can alter Plasmodium falciparum’s investment in sexual versus asexual growth. Using a multiscale mathematical model, we demonstrate how the proportion of polyclonal infections, which decreases as parasite prevalence declines, affects the optimal sexual development strategy: Within-host competition in multiclone infections favors a greater investment in asexual growth whereas single-clone infections benefit from higher conversion to sexual forms. At the same time, drug treatment also imposes selection pressure on sexual development by shortening infection length and reducing within-host competition. We assess these models using 148 P. falciparum parasite genomes sampled in French Guiana over an 18-y period of intensive intervention (1998 to 2015). During this time frame, multiple public health measures, including the introduction of new drugs and expanded rapid diagnostic testing, were implemented, reducing P. falciparum malaria cases by an order of magnitude. Consistent with this prevalence decline, we see an increase in the relatedness among parasites, but no single clonal background grew to dominate the population. Analyzing individual allele frequency trajectories, we identify genes that likely experienced selective sweeps. Supporting our model predictions, genes showing the strongest signatures of selection include transcription factors involved in the development of P. falciparum’s sexual gametocyte form. These results highlight how public health interventions impose wide-ranging selection pressures that affect basic parasite life history traits.
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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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Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz MC, Ramakrishnan S, Iqbal Z. Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biol 2022; 23:147. [PMID: 35791022 PMCID: PMC9254434 DOI: 10.1186/s13059-022-02714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/20/2022] [Indexed: 12/30/2022] Open
Abstract
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).
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Affiliation(s)
- Martin Hunt
- EMBL-EBI, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | | | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Kumar S, Li X, McDew-White M, Reyes A, Delgado E, Sayeed A, Haile MT, Abatiyow BA, Kennedy SY, Camargo N, Checkley LA, Brenneman KV, Button-Simons KA, Duraisingh MT, Cheeseman IH, Kappe SHI, Nosten F, Ferdig MT, Vaughan AM, Anderson TJC. A Malaria Parasite Cross Reveals Genetic Determinants of Plasmodium falciparum Growth in Different Culture Media. Front Cell Infect Microbiol 2022; 12:878496. [PMID: 35711667 PMCID: PMC9197316 DOI: 10.3389/fcimb.2022.878496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/28/2022] [Indexed: 12/21/2022] Open
Abstract
What genes determine in vitro growth and nutrient utilization in asexual blood-stage malaria parasites? Competition experiments between NF54, clone 3D7, a lab-adapted African parasite, and a recently isolated Asian parasite (NHP4026) reveal contrasting outcomes in different media: 3D7 outcompetes NHP4026 in media containing human serum, while NHP4026 outcompetes 3D7 in media containing AlbuMAX, a commercial lipid-rich bovine serum formulation. To determine the basis for this polymorphism, we conducted parasite genetic crosses using humanized mice and compared genome-wide allele frequency changes in three independent progeny populations cultured in media containing human serum or AlbuMAX. This bulk segregant analysis detected three quantitative trait loci (QTL) regions [on chromosome (chr) 2 containing aspartate transaminase AST; chr 13 containing EBA-140; and chr 14 containing cysteine protease ATG4] linked with differential growth in serum or AlbuMAX in each of the three independent progeny pools. Selection driving differential growth was strong (s = 0.10 – 0.23 per 48-hour lifecycle). We conducted validation experiments for the strongest QTL on chr 13: competition experiments between ΔEBA-140 and 3D7 wildtype parasites showed fitness reversals in the two medium types as seen in the parental parasites, validating this locus as the causative gene. These results (i) demonstrate the effectiveness of bulk segregant analysis for dissecting fitness traits in P. falciparum genetic crosses, and (ii) reveal intimate links between red blood cell invasion and nutrient composition of growth media. Use of parasite crosses combined with bulk segregant analysis will allow systematic dissection of key nutrient acquisition/metabolism and red blood cell invasion pathways in P. falciparum.
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Affiliation(s)
- Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Marina McDew-White
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ann Reyes
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Elizabeth Delgado
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Abeer Sayeed
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Spencer Y. Kennedy
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Nelly Camargo
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Lisa A. Checkley
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Katelyn V. Brenneman
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Katrina A. Button-Simons
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Manoj T. Duraisingh
- Immunology and Infectious Diseases Department, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Ian H. Cheeseman
- Program in Host Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Oxford, United Kingdom
| | - Michael T. Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- *Correspondence: Ashley M. Vaughan, ; Tim J. C. Anderson,
| | - Tim J. C. Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Ashley M. Vaughan, ; Tim J. C. Anderson,
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LaVerriere E, Schwabl P, Carrasquilla M, Taylor AR, Johnson ZM, Shieh M, Panchal R, Straub TJ, Kuzma R, Watson S, Buckee CO, Andrade CM, Portugal S, Crompton PD, Traore B, Rayner JC, Corredor V, James K, Cox H, Early AM, MacInnis BL, Neafsey DE. Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study. Mol Ecol Resour 2022; 22:2285-2303. [PMID: 35437908 DOI: 10.1111/1755-0998.13622] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, and shows strong potential for genomic epidemiology of infectious disease. AmpSeq data from infectious microbes can inform disease control in multiple ways, including measuring drug resistance marker prevalence, distinguishing imported from local cases, and determining the effectiveness of therapeutics. We describe the design and comparative evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites: a four-locus panel ('4CAST') composed of highly diverse antigens, and a 129-locus panel ('AMPLseq') composed of drug resistance markers, highly diverse loci for inferring relatedness, and a locus to detect Plasmodium vivax co-infection. We explore the performance of each panel in various public health use cases with in silico simulations as well as empirical experiments. The 4CAST panel appears highly suitable for evaluating the number of distinct parasite strains within samples (complexity of infection), showing strong performance across a wide range of parasitemia levels without a DNA pre-amplification step. For relatedness inference, the larger AMPLseq panel performs similarly to two existing panels of comparable size, despite differences in the data and approach used for designing each panel. Finally, we describe an R package (paneljudge) that facilitates the design and comparative evaluation of genetic panels for relatedness estimation, and we provide general guidance on the design and implementation of AmpSeq panels for genomic epidemiology of infectious disease.
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Affiliation(s)
- Emily LaVerriere
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manuela Carrasquilla
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zachary M Johnson
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Meg Shieh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruchit Panchal
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy J Straub
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca Kuzma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean Watson
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caroline O Buckee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carolina M Andrade
- Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Silvia Portugal
- Max Planck Institute for Infection Biology, Berlin, Germany.,Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, BP 1805, Point G, Bamako, Mali
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Kashana James
- Guyana National Malaria Control Program, Ministry of Health, 0592, Georgetown, Guyana
| | - Horace Cox
- Guyana Vector Control Services, Ministry of Health, 0592, Georgetown, Guyana
| | - Angela M Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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48
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Brenneman KV, Li X, Kumar S, Delgado E, Checkley LA, Shoue DA, Reyes A, Abatiyow BA, Haile MT, Tripura R, Peto T, Lek D, Button-Simons KA, Kappe SH, Dhorda M, Nosten F, Nkhoma SC, Cheeseman IH, Vaughan AM, Ferdig MT, Anderson TJ. Optimizing bulk segregant analysis of drug resistance using Plasmodium falciparum genetic crosses conducted in humanized mice. iScience 2022; 25:104095. [PMID: 35372813 PMCID: PMC8971943 DOI: 10.1016/j.isci.2022.104095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 01/15/2023] Open
Abstract
Classical malaria parasite genetic crosses involve isolation, genotyping, and phenotyping of progeny parasites, which is time consuming and laborious. We tested a rapid alternative approach-bulk segregant analysis (BSA)-that utilizes sequencing of bulk progeny populations with and without drug selection for rapid identification of drug resistance loci. We used dihydroartemisinin (DHA) selection in two genetic crosses and investigated how synchronization, cryopreservation, and the drug selection regimen impacted BSA success. We detected a robust quantitative trait locus (QTL) at kelch13 in both crosses but did not detect QTLs at four other candidate loci. QTLs were detected using synchronized, but not unsynchronized progeny pools, consistent with the stage-specific action of DHA. We also successfully applied BSA to cryopreserved progeny pools, expanding the utility of this approach. We conclude that BSA provides a powerful approach for investigating the genetic architecture of drug resistance in Plasmodium falciparum.
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Affiliation(s)
- Katelyn Vendrely Brenneman
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Elizabeth Delgado
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Lisa A. Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Ann Reyes
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Rupam Tripura
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Tom Peto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Dysoley Lek
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
- School of Public Health, National Institute of Public Health, Phnom Penh, Cambodia
| | - Katrina A. Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stefan H.I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Ian H. Cheeseman
- Program in Host Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Corresponding author
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- Corresponding author
| | - Tim J.C. Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
- Corresponding author
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49
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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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50
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Turnbull LB, Button-Simons KA, Agbayani N, Ferdig MT. Sources of transcription variation in Plasmodium falciparum. J Genet Genomics 2022; 49:965-974. [PMID: 35395422 DOI: 10.1016/j.jgg.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/20/2022]
Abstract
Variation in transcript abundance can contribute to both short-term environmental response and long-term evolutionary adaptation. Most studies are designed to assess differences in mean transcription levels and do not consider other potentially important and confounding sources of transcriptional variation. Detailed quantification of variation sources will improve our ability to detect and identify the mechanisms that contribute to genome-wide transcription changes that underpin adaptive responses. To quantify innate levels of expression variation, we measured mRNA levels for more than 5000 genes in the malaria parasite, Plasmodium falciparum, among clones derived from two parasite strains across biologically and experimentally replicated batches. Using a mixed effects model, we partitioned the total variation among four sources - between strain, within strain, environmental batch effects, and stochastic noise. We found 646 genes with significant variation attributable to at least one of these sources. These genes were categorized by their predominant variation source and further examined using gene ontology enrichment analysis to associate function with each source of variation. Genes with environmental batch effect and within strain transcript variation may contribute to phenotypic plasticity, while genes with between strain variation may contribute to adaptive responses and processes that lead to parasite strain-specific survival under varied conditions.
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Affiliation(s)
- Lindsey B Turnbull
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Katrina A Button-Simons
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nestor Agbayani
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA; Rush School of Medicine, Chicago, IL, 60612, USA
| | - Michael T Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
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