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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
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2
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Vareta J, Horstman NA, Adams M, Seydel KB, McCann RS, Cohee LM, Laufer MK, Takala-Harrison S. Genotyping Plasmodium falciparum gametocytes using amplicon deep sequencing. Malar J 2024; 23:96. [PMID: 38582837 PMCID: PMC10999092 DOI: 10.1186/s12936-024-04920-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/27/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Understanding the dynamics of gametocyte production in polyclonal Plasmodium falciparum infections requires a genotyping method that detects distinct gametocyte clones and estimates their relative frequencies. Here, a marker was identified and evaluated to genotype P. falciparum mature gametocytes using amplicon deep sequencing. METHODS A data set of polymorphic regions of the P. falciparum genome was mined to identify a gametocyte genotyping marker. To assess marker resolution, the number of unique haplotypes in the marker region was estimated from 95 Malawian P. falciparum whole genome sequences. Specificity of the marker for detection of mature gametocytes was evaluated using reverse transcription-polymerase chain reaction of RNA extracted from NF54 mature gametocytes and rings from a non-gametocyte-producing strain of P. falciparum. Amplicon deep sequencing was performed on experimental mixtures of mature gametocytes from two distinct parasite clones, as well as gametocyte-positive P. falciparum field isolates to evaluate the quantitative ability and determine the limit of detection of the genotyping approach. RESULTS A 400 bp region of the pfs230 gene was identified as a gametocyte genotyping marker. A larger number of unique haplotypes was observed at the pfs230 marker (34) compared to the sera-2 (18) and ama-1 (14) markers in field isolates from Malawi. RNA and DNA genotyping accurately estimated gametocyte and total parasite clone frequencies when evaluating agreement between expected and observed haplotype frequencies in gametocyte mixtures, with concordance correlation coefficients of 0.97 [95% CI: 0.92-0.99] and 0.92 [95% CI: 0.83-0.97], respectively. The detection limit of the genotyping method for male gametocytes was 0.41 pfmget transcripts/µl [95% CI: 0.28-0.72] and for female gametocytes was 1.98 ccp4 transcripts/µl [95% CI: 1.35-3.68]. CONCLUSIONS A region of the pfs230 gene was identified as a marker to genotype P. falciparum gametocytes. Amplicon deep sequencing of this marker can be used to estimate the number and relative frequency of parasite clones among mature gametocytes within P. falciparum infections. This gametocyte genotyping marker will be an important tool for studies aimed at understanding dynamics of gametocyte production in polyclonal P. falciparum infections.
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Affiliation(s)
- Jimmy Vareta
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Natalie A Horstman
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Karl B Seydel
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Robert S McCann
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lauren M Cohee
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Miriam K Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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3
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
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Garcia OA, Arslanian K, Whorf D, Thariath S, Shriver M, Li JZ, Bigham AW. The Legacy of Infectious Disease Exposure on the Genomic Diversity of Indigenous Southern Mexicans. Genome Biol Evol 2023; 15:7023365. [PMID: 36726304 PMCID: PMC10016042 DOI: 10.1093/gbe/evad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 12/19/2022] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
To characterize host risk factors for infectious disease in Mesoamerican populations, we interrogated 857,481 SNPs assayed using the Affymetrix 6.0 genotyping array for signatures of natural selection in immune response genes. We applied three statistical tests to identify signatures of natural selection: locus-specific branch length (LSBL), the cross-population extended haplotype homozygosity (XP-EHH), and the integrated haplotype score (iHS). Each of the haplotype tests (XP-EHH and iHS) were paired with LSBL and significance was determined at the 1% level. For the paired analyses, we identified 95 statistically significant windows for XP-EHH/LSBL and 63 statistically significant windows for iHS/LSBL. Among our top immune response loci, we found evidence of recent directional selection associated with the major histocompatibility complex (MHC) and the peroxisome proliferator-activated receptor gamma (PPAR-γ) signaling pathway. These findings illustrate that Mesoamerican populations' immunity has been shaped by exposure to infectious disease. As targets of selection, these variants are likely to encode phenotypes that manifest themselves physiologically and therefore may contribute to population-level variation in immune response. Our results shed light on past selective events influencing the host response to modern diseases, both pathogenic infection as well as autoimmune disorders.
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Affiliation(s)
- Obed A Garcia
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan.,Department of Biomedical Data Science, Stanford University, Stanford, California
| | | | - Daniel Whorf
- College of Medicine, University of Illinois, Peoria, Illinois
| | - Serena Thariath
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee
| | - Mark Shriver
- Department of Anthropology, Penn State University, State College, Pennsylvania
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, California
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5
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Liu Y, Zhang T, Chen SB, Cui YB, Wang SQ, Zhang HW, Shen HM, Chen JH. Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s. Front Microbiol 2023; 14:1071689. [PMID: 36846776 PMCID: PMC9948256 DOI: 10.3389/fmicb.2023.1071689] [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: 10/16/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction In malaria-free countries, imported cases are challenging because interconnections with neighboring countries with higher transmission rates increase the risk of parasite reintroduction. Establishing a genetic database for rapidly identifying malaria importation or reintroduction is crucial in addressing these challenges. This study aimed to examine genomic epidemiology during the pre-elimination stage by retrospectively reporting whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China. Methods The samples were collected during the last few inland outbreaks from 2011 to 2012 when China implemented a malaria control plan. After next-generation sequencing, we completed a genetic analysis of the population, explored the geographic specificity of the samples, and examined clustering of selection pressures. We also scanned genes for signals of positive selection. Results China's inland populations were highly structured compared to the surrounding area, with a single potential ancestor. Additionally, we identified genes under selection and evaluated the selection pressure on drug-resistance genes. In the inland population, positive selection was detected in some critical gene families, including sera, msp3, and vir. Meanwhile, we identified selection signatures in drug resistance, such as ugt, krs1, and crt, and noticed that the ratio of wild-type dhps and dhfr-ts increased after China banned sulfadoxine-pyrimethamine (SP) for decades. Discussion Our data provides an opportunity to investigate the molecular epidemiology of pre-elimination inland malaria populations, which exhibited lower selection pressure on invasion and immune evasion genes than neighbouring areas, but increased drug resistance in low transmission settings. Our results revealed that the inland population was severely fragmented with low relatedness among infections, despite a higher incidence of multiclonal infections, suggesting that superinfection or co-transmission events are rare in low-endemic circumstances. We identified selective signatures of resistance and found that the proportion of susceptible isolates fluctuated in response to the prohibition of specific drugs. This finding is consistent with the alterations in medication strategies during the malaria elimination campaign in inland China. Such findings could provide a genetic basis for future population studies, assessing changes in other pre-elimination countries.
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Affiliation(s)
- Ying Liu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Tao Zhang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shu-Qi Wang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hong-Wei Zhang
- Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Hai-Mo Shen, ✉
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Jun-Hu Chen, ✉
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6
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Mbye H, Mane K, Diop MF, Demba MA, Bojang F, Mohammed NI, Jeffries D, Quashie NB, D'Alessandro U, Amambua-Ngwa A. Plasmodium falciparum merozoite invasion ligands, linked antimalarial resistance loci and ex vivo responses to antimalarials in The Gambia. J Antimicrob Chemother 2022; 77:2946-2955. [PMID: 35904009 PMCID: PMC9616547 DOI: 10.1093/jac/dkac244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/23/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Artemether/lumefantrine is the most commonly used artemisinin-based combination treatment (ACT) for malaria in sub-Saharan Africa. Drug resistance to ACT components is a major threat to malaria elimination efforts. Therefore, rigorous monitoring of drug efficacy is required for adequate management of malaria and to sustain the effectiveness of ACTs. OBJECTIVES This study identified and described genomic loci that correlate with differences in ex vivo responses of natural Plasmodium falciparum isolates from The Gambia to antimalarial drugs. METHODS Natural P. falciparum isolates from The Gambia were assayed for IC50 responses to four antimalarial drugs (artemether, dihydroartemisinin, amodiaquine and lumefantrine). Genome-wide SNPs from 56 of these P. falciparum isolates were applied to mixed-model regression and network analyses to determine linked loci correlating with drug responses. Genomic regions of shared haplotypes and positive selection within and between Gambian and Cambodian P. falciparum isolates were mapped by identity-by-descent (IBD) analysis of 209 genomes. RESULTS SNPs in 71 genes, mostly involved in stress and drug resistance mechanisms correlated with drug responses. Additionally, erythrocyte invasion and permeability loci, including merozoite surface proteins (Pfdblmsp, Pfsurfin), and high-molecular-weight rhoptry protein 2 (Pfrhops2) were correlated with responses to multiple drugs. Haplotypes of pfdblmsp2 and known drug resistance loci (pfaat1, pfcrt and pfdhfr) from The Gambia showed high IBD with those from Cambodia, indicating co-ancestry, with significant linkage disequilibrium between their alleles. CONCLUSIONS Multiple linked genic loci correlating with drug response phenotypes suggest a genomic backbone may be under selection by antimalarials. This calls for further analysis of molecular pathways to drug resistance in African P. falciparum.
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Affiliation(s)
- Haddijatou Mbye
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Karim Mane
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Mouhamadou Fadel Diop
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Martha Anita Demba
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Fatoumata Bojang
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - David Jeffries
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Umberto D'Alessandro
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Alfred Amambua-Ngwa
- Medical Research Council at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
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7
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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Wunderlich J. Updated List of Transport Proteins in Plasmodium falciparum. Front Cell Infect Microbiol 2022; 12:926541. [PMID: 35811673 PMCID: PMC9263188 DOI: 10.3389/fcimb.2022.926541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria remains a leading cause of death and disease in many tropical and subtropical regions of the world. Due to the alarming spread of resistance to almost all available antimalarial drugs, novel therapeutic strategies are urgently needed. As the intracellular human malaria parasite Plasmodium falciparum depends entirely on the host to meet its nutrient requirements and the majority of its transmembrane transporters are essential and lack human orthologs, these have often been suggested as potential targets of novel antimalarial drugs. However, membrane proteins are less amenable to proteomic tools compared to soluble parasite proteins, and have thus not been characterised as well. While it had been proposed that P. falciparum had a lower number of transporters (2.5% of its predicted proteome) in comparison to most reference genomes, manual curation of information from various sources led to the identification of 197 known and putative transporter genes, representing almost 4% of all parasite genes, a proportion that is comparable to well-studied metazoan species. This transporter list presented here was compiled by collating data from several databases along with extensive literature searches, and includes parasite-encoded membrane-resident/associated channels, carriers, and pumps that are located within the parasite or exported to the host cell. It provides updated information on the substrates, subcellular localisation, class, predicted essentiality, and the presence or absence of human orthologs of P. falciparum transporters to quickly identify essential proteins without human orthologs for further functional characterisation and potential exploitation as novel drug targets.
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Affiliation(s)
- Juliane Wunderlich
- Max Planck Institute for Infection Biology, Berlin, Germany
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- *Correspondence: Juliane Wunderlich,
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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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11
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022; 18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
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Affiliation(s)
- Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Anthony Kocoski
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail:
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12
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Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM, Macharia AW, Hubbart C, Jeffreys AE, Rowlands K, Nguyen T, Gonçalves S, Ariani CV, Stalker J, Pearson RD, Amato R, Drury E, Sirugo G, d'Alessandro U, Bojang KA, Marsh K, Peshu N, Saelens JW, Diakité M, Taylor SM, Conway DJ, Williams TN, Rockett KA, Kwiatkowski DP. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature 2021; 602:106-111. [PMID: 34883497 PMCID: PMC8810385 DOI: 10.1038/s41586-021-04288-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations. A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.
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Affiliation(s)
- Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Muminatou Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Edward Francis Small Teaching Hospital (formerly Royal Victoria Teaching Hospital), Independence Drive, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Thuy Nguyen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Jim Stalker
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA
| | | | | | - Giorgio Sirugo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Umberto d'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kalifa A Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford, UK
| | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - David J Conway
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial College, London, London, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
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13
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Oberstaller J, Zoungrana L, Bannerman CD, Jahangiri S, Dwivedi A, Silva JC, Adams JH, Takala-Harrison S. Integration of population and functional genomics to understand mechanisms of artemisinin resistance in Plasmodium falciparum. Int J Parasitol Drugs Drug Resist 2021; 16:119-128. [PMID: 34102588 PMCID: PMC8187163 DOI: 10.1016/j.ijpddr.2021.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/05/2021] [Accepted: 05/21/2021] [Indexed: 11/05/2022]
Abstract
Resistance to antimalarial drugs, and in particular to the artemisinin derivatives and their partner drugs, threatens recent progress toward regional malaria elimination and eventual global malaria eradication. Population-level studies utilizing whole-genome sequencing approaches have facilitated the identification of regions of the parasite genome associated with both clinical and in vitro drug-resistance phenotypes. However, the biological relevance of genes identified in these analyses and the establishment of a causal relationship between genotype and phenotype requires functional characterization. Here we examined data from population genomic and transcriptomic studies in the context of data generated from recent functional studies, using a new population genetic approach designed to identify potential favored mutations within the region of a selective sweep (iSAFE). We identified several genes functioning in pathways now known to be associated with artemisinin resistance that were supported in early population genomic studies, as well as potential new drug targets/pathways for further validation and consideration for treatment of artemisinin-resistant Plasmodium falciparum. In addition, we establish the utility of iSAFE in identifying positively-selected mutations in population genomic studies, potentially accelerating the time to functional validation of candidate genes.
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Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Linda Zoungrana
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Carl D Bannerman
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Samira Jahangiri
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - John H Adams
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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14
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Abstract
Although the last two decades have seen a substantial decline in malaria incidence and mortality due to the use of insecticide-treated bed nets and artemisinin combination therapy, the threat of drug resistance is a constant obstacle to sustainable malaria control. Given that patients can die quickly from this disease, public health officials and doctors need to understand whether drug resistance exists in the parasite population, as well as how prevalent it is so they can make informed decisions about treatment. As testing for drug efficacy before providing treatment to malaria patients is impractical, researchers need molecular markers of resistance that can be more readily tracked in parasite populations. To this end, much work has been done to unravel the genetic underpinnings of drug resistance in Plasmodium falciparum. The aim of this review is to provide a broad overview of common genomic approaches that have been used to discover the alleles that drive drug response phenotypes in the most lethal human malaria parasite.
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Affiliation(s)
- Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
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15
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Gendrot M, Delandre O, Robert MG, Foguim FT, Benoit N, Amalvict R, Fonta I, Mosnier J, Madamet M, Pradines B. Absence of Association between Methylene Blue Reduced Susceptibility and Polymorphisms in 12 Genes Involved in Antimalarial Drug Resistance in African Plasmodium falciparum. Pharmaceuticals (Basel) 2021; 14:ph14040351. [PMID: 33918981 PMCID: PMC8069138 DOI: 10.3390/ph14040351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/26/2021] [Accepted: 04/07/2021] [Indexed: 11/17/2022] Open
Abstract
Half the human population is exposed to malaria. Plasmodium falciparum antimalarial drug resistance monitoring and development of new drugs are major issues related to the control of malaria. Methylene blue (MB), the oldest synthetic antimalarial, is again a promising drug after the break of its use as an antimalarial drug for more than 80 years and a potential partner for triple combination. Very few data are available on the involvement of polymorphisms on genes known to be associated with standard antimalarial drugs and parasite in vitro susceptibility to MB (cross-resistance). In this context, MB susceptibility was evaluated against 482 isolates of imported malaria from Africa by HRP2-based ELISA chemosusceptibility assay. A total of 12 genes involved in antimalarial drug resistance (Pfcrt, Pfdhfr, Pfmdr1, Pfmdr5, Pfmdr6, PfK13, Pfubq, Pfcarl, Pfugt, Pfact, Pfcoronin, and copy number of Pfpm2) were sequenced by Sanger method and quantitative PCR. On the Pfmdr1 gene, the mutation 86Y combined with 184F led to more susceptible isolates to MB (8.0 nM vs. 11.6 nM, p = 0.03). Concerning Pfmdr6, the isolates bearing 12 Asn repetitions were more susceptible to MB (4.6 nM vs. 11.6 nM, p = 0.005). None of the polymorphisms previously described as involved in antimalarial drug resistance was shown to be associated with reduced susceptibility to MB. Some genes (particularly PfK13, Pfugt, Pfact, Pfpm2) did not present enough genetic variability to draw conclusions about their involvement in reduced susceptibility to MB. None of the polymorphisms analyzed by multiple correspondence analysis (MCA) had an impact on the MB susceptibility of the samples successfully included in the analysis. It seems that there is no in vitro cross-resistance between MB and commonly used antimalarial drugs.
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Affiliation(s)
- Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Marie Gladys Robert
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Francis Tsombeng Foguim
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Nicolas Benoit
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Rémy Amalvict
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Marylin Madamet
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.G.); (O.D.); (M.G.R.); (F.T.F.); (N.B.); (R.A.); (I.F.); (J.M.); (M.M.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
- Correspondence:
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16
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Slater L, Betson M, Ashraf S, Sargison N, Chaudhry U. Current methods for the detection of antimalarial drug resistance in Plasmodium parasites infecting humans. Acta Trop 2021; 216:105828. [PMID: 33465353 DOI: 10.1016/j.actatropica.2021.105828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 12/19/2022]
Abstract
Malaria is the world's deadliest parasitic disease. Great progress has been made in the fight against malaria over the past two decades, but this has recently begun to plateau, in part due to the global development of antimalarial drug resistance. The ability to track drug resistance is necessary to achieve progress in treatment, disease surveillance and epidemiology, which has prompted the development of advanced diagnostic methods. These new methods provide unprecedented access to information that can help to guide public health policies. Development of new technologies increases the potential for high throughput and reduced costs of diagnostic tests; improving the accessibility of tools to investigate the forces driving disease dynamics and, ultimately, clinical outcomes for malaria patients and public health. This literature review provides a summary of the methods currently available for the detection of antimalarial drug resistance from the examination of patients' blood samples. While no single method is perfect for every application, many of the newly developed methods give promise for more reliable and efficient characterisation of Plasmodium resistance in a range of settings. By exploiting the strengths of the tools available, we can develop a deeper understanding of the evolutionary and spatiotemporal dynamics of this disease. This will translate into more effective disease control, better-informed policy, and more timely and successful treatment for malaria patients.
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17
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Kassegne K, Komi Koukoura K, Shen HM, Chen SB, Fu HT, Chen YQ, Zhou XN, Chen JH, Cheng Y. Genome-Wide Analysis of the Malaria Parasite Plasmodium falciparum Isolates From Togo Reveals Selective Signals in Immune Selection-Related Antigen Genes. Front Immunol 2020; 11:552698. [PMID: 33193320 PMCID: PMC7645038 DOI: 10.3389/fimmu.2020.552698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022] Open
Abstract
Malaria is a public health concern worldwide, and Togo has proven to be no exception. Effective approaches to provide information on biological insights for disease elimination are therefore a research priority. Local selection on malaria pathogens is due to multiple factors including host immunity. We undertook genome-wide analysis of sequence variation on a sample of 10 Plasmodium falciparum (Pf) clinical isolates from Togo to identify local-specific signals of selection. Paired-end short-read sequences were mapped and aligned onto > 95% of the 3D7 Pf reference genome sequence in high fold coverage. Data on 266 963 single nucleotide polymorphisms were obtained, with average nucleotide diversity π = 1.79 × 10−3. Both principal component and neighbor-joining tree analyses showed that the Togo parasites clustered according to their geographic (Africa) origin. In addition, the average genome-wide diversity of Pf from Togo was much higher than that from other African samples. Tajima’s D value of the Togo isolates was −0.56, suggesting evidence of directional selection and/or recent population expansion. Against this background, within-population analyses identifying loci of balancing and recent positive selections evidenced that host immunity has been the major selective agent. Importantly, 87 and 296 parasite antigen genes with Tajima’s D values > 1 and in the top 1% haplotype scores, respectively, include a significant representation of membrane proteins at the merozoite stage that invaded red blood cells (RBCs) and parasitized RBCs surface proteins that play roles in immunoevasion, adhesion, or rosetting. This is consistent with expectations that elevated signals of selection due to allele-specific acquired immunity are likely to operate on antigenic targets. Collectively, our data suggest a recent expansion of Pf population in Togo and evidence strong host immune selection on membrane/surface antigens reflected in signals of balancing/positive selection of important gene loci. Findings from this study provide a fundamental basis to engage studies for effective malaria control in Togo.
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Affiliation(s)
- Kokouvi Kassegne
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Komi Komi Koukoura
- Laboratoire des Sciences Biomédicales, Alimentaires et Santé Environnementale, Département des Analyses Biomédicales, Ecole Supérieure des Techniques Biologiques et Alimentaires, Université de Lomé, Lomé, Togo
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Hai-Tian Fu
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yong-Quan Chen
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yang Cheng
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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18
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Jankowska-Döllken M, Sanchez CP, Cyrklaff M, Lanzer M. Overexpression of the HECT ubiquitin ligase PfUT prolongs the intraerythrocytic cycle and reduces invasion efficiency of Plasmodium falciparum. Sci Rep 2019; 9:18333. [PMID: 31797898 PMCID: PMC6893019 DOI: 10.1038/s41598-019-54854-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/18/2019] [Indexed: 11/22/2022] Open
Abstract
The glms ribozyme system has been used as an amenable tool to conditionally control expression of genes of interest. It is generally assumed that insertion of the ribozyme sequence does not affect expression of the targeted gene in the absence of the inducer glucosamine-6-phosphate, although experimental support for this assumption is scarce. Here, we report the unexpected finding that integration of the glms ribozyme sequence in the 3′ untranslated region of a gene encoding a HECT E3 ubiquitin ligase, termed Plasmodium falciparum ubiquitin transferase (PfUT), increased steady state RNA and protein levels 2.5-fold in the human malaria parasite P. falciparum. Overexpression of pfut resulted in an S/M phase-associated lengthening of the parasite’s intraerythrocytic developmental cycle and a reduced merozoite invasion efficiency. The addition of glucosamine partially restored the wild type phenotype. Our study suggests a role of PfUT in controlling cell cycle progression and merozoite invasion. Our study further raises awareness regarding unexpected effects on gene expression when inserting the glms ribozyme sequence into a gene locus.
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Affiliation(s)
- Monika Jankowska-Döllken
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Cecilia P Sanchez
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Marek Cyrklaff
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
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19
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Zhao Y, Liu Z, Soe MT, Wang L, Soe TN, Wei H, Than A, Aung PL, Li Y, Zhang X, Hu Y, Wei H, Zhang Y, Burgess J, Siddiqui FA, Menezes L, Wang Q, Kyaw MP, Cao Y, Cui L. Genetic Variations Associated with Drug Resistance Markers in Asymptomatic Plasmodium falciparum Infections in Myanmar. Genes (Basel) 2019; 10:genes10090692. [PMID: 31505774 PMCID: PMC6770986 DOI: 10.3390/genes10090692] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/31/2019] [Accepted: 09/04/2019] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of drug resistance is a problem hindering malaria elimination in Southeast Asia. In this study, genetic variations in drug resistance markers of Plasmodium falciparum were determined in parasites from asymptomatic populations located in three geographically dispersed townships of Myanmar by PCR and sequencing. Mutations in dihydrofolate reductase (pfdhfr), dihydropteroate synthase (pfdhps), chloroquine resistance transporter (pfcrt), multidrug resistance protein 1 (pfmdr1), multidrug resistance-associated protein 1 (pfmrp1), and Kelch protein 13 (k13) were present in 92.3%, 97.6%, 84.0%, 98.8%, and 68.3% of the parasites, respectively. The pfcrt K76T, pfmdr1 N86Y, pfmdr1 I185K, and pfmrp1 I876V mutations were present in 82.7%, 2.5%, 87.5%, and 59.8% isolates, respectively. The most prevalent haplotypes for pfdhfr, pfdhps, pfcrt and pfmdr1 were 51I/59R/108N/164L, 436A/437G/540E/581A, 74I/75E/76T/220S/271E/326N/356T/371I, and 86N/130E/184Y/185K/1225V, respectively. In addition, 57 isolates had three different point mutations (K191T, F446I, and P574L) and three types of N-terminal insertions (N, NN, NNN) in the k13 gene. In total, 43 distinct haplotypes potentially associated with multidrug resistance were identified. These findings demonstrate a high prevalence of multidrug-resistant P. falciparum in asymptomatic infections from diverse townships in Myanmar, emphasizing the importance of targeting asymptomatic infections to prevent the spread of drug-resistant P.falciparum.
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Affiliation(s)
- Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Ziling Liu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Myat Thu Soe
- Myanmar Health Network Organization, Yangon 11211, Myanmar.
| | - Lin Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Than Naing Soe
- Department of Public Health, Ministry of Health and Sports, Nay Pyi Taw 15011, Myanmar.
| | - Huanping Wei
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Aye Than
- Myanmar Health Network Organization, Yangon 11211, Myanmar.
| | - Pyae Linn Aung
- Myanmar Health Network Organization, Yangon 11211, Myanmar.
| | - Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Xuexing Zhang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Haichao Wei
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Yangminghui Zhang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Jessica Burgess
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA.
| | - Faiza A Siddiqui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA.
| | - Lynette Menezes
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA.
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | | | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang 110122, China.
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA.
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20
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Apinjoh TO, Ouattara A, Titanji VPK, Djimde A, Amambua-Ngwa A. Genetic diversity and drug resistance surveillance of Plasmodium falciparum for malaria elimination: is there an ideal tool for resource-limited sub-Saharan Africa? Malar J 2019; 18:217. [PMID: 31242921 PMCID: PMC6595576 DOI: 10.1186/s12936-019-2844-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
The intensification of malaria control interventions has resulted in its global decline, but it remains a significant public health burden especially in sub-Saharan Africa (sSA). Knowledge on the parasite diversity, its transmission dynamics, mechanisms of adaptation to environmental and interventional pressures could help refine or develop new control and elimination strategies. Critical to this is the accurate assessment of the parasite’s genetic diversity and monitoring of genetic markers of anti-malarial resistance across all susceptible populations. Such wide molecular surveillance will require selected tools and approaches from a variety of ever evolving advancements in technology and the changing epidemiology of malaria. The choice of an effective approach for specific endemic settings remains challenging, particularly for countries in sSA with limited access to advanced technologies. This article examines the current strategies and tools for Plasmodium falciparum genetic diversity typing and resistance monitoring and proposes how the different tools could be employed in resource-poor settings. Advanced approaches enabling targeted deep sequencing is valued as a sensitive method for assessing drug resistance and parasite diversity but remains out of the reach of most laboratories in sSA due to the high cost of development and maintenance. It is, however, feasible to equip a limited number of laboratories as Centres of Excellence in Africa (CEA), which will receive and process samples from a network of peripheral laboratories in the continent. Cheaper, sensitive and portable real-time PCR methods can be used in peripheral laboratories to pre-screen and select samples for targeted deep sequence or genome wide analyses at these CEAs.
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Affiliation(s)
- Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Amed Ouattara
- School of Medicine, University of Maryland, College Park, Baltimore, USA
| | - Vincent P K Titanji
- Faculty of Science, Engineering and Technology, Cameroon Christian University, Bali, Cameroon
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
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21
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Genome-wide Approaches to Investigate Anthelmintic Resistance. Trends Parasitol 2019; 35:289-301. [DOI: 10.1016/j.pt.2019.01.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 01/09/2023]
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22
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Castillo AI, Nelson ADL, Lyons E. Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp. Genome Biol Evol 2019; 11:497-507. [PMID: 30689842 PMCID: PMC6385630 DOI: 10.1093/gbe/evz015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2019] [Indexed: 01/16/2023] Open
Abstract
Plasmodium parasites are valuable models to understand how nucleotide composition affects mutation, diversification, and adaptation. No other observed eukaryotes have undergone such large changes in genomic Guanine-Cytosine (GC) content as seen in the genus Plasmodium (∼30% within 35-40 Myr). Although mutational biases are known to influence GC content in the human-infective Plasmodium vivax and Plasmodium falciparum; no study has addressed how different gene functional classes contribute to genus-wide compositional changes, or if Plasmodium GC content variation is driven by natural selection. Here, we tested the hypothesis that certain gene processes and functions drive variation in global GC content between Plasmodium species. We performed a large-scale comparative genomic analysis using the genomes and predicted genes of 17 Plasmodium species encompassing a wide genomic GC content range. Genic GC content was sorted and divided into ten equally sized quantiles that were then assessed for functional enrichment classes. In agreement that selection on gene classes may drive genomic GC content, trans-membrane proteins were enriched within extreme GC content quantiles (Q1 and Q10). Specifically, variant surface antigens, which primarily interact with vertebrate immune systems, showed skewed GC content distributions compared with other trans-membrane proteins. Although a definitive causation linking GC content, expression, and positive selection within variant surface antigens from Plasmodium vivax, Plasmodium berghei, and Plasmodium falciparum could not be established, we found that regardless of genomic nucleotide composition, genic GC content and expression were positively correlated during trophozoite stages. Overall, these data suggest that, alongside mutational biases, functional protein classes drive Plasmodium GC content change.
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Affiliation(s)
- Andreina I Castillo
- School of Environmental Science, Policy, and Management, University of California, Berkeley
| | | | - Eric Lyons
- BIO5 Institute, School of Plant Sciences, University of Arizona
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23
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Mutations in Plasmodium falciparum actin-binding protein coronin confer reduced artemisinin susceptibility. Proc Natl Acad Sci U S A 2018; 115:12799-12804. [PMID: 30420498 PMCID: PMC6294886 DOI: 10.1073/pnas.1812317115] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The spread of Plasmodium falciparum with reduced susceptibility to artemisinin (ART) in Southeast Asia threatens global malaria control. Most failures of ART treatment are attributed to mutations in the pfkelch13 locus acting through an unclear mechanism. The role of pfkelch13 in reducing ART susceptibility was first identified in an in vitro selection experiment. We carried out a similar in vitro selection and discovered mutations in a different gene that reduce susceptibility to ART. The gene encodes PfCoronin, a conserved protein that in other organisms binds with actin to enhance cytoskeletal plasticity or is involved in vesicular transport. PfCoronin and PfKelch13 share structural similarities, and this finding may yield insights into the molecular mechanisms of ART resistance. Drug resistance is an obstacle to global malaria control, as evidenced by the recent emergence and rapid spread of delayed artemisinin (ART) clearance by mutant forms of the PfKelch13 protein in Southeast Asia. Identifying genetic determinants of ART resistance in African-derived parasites is important for surveillance and for understanding the mechanism of resistance. In this study, we carried out long-term in vitro selection of two recently isolated West African parasites (from Pikine and Thiès, Senegal) with increasing concentrations of dihydroartemisinin (DHA), the biologically active form of ART, over a 4-y period. We isolated two parasite clones, one from each original isolate, that exhibited enhanced survival to DHA in the ring-stage survival assay. Whole-genome sequence analysis identified 10 mutations in seven different genes. We chose to focus on the gene encoding PfCoronin, a member of the WD40-propeller domain protein family, because mutations in this gene occurred in both independent selections, and the protein shares the β-propeller motif with PfKelch13 protein. For functional validation, when pfcoronin mutations were introduced into the parental parasites by CRISPR/Cas9-mediated gene editing, these mutations were sufficient to reduce ART susceptibility in the parental lines. The discovery of a second gene for ART resistance may yield insights into the molecular mechanisms of resistance. It also suggests that pfcoronin mutants could emerge as a nonkelch13 type of resistance to ART in natural settings.
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24
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Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens. PLoS Genet 2018; 14:e1007279. [PMID: 29791438 PMCID: PMC5988311 DOI: 10.1371/journal.pgen.1007279] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 06/05/2018] [Accepted: 02/26/2018] [Indexed: 12/30/2022] Open
Abstract
Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized in analysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections. Using the inferred IBD status at genomic locations, we have also developed a novel statistic for identifying loci under positive selection and propose relatedness networks as a means of exploring shared haplotypes within populations. We evaluate the performance of our methodologies for detecting IBD and selection, including comparisons with existing tools, then perform an exploratory analysis of whole genome sequencing data from a global Plasmodium falciparum dataset of more than 2500 genomes. This analysis identifies Southeast Asia as having many highly related isolates, possibly as a result of both reduced transmission from intensified control efforts and population bottlenecks following the emergence of antimalarial drug resistance. Many signals of selection are also identified, most of which overlap genes that are known to be associated with drug resistance, in addition to two novel signals observed in multiple countries that have yet to be explored in detail. Additionally, we investigate relatedness networks over the selected loci and determine that one of these sweeps has spread between continents while the other has arisen independently in different countries. IBD analysis of microorganisms using isoRelate can be used for exploring population structure, positive selection and haplotype distributions, and will be a valuable tool for monitoring disease control and elimination efforts of many diseases. There are growing concerns over the emergence of antimicrobial drug resistance, which threatens the efficacy of treatments for infectious diseases such as malaria. As such, it is important to understand the dynamics of resistance by investigating population structure, natural selection and disease transmission in microorganisms. The study of disease dynamics has been hampered by the lack of suitable statistical models for analysis of isolates containing multiple infections. We introduce a statistical model that uses population genomic data to identify genomic regions (loci) that are inherited from a common ancestor, in the presence of multiple infections. We demonstrate its potential for biological discovery using a global Plasmodium falciparum dataset. We identify low genetic diversity in isolates from Southeast Asia, possibly from clonal expansion following intensified control efforts after the emergence of artemisinin resistance. We also identify loci under positive selection, most of which contain genes that have been associated with antimalarial drug resistance. We discover two loci under strong selection in multiple countries throughout Southeast Asia and Africa where the selection pressure is currently unknown. We find that the selection pressure at one of these loci has originated from gene flow, while the other loci has originated from multiple independent events.
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25
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Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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26
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Gendrot M, Foguim FT, Robert MG, Amalvict R, Mosnier J, Benoit N, Madamet M, Pradines B. The D113N mutation in the RING E3 ubiquitin protein ligase gene is not associated with ex vivo susceptibility to common anti-malarial drugs in African Plasmodium falciparum isolates. Malar J 2018. [PMID: 29530046 PMCID: PMC5848522 DOI: 10.1186/s12936-018-2252-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium falciparum resistance to artemisinin-based combination therapy has emerged and spread in Southeast Asia. In areas where artemisinin resistance is emerging, the efficacy of combination is now based on partner drugs. In this context, the identification of novel markers of resistance is essential to monitor the emergence and spread of resistance to these partner drugs. The ubiquitylation pathway could be a possible target for anti-malarial compounds and might be involved in resistance. Polymorphisms in the E3 ubiquitin-protein ligase (PF3D7_0627300) gene could be associated with decreased in vitro susceptibility to anti-malarial drugs. METHODS Plasmodium falciparum isolates were collected from patients hospitalized in France with imported malaria from a malaria-endemic country from January 2015 to December 2016 and, more particularly, from African French-speaking countries. In total, 215 isolates were successfully sequenced for the E3 ubiquitin-protein ligase gene and assessed for ex vivo susceptibility to anti-malarial drugs. RESULTS The D113N mutation in the RING E3 ubiquitin-protein ligase gene was present in 147 out of the 215 samples (68.4%). The IC50 values for the ten anti-malarial drugs were not significantly different between the wild-type and mutant parasites (p values between 0.225 and 0.933). There was no significant difference in terms of the percentage of parasites with decreased susceptibility between the D113 wild-type and the 133N mutated P. falciparum strains (p values between 0.541 and 1). CONCLUSION The present data confirmed the absence of the association between polymorphisms in the RING E3 ubiquitin-protein ligase gene and the ex vivo susceptibility to common anti-malarial drugs in African P. falciparum isolates.
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Affiliation(s)
- Mathieu Gendrot
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Francis Tsombeng Foguim
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Marie Gladys Robert
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Rémy Amalvict
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,Centre national de référence du Paludisme, Institut hospitalo-universitaire (IHU) Méditerranée Infection, Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,Centre national de référence du Paludisme, Institut hospitalo-universitaire (IHU) Méditerranée Infection, Marseille, France
| | - Nicolas Benoit
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,Centre national de référence du Paludisme, Institut hospitalo-universitaire (IHU) Méditerranée Infection, Marseille, France
| | - Marylin Madamet
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,Centre national de référence du Paludisme, Institut hospitalo-universitaire (IHU) Méditerranée Infection, Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et entomologie, Département des maladies infectieuses, Institut de recherche biomédicale des armées, Institut hospitalo-universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France. .,Centre national de référence du Paludisme, Institut hospitalo-universitaire (IHU) Méditerranée Infection, Marseille, France.
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27
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Nilsson Bark SK, Ahmad R, Dantzler K, Lukens AK, De Niz M, Szucs MJ, Jin X, Cotton J, Hoffmann D, Bric-Furlong E, Oomen R, Parrington M, Milner D, Neafsey DE, Carr SA, Wirth DF, Marti M. Quantitative Proteomic Profiling Reveals Novel Plasmodium falciparum Surface Antigens and Possible Vaccine Candidates. Mol Cell Proteomics 2017; 17:43-60. [PMID: 29162636 DOI: 10.1074/mcp.ra117.000076] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/20/2017] [Indexed: 12/30/2022] Open
Abstract
Despite recent efforts toward control and elimination, malaria remains a major public health problem worldwide. Plasmodium falciparum resistance against artemisinin, used in front line combination drugs, is on the rise, and the only approved vaccine shows limited efficacy. Combinations of novel and tailored drug and vaccine interventions are required to maintain the momentum of the current malaria elimination program. Current evidence suggests that strain-transcendent protection against malaria infection can be achieved using whole organism vaccination or with a polyvalent vaccine covering multiple antigens or epitopes. These approaches have been successfully applied to the human-infective sporozoite stage. Both systemic and tissue-specific pathology during infection with the human malaria parasite P. falciparum is caused by asexual blood stages. Tissue tropism and vascular sequestration are the result of specific binding interactions between antigens on the parasite-infected red blood cell (pRBC) surface and endothelial receptors. The major surface antigen and parasite ligand binding to endothelial receptors, PfEMP1 is encoded by about 60 variants per genome and shows high sequence diversity across strains. Apart from PfEMP1 and three additional variant surface antigen families RIFIN, STEVOR, and SURFIN, systematic analysis of the infected red blood cell surface is lacking. Here we present the most comprehensive proteomic investigation of the parasitized red blood cell surface so far. Apart from the known variant surface antigens, we identified a set of putative single copy surface antigens with low sequence diversity, several of which are validated in a series of complementary experiments. Further functional and immunological investigation is underway to test these novel P. falciparum blood stage proteins as possible vaccine candidates.
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Affiliation(s)
- Sandra K Nilsson Bark
- From the ‡Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Rushdy Ahmad
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Kathleen Dantzler
- From the ‡Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115.,¶Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Amanda K Lukens
- From the ‡Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115.,§The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Mariana De Niz
- ¶Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Matthew J Szucs
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Xiaoying Jin
- ‖Sanofi Biopharmaceutics Development, Framingham, Massachusetts 02142
| | - Joanne Cotton
- ‖Sanofi Biopharmaceutics Development, Framingham, Massachusetts 02142
| | | | | | - Ray Oomen
- **Sanofi Pasteur Biologics, Cambridge, Massachusetts 02139
| | | | - Dan Milner
- From the ‡Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115.,‡‡Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Daniel E Neafsey
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Steven A Carr
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Dyann F Wirth
- From the ‡Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115.,§The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Matthias Marti
- From the ‡Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115; .,¶Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow G12 8TA, UK
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Seck MC, Thwing J, Fall FB, Gomis JF, Deme A, Ndiaye YD, Daniels R, Volkman SK, Ndiop M, Ba M, Ndiaye D. Malaria prevalence, prevention and treatment seeking practices among nomadic pastoralists in northern Senegal. Malar J 2017; 16:413. [PMID: 29029619 PMCID: PMC5640937 DOI: 10.1186/s12936-017-2055-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/05/2017] [Indexed: 12/26/2022] Open
Abstract
Background Malaria transmission in Senegal is highly stratified, from low in the dry north to moderately high in the moist south. In northern Senegal, along the Senegal River Valley and in the Ferlo semi-desert region, annual incidence is less than five cases per 1000 inhabitants. Many nomadic pastoralists have permanent dwellings in the Ferlo Desert and Senegal River Valley, but spend dry season in the south with their herds, returning north when the rains start, leading to a concern that this population could contribute to ongoing transmission in the north. Methods A modified snowball sampling survey was conducted at six sites in northern Senegal to determine the malaria prevention and treatment seeking practices and parasite prevalence among nomadic pastoralists in the Senegal River Valley and the Ferlo Desert. Nomadic pastoralists aged 6 months and older were surveyed during September and October 2014, and data regarding demographics, access to care and preventive measures were collected. Parasite infection was detected using rapid diagnostic tests (RDTs), microscopy (thin and thick smears) and polymerase chain reaction (PCR). Molecular barcodes were determined by high resolution melting (HRM). Results Of 1800 participants, 61% were male. Sixty-four percent had at least one bed net in the household, and 53% reported using a net the night before. Only 29% had received a net from a mass distribution campaign. Of the 8% (142) who reported having had fever in the last month, 55% sought care, 20% of whom received a diagnostic test, one-third of which (n = 5) were reported to be positive. Parasite prevalence was 0.44% by thick smear and 0.50% by PCR. None of the molecular barcodes identified among the nomadic pastoralists had been previously identified in Senegal. Conclusions While access to and utilization of malaria control interventions among nomadic pastoralists was lower than the general population, parasite prevalence was lower than expected and sheds doubt on the perception that they are a source of ongoing transmission in the north. The National Malaria Control Program is making efforts to improve access to malaria prevention and case management for nomadic populations. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-2055-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mame Cheikh Seck
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, U.S. Centers for Disease Control and Prevention, President's Malaria Initiative, Atlanta, GA, USA.
| | - Fatou Ba Fall
- Senegal National Malaria Control Program, Dakar, Senegal
| | - Jules Francois Gomis
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Awa Deme
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Yaye Die Ndiaye
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Rachel Daniels
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | | | - Medoune Ndiop
- Senegal National Malaria Control Program, Dakar, Senegal
| | - Mady Ba
- Senegal National Malaria Control Program, Dakar, Senegal
| | - Daouda Ndiaye
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
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QnAs with Pardis Sabeti. Proc Natl Acad Sci U S A 2017; 114:9757-9758. [DOI: 10.1073/pnas.1714015114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Doyle SR, Bourguinat C, Nana-Djeunga HC, Kengne-Ouafo JA, Pion SDS, Bopda J, Kamgno J, Wanji S, Che H, Kuesel AC, Walker M, Basáñez MG, Boakye DA, Osei-Atweneboana MY, Boussinesq M, Prichard RK, Grant WN. Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity. PLoS Negl Trop Dis 2017; 11:e0005816. [PMID: 28746337 PMCID: PMC5546710 DOI: 10.1371/journal.pntd.0005816] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/07/2017] [Accepted: 07/19/2017] [Indexed: 12/30/2022] Open
Abstract
Background Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana—exposed to more than a decade of regular ivermectin treatment—have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread. Methodology/Principal findings Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR. Conclusions/Significance This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations. Onchocerciasis is a human parasitic disease endemic across large areas of Sub-Saharan Africa, where more than 99% of the estimated 100 million people globally at-risk live. The microfilarial stage of Onchocerca volvulus causes pathologies ranging from mild itching to visual impairment and ultimately, irreversible blindness. Mass administration of ivermectin kills microfilariae and has an anti-fecundity effect on adult worms by temporarily inhibiting the development in utero and/or release into the skin of new microfilariae, thereby reducing morbidity and transmission. Phenotypic and genetic changes in some parasite populations that have undergone multiple ivermectin treatments in Cameroon and Ghana have raised concern that sub-optimal response to ivermectin's anti-fecundity effect may increase in frequency, reducing the impact of ivermectin-based control measures. We used next generation sequencing of small pools of parasites to define genome-wide genetic differences between phenotypically characterised good and sub-optimal responder parasites from Cameroon and Ghana, and identified multiple regions of the genome that differentiated the response types. These regions were largely different between parasites from these two countries but revealed common molecular pathways that might be involved in determining the extent of response to ivermectin's anti-fecundity effect. These data reveal a more complex than previously described pattern of genetic diversity among O. volvulus populations that differ in their geography and response to ivermectin treatment.
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Affiliation(s)
- Stephen R. Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- * E-mail: (SRD); (RKP); (WNG)
| | - Catherine Bourguinat
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
| | - Hugues C. Nana-Djeunga
- Parasitology and Ecology Laboratory, Department of Animal Biology and Physiology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
| | - Jonas A. Kengne-Ouafo
- Research Foundation in Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Sébastien D. S. Pion
- Institut de Recherche pour le Développement (IRD), IRD UMI 233 TransVIHMI – Université Montpellier – INSERM U1175, Montpellier, France
| | - Jean Bopda
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Joseph Kamgno
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Samuel Wanji
- Research Foundation in Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Hua Che
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
| | - Annette C. Kuesel
- UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (WHO/TDR), World Health Organization, Geneva, Switzerland
| | - Martin Walker
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, United Kingdom
| | - Maria-Gloria Basáñez
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, United Kingdom
| | - Daniel A. Boakye
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mike Y. Osei-Atweneboana
- Department of Environmental Biology and Health Water Research Institute, Council for Scientific and Industrial Research (CSIR), Accra, Ghana
| | - Michel Boussinesq
- Institut de Recherche pour le Développement (IRD), IRD UMI 233 TransVIHMI – Université Montpellier – INSERM U1175, Montpellier, France
| | - Roger K. Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
- * E-mail: (SRD); (RKP); (WNG)
| | - Warwick N. Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
- * E-mail: (SRD); (RKP); (WNG)
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Oyebola KM, Idowu ET, Olukosi YA, Awolola TS, Amambua-Ngwa A. Pooled-DNA sequencing identifies genomic regions of selection in Nigerian isolates of Plasmodium falciparum. Parasit Vectors 2017; 10:320. [PMID: 28662682 PMCID: PMC5492182 DOI: 10.1186/s13071-017-2260-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/22/2017] [Indexed: 01/22/2023] Open
Abstract
Background The burden of falciparum malaria is especially high in sub-Saharan Africa. Differences in pressure from host immunity and antimalarial drugs lead to adaptive changes responsible for high level of genetic variations within and between the parasite populations. Population-specific genetic studies to survey for genes under positive or balancing selection resulting from drug pressure or host immunity will allow for refinement of interventions. Methods We performed a pooled sequencing (pool-seq) of the genomes of 100 Plasmodium falciparum isolates from Nigeria. We explored allele-frequency based neutrality test (Tajima’s D) and integrated haplotype score (iHS) to identify genes under selection. Results Fourteen shared iHS regions that had at least 2 SNPs with a score > 2.5 were identified. These regions code for genes that were likely to have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (CRT) on chromosome 7 and the multidrug resistance 1 (MDR1) on chromosome 5. There was a weak signature of selection in the dihydrofolate reductase (DHFR) gene on chromosome 4 and MDR5 genes on chromosome 13, with only 2 and 3 SNPs respectively identified within the iHS window. We observed strong selection pressure attributable to continued chloroquine and sulfadoxine-pyrimethamine use despite their official proscription for the treatment of uncomplicated malaria. There was also a major selective sweep on chromosome 6 which had 32 SNPs within the shared iHS region. Tajima’s D of circumsporozoite protein (CSP), erythrocyte-binding antigen (EBA-175), merozoite surface proteins - MSP3 and MSP7, merozoite surface protein duffy binding-like (MSPDBL2) and serine repeat antigen (SERA-5) were 1.38, 1.29, 0.73, 0.84 and 0.21, respectively. Conclusion We have demonstrated the use of pool-seq to understand genomic patterns of selection and variability in P. falciparum from Nigeria, which bears the highest burden of infections. This investigation identified known genomic signatures of selection from drug pressure and host immunity. This is evidence that P. falciparum populations explore common adaptive strategies that can be targeted for the development of new interventions. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2260-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kolapo M Oyebola
- Medical Research Council Unit The Gambia, Atlantic Road, Fajara, Gambia.,Parasitology and Bioinformatics, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria.,Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Emmanuel T Idowu
- Parasitology and Bioinformatics, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
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Shen HM, Chen SB, Wang Y, Xu B, Abe EM, Chen JH. Genome-wide scans for the identification of Plasmodium vivax genes under positive selection. Malar J 2017; 16:238. [PMID: 28587615 PMCID: PMC5461743 DOI: 10.1186/s12936-017-1882-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current trend of Plasmodium vivax cases imported from Southeast Asia into China has sharply increased recently, especially from the China-Myanmar border (CMB) area. High recombination rates of P. vivax populations associated with varied transmission intensity might cause distinct local selective pressures. The information on the genetic variability of P. vivax in this area is scant. Hence, this study assessed the genetic diversity of P. vivax genome sequence in CMB area and aimed to provide information on the positive selection of new gene loci. RESULTS This study reports a genome-wide survey of P. vivax in CMB area, using blood samples from local patients to identify population-specific selective processes. The result showed that considerable genetic diversity and mean pair-wise divergence among the sequenced P. vivax isolates were higher in some important gene families. Using the standardized integrated haplotype score (|iHS|) for all SNPs in chromosomal regions with SNPs above the top 1% distribution, it was observed that the top score locus involved 356 genes and most of them are associated with red blood cell invasion and immune evasion. The XP-EHH test was also applied and some important genes associated with anti-malarial drug resistance were observed in high positive scores list. This result suggests that P. vivax in CMB area is facing more pressure to survive than any other region and this has led to the strong positive selection of genes that are associated with host-parasite interactions. CONCLUSIONS This study suggests that greater genetic diversity in P. vivax from CMB area and positive selection signals in invasion and drug resistance genes are consistent with the history of drug use during malaria elimination programme in CMB area. Furthermore, this result also demonstrates that haplotype-based detecting selection can assist the genome-wide methods to identify the determinants of P. vivax diversity.
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Affiliation(s)
- Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Yue Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China.,Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, People's Republic of China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Eniola Michael Abe
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China.
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Cerqueira GC, Cheeseman IH, Schaffner SF, Nair S, McDew-White M, Phyo AP, Ashley EA, Melnikov A, Rogov P, Birren BW, Nosten F, Anderson TJC, Neafsey DE. Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance. Genome Biol 2017; 18:78. [PMID: 28454557 PMCID: PMC5410087 DOI: 10.1186/s13059-017-1204-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
Background Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutations in the kelch13 gene have been implicated in this resistance. We used longitudinal genomic surveillance to detect signals in kelch13 and other loci that contribute to artemisinin or partner drug resistance. We retrospectively sequenced the genomes of 194 P. falciparum isolates from five sites in Northwest Thailand, over the period of a rapid increase in the emergence of artemisinin resistance (2001–2014). Results We evaluate statistical metrics for temporal change in the frequency of individual SNPs, assuming that SNPs associated with resistance increase in frequency over this period. After Kelch13-C580Y, the strongest temporal change is seen at a SNP in phosphatidylinositol 4-kinase, which is involved in a pathway recently implicated in artemisinin resistance. Furthermore, other loci exhibit strong temporal signatures which warrant further investigation for involvement in artemisinin resistance evolution. Through genome-wide association analysis we identify a variant in a kelch domain-containing gene on chromosome 10 that may epistatically modulate artemisinin resistance. Conclusions This analysis demonstrates the potential of a longitudinal genomic surveillance approach to detect resistance-associated gene loci to improve our mechanistic understanding of how resistance develops. Evidence for additional genomic regions outside of the kelch13 locus associated with artemisinin-resistant parasites may yield new molecular markers for resistance surveillance, which may be useful in efforts to reduce the emergence or spread of artemisinin resistance in African parasite populations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1204-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Ian H Cheeseman
- Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | | | - Shalini Nair
- Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | | | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol University, Mae Sot, Thailand
| | - Elizabeth A Ashley
- Shoklo Malaria Research Unit, Mahidol University, Mae Sot, Thailand.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Peter Rogov
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol University, Mae Sot, Thailand.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome Biol 2017; 18:71. [PMID: 28424085 PMCID: PMC5395877 DOI: 10.1186/s13059-017-1196-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/21/2017] [Indexed: 12/22/2022] Open
Abstract
Background Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics. Results By combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance. Conclusions Our findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1196-0) contains supplementary material, which is available to authorized users.
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Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia. Proc Natl Acad Sci U S A 2016; 113:E8096-E8105. [PMID: 27911780 DOI: 10.1073/pnas.1608828113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cambodia, in which both Plasmodium vivax and Plasmodium falciparum are endemic, has been the focus of numerous malaria-control interventions, resulting in a marked decline in overall malaria incidence. Despite this decline, the number of P vivax cases has actually increased. To understand better the factors underlying this resilience, we compared the genetic responses of the two species to recent selective pressures. We sequenced and studied the genomes of 70 P vivax and 80 P falciparum isolates collected between 2009 and 2013. We found that although P falciparum has undergone population fracturing, the coendemic P vivax population has grown undisrupted, resulting in a larger effective population size, no discernable population structure, and frequent multiclonal infections. Signatures of selection suggest recent, species-specific evolutionary differences. Particularly, in contrast to P falciparum, P vivax transcription factors, chromatin modifiers, and histone deacetylases have undergone strong directional selection, including a particularly strong selective sweep at an AP2 transcription factor. Together, our findings point to different population-level adaptive mechanisms used by P vivax and P falciparum parasites. Although population substructuring in P falciparum has resulted in clonal outgrowths of resistant parasites, P vivax may use a nuanced transcriptional regulatory approach to population maintenance, enabling it to preserve a larger, more diverse population better suited to facing selective threats. We conclude that transcriptional control may underlie P vivax's resilience to malaria control measures. Novel strategies to target such processes are likely required to eradicate P vivax and achieve malaria elimination.
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Auburn S, Barry AE. Dissecting malaria biology and epidemiology using population genetics and genomics. Int J Parasitol 2016; 47:77-85. [PMID: 27825828 DOI: 10.1016/j.ijpara.2016.08.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
Abstract
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia.
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Goswami AM. Computational analysis, structural modeling and ligand binding site prediction of Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate synthase. Comput Biol Chem 2016; 66:1-10. [PMID: 27842226 DOI: 10.1016/j.compbiolchem.2016.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 11/27/2022]
Abstract
Malaria remains one of the most serious infectious diseases in the world. There are five human species of the Plasmodium genus, of which Plasmodium falciparum is the most virulent and responsible for the vast majority of malaria related deaths. The unique biochemical processes that exist in Plasmodium falciparum provide a useful way to develop novel inhibitors. One such biochemical pathway is the methyl erythritol phosphate pathway (MEP), required to synthesize isoprenoid precursors. In the present study, a detailed computational analysis has been performed for 1-deoxy-d-xylulose-5-phosphate synthase, a key enzyme in MEP. The protein is found to be stable and residues from 825 to 971 are highly conserved across species. The homology model of the enzyme is developed using three web-based servers and Modeller software. It has twelve disordered regions indicating its druggability. Virtual screening of ZINC database identifies ten potential compounds in thiamine diphosphate binding region of the enzyme.
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Affiliation(s)
- Achintya Mohan Goswami
- Department of Physiology, Krishnagar Govt. College, Krishnagar, Nadia, West Bengal, India.
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Volkman SK, Herman J, Lukens AK, Hartl DL. Genome-Wide Association Studies of Drug-Resistance Determinants. Trends Parasitol 2016; 33:214-230. [PMID: 28179098 DOI: 10.1016/j.pt.2016.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/26/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
Abstract
Population genetic strategies that leverage association, selection, and linkage have identified drug-resistant loci. However, challenges and limitations persist in identifying drug-resistance loci in malaria. In this review we discuss the genetic basis of drug resistance and the use of genome-wide association studies, complemented by selection and linkage studies, to identify and understand mechanisms of drug resistance and response. We also discuss the implications of nongenetic mechanisms of drug resistance recently reported in the literature, and present models of the interplay between nongenetic and genetic processes that contribute to the emergence of drug resistance. Throughout, we examine artemisinin resistance as an example to emphasize challenges in identifying phenotypes suitable for population genetic studies as well as complications due to multiple-factor drug resistance.
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Affiliation(s)
- Sarah K Volkman
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA; Simmons College, School of Nursing and Health Science, Boston, MA, USA.
| | - Jonathan Herman
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Amanda K Lukens
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA
| | - Daniel L Hartl
- The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA; Harvard University, Organismic and Evolutionary Biology, Cambridge, MA, USA
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Amambua-Ngwa A, Danso B, Worwui A, Ceesay S, Davies N, Jeffries D, D'Alessandro U, Conway D. Exceptionally long-range haplotypes in Plasmodium falciparum chromosome 6 maintained in an endemic African population. Malar J 2016; 15:515. [PMID: 27769292 PMCID: PMC5073846 DOI: 10.1186/s12936-016-1560-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous genome-wide analyses of single nucleotide variation in Plasmodium falciparum identified evidence of an extended haplotype region on chromosome 6 in West Africa, suggesting recent positive selection. Such a pattern is not seen in samples from East Africa or South East Asia, so it could be marking a selective process specific to West Africa. Analyses of the haplotype structure in samples taken at different times could give clues to possible causes of selection. METHODS This study investigates chromosome 6 extended haplotypes in The Gambia by analysing alleles at multiple microsatellite loci using genome sequence data previously obtained from clinical isolates collected in 2008, followed by genotyping of 13 loci in 439 isolates from 1984, 1991, 2008 and 2014. Temporal changes in haplotype structure and frequencies were determined. RESULTS A region of high linkage disequilibrium spanning over 170 kilobases (kb) was identified with both NGS and laboratory determined microsatellite alleles. Multiple long haplotypes were found in all temporal populations from The Gambia. Two of the haplotypes were detected in samples from 1984 and 1991. The frequency of long-range haplotypes increased in 2008 and 2014 populations. There was higher Fst between older and more recent populations at loci in proximity to genes involved in drug metabolism pathways. CONCLUSIONS The occurrence of several long haplotypes at intermediate frequencies suggests an unusual mode of selection in chromosome 6, possibly combined with recombination suppression on specific haplotypes. Such selection apparently occurred before the emergence of known anti-malarial drug resistance alleles, and could be due to effects of other drugs or unknown processes that have long been operating in this endemic region.
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Affiliation(s)
- Alfred Amambua-Ngwa
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia.
| | - Bakary Danso
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Sukai Ceesay
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Nwakanma Davies
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia.,London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - David Conway
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
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Genome-wide association analysis identifies genetic loci associated with resistance to multiple antimalarials in Plasmodium falciparum from China-Myanmar border. Sci Rep 2016; 6:33891. [PMID: 27694982 PMCID: PMC5046179 DOI: 10.1038/srep33891] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/05/2016] [Indexed: 12/02/2022] Open
Abstract
Drug resistance has emerged as one of the greatest challenges facing malaria control. The recent emergence of resistance to artemisinin (ART) and its partner drugs in ART-based combination therapies (ACT) is threatening the efficacy of this front-line regimen for treating Plasmodium falciparum parasites. Thus, an understanding of the molecular mechanisms that underlie the resistance to ART and the partner drugs has become a high priority for resistance containment and malaria management. Using genome-wide association studies, we investigated the associations of genome-wide single nucleotide polymorphisms with in vitro sensitivities to 10 commonly used antimalarial drugs in 94 P. falciparum isolates from the China-Myanmar border area, a region with the longest history of ART usage. We identified several loci associated with various drugs, including those containing pfcrt and pfdhfr. Of particular interest is a locus on chromosome 10 containing the autophagy-related protein 18 (ATG18) associated with decreased sensitivities to dihydroartemisinin, artemether and piperaquine – an ACT partner drug in this area. ATG18 is a phosphatidylinositol-3-phosphate binding protein essential for autophagy and recently identified as a potential ART target. Further investigations on the ATG18 and genes at the chromosome 10 locus may provide an important lead for a connection between ART resistance and autophagy.
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Chang HH, Childs LM, Buckee CO. Variation in infection length and superinfection enhance selection efficiency in the human malaria parasite. Sci Rep 2016; 6:26370. [PMID: 27193195 PMCID: PMC4872237 DOI: 10.1038/srep26370] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/28/2016] [Indexed: 01/08/2023] Open
Abstract
The capacity for adaptation is central to the evolutionary success of the human malaria parasite Plasmodium falciparum. Malaria epidemiology is characterized by the circulation of multiple, genetically diverse parasite clones, frequent superinfection, and highly variable infection lengths, a large number of which are chronic and asymptomatic. The impact of these characteristics on the evolution of the parasite is largely unknown, however, hampering our understanding of the impact of interventions and the emergence of drug resistance. In particular, standard population genetic frameworks do not accommodate variation in infection length or superinfection. Here, we develop a population genetic model of malaria including these variations, and show that these aspects of malaria infection dynamics enhance both the probability and speed of fixation for beneficial alleles in complex and non-intuitive ways. We find that populations containing a mixture of short- and long-lived infections promote selection efficiency. Interestingly, this increase in selection efficiency occurs even when only a small fraction of the infections are chronic, suggesting that selection can occur efficiently in areas of low transmission intensity, providing a hypothesis for the repeated emergence of drug resistance in the low transmission setting of Southeast Asia.
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Affiliation(s)
- Hsiao-Han Chang
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lauren M Childs
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Absence of Association between Polymorphisms in the RING E3 Ubiquitin Protein Ligase Gene and Ex Vivo Susceptibility to Conventional Antimalarial Drugs in Plasmodium falciparum Isolates from Dakar, Senegal. Antimicrob Agents Chemother 2016; 60:5010-3. [PMID: 27185795 DOI: 10.1128/aac.03105-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 05/08/2016] [Indexed: 11/20/2022] Open
Abstract
The RING E3 ubiquitin protein ligase is crucial for facilitating the transfer of ubiquitin. The only polymorphism identified in the E3 ubiquitin protein ligase gene was the D113N mutation (62.5%) but was not significantly associated with the 50% inhibitory concentration (IC50) of conventional antimalarial drugs. However, some mutated isolates (D113N) present a trend of reduced susceptibility to piperaquine (P = 0.0938). To evaluate the association of D113N polymorphism with susceptibility to antimalarials, more isolates are necessary.
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43
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Gunawardena S, Karunaweera ND. Advances in genetics and genomics: use and limitations in achieving malaria elimination goals. Pathog Glob Health 2016; 109:123-41. [PMID: 25943157 DOI: 10.1179/2047773215y.0000000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Success of the global research agenda towards eradication of malaria will depend on the development of new tools, including drugs, vaccines, insecticides and diagnostics. Genetic and genomic information now available for the malaria parasites, their mosquito vectors and human host, can be harnessed to both develop these tools and monitor their effectiveness. Here we review and provide specific examples of current technological advances and how these genetic and genomic tools have increased our knowledge of host, parasite and vector biology in relation to malaria elimination and in turn enhanced the potential to reach that goal. We then discuss limitations of these tools and future prospects for the successful achievement of global malaria elimination goals.
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Herman JD, Pepper LR, Cortese JF, Estiu G, Galinsky K, Zuzarte-Luis V, Derbyshire ER, Ribacke U, Lukens AK, Santos SA, Patel V, Clish CB, Sullivan WJ, Zhou H, Bopp SE, Schimmel P, Lindquist S, Clardy J, Mota MM, Keller TL, Whitman M, Wiest O, Wirth DF, Mazitschek R. The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs. Sci Transl Med 2016; 7:288ra77. [PMID: 25995223 DOI: 10.1126/scitranslmed.aaa3575] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The emergence of drug resistance is a major limitation of current antimalarials. The discovery of new druggable targets and pathways including those that are critical for multiple life cycle stages of the malaria parasite is a major goal for developing next-generation antimalarial drugs. Using an integrated chemogenomics approach that combined drug resistance selection, whole-genome sequencing, and an orthogonal yeast model, we demonstrate that the cytoplasmic prolyl-tRNA (transfer RNA) synthetase (PfcPRS) of the malaria parasite Plasmodium falciparum is a biochemical and functional target of febrifugine and its synthetic derivative halofuginone. Febrifugine is the active principle of a traditional Chinese herbal remedy for malaria. We show that treatment with febrifugine derivatives activated the amino acid starvation response in both P. falciparum and a transgenic yeast strain expressing PfcPRS. We further demonstrate in the Plasmodium berghei mouse model of malaria that halofuginol, a new halofuginone analog that we developed, is active against both liver and asexual blood stages of the malaria parasite. Halofuginol, unlike halofuginone and febrifugine, is well tolerated at efficacious doses and represents a promising lead for the development of dual-stage next-generation antimalarials.
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Affiliation(s)
- Jonathan D Herman
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Biological and Biomedical Sciences, Boston, MA 02115, USA. Harvard/Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Boston, MA 02115, USA. Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren R Pepper
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Joseph F Cortese
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA
| | - Guillermina Estiu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Kevin Galinsky
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA
| | - Vanessa Zuzarte-Luis
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa,1649-028 Lisbon, Portugal
| | - Emily R Derbyshire
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ulf Ribacke
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amanda K Lukens
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sofia A Santos
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA. Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Professor Gama Pinto, Lisbon 1640-003, Portugal
| | - Vishal Patel
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Clary B Clish
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA
| | - William J Sullivan
- Departments of Pharmacology and Toxicology and Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Huihao Zhou
- Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Selina E Bopp
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Paul Schimmel
- Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. The Scripps Research Institute, Florida, Jupiter, FL 33458, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Jon Clardy
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Maria M Mota
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa,1649-028 Lisbon, Portugal
| | - Tracy L Keller
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA. School of Chemical Biology and Biotechnology, Laboratory for Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Dyann F Wirth
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Ralph Mazitschek
- Infectious Diseases Program, Broad Institute, Cambridge, MA 02142, USA. Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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Gabryszewski SJ, Modchang C, Musset L, Chookajorn T, Fidock DA. Combinatorial Genetic Modeling of pfcrt-Mediated Drug Resistance Evolution in Plasmodium falciparum. Mol Biol Evol 2016; 33:1554-70. [PMID: 26908582 PMCID: PMC4868112 DOI: 10.1093/molbev/msw037] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The emergence of drug resistance continuously threatens global control of infectious diseases, including malaria caused by the protozoan parasite Plasmodium falciparum. A critical parasite determinant is the P. falciparum chloroquine resistance transporter (PfCRT), the primary mediator of chloroquine (CQ) resistance (CQR), and a pleiotropic modulator of susceptibility to several first-line artemisinin-based combination therapy partner drugs. Aside from the validated CQR molecular marker K76T, P. falciparum parasites have acquired at least three additional pfcrt mutations, whose contributions to resistance and fitness have been heretofore unclear. Focusing on the quadruple-mutant Ecuadorian PfCRT haplotype Ecu1110 (K76T/A220S/N326D/I356L), we genetically modified the pfcrt locus of isogenic, asexual blood stage P. falciparum parasites using zinc-finger nucleases, producing all possible combinations of intermediate pfcrt alleles. Our analysis included the related quintuple-mutant PfCRT haplotype 7G8 (Ecu1110 + C72S) that is widespread throughout South America and the Western Pacific. Drug susceptibilities and in vitro growth profiles of our combinatorial pfcrt-modified parasites were used to simulate the mutational trajectories accessible to parasites as they evolved CQR. Our results uncover unique contributions to parasite drug resistance and growth for mutations beyond K76T and predict critical roles for the CQ metabolite monodesethyl-CQ and the related quinoline-type drug amodiaquine in driving mutant pfcrt evolution. Modeling outputs further highlight the influence of parasite proliferation rates alongside gains in drug resistance in dictating successful trajectories. Our findings suggest that P. falciparum parasites have navigated constrained pfcrt adaptive landscapes by means of probabilistically rare mutational bursts that led to the infrequent emergence of pfcrt alleles in the field.
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Affiliation(s)
| | - Charin Modchang
- Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Lise Musset
- Laboratoire de Parasitologie, WHO Collaborating Center for Surveillance of Anti-Malarial Drug Resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit, Center of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY
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Winter DJ, Pacheco MA, Vallejo AF, Schwartz RS, Arevalo-Herrera M, Herrera S, Cartwright RA, Escalante AA. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia. PLoS Negl Trop Dis 2015; 9:e0004252. [PMID: 26709695 PMCID: PMC4692395 DOI: 10.1371/journal.pntd.0004252] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/30/2015] [Indexed: 11/24/2022] Open
Abstract
Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America.
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Affiliation(s)
- David J. Winter
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - M. Andreína Pacheco
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
| | | | - Rachel S. Schwartz
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Myriam Arevalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | | | - Reed A. Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- The School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Ananias A. Escalante
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
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Vatsiou AI, Bazin E, Gaggiotti OE. Detection of selective sweeps in structured populations: a comparison of recent methods. Mol Ecol 2015; 25:89-103. [DOI: 10.1111/mec.13360] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/27/2015] [Accepted: 08/25/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Alexandra I. Vatsiou
- Laboratoire d'Ecologie Alpine UMR CNRS 5553 Université Joseph Fourier Grenoble France
- Scottish Oceans Institute East Sands University of St Andrews St Andrews KY16 8LB UK
| | - Eric Bazin
- Laboratoire d'Ecologie Alpine UMR CNRS 5553 Université Joseph Fourier Grenoble France
| | - Oscar E. Gaggiotti
- Laboratoire d'Ecologie Alpine UMR CNRS 5553 Université Joseph Fourier Grenoble France
- Scottish Oceans Institute East Sands University of St Andrews St Andrews KY16 8LB UK
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48
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Haasl RJ, Payseur BA. Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication. Mol Ecol 2015. [PMID: 26224644 DOI: 10.1111/mec.13339] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example F(ST), cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.
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Affiliation(s)
- Ryan J Haasl
- Department of Biology, University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI, 53818, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA
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Cravo P, Napolitano H, Culleton R. How genomics is contributing to the fight against artemisinin-resistant malaria parasites. Acta Trop 2015; 148:1-7. [PMID: 25910626 DOI: 10.1016/j.actatropica.2015.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/06/2015] [Accepted: 04/11/2015] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum, the malignant malaria parasite, has developed resistance to artemisinin, the most important and widely used antimalarial drug at present. Currently confined to Southeast Asia, the spread of resistant parasites to Africa would constitute a public health catastrophe. In this review we highlight the recent contributions of genomics to our understanding how the parasite develops resistance to artemisinin and its derivatives, and how resistant parasites may be monitored and tracked in real-time, using molecular approaches.
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Affiliation(s)
- Pedro Cravo
- Laboratory of Genomics and Biotechnology (GenoBio), IPTSP, Universidade Federal de Goiás, Goiânia 74605050, GO, Brazil; PPSTMA, Centro Universitário de Anápolis (UniEVANGÉLICA), Anápolis 75083515, GO, Brazil; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon 1349-008, Portugal.
| | - Hamilton Napolitano
- PPSTMA, Centro Universitário de Anápolis (UniEVANGÉLICA), Anápolis 75083515, GO, Brazil; Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás. 459, 75001970 Anápolis, GO, Brazil
| | - Richard Culleton
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 8528523, Japan
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50
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Duffy CW, Assefa SA, Abugri J, Amoako N, Owusu-Agyei S, Anyorigiya T, MacInnis B, Kwiatkowski DP, Conway DJ, Awandare GA. Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity. BMC Genomics 2015; 16:527. [PMID: 26173872 PMCID: PMC4502944 DOI: 10.1186/s12864-015-1746-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome wide sequence analyses of malaria parasites from widely separated areas of the world have identified contrasting population structures and signatures of selection. To compare relatively closely situated but ecologically contrasting regions within an endemic African country, population samples of Plasmodium falciparum clinical isolates were collected in Ghana from Kintampo in the central forest-savannah area, and Navrongo in a drier savannah area ~350 km to the north with more seasonally-restricted transmission. Parasite DNA was sequenced and paired-end reads mapped to the P. falciparum reference genome. RESULTS High coverage genome wide sequence data for 85 different clinical isolates enabled analysis of 121,712 single nucleotide polymorphisms (SNPs). The local populations had similar proportions of mixed genotype infections, similar SNP allele frequency distributions, and eleven chromosomal regions had elevated integrated haplotype scores (|iHS|) in both. A between-population Rsb metric comparing extended haplotype homozygosity indicated a stronger signal within Kintampo for one of these regions (on chromosome 14) and in Navrongo for two of these regions (on chromosomes 10 and 13). At least one gene in each of these identified regions is a potential target of locally varying selection. The candidates include genes involved in parasite development in mosquitoes, members of variant-expressed multigene families, and a leading vaccine-candidate target of immunity. CONCLUSIONS Against a background of very similar population structure and selection signatures in the P. falciparum populations of Ghana, three narrow genomic regions showed evidence indicating local differences in historical timing or intensity of selection. Sampling of closely situated populations across heterogeneous environments has potential to refine the mapping of important loci under temporally or spatially varying selection.
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Affiliation(s)
- Craig W Duffy
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Samuel A Assefa
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - James Abugri
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Box LG 54, Volta Road, Legon, Accra, Ghana. .,Department of Applied Chemistry and Biochemistry, University for Development Studies, Tamale, Ghana.
| | | | - Seth Owusu-Agyei
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK. .,Kintampo Health Research Centre, Kintampo, Ghana.
| | | | | | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, UK. .,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Box LG 54, Volta Road, Legon, Accra, Ghana.
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