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Guo B, Takala-Harrison S, O’Connor TD. Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592538. [PMID: 38746392 PMCID: PMC11092787 DOI: 10.1101/2024.05.04.592538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Genomic surveillance is crucial for identifying at-risk populations for targeted malaria control and elimination. Identity-by-descent (IBD) is being used in Plasmodium population genomics to estimate genetic relatedness, effective population size ( N e ) , population structure, and positive selection. However, a comprehensive evaluation of IBD segment detection tools is lacking for species with high rates of recombination. Here, we employ genetic simulations reflecting P. falciparum's high recombination rate and decreasing N e to benchmark IBD callers, including probabilistic (hmmIBD, isoRelate), identity-by-state-based (hap-IBD, phased IBD) and others (Refined IBD), using genealogy-based true IBD and downstream inference of population characteristics. Our findings reveal that low marker density per genetic unit, related to high recombination rates relative to mutation rates, significantly affects the quality of detected IBD segments. Most IBD callers suffer from high false negative rates, which can be improved with parameter optimization. Optimized parameters allow for more accurate capture of selection signals and population structure, but hmmIBD is unique in providing less biased estimates of N e . Empirical data subsampled from the MalariaGEN Pf7 database, representing different transmission settings, confirmed these patterns. We conclude that the detection of IBD in high-recombining species requires context-specific evaluation and parameter optimization and recommend that hmmIBD be used for quality-sensitive analysis, such as estimation of N e in these species.
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Affiliation(s)
- Bing Guo
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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2
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Pacheco MA, Cepeda AS, Miller EA, Beckerman S, Oswald M, London E, Mateus-Pinilla NE, Escalante AA. A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies. Malar J 2024; 23:134. [PMID: 38704592 PMCID: PMC11069185 DOI: 10.1186/s12936-024-04961-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Studies on haemosporidian diversity, including origin of human malaria parasites, malaria's zoonotic dynamic, and regional biodiversity patterns, have used target gene approaches. However, current methods have a trade-off between scalability and data quality. Here, a long-read Next-Generation Sequencing protocol using PacBio HiFi is presented. The data processing is supported by a pipeline that uses machine-learning for analysing the reads. METHODS A set of primers was designed to target approximately 6 kb, almost the entire length of the haemosporidian mitochondrial genome. Amplicons from different samples were multiplexed in an SMRTbell® library preparation. A pipeline (HmtG-PacBio Pipeline) to process the reads is also provided; it integrates multiple sequence alignments, a machine-learning algorithm that uses modified variational autoencoders, and a clustering method to identify the mitochondrial haplotypes/species in a sample. Although 192 specimens could be studied simultaneously, a pilot experiment with 15 specimens is presented, including in silico experiments where multiple data combinations were tested. RESULTS The primers amplified various haemosporidian parasite genomes and yielded high-quality mt genome sequences. This new protocol allowed the detection and characterization of mixed infections and co-infections in the samples. The machine-learning approach converged into reproducible haplotypes with a low error rate, averaging 0.2% per read (minimum of 0.03% and maximum of 0.46%). The minimum recommended coverage per haplotype is 30X based on the detected error rates. The pipeline facilitates inspecting the data, including a local blast against a file of provided mitochondrial sequences that the researcher can customize. CONCLUSIONS This is not a diagnostic approach but a high-throughput method to study haemosporidian sequence assemblages and perform genotyping by targeting the mitochondrial genome. Accordingly, the methodology allowed for examining specimens with multiple infections and co-infections of different haemosporidian parasites. The pipeline enables data quality assessment and comparison of the haplotypes obtained to those from previous studies. Although a single locus approach, whole mitochondrial data provide high-quality information to characterize species pools of haemosporidian parasites.
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Affiliation(s)
- M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA.
| | - Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Erica A Miller
- University of Pennsylvania, Wildlife Futures Program, Kennett Square, Philadelphia, PA, 19348, USA
| | | | | | - Evan London
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Nohra E Mateus-Pinilla
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA.
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3
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Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum. Nat Commun 2024; 15:2499. [PMID: 38509066 PMCID: PMC10954658 DOI: 10.1038/s41467-024-46659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates. We demonstrate that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discover that the removal of IBD peak regions partially restores the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness and extent of inbreeding. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
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Affiliation(s)
- Bing Guo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michele D Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mariusz Wojnarski
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Brian A Vesely
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisbon, Portugal
| | - Norman C Waters
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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4
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Konaté-Touré A, Gnagne AP, Bedia-Tanoh AV, Menan EIH, Yavo W. Increase of Plasmodium falciparum parasites carrying lumefantrine-tolerance molecular markers and lack of South East Asian pfk13 artemisinin-resistance mutations in samples collected from 2013 to 2016 in Côte d'Ivoire. J Parasit Dis 2024; 48:59-66. [PMID: 38440764 PMCID: PMC10908703 DOI: 10.1007/s12639-023-01640-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/21/2023] [Indexed: 03/06/2024] Open
Abstract
One of the major obstacles to malaria elimination in the world is the resistance in Plasmodium falciparum to most antimalarial drugs. This study aimed to estimate the prevalence of molecular markers of antimalarial drugs resistance in Côte d'Ivoire. Samples were collected from 2013 to 2016 from asymptomatic and symptomatic subjects in Abengourou, Abidjan, Grand Bassam, and San Pedro. A total of 704 participants aged between 1 year and 65 years (Mean age: 9 years ± 7.7) were enrolled. All the dried filter paper blood spots were genotyped by sequencing. Plasmodium falciparum kelch propeller domain 13 (pfk13) gene were analyzed for all the samples, while 344 samples were examined for Plasmodium falciparum multi-drug resistance 1 (pfmdr1). Overall, the success rate of molecular tests was 98.8% (340/344), 99.1% (341/344), and 94.3% (664/704) for pfmdr1 N86Y, pfmdr1 Y184F, and pfk13 genes respectively. Molecular analysis revealed twenty (5.9%; 20/340) and 219 (64.2%; 219/341) mutant alleles for pfmdr1 86Y and pfmdr1 184 F, respectively. Twenty-nine mutations in pfk13 gene (4.4%; 29/664) with 2.7% (18/664) of non-synonymous mutations was found. None of the mutations previously described in South East Asia (SEA) involved in P. falciparum resistance to artemisinin derivatives were observed in this study. According to year of collection, a decrease of the prevalence of pfk13 mutation (from 3.6 to 1.8%) and pfmdr1 N86Y mutation (from 8.5 to 4.5%) and an increase of mutant allele of pfmdr1 Y184F proportion (from 39.8 to 66.4%) were found. Comparing to previous studies in the country, this study showed an increase in lumefantrine tolerance of P. falciparum strains. This demonstrates the importance of establishing a strong system for molecular surveillance of malaria in Côte d'Ivoire.
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Affiliation(s)
- Abibatou Konaté-Touré
- Department of Parasitology, Mycology, Animal Biology and, Zoology, Felix Houphouët-Boigny University, BPV 34, Abidjan, Côte d’Ivoire
- Malaria Research and Control Centre, National Institute of Public Health, BPV 47, Abidjan, Côte d’Ivoire
| | - Akpa Paterne Gnagne
- Malaria Research and Control Centre, National Institute of Public Health, BPV 47, Abidjan, Côte d’Ivoire
| | - Akoua Valérie Bedia-Tanoh
- Department of Parasitology, Mycology, Animal Biology and, Zoology, Felix Houphouët-Boigny University, BPV 34, Abidjan, Côte d’Ivoire
- Malaria Research and Control Centre, National Institute of Public Health, BPV 47, Abidjan, Côte d’Ivoire
| | - Eby Ignace Hervé Menan
- Department of Parasitology, Mycology, Animal Biology and, Zoology, Felix Houphouët-Boigny University, BPV 34, Abidjan, Côte d’Ivoire
| | - William Yavo
- Department of Parasitology, Mycology, Animal Biology and, Zoology, Felix Houphouët-Boigny University, BPV 34, Abidjan, Côte d’Ivoire
- Malaria Research and Control Centre, National Institute of Public Health, BPV 47, Abidjan, Côte d’Ivoire
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5
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Su X, Stadler RV, Xu F, Wu J. Malaria Genomics, Vaccine Development, and Microbiome. Pathogens 2023; 12:1061. [PMID: 37624021 PMCID: PMC10459703 DOI: 10.3390/pathogens12081061] [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: 07/21/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Recent advances in malaria genetics and genomics have transformed many aspects of malaria research in areas of molecular evolution, epidemiology, transmission, host-parasite interaction, drug resistance, pathogenicity, and vaccine development. Here, in addition to introducing some background information on malaria parasite biology, parasite genetics/genomics, and genotyping methods, we discuss some applications of genetic and genomic approaches in vaccine development and in studying interactions with microbiota. Genetic and genomic data can be used to search for novel vaccine targets, design an effective vaccine strategy, identify protective antigens in a whole-organism vaccine, and evaluate the efficacy of a vaccine. Microbiota has been shown to influence disease outcomes and vaccine efficacy; studying the effects of microbiota in pathogenicity and immunity may provide information for disease control. Malaria genetics and genomics will continue to contribute greatly to many fields of malaria research.
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Affiliation(s)
- Xinzhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (R.V.S.); (F.X.); (J.W.)
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6
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Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong Positive Selection Biases Identity-By-Descent-Based Inferences of Recent Demography and Population Structure in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549114. [PMID: 37502843 PMCID: PMC10370022 DOI: 10.1101/2023.07.14.549114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD). Yet, strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we utilized simulations, a true IBD inference algorithm, and empirical datasets from different malaria transmission settings to investigate the extent of such bias and explore potential correction strategies. We analyzed whole genome sequence data generated from 640 new and 4,026 publicly available Plasmodium falciparum clinical isolates. Our findings demonstrated that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discovered that the removal of IBD peak regions partially restored the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
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Affiliation(s)
- Bing Guo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michele D Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mariusz Wojnarski
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Brian A Vesely
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Norman C Waters
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
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7
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Morano AA, Rudlaff RM, Dvorin JD. A PPP-type pseudophosphatase is required for the maintenance of basal complex integrity in Plasmodium falciparum. Nat Commun 2023; 14:3916. [PMID: 37400439 DOI: 10.1038/s41467-023-39435-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/13/2023] [Indexed: 07/05/2023] Open
Abstract
During its asexual blood stage, P. falciparum replicates via schizogony, wherein dozens of daughter cells are formed within a single parent. The basal complex, a contractile ring that separates daughter cells, is critical for schizogony. In this study, we identify a Plasmodium basal complex protein essential for basal complex maintenance. Using multiple microscopy techniques, we demonstrate that PfPPP8 is required for uniform basal complex expansion and maintenance of its integrity. We characterize PfPPP8 as the founding member of a novel family of pseudophosphatases with homologs in other Apicomplexan parasites. By co-immunoprecipitation, we identify two additional new basal complex proteins. We characterize the unique temporal localizations of these new basal complex proteins (late-arriving) and of PfPPP8 (early-departing). In this work, we identify a novel basal complex protein, determine its specific role in segmentation, identify a new pseudophosphatase family, and establish that the P. falciparum basal complex is a dynamic structure.
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Affiliation(s)
- Alexander A Morano
- Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Rachel M Rudlaff
- Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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8
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Escalante AA, Cepeda AS, Pacheco MA. Why Plasmodium vivax and Plasmodium falciparum are so different? A tale of two clades and their species diversities. Malar J 2022; 21:139. [PMID: 35505356 PMCID: PMC9066883 DOI: 10.1186/s12936-022-04130-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/18/2022] [Indexed: 11/29/2022] Open
Abstract
The global malaria burden sometimes obscures that the genus Plasmodium comprises diverse clades with lineages that independently gave origin to the extant human parasites. Indeed, the differences between the human malaria parasites were highlighted in the classical taxonomy by dividing them into two subgenera, the subgenus Plasmodium, which included all the human parasites but Plasmodium falciparum that was placed in its separate subgenus, Laverania. Here, the evolution of Plasmodium in primates will be discussed in terms of their species diversity and some of their distinct phenotypes, putative molecular adaptations, and host–parasite biocenosis. Thus, in addition to a current phylogeny using genome-level data, some specific molecular features will be discussed as examples of how these parasites have diverged. The two subgenera of malaria parasites found in primates, Plasmodium and Laverania, reflect extant monophyletic groups that originated in Africa. However, the subgenus Plasmodium involves species in Southeast Asia that were likely the result of adaptive radiation. Such events led to the Plasmodium vivax lineage. Although the Laverania species, including P. falciparum, has been considered to share “avian characteristics,” molecular traits that were likely in the common ancestor of primate and avian parasites are sometimes kept in the Plasmodium subgenus while being lost in Laverania. Assessing how molecular traits in the primate malaria clades originated is a fundamental science problem that will likely provide new targets for interventions. However, given that the genus Plasmodium is paraphyletic (some descendant groups are in other genera), understanding the evolution of malaria parasites will benefit from studying “non-Plasmodium” Haemosporida.
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Affiliation(s)
- Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine [iGEM], Temple University, Philadelphia, PA, 19122-1801, USA.
| | - Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine [iGEM], Temple University, Philadelphia, PA, 19122-1801, USA
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine [iGEM], Temple University, Philadelphia, PA, 19122-1801, USA
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9
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Shaw WR, Marcenac P, Catteruccia F. Plasmodium development in Anopheles: a tale of shared resources. Trends Parasitol 2022; 38:124-135. [PMID: 34548252 PMCID: PMC8758519 DOI: 10.1016/j.pt.2021.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023]
Abstract
Interactions between the Anopheles mosquito vector and Plasmodium parasites shape how malaria is transmitted in endemic regions. The long association of these two organisms has led to evolutionary processes that minimize fitness costs of infection and benefit both players through shared nutrient resources, parasite immune suppression, and mosquito tolerance to infection. In this review we explore recent data describing how Plasmodium falciparum, the deadliest malaria parasite, associates with one of its most important natural mosquito hosts, Anopheles gambiae, and we discuss the implications of these findings for parasite transmission and vector control strategies currently in development.
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Affiliation(s)
- W Robert Shaw
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Perrine Marcenac
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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10
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Vythilingam I, Chua TH, Liew JWK, Manin BO, Ferguson HM. The vectors of Plasmodium knowlesi and other simian malarias Southeast Asia: challenges in malaria elimination. ADVANCES IN PARASITOLOGY 2021; 113:131-189. [PMID: 34620382 DOI: 10.1016/bs.apar.2021.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Plasmodium knowlesi, a simian malaria parasite of great public health concern has been reported from most countries in Southeast Asia and exported to various countries around the world. Currently P. knowlesi is the predominant species infecting humans in Malaysia. Besides this species, other simian malaria parasites such as P. cynomolgi and P. inui are also infecting humans in the region. The vectors of P. knowlesi and other Asian simian malarias belong to the Leucosphyrus Group of Anopheles mosquitoes which are generally forest dwelling species. Continual deforestation has resulted in these species moving into forest fringes, farms, plantations and human settlements along with their macaque hosts. Limited studies have shown that mosquito vectors are attracted to both humans and macaque hosts, preferring to bite outdoors and in the early part of the night. We here review the current status of simian malaria vectors and their parasites, knowledge of vector competence from experimental infections and discuss possible vector control measures. The challenges encountered in simian malaria elimination are also discussed. We highlight key knowledge gaps on vector distribution and ecology that may impede effective control strategies.
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Affiliation(s)
- Indra Vythilingam
- Department of Parasitology, University of Malaya, Kuala Lumpur, Malaysia.
| | - Tock Hing Chua
- Department of Pathobiology and Microbiology, Faculty of Medicine and Health Sciences, Universiti Sabah Malaysia, Kota Kinabalu, Sabah, Malaysia.
| | - Jonathan Wee Kent Liew
- Department of Parasitology, University of Malaya, Kuala Lumpur, Malaysia; Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Benny O Manin
- Department of Pathobiology and Microbiology, Faculty of Medicine and Health Sciences, Universiti Sabah Malaysia, Kota Kinabalu, Sabah, Malaysia
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
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11
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Rougeron V, Boundenga L, Arnathau C, Durand P, Renaud F, Prugnolle F. A population genetic perspective on the origin, spread and adaptation of the human malaria agents Plasmodium falciparum and Plasmodium vivax. FEMS Microbiol Rev 2021; 46:6373923. [PMID: 34550355 DOI: 10.1093/femsre/fuab047] [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: 02/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
Malaria is considered one of the most important scourges that humanity has faced during its history, being responsible every year for numerous deaths worldwide. The disease is caused by protozoan parasites, among which two species are responsible of the majority of the burden, Plasmodium falciparum and Plasmodium vivax. For these two parasite species, the questions of their origin (how and when they appeared in humans), of their spread throughout the world, as well as how they have adapted to humans have long been of interest to the scientific community. Here, we review the current knowledge that has accumulated on these different questions, thanks in particular to the analysis of the genetic and genomic variability of these parasites and comparison with related Plasmodium species infecting other host species (like non-human primates). In this paper we review the existing body of knowledge, including current research dealing with these questions, focusing particularly on genetic analysis and genomic variability of these parasites and comparison with related Plasmodium species infecting other species of host (such as non-human primates).
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Affiliation(s)
- Virginie Rougeron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Larson Boundenga
- CIRMF, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Patrick Durand
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - François Renaud
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Franck Prugnolle
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
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12
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Study of the Antimalarial Activity of the Leaf Extracts and Fractions of Persea americana and Dacryodes edulis and Their HPLC Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:5218294. [PMID: 34335810 PMCID: PMC8313334 DOI: 10.1155/2021/5218294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/10/2021] [Indexed: 11/18/2022]
Abstract
In the present study, the antimalarial activity of the extracts and fractions of the leaves of Persea americana and Dacryodes edulis as well as their phytochemical compositions were examined. Each of the extracts of the plants was successively fractionated to obtain hexane, ethyl acetate, methanol, and water fractions. The extracts and fractions were tested against Plasmodium berghei in both curative and suppressive antimalarial mouse models. Their major phytochemical composition was studied by the standard chemical tests and HPLC analysis. The extracts and fractions of P. americana and D. edulis demonstrated significant (p < 0.05) maximal plasmodial inhibition as 52.16 ± 2.77% and 57.10 ± 1.98%, respectively, and chemosuppression of parasitemia as 64.01 ± 0.08% and 71.99 ± 0.06%, respectively. The major secondary metabolites identified in the plants include alkaloids, flavonoids, and saponins. It was concluded that P. americana and D. edulis possess promising antimalarial activity and they are potential sources of new lead compounds against malaria.
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13
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Abstract
African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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14
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Mallory KL, Taylor JA, Zou X, Waghela IN, Schneider CG, Sibilo MQ, Punde NM, Perazzo LC, Savransky T, Sedegah M, Dutta S, Janse CJ, Pardi N, Lin PJC, Tam YK, Weissman D, Angov E. Messenger RNA expressing PfCSP induces functional, protective immune responses against malaria in mice. NPJ Vaccines 2021; 6:84. [PMID: 34145286 PMCID: PMC8213722 DOI: 10.1038/s41541-021-00345-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/24/2021] [Indexed: 02/05/2023] Open
Abstract
Human malaria affects the vast majority of the world's population with the Plasmodium falciparum species causing the highest rates of morbidity and mortality. With no licensed vaccine and leading candidates achieving suboptimal protection in the field, the need for an effective immunoprophylactic option continues to motivate the malaria research community to explore alternative technologies. Recent advances in the mRNA discipline have elevated the long-neglected platform to the forefront of infectious disease research. As the immunodominant coat protein of the invasive stage of the malaria parasite, circumsporozoite protein (PfCSP) was selected as the antigen of choice to assess the immunogenic and protective potential of an mRNA malaria vaccine. In mammalian cell transfection experiments, PfCSP mRNA was well expressed and cell associated. In the transition to an in vivo murine model, lipid nanoparticle (LNP) encapsulation was applied to protect and deliver the mRNA to the cell translation machinery and supply adjuvant activity. The immunogenic effect of an array of factors was explored, such as formulation, dose, number, and interval of immunizations. PfCSP mRNA-LNP achieved sterile protection against infection with two P. berghei PfCSP transgenic parasite strains, with mRNA dose and vaccination interval having a greater effect on outcome. This investigation serves as the assessment of pre-erythrocytic malaria, PfCSP mRNA vaccine candidate resulting in sterile protection, with numerous factors affecting protective efficacy, making it a compelling candidate for further investigation.
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Affiliation(s)
- Katherine L Mallory
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Parsons Corporation, Centreville, VA, USA
| | - Justin A Taylor
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Geneva Foundation, Tacoma, WA, USA
| | - Xiaoyan Zou
- Naval Medical Research Center, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ishita N Waghela
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Parsons Corporation, Centreville, VA, USA
| | - Cosette G Schneider
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Michael Q Sibilo
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Parsons Corporation, Centreville, VA, USA
| | - Neeraja M Punde
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Geneva Foundation, Tacoma, WA, USA
| | - Leah C Perazzo
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- General Dynamics Information Technology, Falls Church, VA, USA
| | - Tatyana Savransky
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- General Dynamics Information Technology, Falls Church, VA, USA
| | | | - Sheetij Dutta
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Chris J Janse
- Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Ying K Tam
- Acuitas Therapeutics, Vancouver, BC, Canada
| | | | - Evelina Angov
- Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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15
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Menardo F, Gagneux S, Freund F. Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis. Mol Biol Evol 2021; 38:290-306. [PMID: 32667991 PMCID: PMC8480183 DOI: 10.1093/molbev/msaa179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders). Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabian Freund
- Department of Plant Biodiversity and Breeding Informatics, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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16
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Fu R, Li J, Yu H, Zhang Y, Xu Z, Martin C. The Yin and Yang of traditional Chinese and Western medicine. Med Res Rev 2021; 41:3182-3200. [PMID: 33599314 DOI: 10.1002/med.21793] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 01/22/2023]
Abstract
The success of Western Scientific approaches to medicine, over the last 150 years, can be measured by substantial increases in life expectancy, reductions in infant mortality and the virtual elimination of many infectious diseases accompanied by development of effective management practices for noncommunicable diseases. However, major challenges remain in the form of infectious diseases that evolve resistance to pharmaceuticals rapidly, new diseases, particularly those caused by viruses and effective long-term treatments for chronic, noncommunicable diseases. Traditional Chinese Medicine (TCM) can offer complementary treatments based on personalised interventions, informed by knowledge accumulated from empirical observations gathered over centuries of practice, that address the impact of disease on the whole body. We provide examples of both infectious and noncommunicable diseases where the combination of Western Scientific Medicine (WSM) and TCM can benefit patients in terms of the speed and efficacy of recovery or disease management. TCM is a healing skill based on practice, while WSM is scientific, based on experiments. Against this background, an understanding of the mechanisms of action of traditional Chinese medicinal preparations will offer fresh routes to discovery and development of new therapeutics as well as patented medical prescriptions, which will rely heavily on modern scientific methodologies for their adoption and success, particularly those in plant genomics, plant breeding and synthetic biology.
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Affiliation(s)
- Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jie Li
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Huatao Yu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhihong Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Science, Peking University, Beijing, China
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
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17
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Ribeiro de Castro Duarte AM, Fernandes LN, Silva FS, Sicchi IL, Mucci LF, Curado I, Fernandes A, Medeiros-Sousa AR, Ceretti-Junior W, Marrelli MT, Evangelista E, Teixeira R, Summa JL, Nardi MS, Garnica MR, Loss AC, Buery JC, Cerutti Jr. C, Pacheco MA, Escalante AA, Mureb Sallum MA, Laporta GZ. Complexity of malaria transmission dynamics in the Brazilian Atlantic Forest. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2021; 1:100032. [PMID: 35284897 PMCID: PMC8906072 DOI: 10.1016/j.crpvbd.2021.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/23/2021] [Indexed: 11/26/2022]
Abstract
Plasmodium malariae and Plasmodium vivax are protozoan parasites that can cause malaria in humans. They are genetically indistinguishable from, respectively, Plasmodium brasilianum and Plasmodium simium, i.e. parasites infecting New World non-human primates in South America. In the tropical rainforests of the Brazilian Atlantic coast, it has long been hypothesized that P. brasilianum and P. simium in platyrrhine primates originated from P. malariae and P. vivax in humans. A recent hypothesis proposed the inclusion of Plasmodium falciparum into the transmission dynamics between humans and non-human primates in the Brazilian Atlantic tropical rainforest. Herein, we assess the occurrence of human malaria in simians and sylvatic anophelines using field-collected samples in the Capivari-Monos Environmental Protection Area from 2015 to 2017. We first tested simian blood and anopheline samples. Two simian (Aloutta) blood samples (18%, n = 11) showed Plasmodium cytb DNA sequences, one for P. vivax and another for P. malariae. From a total of 9,416 anopheline females, we found 17 pools positive for Plasmodium species with a 18S qPCR assay. Only three showed P. cytb DNA sequence, one for P. vivax and the others for rodent malaria species (similar to Plasmodium chabaudi and Plasmodium berghei). Based on these results, we tested 25 rodent liver samples for the presence of Plasmodium and obtained P. falciparum cytb DNA sequence in a rodent (Oligoryzomys sp.) liver. The findings of this study indicate complex malaria transmission dynamics composed by parallel spillover-spillback of human malaria parasites, i.e. P. malariae, P. vivax, and P. falciparum, in the Brazilian Atlantic forest. Human malaria parasites circulate in sylvatic cycles in the Brazilian Atlantic forest. Plasmodium vivax and Plasmodium malariae identified in simian blood samples. Plasmodium falciparum detected in a rodent liver sample. Anopheline vectors found to carry human and rodent malaria parasites. Local vector ecology and biology are key to the spillover-spillback of human malaria parasites.
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18
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Derilus D, Rahman MZ, Serrano AE, Massey SE. Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. INFECTION GENETICS AND EVOLUTION 2020; 87:104642. [PMID: 33296723 DOI: 10.1016/j.meegid.2020.104642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 11/29/2022]
Abstract
Apicomplexans are alveolate parasites which include Plasmodium falciparum, the main cause of malaria, one of the world's biggest killers from infectious disease. Apicomplexans are characterized by a reduction in proteome size, which appears to result from metabolic and functional simplification, commensurate with their parasitic lifestyle. However, other factors may also help to explain gene loss such as population bottlenecks experienced during transmission, and the effect of reducing the overall genomic information content. The latter constitutes an 'informational constraint', which is proposed to exert a selective pressure to evolve and maintain genes involved in informational fidelity and error correction, proportional to the quantity of information in the genome (which approximates to proteome size). The dynamics of gene loss was examined in 41 Apicomplexan genomes using orthogroup analysis. We show that loss of genes involved in amino acid metabolism and steroid biosynthesis can be explained by metabolic redundancy with the host. We also show that there is a marked tendency to lose DNA repair genes as proteome size is reduced. This may be explained by a reduction in size of the informational constraint and can help to explain elevated mutation rates in pathogens with reduced genome size. Multiple Sequentially Markovian Coalescent (MSMC) analysis indicates a recent bottleneck, consistent with predictions generated using allele-based population genetics approaches, implying that relaxed selection pressure due to reduced population size might have contributed to gene loss. However, the non-randomness of pathways that are lost challenges this scenario. Lastly, we identify unique orthogroups in malaria-causing Plasmodium species that infect humans, with a high proportion of membrane associated proteins. Thus, orthogroup analysis appears useful for identifying novel candidate pathogenic factors in parasites, when there is a wide sample of genomes available.
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Affiliation(s)
- D Derilus
- Environmental Sciences Department, University of Puerto Rico-Rio Piedras, United States of America
| | - M Z Rahman
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America
| | - A E Serrano
- Department of Microbiology, University of Puerto Rico-School of Medicine, Medical Sciences, United States of America
| | - S E Massey
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America.
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19
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Mwamuye MM, Obara I, Elati K, Odongo D, Bakheit MA, Jongejan F, Nijhof AM. Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria parva Vaccine and Buffalo-Derived Strains. Life (Basel) 2020; 10:life10120334. [PMID: 33302571 PMCID: PMC7764068 DOI: 10.3390/life10120334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 11/18/2022] Open
Abstract
Distinct pathogenic and epidemiological features underlie different Theileria parva strains resulting in different clinical manifestations of East Coast Fever and Corridor Disease in susceptible cattle. Unclear delineation of these strains limits the control of these diseases in endemic areas. Hence, an accurate characterization of strains can improve the treatment and prevention approaches as well as investigate their origin. Here, we describe a set of single nucleotide polymorphisms (SNPs) based on 13 near-complete mitogenomes of T. parva strains originating from East and Southern Africa, including the live vaccine stock strains. We identified 11 SNPs that are non-preferentially distributed within the coding and non-coding regions, all of which are synonymous except for two within the cytochrome b gene of buffalo-derived strains. Our analysis ascertains haplotype-specific mutations that segregate the different vaccine and the buffalo-derived strains except T. parva-Muguga and Serengeti-transformed strains suggesting a shared lineage between the latter two vaccine strains. Phylogenetic analyses including the mitogenomes of other Theileria species: T. annulata, T. taurotragi, and T. lestoquardi, with the latter two sequenced in this study for the first time, were congruent with nuclear-encoded genes. Importantly, we describe seven T. parva haplotypes characterized by synonymous SNPs and parsimony-informative characters with the other three transforming species mitogenomes. We anticipate that tracking T. parva mitochondrial haplotypes from this study will provide insight into the parasite’s epidemiological dynamics and underpin current control efforts.
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Affiliation(s)
- Micky M. Mwamuye
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany; (I.O.); (K.E.)
- Correspondence: (M.M.M.); (A.M.N.); Tel.: +49-30-838-62326 (A.M.N.)
| | - Isaiah Obara
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany; (I.O.); (K.E.)
| | - Khawla Elati
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany; (I.O.); (K.E.)
| | - David Odongo
- School of Biological Sciences, University of Nairobi, P.O. Box 30197-00100 Nairobi, Kenya;
| | - Mohammed A. Bakheit
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, P.O. Box 321-11115 Khartoum, Sudan;
| | - Frans Jongejan
- Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, 0110 Onderstepoort, South Africa;
| | - Ard M. Nijhof
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany; (I.O.); (K.E.)
- Correspondence: (M.M.M.); (A.M.N.); Tel.: +49-30-838-62326 (A.M.N.)
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20
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Hoh BP, Zhang X, Deng L, Yuan K, Yew CW, Saw WY, Hoque MZ, Aghakhanian F, Phipps ME, Teo YY, Subbiah VK, Xu S. Shared Signature of Recent Positive Selection on the TSBP1-BTNL2-HLA-DRA Genes in Five Native Populations from North Borneo. Genome Biol Evol 2020; 12:2245-2257. [PMID: 33022050 PMCID: PMC7738747 DOI: 10.1093/gbe/evaa207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
North Borneo (NB) is home to more than 40 native populations. These natives are believed to have undergone local adaptation in response to environmental challenges such as the mosquito-abundant tropical rainforest. We attempted to trace the footprints of natural selection from the genomic data of NB native populations using a panel of ∼2.2 million genome-wide single nucleotide polymorphisms. As a result, an ∼13-kb haplotype in the Major Histocompatibility Complex Class II region encompassing candidate genes TSBP1–BTNL2–HLA-DRA was identified to be undergoing natural selection. This putative signature of positive selection is shared among the five NB populations and is estimated to have arisen ∼5.5 thousand years (∼220 generations) ago, which coincides with the period of Austronesian expansion. Owing to the long history of endemic malaria in NB, the putative signature of positive selection is postulated to be driven by Plasmodium parasite infection. The findings of this study imply that despite high levels of genetic differentiation, the NB populations might have experienced similar local genetic adaptation resulting from stresses of the shared environment.
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Affiliation(s)
- Boon-Peng Hoh
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, Malaysia Cheras, Kuala Lumpur
| | - Xiaoxi Zhang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lian Deng
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chee-Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Woei-Yuh Saw
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Mohammad Zahirul Hoque
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Farhang Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - Yik-Ying Teo
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Shuhua Xu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Centre of Genetics and Development, Shanghai, China
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21
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Su XZ, Zhang C, Joy DA. Host-Malaria Parasite Interactions and Impacts on Mutual Evolution. Front Cell Infect Microbiol 2020; 10:587933. [PMID: 33194831 PMCID: PMC7652737 DOI: 10.3389/fcimb.2020.587933] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Malaria is the most deadly parasitic disease, affecting hundreds of millions of people worldwide. Malaria parasites have been associated with their hosts for millions of years. During the long history of host-parasite co-evolution, both parasites and hosts have applied pressure on each other through complex host-parasite molecular interactions. Whereas the hosts activate various immune mechanisms to remove parasites during an infection, the parasites attempt to evade host immunity by diversifying their genome and switching expression of targets of the host immune system. Human intervention to control the disease such as antimalarial drugs and vaccination can greatly alter parasite population dynamics and evolution, particularly the massive applications of antimalarial drugs in recent human history. Vaccination is likely the best method to prevent the disease; however, a partially protective vaccine may have unwanted consequences that require further investigation. Studies of host-parasite interactions and co-evolution will provide important information for designing safe and effective vaccines and for preventing drug resistance. In this essay, we will discuss some interesting molecules involved in host-parasite interactions, including important parasite antigens. We also discuss subjects relevant to drug and vaccine development and some approaches for studying host-parasite interactions.
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Affiliation(s)
- Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Cui Zhang
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Deirdre A Joy
- Parasitology and International Programs Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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22
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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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23
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Tagliamonte MS, Yowell CA, Elbadry MA, Boncy J, Raccurt CP, Okech BA, Goss EM, Salemi M, Dame JB. Genetic Markers of Adaptation of Plasmodium falciparum to Transmission by American Vectors Identified in the Genomes of Parasites from Haiti and South America. mSphere 2020; 5:e00937-20. [PMID: 33087522 PMCID: PMC7580960 DOI: 10.1128/msphere.00937-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, was introduced into Hispaniola and other regions of the Americas through the slave trade spanning the 16th through the 19th centuries. During this period, more than 12 million Africans were brought across the Atlantic to the Caribbean and other regions of the Americas. Since malaria is holoendemic in West Africa, a substantial percentage of these individuals carried the parasite. St. Domingue on Hispaniola, now modern-day Haiti, was a major port of disembarkation, and malaria is still actively transmitted there. We undertook a detailed study of the phylogenetics of the Haitian parasites and those from Colombia and Peru utilizing whole-genome sequencing. Principal-component and phylogenetic analyses, based upon single nucleotide polymorphisms (SNPs) in protein coding regions, indicate that, despite the potential for millions of introductions from Africa, the Haitian parasites share an ancestral relationship within a well-supported monophyletic clade with parasites from South America, while belonging to a distinct lineage. This result, in stark contrast to the historical record of parasite introductions, is best explained by a severe population bottleneck experienced by the parasites introduced into the Americas. Here, evidence is presented for targeted selection of rare African alleles in genes which are expressed in the mosquito stages of the parasite's life cycle. These genetic markers support the hypothesis that the severe population bottleneck was caused by the required adaptation of the parasite to transmission by new definitive hosts among the Anopheles (Nyssorhynchus) spp. found in the Caribbean and South America.IMPORTANCE Historical data suggest that millions of P. falciparum parasite lineages were introduced into the Americas during the trans-Atlantic slave trade, which would suggest a paraphyletic origin of the extant isolates in the Western Hemisphere. Our analyses of whole-genome variants show that the American parasites belong to a well-supported monophyletic clade. We hypothesize that the required adaptation to American vectors created a severe bottleneck, reducing the effective introduction to a few lineages. In support of this hypothesis, we discovered genes expressed in the mosquito stages of the life cycle that have alleles with multiple, high-frequency or fixed, nonsynonymous mutations in the American populations which are rarely found in African isolates. These alleles appear to be in gene products critical for transmission through the anopheline vector. Thus, these results may inform efforts to develop novel transmission-blocking vaccines by identifying parasite proteins functionally interacting with the vector that are important for successful transmission. Further, to the best of our knowledge, these are the first whole-genome data available from Haitian P. falciparum isolates. Defining the genome of these parasites provides genetic markers useful for mapping parasite populations and monitoring parasite movements/introductions.
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Affiliation(s)
- Massimiliano S Tagliamonte
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Charles A Yowell
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Maha A Elbadry
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jacques Boncy
- Laboratoire National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Christian P Raccurt
- Department of Tropical Medicine and Infectious Diseases, Faculty of Medicine, University of Quisqueya, Port-au-Prince, Haiti
| | - Bernard A Okech
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, College of Agricultural and Life Sciences, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - John B Dame
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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24
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Hu S, Sun S, Fu D, Lü J, Wang X, Yu Y, Dong L, Chen S, Ye H. Migration sources and pathways of the pest species Sogatella furcifera in Yunnan, China, and across the border inferred from DNA and wind analyses. Ecol Evol 2020; 10:8235-8250. [PMID: 32788975 PMCID: PMC7417236 DOI: 10.1002/ece3.6531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/20/2020] [Accepted: 06/03/2020] [Indexed: 01/31/2023] Open
Abstract
The migration sources and pathways of Sogatella furcifera (Horváth) in topologically complex regions like Yunnan, China, and adjacent montane areas have long been a challenging task and a bottleneck in effective pest forecast and control. The present research reinvestigated this issue using a combination of mtDNA and long-term historical wind field data in an attempt to provide new insights. Genetic analyses showed that the 60 populations of S. furcufera collected across Myanmar, Thailand, Laos, Vietnam, Yunnan, Guizhou, and Sichuan lack genetic structure and geographic isolation, while spatial analysis of haplotype and diversity indices discovered geographic relevance between populations. Migration rate analysis combined with high-resolution 10-year wind field analysis detected the following migration sources, pathways, and impacted areas which could explain the outbreak pattern in Yunnan. (a) Dominating stepwise northward migrations originated from northern Indochina, southern Yunnan, and central-eastern Yunnan, impacting their northern areas. (b) Concurring summer-autumn southward (return) migration originated from nearly all latitude belts of Sichuan and Yunnan mainly impacting central and southern Yunnan. (c) Regular eastward and summer-autumn westward migrations across Yunnan. The northward migration reflects the temporal rhythm of gradual outbreaks from the south to the north in a year, while the return migration may explain the repeated or very severe outbreaks in the impacted areas. To form a better pest forecast and control network, attention must also be paid to the northern part of Yunnan to suppress the impact of return migration in summers and autumns.
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Affiliation(s)
- Shao‐Ji Hu
- Yunnan Key Laboratory of International Rivers and Transboundary Eco‐securityYunnan UniversityKunmingChina
- Institute of International Rivers and Eco‐securityYunnan UniversityKunmingChina
| | - Shan‐Shan Sun
- Department of Atmospheric SciencesSchool of Resource Environment and Earth ScienceYunnan UniversityKunmingChina
| | - Da‐Ying Fu
- School of Life SciencesSouthwest Forest UniversityKunmingChina
| | - Jian‐Ping Lü
- Plant Protection and Quarantine Station of Yunnan ProvinceKunmingChina
| | - Xue‐Ying Wang
- School of Life SciencesYunnan UniversityKunmingChina
| | - Yan‐Ping Yu
- School of Life SciencesYunnan UniversityKunmingChina
| | - Li‐Min Dong
- School of Life SciencesYunnan UniversityKunmingChina
| | - Sui‐Yun Chen
- Biocontrol Engineering Research Centre of Crop Disease and PestYunnan UniversityKunmingChina
- Biocontrol Engineering Research Centre of Plant Disease and PestYunnan UniversityKunmingChina
| | - Hui Ye
- School of AgricultureYunnan UniversityKunmingChina
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25
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Noviyanti R, Miotto O, Barry A, Marfurt J, Siegel S, Thuy-Nhien N, Quang HH, Anggraeni ND, Laihad F, Liu Y, Sumiwi ME, Trimarsanto H, Coutrier F, Fadila N, Ghanchi N, Johora FT, Puspitasari AM, Tavul L, Trianty L, Utami RAS, Wang D, Wangchuck K, Price RN, Auburn S. Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia-Pacific region. Malar J 2020; 19:271. [PMID: 32718342 PMCID: PMC7385952 DOI: 10.1186/s12936-020-03330-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/09/2020] [Indexed: 01/13/2023] Open
Abstract
The Asia-Pacific region faces formidable challenges in achieving malaria elimination by the proposed target in 2030. Molecular surveillance of Plasmodium parasites can provide important information on malaria transmission and adaptation, which can inform national malaria control programmes (NMCPs) in decision-making processes. In November 2019 a parasite genotyping workshop was held in Jakarta, Indonesia, to review molecular approaches for parasite surveillance and explore ways in which these tools can be integrated into public health systems and inform policy. The meeting was attended by 70 participants from 8 malaria-endemic countries and partners of the Asia Pacific Malaria Elimination Network. The participants acknowledged the utility of multiple use cases for parasite genotyping including: quantifying the prevalence of drug resistant parasites, predicting risks of treatment failure, identifying major routes and reservoirs of infection, monitoring imported malaria and its contribution to local transmission, characterizing the origins and dynamics of malaria outbreaks, and estimating the frequency of Plasmodium vivax relapses. However, the priority of each use case varies with different endemic settings. Although a one-size-fits-all approach to molecular surveillance is unlikely to be applicable across the Asia-Pacific region, consensus on the spectrum of added-value activities will help support data sharing across national boundaries. Knowledge exchange is needed to establish local expertise in different laboratory-based methodologies and bioinformatics processes. Collaborative research involving local and international teams will help maximize the impact of analytical outputs on the operational needs of NMCPs. Research is also needed to explore the cost-effectiveness of genetic epidemiology for different use cases to help to leverage funding for wide-scale implementation. Engagement between NMCPs and local researchers will be critical throughout this process.
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Affiliation(s)
| | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alyssa Barry
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Burnet Institute, Melbourne, VIC, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Sasha Siegel
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Nguyen Thuy-Nhien
- Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Huynh Hong Quang
- Institute of Malariology, Parasitology and Entomology, Quy Nhon, Vietnam
| | | | | | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | | | | | - Farah Coutrier
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Nadia Fadila
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Najia Ghanchi
- Pathology, Aga Khan University Hospital, Karachi, Pakistan
| | - Fatema Tuj Johora
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh Mohakhali, Dhaka, Bangladesh
| | | | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Leily Trianty
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Duoquan Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Kesang Wangchuck
- Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Ric N Price
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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26
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Abstract
The medical, public health, and scientific communities are grappling with monumental imperatives to contain COVID-19, develop effective vaccines, identify efficacious treatments for the infection and its complications, and find biomarkers that detect patients at risk of severe disease. The focus of this communication is on a potential biomarker, short telomere length (TL), that might serve to identify patients more likely to die from the SARS-CoV-2 infection, regardless of age. The common thread linking these patients is lymphopenia, which largely reflects a decline in the numbers of CD4/CD8 T cells but not B cells. These findings are consistent with data that lymphocyte TL dynamics impose a limit on T-cell proliferation. They suggest that T-cell lymphopoiesis might stall in individuals with short TL who are infected with SARS-CoV-2.
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Affiliation(s)
- Abraham Aviv
- Center of Human Development and AgingRutgers, The State University of New JerseyNew Jersey Medical SchoolNewarkNJUSA
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27
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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28
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Amambua-Ngwa A, Amenga-Etego L, Kamau E, Amato R, Ghansah A, Golassa L, Randrianarivelojosia M, Ishengoma D, Apinjoh T, Maïga-Ascofaré O, Andagalu B, Yavo W, Bouyou-Akotet M, Kolapo O, Mane K, Worwui A, Jeffries D, Simpson V, D'Alessandro U, Kwiatkowski D, Djimde AA. Major subpopulations of Plasmodium falciparum in sub-Saharan Africa. Science 2020; 365:813-816. [PMID: 31439796 DOI: 10.1126/science.aav5427] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/05/2019] [Indexed: 01/04/2023]
Abstract
Understanding genomic variation and population structure of Plasmodium falciparum across Africa is necessary to sustain progress toward malaria elimination. Genome clustering of 2263 P. falciparum isolates from 24 malaria-endemic settings in 15 African countries identified major western, central, and eastern ancestries, plus a highly divergent Ethiopian population. Ancestry aligned to these regional blocs, overlapping with both the parasite's origin and with historical human migration. The parasite populations are interbred and shared genomic haplotypes, especially across drug resistance loci, which showed the strongest recent identity-by-descent between populations. A recent signature of selection on chromosome 12 with candidate resistance loci against artemisinin derivatives was evident in Ghana and Malawi. Such selection and the emerging substructure may affect treatment-based intervention strategies against P. falciparum malaria.
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Affiliation(s)
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Edwin Kamau
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya.,Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research (NMIMR), Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Deus Ishengoma
- National Institute for Medical Research (NIMR), Tanga, Tanzania
| | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | - William Yavo
- Unite des Sciences Pharmaceutiques et Biologiques, University Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | | | - Oyebola Kolapo
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia.,Department of Zoology, University of Lagos, Lagos, Nigeria
| | - Karim Mane
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - Vikki Simpson
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Dominic Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Abdoulaye A Djimde
- Wellcome Sanger Institute, Hinxton, UK. .,Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
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29
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Liang X, Chen J, Ma Y, Huang H, Xie D, Monte‐Nguba S, Ehapo CS, Eyi UM, Zheng Y, Liu X, Zha G, Lin L, Chen W, Zhou X, Lin M. Evidence of positively selected G6PD A- allele reduces risk of Plasmodium falciparum infection in African population on Bioko Island. Mol Genet Genomic Med 2020; 8:e1061. [PMID: 31872983 PMCID: PMC7005621 DOI: 10.1002/mgg3.1061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase (G6PD) is an essential enzyme that protects red blood cells from oxidative damage. Although G6PD-deficient alleles appear to confer a protective effect of malaria, the link with clinical protection against Plasmodium infection is conflicting. METHODS A case-control study was conducted on Bioko Island, Equatorial Guinea and further genotyping analysis used to detect natural selection of the G6PD A- allele. RESULTS Our results showed G6PD A- allele could significantly reduce the risk of Plasmodium falciparum infection in male individuals (adjusted odds ratio [AOR], 0.43; 95% confidence interval [CI], 0.20-0.93; p < .05) and homozygous female individuals (AOR, 0.11; 95% CI, 0.01-0.84; p < .05). Additionally, the parasite densities were significantly different in the individuals with different G6PD A- alleles and individual levels of G6PD enzyme activity. The pattern of linkage disequilibrium and results of the long-range haplotype test revealed a strong selective signature in the region encompassing the G6PD A- allele over the past 6,250 years. The network of inferred haplotypes suggested a single origin of the G6PD A- allele in Africans. CONCLUSION Our findings demonstrate that glucose-6-phosphate dehydrogenase (G6PD) A- allele could reduce the risk of P. falciparum infection in the African population and indicate that malaria has a recent positive selection on G6PD A- allele.
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Affiliation(s)
- Xue‐Yan Liang
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
- Department of Medical GeneticsShantou University Medical CollegeShantouGuangdong ProvincePeople’s Republic of China
| | - Jiang‐Tao Chen
- The Chinese Medical Aid Team to the Republic of Equatorial GuineaGuangzhouGuangdong ProvincePeople’s Republic of China
- Department of Medical LaboratoryHuizhou Central HospitalHuizhouGuangdong ProvincePeople’s Republic of China
| | - Yan‐Bo Ma
- School of Mathematics and StatisticsHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Hui‐Ying Huang
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
- Department of Medical GeneticsShantou University Medical CollegeShantouGuangdong ProvincePeople’s Republic of China
| | - Dong‐De Xie
- The Chinese Medical Aid Team to the Republic of Equatorial GuineaGuangzhouGuangdong ProvincePeople’s Republic of China
- Department of Medical LaboratoryHuizhou Central HospitalHuizhouGuangdong ProvincePeople’s Republic of China
| | | | - Carlos Salas Ehapo
- Department of Medical LaboratoryMalabo Regional HospitalMalaboEquatorial Guinea
| | - Urbano Monsuy Eyi
- Department of Medical LaboratoryMalabo Regional HospitalMalaboEquatorial Guinea
| | - Yu‐Zhong Zheng
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Xiang‐Zhi Liu
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
| | - Guang‐Cai Zha
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Li‐Yun Lin
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Wei‐Zhong Chen
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
| | - Xia Zhou
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
| | - Min Lin
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
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30
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Diakité SAS, Traoré K, Sanogo I, Clark TG, Campino S, Sangaré M, Dabitao D, Dara A, Konaté DS, Doucouré F, Cissé A, Keita B, Doumbouya M, Guindo MA, Toure MB, Sogoba N, Doumbia S, Awandare GA, Diakité M. A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali. Malar J 2019; 18:361. [PMID: 31718631 PMCID: PMC6849310 DOI: 10.1186/s12936-019-2986-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/24/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drug resistance is one of the greatest challenges of malaria control programme in Mali. Recent advances in next-generation sequencing (NGS) technologies provide new and effective ways of tracking drug-resistant malaria parasites in Africa. The diversity and the prevalence of Plasmodium falciparum drug-resistance molecular markers were assessed in Dangassa and Nioro-du-Sahel in Mali, two sites with distinct malaria transmission patterns. Dangassa has an intense seasonal malaria transmission, whereas Nioro-du-Sahel has an unstable and short seasonal malaria transmission. METHODS Up to 270 dried blood spot samples (214 in Dangassa and 56 in Nioro-du-Sahel) were collected from P. falciparum positive patients in 2016. Samples were analysed on the Agena MassARRAY® iPLEX platform. Specific codons were targeted in Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps, Pfarps10, Pfferredoxin, Pfexonuclease and Pfmdr2 genes. The Sanger's 101-SNPs-barcode method was used to assess the genetic diversity of P. falciparum and to determine the parasite species. RESULTS The Pfcrt_76T chloroquine-resistance genotype was found at a rate of 64.4% in Dangassa and 45.2% in Nioro-du-Sahel (p = 0.025). The Pfdhfr_51I-59R-108N pyrimethamine-resistance genotype was 14.1% and 19.6%, respectively in Dangassa and Nioro-du-Sahel. Mutations in the Pfdhps_S436-A437-K540-A581-613A sulfadoxine-resistance gene was significantly more prevalent in Dangassa as compared to Nioro-du-Sahel (p = 0.035). Up to 17.8% of the isolates from Dangassa vs 7% from Nioro-du-Sahel harboured at least two codon substitutions in this haplotype. The amodiaquine-resistance Pfmdr1_N86Y mutation was identified in only three samples (two in Dangassa and one in Nioro-du-Sahel). The lumefantrine-reduced susceptibility Pfmdr1_Y184F mutation was found in 39.9% and 48.2% of samples in Dangassa and Nioro-du-Sahel, respectively. One piperaquine-resistance Exo_E415G mutation was found in Dangassa, while no artemisinin resistance genetic-background were identified. A high P. falciparum diversity was observed, but no clear genetic aggregation was found at either study sites. Higher multiplicity of infection was observed in Dangassa with both COIL (p = 0.04) and Real McCOIL (p = 0.02) methods relative to Nioro-du-Sahel. CONCLUSIONS This study reveals high prevalence of chloroquine and pyrimethamine-resistance markers as well as high codon substitution rate in the sulfadoxine-resistance gene. High genetic diversity of P. falciparum was observed. These observations suggest that the use of artemisinins is relevant in both Dangassa and Nioro-du-Sahel.
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Affiliation(s)
- Seidina A S Diakité
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali.
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ibrahim Sanogo
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Modibo Sangaré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Dabitao
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antoine Dara
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Drissa S Konaté
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fousseyni Doucouré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Cissé
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourama Keita
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mory Doumbouya
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Merepen A Guindo
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamoudou B Toure
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nafomon Sogoba
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
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Qureshi NA, Fatima H, Afzal M, Khattak AA, Nawaz MA. Occurrence and seasonal variation of human Plasmodium infection in Punjab Province, Pakistan. BMC Infect Dis 2019; 19:935. [PMID: 31694574 PMCID: PMC6836532 DOI: 10.1186/s12879-019-4590-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/23/2019] [Indexed: 11/26/2022] Open
Abstract
Background Malaria is the fifth leading cause of death worldwide. Pakistan is considered as a moderate malaria-endemic country but still, 177 million individuals are at risk of malaria. Roughly 60% of Pakistan’s population, live in malaria-endemic regions. The present study is based upon the survey of various health care centers in 10 major cities of Northern and Southern Punjab to find out the malarial infection patterns in 2015. The diagnosis, seasonal variations, age and gender-wise distribution of Plasmodium spp. circulating in the study area were also included in the objectives. Methods The malaria-suspected patients ‘16075’ were enrolled for malaria diagnosis using microscopy, out of which 925 were malaria positive which were processed for molecular analysis using nested PCR. The 18S rRNA genes of Plasmodium species were amplified, sequenced, blast and the phylogenetic tree was constructed based on sequences using online integrated tool MEGA7. Results The 364 cases recruited from Northern Punjab with the highest incidence in Rawalpindi (25.5%) and lowest in Chakwal (15.9%). From Southern Punjab 561 cases were enlisted Rajanpur (21.4%) maximum and lowest from Multan and Rahim Yar Khan (18%). The slide positivity rate, annual parasite incidence, and annual blood examination rates were 5.7 per 1000 population, 0.1, and 0.2% respectively. The only P. vivax (66.7%), P. falciparum (23.7%) and mixed infection by these two species (9.6%) were diagnosed. The same trend (P. vivax > P. falciparum > mixed infection) in species identification %age was confirmed from molecular analysis. However, the occurrence of malaria was higher in Southern Punjab (5.5%) as compared to the Northern Punjab (4.0%). The overall malaria percentage occurrence of treatment-seeking patients in all recruited cities of Punjab was 4.9%. The age-group of 1–20 and males among genders were more affected by malaria. The comparison of different seasons showed that the malaria infection was at a peak in Summer and post-monsoon. Conclusion The incidence of malaria was high in the flood infected rural areas of Southern Punjab, Summer, and post-monsoon. The age group (1–20) and gender-wise males were more affected by malaria.
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Affiliation(s)
- Naveeda Akhtar Qureshi
- Department of Animal Science, Faculty of Biological Science, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Huma Fatima
- Department of Animal Science, Faculty of Biological Science, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Afzal
- Department of Animal Science, Faculty of Biological Science, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Aamer Ali Khattak
- Department of Medical Laboratory Technology, University of Haripur, Haripur, Khyber Pakhtunkhwa, 26220, Pakistan
| | - Muhammad Ali Nawaz
- Department of Animal Science, Faculty of Biological Science, Quaid-i-Azam University, Islamabad, 45320, Pakistan
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Ye R, Tian Y, Huang Y, Zhang Y, Wang J, Sun X, Zhou H, Zhang D, Pan W. Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China-Myanmar Border. Front Genet 2019; 10:1065. [PMID: 31737048 PMCID: PMC6830057 DOI: 10.3389/fgene.2019.01065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/03/2019] [Indexed: 12/29/2022] Open
Abstract
Plasmodium falciparum isolates from China-Myanmar border (CMB) have experienced regional special selective pressures and adaptive evolution. However, the genomes of P. falciparum isolates from this region to date are poorly characterized. Herein, we performed whole-genome sequencing of 34 P. falciparum isolates from CMB and a series of genome-wide sequence analyses to reveal their genetic diversity, population structures, and comparisons with the isolates from other epidemic regions (Thai-Cambodia border, Thai-Myanmar border, and West Africa). Totally 59,720 high-quality single-nucleotide polymorphisms (SNPs) were identified in the P. falciparum isolates from CMB, with average nucleotide diversity (π = 4.59 × 10-4) and LD decay (132 bp). The Tajima's D and Fu and Li's D values of the CMB isolates were -0.8 (p < 0.05) and -0.84 (p < 0.05), respectively, suggesting a demographic history of recent population expansion or purifying selection. Moreover, 78 genes of the parasite were identified that could be under positive selection, including those genes conferring drug resistance such as pfubp1. In addition, 33 SNPs were identified for tracing the source of the parasites with a high accuracy by analysis of the most differential SNPs among the four epidemic regions. Collectively, our data demonstrated high diversity of the CMB isolates' genomes forming a distinct population, and the identification of 33-SNP barcode provides a valuable surveillance of parasite migration among the regions.
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Affiliation(s)
- Run Ye
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Yini Tian
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Yufu Huang
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Yilong Zhang
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Jian Wang
- Yunnan Institute of Parasitic Diseases, Puer, China
| | - Xiaodong Sun
- Yunnan Institute of Parasitic Diseases, Puer, China
| | | | - Dongmei Zhang
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Weiqing Pan
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
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The Diversity of the Plasmodium falciparum K13 Propeller Domain Did Not Increase after Implementation of Artemisinin-Based Combination Therapy in Uganda. Antimicrob Agents Chemother 2019; 63:AAC.01234-19. [PMID: 31358588 DOI: 10.1128/aac.01234-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
Artemisinin-based combination therapies (ACTs) are the standard of care to treat uncomplicated falciparum malaria. However, resistance to artemisinins, defined as delayed parasite clearance after therapy, has emerged in Southeast Asia, and the spread of resistance to sub-Saharan Africa could have devastating consequences. Artemisinin resistance has been associated in Southeast Asia with multiple nonsynonymous single nucleotide polymorphisms (NS-SNPs) in the propeller domain of the gene encoding the Plasmodium falciparum K13 protein (K13PD). Some K13PD NS-SNPs have been seen in Africa, but the relevance of these mutations is unclear. To assess whether ACT use has selected for specific K13PD mutations, we compared the K13PD genetic diversity in clinical isolates collected before and after the implementation of ACT use from seven sites across Uganda. We detected K13PD NS-SNPs in 16 of 683 (2.3%) clinical isolates collected between 1999 and 2004 and in 26 of 716 (3.6%) isolates collected between 2012 and 2016 (P = 0.16), representing a total of 29 different polymorphisms at 27 codons. Individual NS-SNPs were usually detected only once, and none were found in more than 0.7% of the isolates. Three SNPs (C469F, P574L, and A675V) associated with delayed clearance in Southeast Asia were seen in samples collected between 2012 and 2016, each in a single isolate. No differences in diversity following implementation of ACT use were found at any of the seven sites, nor was there evidence of selective pressures acting on the locus. Our results suggest that selection by ACTs is not impacting on K13PD diversity in Uganda.
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Schmedes SE, Patel D, Kelley J, Udhayakumar V, Talundzic E. Using the Plasmodium mitochondrial genome for classifying mixed-species infections and inferring the geographical origin of P. falciparum parasites imported to the U.S. PLoS One 2019; 14:e0215754. [PMID: 31039178 PMCID: PMC6490880 DOI: 10.1371/journal.pone.0215754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/08/2019] [Indexed: 12/20/2022] Open
Abstract
The ability to identify mixed-species infections and track the origin of Plasmodium parasites can further enhance the development of treatment and prevention recommendations as well as outbreak investigations. Here, we explore the utility of using the full Plasmodium mitochondrial genome to classify Plasmodium species, detect mixed infections, and infer the geographical origin of imported P. falciparum parasites to the United States (U.S.). Using the recently developed standardized, high-throughput Malaria Resistance Surveillance (MaRS) protocol, the full Plasmodium mitochondrial genomes of 265 malaria cases imported to the U.S. from 2014–2017 were sequenced and analyzed. P. falciparum infections were found in 94.7% (251/265) of samples. Five percent (14/265) of samples were identified as mixed- Plasmodium species or non-P. falciparum, including P. vivax, P. malariae, P. ovale curtisi, and P. ovale wallikeri. P. falciparum mitochondrial haplotypes analysis revealed greater than eighteen percent of samples to have at least two P. falciparum mitochondrial genome haplotypes, indicating either heteroplasmy or multi-clonal infections. Maximum-likelihood phylogenies of 912 P. falciparum mitochondrial genomes with known country origin were used to infer the geographical origin of thirteen samples from persons with unknown travel histories as: Africa (country unspecified) (n = 10), Ghana (n = 1), Southeast Asia (n = 1), and the Philippines (n = 1). We demonstrate the utility and current limitations of using the Plasmodium mitochondrial genome to classify samples with mixed-infections and infer the geographical origin of imported P. falciparum malaria cases to the U.S. with unknown travel history.
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Affiliation(s)
- Sarah E. Schmedes
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States America
- Association of Public Health Laboratories, Silver Spring, Maryland, United States America
- * E-mail:
| | - Dhruviben Patel
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States America
- Williams Consulting LLC, Baltimore, Maryland, United States America
| | - Julia Kelley
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States America
- Atlanta Research and Education Foundation, Atlanta, Georgia, United States America
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States America
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States America
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Abstract
The fractional coalescent is a generalization of Kingman’s n-coalescent. It facilitates the development of the theory of population genetic processes that deviate from Poisson-distributed waiting times. It also marks the use of methods developed in fractional calculus in population genetics. The fractional coalescent is an extension of Canning’s model, where the variance of the number of offspring per parent is a random variable. The distribution of the number of offspring depends on a parameter α, which is a potential measure of the environmental heterogeneity that is commonly ignored in current inferences. An approach to the coalescent, the fractional coalescent (f-coalescent), is introduced. The derivation is based on the discrete-time Cannings population model in which the variance of the number of offspring depends on the parameter α. This additional parameter α affects the variability of the patterns of the waiting times; values of α<1 lead to an increase of short time intervals, but occasionally allow for very long time intervals. When α=1, the f-coalescent and the Kingman’s n-coalescent are equivalent. The distribution of the time to the most recent common ancestor and the probability that n genes descend from m ancestral genes in a time interval of length T for the f-coalescent are derived. The f-coalescent has been implemented in the population genetic model inference software Migrate. Simulation studies suggest that it is possible to accurately estimate α values from data that were generated with known α values and that the f-coalescent can detect potential environmental heterogeneity within a population. Bayes factor comparisons of simulated data with α<1 and real data (H1N1 influenza and malaria parasites) showed an improved model fit of the f-coalescent over the n-coalescent. The development of the f-coalescent and its inclusion into the inference program Migrate facilitates testing for deviations from the n-coalescent.
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Pacheco MA, Matta NE, Valkiunas G, Parker PG, Mello B, Stanley CE, Lentino M, Garcia-Amado MA, Cranfield M, Kosakovsky Pond SL, Escalante AA. Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites. Mol Biol Evol 2019; 35:383-403. [PMID: 29126122 PMCID: PMC5850713 DOI: 10.1093/molbev/msx285] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites’ diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes’ evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium. Contrary to previous assertions, the mtDNA is phylogenetically informative. The inferred phylogeny showed that, like the genus Plasmodium, the Leucocytozoon and Haemoproteus genera are not monophyletic groups. Although sensitive to the assumptions of the molecular dating method used, the estimated times indicate that the diversification of the avian haemosporidian subgenera/genera took place after the Cretaceous–Paleogene boundary following the radiation of modern birds. Furthermore, parasite clade differences in mtDNA substitution rates and strength of negative selection were detected. These differences may affect the biological interpretation of mtDNA gene lineages used as a proxy to species in ecological and parasitological investigations. Given that the mitochondria are critically important in the parasite life cycle stages that take place in the vector and that the transmission of parasites belonging to particular clades has been linked to specific insect families/subfamilies, this study suggests that differences in vectors have affected the mode of evolution of haemosporidian mtDNA genes. The observed patterns also suggest that the radiation of haemosporidian parasites may be the result of community-level evolutionary processes between their vertebrate and invertebrate hosts.
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Affiliation(s)
- M Andreína Pacheco
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | - Nubia E Matta
- Departamento de Biología, Grupo de Investigación Caracterización Genética e Inmunología, Sede Bogotá-Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Patricia G Parker
- Department of Biology, Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO
| | - Beatriz Mello
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | - Craig E Stanley
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | | | - Maria Alexandra Garcia-Amado
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas (IVIC), Miranda, Venezuela
| | - Michael Cranfield
- Gorilla Doctors, the Wildlife Health Center School of Veterinary Medicine, University of California, Davis, CA
| | - Sergei L Kosakovsky Pond
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | - Ananias A Escalante
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
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Estimating effective population size for a cestode parasite infecting three-spined sticklebacks. Parasitology 2019; 146:883-896. [PMID: 30720409 DOI: 10.1017/s0031182018002226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Remarkably few attempts have been made to estimate contemporary effective population size (Ne) for parasitic species, despite the valuable perspectives it can offer on the tempo and pace of parasite evolution as well as coevolutionary dynamics of host-parasite interactions. In this study, we utilized multi-locus microsatellite data to derive single-sample and temporal estimates of contemporary Ne for a cestode parasite (Schistocephalus solidus) as well as three-spined stickleback hosts (Gasterosteus aculeatus) in lakes across Alaska. Consistent with prior studies, both approaches recovered small and highly variable estimates of parasite and host Ne. We also found that estimates of host Ne and parasite Ne were sensitive to assumptions about population genetic structure and connectivity. And, while prior work on the stickleback-cestode system indicates that physiographic factors external to stickleback hosts largely govern genetic variation in S. solidus, our findings indicate that stickleback host attributes and factors internal to the host - namely body length, genetic diversity and infection - shape contemporary Ne of cestode parasites.
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Origin of the New World Plasmodium vivax: Facts and New Approaches. Int Microbiol 2019; 22:337-342. [PMID: 30810995 DOI: 10.1007/s10123-018-00053-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023]
Abstract
Malaria is one of the most important human diseases throughout tropical and sub-tropical regions of the world. Global distribution and ample host range have contributed to the genetic diversity of the etiological agent, Plasmodium. Phylogeographical analyses demonstrated that Plasmodium falciparum and Plasmodium vivax follow an Out of Africa (OOA) expansion, having a higher genetic diversity in African populations and a low genetic diversity in South American populations. Modeling the evolutionary rate of conserved genes for both P. falciparum and P. vivax determined the approximate arrival of human malaria in South America. Bayesian computational methods suggest that P. falciparum originated in Africa and arrived in South America through multiple independent introductions by the transatlantic African slave trade; however, in South America, P. vivax could have been introduced through an alternate migratory route. Alignments of P. vivax mitogenomes have revealed low genetic variation between the South American and Southeast Asian populations suggesting introduction through either pre-Columbian human migration or post-colonization events. To confirm the findings of these phylogeographical analyses, molecular methods were used to diagnose malaria infection in archeological remains of pre-Columbian ethnic groups. Immunohistochemistry tests were used and identified P. vivax but not P. falciparum in histologically prepared tissues from pre-Columbian Peruvian mummies, whereas shotgun metagenomics sequencing of DNA isolated from pre-Columbian Caribbean coprolites revealed Plasmodium-homologous reads; current evidence suggests that only P. vivax might have been present in pre-Columbian South America.
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Harvey JA, Voelker G. Host associations and climate influence avian haemosporidian distributions in Benin. Int J Parasitol 2019; 49:27-36. [DOI: 10.1016/j.ijpara.2018.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 10/27/2022]
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Hecht LBB, Thompson PC, Rosenthal BM. Comparative demography elucidates the longevity of parasitic and symbiotic relationships. Proc Biol Sci 2018; 285:rspb.2018.1032. [PMID: 30282650 PMCID: PMC6191686 DOI: 10.1098/rspb.2018.1032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022] Open
Abstract
Parasitic and symbiotic relationships govern vast nutrient and energy flows, yet controversy surrounds their longevity. Enduring relationships may engender parallel phylogenies among hosts and parasites, but so may ephemeral relationships when parasites colonize related hosts. An understanding of whether symbiont and host populations have grown and contracted in concert would be useful when considering the temporal durability of these relationships. Here, we devised methods to compare demographic histories derived from genomic data. We compared the historical growth of the agent of severe human malaria, Plasmodium falciparum, and its mosquito vector, Anopheles gambiae, to human and primate histories, thereby discerning long-term parallels and anthropogenic population explosions. The growth history of Trichinella spiralis, a zoonotic parasite disseminated by swine, proved regionally specific, paralleling distinctive growth histories for wild boar in Asia and Europe. Parallel histories were inferred for an anemone and its algal symbiont (Exaiptasia pallida and Symbiodinium minutum). Concerted growth in potatoes and the agent of potato blight (Solanum tuberosum and Phytophthora infestans) did not commence until the age of potato domestication. Through these examples, we illustrate the utility of comparative historical demography as a new exploratory tool by which to interrogate the origins and durability of myriad ecological relationships. To facilitate future use of this approach, we introduce a tool called C-PSMC to align and evaluate the similarity of demographic history curves.
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Affiliation(s)
- Luke B B Hecht
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.,US Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Peter C Thompson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.,US Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Benjamin M Rosenthal
- US Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
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Shapiro LR, Paulson JN, Arnold BJ, Scully ED, Zhaxybayeva O, Pierce NE, Rocha J, Klepac-Ceraj V, Holton K, Kolter R. An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila. mBio 2018; 9:e01307-18. [PMID: 30279283 PMCID: PMC6168856 DOI: 10.1128/mbio.01307-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/17/2018] [Indexed: 12/14/2022] Open
Abstract
Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits, an economically important phytopathogen affecting an economically important phytopathogen affecting few cultivated Cucurbitaceae few cultivated Cucurbitaceae host plant species in temperate eastern North America. However, essentially nothing is known about E. tracheiphila population structure or genetic diversity. To address this shortcoming, a representative collection of 88 E. tracheiphila isolates was gathered from throughout its geographic range, and their genomes were sequenced. Phylogenomic analysis revealed three genetic clusters with distinct hrpT3SS virulence gene repertoires, host plant association patterns, and geographic distributions. Low genetic heterogeneity within each cluster suggests a recent population bottleneck followed by population expansion. We showed that in the field and greenhouse, cucumber (Cucumis sativus), which was introduced to North America by early Spanish conquistadors, is the most susceptible host plant species and the only species susceptible to isolates from all three lineages. The establishment of large agricultural populations of highly susceptible C. sativus in temperate eastern North America may have facilitated the original emergence of E. tracheiphila into cucurbit agroecosystems, and this introduced plant species may now be acting as a highly susceptible reservoir host. Our findings have broad implications for agricultural sustainability by drawing attention to how worldwide crop plant movement, agricultural intensification, and locally unique environments may affect the emergence, evolution, and epidemic persistence of virulent microbial pathogens.IMPORTANCEErwinia tracheiphila is a virulent phytopathogen that infects two genera of cucurbit crop plants, Cucurbita spp. (pumpkin and squash) and Cucumis spp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate eastern North America. Here, we complete the first large-scale sequencing of an E. tracheiphila isolate collection. From phylogenomic, comparative genomic, and empirical analyses, we find that introduced Cucumis spp. crop plants are driving the diversification of E. tracheiphila into multiple lineages. Together, the results from this study show that locally unique biotic (plant population) and abiotic (climate) conditions can drive the evolutionary trajectories of locally endemic pathogens in unexpected ways.
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Affiliation(s)
- Lori R Shapiro
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., San Francisco, California, USA
| | - Brian J Arnold
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research, Manhattan, Kansas, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
| | - Naomi E Pierce
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jorge Rocha
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
- CIDEA Consortium Conacyt-Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA
| | - Kristina Holton
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Roberto Kolter
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
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Moore CS, Ruocchio MJ, Blakeslee AM. Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries. PeerJ 2018; 6:e5380. [PMID: 30123709 PMCID: PMC6086083 DOI: 10.7717/peerj.5380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/11/2018] [Indexed: 11/25/2022] Open
Abstract
Many species of fish produce larvae that undergo a prolonged dispersal phase. However, evidence from a number of recent studies on demersal fishes suggests that the dispersal of propagules may not be strongly correlated with gene flow. Instead, other factors like larval behavior and the availability of preferred settlement habitat may be more important to maintaining population structure. We used an ecologically important benthic fish species, Gobiosoma bosc (naked goby), to investigate local and regional scale population structure and gene flow along a salinity gradient (∼3 ppt to ∼18 ppt) in two North Carolina estuaries. G. bosc is an abundant and geographically widespread species that requires complex but patchy microhabitat (e.g. oyster reefs, rubble, woody debris) for reproduction and refuge. We sequenced 155 fish from 10 sites, using a common barcoding gene (COI). We also included recent sequence data from GenBank to determine how North Carolina populations fit into the larger biogeographic understanding of this species. In North Carolina, we found a significant amount of gene flow within and between estuaries. Our analysis also showed high predicted genetic diversity based upon a large number of rare haplotypes found within many of our sampled populations. Moreover, we detected a number of new haplotypes in North Carolina that had not yet been observed in prior work. Sampling along a salinity gradient did not reveal any significant positive or negative correlations between salinity and genetic diversity, nor the proportion of singleton haplotypes, with the exception of a positive correlation between salinity standard deviation and genetic diversity. We also found evidence that an introduced European population of naked gobies may have originated from an Atlantic source population. Altogether, this system offers a compelling way to evaluate whether factors other than dispersal per se mediate recruitment in an estuarine-dependent species of fish with a larval dispersal phase. It also demonstrates the importance of exploring both smaller and larger scale population structure in marine organisms to better understand local and regional patterns of population connectivity and gene flow.
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Affiliation(s)
- Christopher S. Moore
- Biology Department, East Carolina University, Greenville, NC, United States of America
| | - Matthew J. Ruocchio
- Biology Department, East Carolina University, Greenville, NC, United States of America
| | - April M.H. Blakeslee
- Biology Department, East Carolina University, Greenville, NC, United States of America
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Mita T, Hombhanje F, Takahashi N, Sekihara M, Yamauchi M, Tsukahara T, Kaneko A, Endo H, Ohashi J. Rapid selection of sulphadoxine-resistant Plasmodium falciparum and its effect on within-population genetic diversity in Papua New Guinea. Sci Rep 2018; 8:5565. [PMID: 29615786 PMCID: PMC5882878 DOI: 10.1038/s41598-018-23811-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
The ability of the human malarial parasite Plasmodium falciparum to adapt to environmental changes depends considerably on its ability to maintain within-population genetic variation. Strong selection, consequent to widespread antimalarial drug usage, occasionally elicits a rapid expansion of drug-resistant isolates, which can act as founders. To investigate whether this phenomenon induces a loss of within-population genetic variation, we performed a population genetic analysis on 302 P. falciparum cases detected during two cross-sectional surveys in 2002/2003, just after the official introduction of sulphadoxine/pyrimethamine as a first-line treatment, and again in 2010/2011, in highly endemic areas in Papua New Guinea. We found that a single-origin sulphadoxine-resistant parasite isolate rapidly increased from 0% in 2002/2003 to 54% in 2010 and 84% in 2011. However, a considerable number of pairs exhibited random associations among 10 neutral microsatellite markers located in various chromosomes, suggesting that outcrossing effectively reduced non-random associations, albeit at a low average multiplicity of infection (1.35–1.52). Within-population genetic diversity was maintained throughout the study period. This indicates that the parasites maintained within-population variation, even after a clonal expansion of drug-resistant parasites. Outcrossing played a role in the preservation of within-population genetic diversity despite low levels of multiplicity of infection.
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Affiliation(s)
- Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Nabasa Road, P.O. Box 483, Madang, Papua New Guinea
| | - Nobuyuki Takahashi
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Makoto Sekihara
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Masato Yamauchi
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Takahiro Tsukahara
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Akira Kaneko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.,Department of Parasitology, Osaka City University Graduate School of Medicine, Asahi-cho 1-4-3, Abeno-ku, Osaka, 545-8585, Japan
| | - Hiroyoshi Endo
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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de Laurent ZR, Chebon LJ, Ingasia LA, Akala HM, Andagalu B, Ochola-Oyier LI, Kamau E. Polymorphisms in the K13 Gene in Plasmodium falciparum from Different Malaria Transmission Areas of Kenya. Am J Trop Med Hyg 2018; 98:1360-1366. [PMID: 29582728 DOI: 10.4269/ajtmh.17-0505] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The development of artemisinin (ART)-resistant parasites in Southeast Asia (SEA) threatens malaria control globally. Mutations in the Kelch 13 (K13)-propeller domain have been useful in identifying ART resistance in SEA. ART combination therapy (ACT) remains highly efficacious in the treatment of uncomplicated malaria in Sub-Saharan Africa (SSA). However, it is crucial that the efficacy of ACT is closely monitored. Toward this effort, this study profiled the prevalence of K13 nonsynonymous mutations in different malaria ecological zones of Kenya and in different time periods, before (pre) and after (post) the introduction of ACT as the first-line treatment of malaria. Nineteen nonsynonymous mutations were present in the pre-ACT samples (N = 64) compared with 22 in the post-ACT samples (N = 251). Eight of these mutations were present in both pre- and post-ACT parasites. Interestingly, seven of the shared single-nucleotide polymorphisms were at higher frequencies in the pre-ACT than the post-ACT parasites. The A578S mutation reported in SSA and the V568G mutation reported in SEA were found in both pre- and post-ACT parasites, with their frequencies declining post-ACT. D584Y and R539K mutations were found only in post-ACT parasites; changes in these codons have also been reported in SEA with different amino acids. The N585K mutation described for the first time in this study was present only in post-ACT parasites, and it was the most prevalent mutation at a frequency of 5.2%. This study showed the type, prevalence, and frequency of K13 mutations that varied based on the malaria ecological zones and also between the pre- and post-ACT time periods.
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Affiliation(s)
- Zaydah R de Laurent
- Center for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya.,Kenya Medical Research Institute/United States Army Medical Research Directorate-Kenya, Kisumu, Kenya
| | - Lorna J Chebon
- Kenya Medical Research Institute/United States Army Medical Research Directorate-Kenya, Kisumu, Kenya
| | - Luicer A Ingasia
- Kenya Medical Research Institute/United States Army Medical Research Directorate-Kenya, Kisumu, Kenya
| | - Hoseah M Akala
- Kenya Medical Research Institute/United States Army Medical Research Directorate-Kenya, Kisumu, Kenya
| | - Ben Andagalu
- Kenya Medical Research Institute/United States Army Medical Research Directorate-Kenya, Kisumu, Kenya
| | - Lynette Isabella Ochola-Oyier
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Center for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Edwin Kamau
- Kenya Medical Research Institute/United States Army Medical Research Directorate-Kenya, Kisumu, Kenya.,Walter Reed National Military Medical Center (WRNMMC), Bethesda, Maryland
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45
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Ma S, Cahalan S, LaMonte G, Grubaugh ND, Zeng W, Murthy SE, Paytas E, Gamini R, Lukacs V, Whitwam T, Loud M, Lohia R, Berry L, Khan SM, Janse CJ, Bandell M, Schmedt C, Wengelnik K, Su AI, Honore E, Winzeler EA, Andersen KG, Patapoutian A. Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection. Cell 2018; 173:443-455.e12. [PMID: 29576450 DOI: 10.1016/j.cell.2018.02.047] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/06/2018] [Accepted: 02/14/2018] [Indexed: 01/05/2023]
Abstract
Hereditary xerocytosis is thought to be a rare genetic condition characterized by red blood cell (RBC) dehydration with mild hemolysis. RBC dehydration is linked to reduced Plasmodium infection in vitro; however, the role of RBC dehydration in protection against malaria in vivo is unknown. Most cases of hereditary xerocytosis are associated with gain-of-function mutations in PIEZO1, a mechanically activated ion channel. We engineered a mouse model of hereditary xerocytosis and show that Plasmodium infection fails to cause experimental cerebral malaria in these mice due to the action of Piezo1 in RBCs and in T cells. Remarkably, we identified a novel human gain-of-function PIEZO1 allele, E756del, present in a third of the African population. RBCs from individuals carrying this allele are dehydrated and display reduced Plasmodium infection in vitro. The existence of a gain-of-function PIEZO1 at such high frequencies is surprising and suggests an association with malaria resistance.
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Affiliation(s)
- Shang Ma
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stuart Cahalan
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gregory LaMonte
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Nathan D Grubaugh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Weizheng Zeng
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Swetha E Murthy
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Emma Paytas
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Ramya Gamini
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Viktor Lukacs
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tess Whitwam
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meaghan Loud
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rakhee Lohia
- DIMNP, CNRS, INSERM, University Montpellier, Montpellier, France
| | - Laurence Berry
- DIMNP, CNRS, INSERM, University Montpellier, Montpellier, France
| | - Shahid M Khan
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center (LUMC), 2333ZA Leiden, the Netherlands
| | - Chris J Janse
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center (LUMC), 2333ZA Leiden, the Netherlands
| | - Michael Bandell
- Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Christian Schmedt
- Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Kai Wengelnik
- DIMNP, CNRS, INSERM, University Montpellier, Montpellier, France
| | - Andrew I Su
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Eric Honore
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Paris, France; Institut de Pharmacologie Moléculaire et Cellulaire, Labex ICST, Valbonne, France
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ardem Patapoutian
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Rojas-Velázquez L, Morán P, Serrano-Vázquez A, Fernández LD, Pérez-Juárez H, Poot-Hernández AC, Portillo T, González E, Hernández E, Partida-Rodríguez O, Nieves-Ramírez ME, Magaña U, Torres J, Eguiarte LE, Piñero D, Ximénez C. Genetic Diversity and Distribution of Blastocystis Subtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3916263. [PMID: 29744356 PMCID: PMC5878905 DOI: 10.1155/2018/3916263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/11/2018] [Indexed: 02/01/2023]
Abstract
Blastocystis subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of Blastocystis ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of Blastocystis ST3 from other regions of the planet. Our analyses reveled that diversity of Blastocystis ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity of Blastocystis ST3 worldwide.
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Affiliation(s)
- Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
- Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Circuito de Posgrado S/N, Coyoacán, Cd. Universitaria, 04510 Ciudad de México, Mexico
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
| | - Leonardo D. Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Avenida Viel 1497, Santiago, Chile
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
- Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Circuito de Posgrado S/N, Coyoacán, Cd. Universitaria, 04510 Ciudad de México, Mexico
| | - Augusto C. Poot-Hernández
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Sección de Ingeniería de Sistemas Computacionales, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México (UNAM), Circuito Escolar 3000, Cd. Universitaria, Coyoacán, 04510 Ciudad de México, Mexico
| | - Tobías Portillo
- Unidad de Bioinformática, Bioestadística y Biología Computacional, Red de Apoyo a la Investigación, Coordinación de la Investigación Científica, UNAM, Instituto Nacional de Ciencias Médicas y Nutrición, Vasco de Quiroga 15, Tlalpan, 14080 Ciudad de México, Mexico
| | - Enrique González
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
| | - Eric Hernández
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
| | - Oswaldo Partida-Rodríguez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
| | - Miriam E. Nieves-Ramírez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
| | - Ulises Magaña
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
- Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Circuito de Posgrado S/N, Coyoacán, Cd. Universitaria, 04510 Ciudad de México, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Avenida Cuauhtémoc 330, Doctores, Cuauhtémoc, 06720 Ciudad de México, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior S/N, Junto al Jardín Botánico, Cd. Universitaria, Coyoacán, 04510 Ciudad de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior S/N, Junto al Jardín Botánico, Cd. Universitaria, Coyoacán, 04510 Ciudad de México, Mexico
| | - Cecilia Ximénez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Dr. Balmis 148, Doctores, Cuauhtémoc, 06726 Ciudad de México, Mexico
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Abel L, Fellay J, Haas DW, Schurr E, Srikrishna G, Urbanowski M, Chaturvedi N, Srinivasan S, Johnson DH, Bishai WR. Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectives. THE LANCET. INFECTIOUS DISEASES 2018; 18:e64-e75. [DOI: 10.1016/s1473-3099(17)30623-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 02/07/2023]
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48
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Human migration and the spread of malaria parasites to the New World. Sci Rep 2018; 8:1993. [PMID: 29386521 PMCID: PMC5792595 DOI: 10.1038/s41598-018-19554-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/03/2018] [Indexed: 01/02/2023] Open
Abstract
We examined the mitogenomes of a large global collection of human malaria parasites to explore how and when Plasmodium falciparum and P. vivax entered the Americas. We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans. Importantly, mitochondrial lineages of the P. vivax-like species P. simium are shared by platyrrhine monkeys and humans in the Atlantic Forest ecosystem, but not across the Amazon, which most likely resulted from one or a few recent human-to-monkey transfers. While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax.
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49
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Fu R, Martin C, Zhang Y. Next-Generation Plant Metabolic Engineering, Inspired by an Ancient Chinese Irrigation System. MOLECULAR PLANT 2018; 11:47-57. [PMID: 28893713 DOI: 10.1016/j.molp.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/06/2017] [Accepted: 09/01/2017] [Indexed: 05/03/2023]
Abstract
Specialized secondary metabolites serve not only to protect plants against abiotic and biotic challenges, but have also been used extensively by humans to combat diseases. Due to the great importance of medicinal plants for health, we need to find new and sustainable ways to improve the production of the specialized metabolites. In addition to direct extraction, recent progress in metabolic engineering of plants offers an alternative supply option. We argue that metabolic engineering for producing the secondary metabolites in plants may have distinct advantages over microbial production platforms, and thus propose new approaches of plant metabolic engineering, which are inspired by an ancient Chinese irrigation system. Metabolic engineering strategies work at three levels: introducing biosynthetic genes, using transcription factors, and improving metabolic flux including increasing the supply of precursors, energy, and reducing power. In addition, recent progress in biotechnology contributes markedly to better engineering, such as the use of specific promoters and the deletion of competing branch pathways. We propose that next-generation plant metabolic engineering will improve current engineering strategies, for the purpose of producing valuable metabolites in plants on industrial scales.
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Affiliation(s)
- Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
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Rougeron V, Tiedje KE, Chen DS, Rask TS, Gamboa D, Maestre A, Musset L, Legrand E, Noya O, Yalcindag E, Renaud F, Prugnolle F, Day KP. Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance. Ecol Evol 2017; 7:9376-9390. [PMID: 29187975 PMCID: PMC5696401 DOI: 10.1002/ece3.3425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/07/2017] [Accepted: 08/19/2017] [Indexed: 11/11/2022] Open
Abstract
Strong founder effects resulting from human migration out of Africa have led to geographic variation in single nucleotide polymorphisms (SNPs) and microsatellites (MS) of the malaria parasite, Plasmodium falciparum. This is particularly striking in South America where two major founder populations of P. falciparum have been identified that are presumed to have arisen from the transatlantic slave trade. Given the importance of the major variant surface antigen of the blood stages of P. falciparum as both a virulence factor and target of immunity, we decided to investigate the population genetics of the genes encoding “Plasmodium falciparum Erythrocyte Membrane Protein 1” (PfEMP1) among several countries in South America, in order to evaluate the transmission patterns of malaria in this continent. Deep sequencing of the DBLα domain of var genes from 128 P. falciparum isolates from five locations in South America was completed using a 454 high throughput sequencing protocol. Striking geographic variation in var DBLα sequences, similar to that seen for SNPs and MS markers, was observed. Colombia and French Guiana had distinct var DBLα sequences, whereas Peru and Venezuela showed an admixture. The importance of such geographic variation to herd immunity and malaria vaccination is discussed.
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Affiliation(s)
- Virginie Rougeron
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Kathryn E Tiedje
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Donald S Chen
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA
| | - Thomas S Rask
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt and Departamento de Ciencias Celulares y Moleculares Facultad de Ciencias y Filosofia Universidad Peruana Cayetano Heredia Lima Peru
| | - Amanda Maestre
- Grupo Salud y Comunidad Facultad de Medicina Universidad de Antioquía Medellín Colombia
| | - Lise Musset
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana
| | - Eric Legrand
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana.,Unit of Genetics and Genomics on Insect Vectors Institut Pasteur Paris France
| | - Oscar Noya
- Centro para Estudios Sobre Malaria Instituto de Altos Estudios en Salud "Dr. Arnoldo Gabaldón" Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical Universidad Central de Venezuela Caracas Venezuela
| | - Erhan Yalcindag
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - François Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Franck Prugnolle
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Karen P Day
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
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