1
|
Gupta H, Sharma S, Gilyazova I, Satyamoorthy K. Molecular tools are crucial for malaria elimination. Mol Biol Rep 2024; 51:555. [PMID: 38642192 DOI: 10.1007/s11033-024-09496-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
The eradication of Plasmodium parasites, responsible for malaria, is a daunting global public health task. It requires a comprehensive approach that addresses symptomatic, asymptomatic, and submicroscopic cases. Overcoming this challenge relies on harnessing the power of molecular diagnostic tools, as traditional methods like microscopy and rapid diagnostic tests fall short in detecting low parasitaemia, contributing to the persistence of malaria transmission. By precisely identifying patients of all types and effectively characterizing malaria parasites, molecular tools may emerge as indispensable allies in the pursuit of malaria elimination. Furthermore, molecular tools can also provide valuable insights into parasite diversity, drug resistance patterns, and transmission dynamics, aiding in the implementation of targeted interventions and surveillance strategies. In this review, we explore the significance of molecular tools in the pursuit of malaria elimination, shedding light on their key contributions and potential impact on public health.
Collapse
Affiliation(s)
- Himanshu Gupta
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Sonal Sharma
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Irina Gilyazova
- Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, 450054, Russia
- Bashkir State Medical University, Ufa, 450008, Russia
| | - Kapaettu Satyamoorthy
- SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur, Dharwad, 580009, Karnataka, India
| |
Collapse
|
2
|
Kattenberg JH, Monsieurs P, De Meyer J, De Meulenaere K, Sauve E, de Oliveira TC, Ferreira MU, Gamboa D, Rosanas‐Urgell A. Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America. Ecol Evol 2024; 14:e11103. [PMID: 38529021 PMCID: PMC10961478 DOI: 10.1002/ece3.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility - crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.
Collapse
Affiliation(s)
| | - Pieter Monsieurs
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Julie De Meyer
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Present address:
Integrated Molecular Plant physiology Research (IMPRES) and Plants and Ecosystems (PLECO), Department of BiologyUniversity of AntwerpAntwerpBelgium
| | | | - Erin Sauve
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Thaís C. de Oliveira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical MedicineNova University of LisbonLisbonPortugal
| | - Dionicia Gamboa
- Instituto de Medicina Tropical “Alexander von Humboldt”Universidad Peruana Cayetano HerediaLimaPeru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e IngenieríaUniversidad Peruana Cayetano HerediaLimaPeru
| | | |
Collapse
|
3
|
De Meulenaere K, Cuypers B, Gamboa D, Laukens K, Rosanas-Urgell A. A new Plasmodium vivax reference genome for South American isolates. BMC Genomics 2023; 24:606. [PMID: 37821878 PMCID: PMC10568799 DOI: 10.1186/s12864-023-09707-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering. RESULTS This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions. CONCLUSIONS Our findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.
Collapse
Affiliation(s)
- Katlijn De Meulenaere
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
- Department of Computer Science, University of Antwerp, Antwerp, Belgium.
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
| |
Collapse
|
4
|
Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
Collapse
|
5
|
Kattenberg JH, Nguyen HV, Nguyen HL, Sauve E, Nguyen NTH, Chopo-Pizarro A, Trimarsanto H, Monsieurs P, Guetens P, Nguyen XX, Esbroeck MV, Auburn S, Nguyen BTH, Rosanas-Urgell A. Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales. Front Cell Infect Microbiol 2022; 12:953187. [PMID: 36034708 PMCID: PMC9403277 DOI: 10.3389/fcimb.2022.953187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Although the power of genetic surveillance tools has been acknowledged widely, there is an urgent need in malaria endemic countries for feasible and cost-effective tools to implement in national malaria control programs (NMCPs) that can generate evidence to guide malaria control and elimination strategies, especially in the case of Plasmodium vivax. Several genetic surveillance applications (‘use cases’) have been identified to align research, technology development, and public health efforts, requiring different types of molecular markers. Here we present a new highly-multiplexed deep sequencing assay (Pv AmpliSeq). The assay targets the 33-SNP vivaxGEN-geo panel for country-level classification, and a newly designed 42-SNP within-country barcode for analysis of parasite dynamics in Vietnam and 11 putative drug resistance genes in a highly multiplexed NGS protocol with easy workflow, applicable for many different genetic surveillance use cases. The Pv AmpliSeq assay was validated using: 1) isolates from travelers and migrants in Belgium, and 2) routine collections of the national malaria control program at sentinel sites in Vietnam. The assay targets 229 amplicons and achieved a high depth of coverage (mean 595.7 ± 481) and high accuracy (mean error-rate of 0.013 ± 0.007). P. vivax parasites could be characterized from dried blood spots with a minimum of 5 parasites/µL and 10% of minority-clones. The assay achieved good spatial specificity for between-country prediction of origin using the 33-SNP vivaxGEN-geo panel that targets rare alleles specific for certain countries and regions. A high resolution for within-country diversity in Vietnam was achieved using the designed 42-SNP within-country barcode that targets common alleles (median MAF 0.34, range 0.01-0.49. Many variants were detected in (putative) drug resistance genes, with different predominant haplotypes in the pvmdr1 and pvcrt genes in different provinces in Vietnam. The capacity of the assay for high resolution identity-by-descent (IBD) analysis was demonstrated and identified a high rate of shared ancestry within Gia Lai Province in the Central Highlands of Vietnam, as well as between the coastal province of Binh Thuan and Lam Dong. Our approach performed well in geographically differentiating isolates at multiple spatial scales, detecting variants in putative resistance genes, and can be easily adjusted to suit the needs in other settings in a country or region. We prioritize making this tool available to researchers and NMCPs in endemic countries to increase ownership and ensure data usage for decision-making and malaria policy.
Collapse
Affiliation(s)
- Johanna Helena Kattenberg
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
- *Correspondence: Johanna Helena Kattenberg, ; Anna Rosanas-Urgell,
| | - Hong Van Nguyen
- Department of Clinical Research, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Hieu Luong Nguyen
- Department of Clinical Research, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Erin Sauve
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ngoc Thi Hong Nguyen
- Department of Molecular Biology, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Ana Chopo-Pizarro
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Hidayat Trimarsanto
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Pieter Monsieurs
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Guetens
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Xa Xuan Nguyen
- Department of Epidemiology, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Marjan Van Esbroeck
- Clinical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Binh Thi Huong Nguyen
- Department of Clinical Research, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Anna Rosanas-Urgell
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
- *Correspondence: Johanna Helena Kattenberg, ; Anna Rosanas-Urgell,
| |
Collapse
|
6
|
Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
Collapse
Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| |
Collapse
|
7
|
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).
Collapse
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
| |
Collapse
|
8
|
Buyon LE, Elsworth B, Duraisingh MT. The molecular basis of antimalarial drug resistance in Plasmodium vivax. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2021; 16:23-37. [PMID: 33957488 PMCID: PMC8113647 DOI: 10.1016/j.ijpddr.2021.04.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 01/07/2023]
Abstract
Plasmodium vivax is the most geographically widespread cause of human malaria and is responsible for the majority of cases outside of the African continent. While great progress has been made towards eliminating human malaria, drug resistant parasite strains pose a threat towards continued progress. Resistance has arisen to multiple antimalarials in P. vivax, including to chloroquine, which is currently the first line therapy for P. vivax in most regions. Despite its importance, an understanding of the molecular mechanisms of drug resistance in this species remains elusive, in large part due to the complex biology of P. vivax and the lack of in vitro culture. In this review, we will cover the extent and challenges of measuring clinical and in vitro drug resistance in P. vivax. We will consider the roles of candidate drug resistance genes. We will highlight the development of molecular approaches for studying P. vivax biology that provide the opportunity to validate the role of putative drug resistance mutations as well as identify novel mechanisms of drug resistance in this understudied parasite. Validated molecular determinants and markers of drug resistance are essential for the rapid and cost-effective monitoring of drug resistance in P. vivax, and will be useful for optimizing drug regimens and for informing drug policy in control and elimination settings. Drug resistance is emerging in Plasmodium vivax, an important cause of malaria. The complex biology of P. vivax and the limited range of research tools make it difficult to identify drug resistance. The molecular mechanisms of drug resistance in P. vivax remain elusive. This review highlights the extent of drug resistance, the putative mechanisms of resistance and new technologies for the study of P. vivax drug resistance.
Collapse
Affiliation(s)
- Lucas E Buyon
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA.
| |
Collapse
|
9
|
Yakubu B, Longdet IY, Jen TH, Davou DT, Obishakin E. High-Complexity Plasmodium falciparum Infections, North Central Nigeria, 2015-2018. Emerg Infect Dis 2019; 25:1330-1338. [PMID: 31211682 PMCID: PMC6590735 DOI: 10.3201/eid2507.181614] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mass migration that occurred during 2009–2013 and after the insurgency in northeastern Nigeria could have increased malaria incidence and Plasmodium falciparum genetic diversity in North Central Nigeria. To determine P. falciparum sequence diversity in this region, we screened 282 samples collected in regional clinics during 2015–2018 for Plasmodium spp. and, with positive samples, determined P. falciparum infection complexity and allele diversity using PCR. Of 34 P. falciparum–positive samples, 39 msp1, 31 msp2, and 13 glurp alleles were detected, and 88% of infections were polyclonal. We identified trimorphic and dimorphic allele combinations in a high percentage of samples, indicative of a high infection complexity in the study population. High genetic diversity is a catalyst for the evolution of drug-resistant alleles. Improved measures (e.g., better drug quality, diagnostics) are needed to control P. falciparum transmission and reduce the potential for the emergence of drug resistance in Nigeria.
Collapse
|
10
|
Yadav BS, Chaturvedi N, Marina N. Recent Advances in System Based Study for Anti-Malarial Drug Development Process. Curr Pharm Des 2019; 25:3367-3377. [DOI: 10.2174/1381612825666190902162105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022]
Abstract
Background:
Presently, malaria is one of the most prevalent and deadly infectious disease across Africa,
Asia, and America that has now started to spread in Europe. Despite large research being carried out in the
field, still, there is a lack of efficient anti-malarial therapeutics. In this paper, we highlight the increasing efforts
that are urgently needed towards the development and discovery of potential antimalarial drugs, which must be
safe and affordable. The new drugs thus mentioned are also able to counter the spread of malaria parasites that
have been resistant to the existing agents.
Objective:
The main objective of the review is to highlight the recent development in the use of system biologybased
approaches towards the design and discovery of novel anti-malarial inhibitors.
Method:
A huge literature survey was performed to gain advance knowledge about the global persistence of
malaria, its available treatment and shortcomings of the available inhibitors. Literature search and depth analysis
were also done to gain insight into the use of system biology in drug discovery and how this approach could be
utilized towards the development of the novel anti-malarial drug.
Results:
The system-based analysis has made easy to understand large scale sequencing data, find candidate
genes expression during malaria disease progression further design of drug molecules those are complementary of
the target proteins in term of shape and configuration.
Conclusion:
The review article focused on the recent computational advances in new generation sequencing,
molecular modeling, and docking related to malaria disease and utilization of the modern system and network
biology approach to antimalarial potential drug discovery and development.
Collapse
Affiliation(s)
- Brijesh S. Yadav
- Department of Bioengineering, University of Information Science and Technology, Partizahska, Ohrid, Macedonia, the Former Yugoslav Republic of
| | - Navaneet Chaturvedi
- Department of Bioengineering, University of Information Science and Technology, Partizahska, Ohrid, Macedonia, the Former Yugoslav Republic of
| | - Ninoslav Marina
- Department of Bioengineering, University of Information Science and Technology, Partizahska, Ohrid, Macedonia, the Former Yugoslav Republic of
| |
Collapse
|
11
|
Auburn S, Getachew S, Pearson RD, Amato R, Miotto O, Trimarsanto H, Zhu SJ, Rumaseb A, Marfurt J, Noviyanti R, Grigg MJ, Barber B, William T, Goncalves SM, Drury E, Sriprawat K, Anstey NM, Nosten F, Petros B, Aseffa A, McVean G, Kwiatkowski DP, Price RN. Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms. J Infect Dis 2019; 220:1738-1749. [PMID: 30668735 PMCID: PMC6804337 DOI: 10.1093/infdis/jiz016] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/18/2019] [Indexed: 01/12/2023] Open
Abstract
The Horn of Africa harbors the largest reservoir of Plasmodium vivax in the continent. Most of sub-Saharan Africa has remained relatively vivax-free due to a high prevalence of the human Duffy-negative trait, but the emergence of strains able to invade Duffy-negative reticulocytes poses a major public health threat. We undertook the first population genomic investigation of P. vivax from the region, comparing the genomes of 24 Ethiopian isolates against data from Southeast Asia to identify important local adaptions. The prevalence of the Duffy binding protein amplification in Ethiopia was 79%, potentially reflecting adaptation to Duffy negativity. There was also evidence of selection in a region upstream of the chloroquine resistance transporter, a putative chloroquine-resistance determinant. Strong signals of selection were observed in genes involved in immune evasion and regulation of gene expression, highlighting the need for a multifaceted intervention approach to combat P. vivax in the region.
Collapse
Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Sisay Getachew
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, Cambridge
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, Cambridge
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, Cambridge
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
- Mahidol–Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Agency for Assessment and Application of Technology, Jakarta, Indonesia
| | - Sha Joe Zhu
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Matthew J Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society, Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
| | - Bridget Barber
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society, Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society, Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
- Jesselton Medical Centre, Sabah, Malaysia
| | | | | | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Shoklo Malaria Research Unit, Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Beyene Petros
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Sanger Institute, Hinxton, Cambridge
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| |
Collapse
|
12
|
Sá JM, Kaslow SR, Moraes Barros RR, Brazeau NF, Parobek CM, Tao D, Salzman RE, Gibson TJ, Velmurugan S, Krause MA, Melendez-Muniz V, Kite WA, Han PK, Eastman RT, Kim A, Kessler EG, Abebe Y, James ER, Chakravarty S, Orr-Gonzalez S, Lambert LE, Engels T, Thomas ML, Fasinu PS, Serre D, Gwadz RW, Walker L, DeConti DK, Mu J, Bailey JA, Sim BKL, Hoffman SL, Fay MP, Dinglasan RR, Juliano JJ, Wellems TE. Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross. Nat Commun 2019; 10:4300. [PMID: 31541097 PMCID: PMC6754410 DOI: 10.1038/s41467-019-12256-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
Mainstay treatment for Plasmodium vivax malaria has long relied on chloroquine (CQ) against blood-stage parasites plus primaquine against dormant liver-stage forms (hypnozoites), however drug resistance confronts this regimen and threatens malaria control programs. Understanding the basis of P. vivax chloroquine resistance (CQR) will inform drug discovery and malaria control. Here we investigate the genetics of P. vivax CQR by a cross of parasites differing in drug response. Gametocytogenesis, mosquito infection, and progeny production are performed with mixed parasite populations in nonhuman primates, as methods for P. vivax cloning and in vitro cultivation remain unavailable. Linkage mapping of progeny surviving >15 mg/kg CQ identifies a 76 kb region in chromosome 1 including pvcrt, an ortholog of the Plasmodium falciparum CQR transporter gene. Transcriptional analysis supports upregulated pvcrt expression as a mechanism of CQR.
Collapse
Affiliation(s)
- Juliana M Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah R Kaslow
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Roberto R Moraes Barros
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian M Parobek
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dingyin Tao
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Rebecca E Salzman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyler J Gibson
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Michael A Krause
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Viviana Melendez-Muniz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Whitney A Kite
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul K Han
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard T Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adam Kim
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Evan G Kessler
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | | | | | - Sachy Orr-Gonzalez
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lynn E Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Theresa Engels
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marvin L Thomas
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pius S Fasinu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Robert W Gwadz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Larry Walker
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - Derrick K DeConti
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeffrey A Bailey
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | | | | | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Rhoel R Dinglasan
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Emerging Pathogens Institute, Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
13
|
In silico analysis of putative dormancy genes in Plasmodium vivax. Acta Trop 2018; 186:24-34. [PMID: 29959903 DOI: 10.1016/j.actatropica.2018.06.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/21/2018] [Accepted: 06/26/2018] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax is the most widely spread species causing human malaria. The control of malaria caused by P. vivax has been largely hampered by its ability to develop a dormant liver stage that can generate a new blood infection at different periods of time. Unfortunately, the mechanisms of dormancy in P. vivax have not been thoroughly elucidated to date. In this study, the putative dormancy genes were analyzed to select genes with less genetic variability to maintain the function of relapsing. Expression data concerning these genes were searched to support the selection. Protein interactions among selected gene products were identified based on known and predicted protein-protein interaction using String database. Potentially interacting proteins (n = 15) were used to propose a mechanism involved in dormancy based on the differential vesicular transport due to the iron available in the hepatocyte.
Collapse
|
14
|
Silva SR, Almeida ACG, da Silva GAV, Ramasawmy R, Lopes SCP, Siqueira AM, Costa GL, Sousa TN, Vieira JLF, Lacerda MVG, Monteiro WM, de Melo GC. Chloroquine resistance is associated to multi-copy pvcrt-o gene in Plasmodium vivax malaria in the Brazilian Amazon. Malar J 2018; 17:267. [PMID: 30012145 PMCID: PMC6048775 DOI: 10.1186/s12936-018-2411-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/09/2018] [Indexed: 01/08/2023] Open
Abstract
Background The resistance of Plasmodium vivax to chloroquine has become an obstacle to control strategies based on the use of anti-malarials. The current study investigated the association between P. vivax CQ-resistance in vivo with copy number variation and mutations in the promoter region in pvcrt-o and pvmdr1 genes. Methods The study included patients with P. vivax that received supervised treatment with chloroquine and primaquine. Recurrences were actively recorded during this period. Results Among the 60 patients with P. vivax, 25 were CQ-resistant and 35 CQ-susceptible. A frequency of 7.1% of multi-copy pvcrt-o was observed in CQ-susceptible samples and 7.7% in CQ-resistant at D0 (P > 0.05) and 33.3% in CQ-resistant at DR (P < 0.05). For pvmdr1, 10.7% of the CQ-susceptible samples presented multiple copies compared to 11.1% in CQ-resistant at D0 and 0.0% in CQ-resistant at DR (P > 0.05). A deletion of 19 bp was found in 11/23 (47.6%) of the patients with CQ-susceptible P. vivax and 3/10 (23.1%) of the samples with in CQRPv at D0. At day DR, 55.5% of the samples with CQRPv had the 19 bp deletion. For the pvmdr-1 gene, was no variation in the analysed gene compared to the P. vivax reference Sal-1. Conclusions This was the first study with 42-day clinical follow-up to evaluate the variation of the number of copies and polymorphisms in the promoter region of the pvcrt-o and pvmdr1 genes in relation to treatment outcomes. Significantly higher frequency of multi-copy pvcrt-o was found in CQRPv samples at DR compared to CQ-susceptible, indicating parasite selection of this genotype after CQ treatment and its association with CQ-resistance in vivo. Electronic supplementary material The online version of this article (10.1186/s12936-018-2411-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Siuhelem Rocha Silva
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil.,Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, 69040-000, Brazil
| | - Anne Cristine Gomes Almeida
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil.,Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, 69040-000, Brazil
| | | | - Rajendranath Ramasawmy
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil.,Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, 69040-000, Brazil
| | - Stefanie Costa Pinto Lopes
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil.,Instituto Leônidas & Maria Deane (ILMD), Fiocruz, Manaus, Amazonas, 69057-070, Brazil
| | - André Machado Siqueira
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil.,Instituto Nacional de Infectologia, Evandro Chagas, Fiocruz, Rio de Janeiro, 21040-360, Brazil
| | - Gabriel Luíz Costa
- Centro de Pesquisas René Rachou, Fiocruz, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Taís Nóbrega Sousa
- Centro de Pesquisas René Rachou, Fiocruz, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | | | - Marcus Vinícius Guimarães Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil.,Instituto Leônidas & Maria Deane (ILMD), Fiocruz, Manaus, Amazonas, 69057-070, Brazil
| | - Wuelton Marcelo Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil.,Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, 69040-000, Brazil
| | - Gisely Cardoso de Melo
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, 69040-000, Brazil. .,Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, 69040-000, Brazil.
| |
Collapse
|
15
|
Cowell AN, Valdivia HO, Bishop DK, Winzeler EA. Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing. Genome Med 2018; 10:52. [PMID: 29973248 PMCID: PMC6032790 DOI: 10.1186/s13073-018-0563-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plasmodium vivax poses a significant challenge to malaria elimination due to its ability to cause relapsed infections from reactivation of dormant liver parasites called hypnozoites. We analyzed 69 P. vivax whole genome sequences obtained from subjects residing in three different villages along the Peruvian Amazon. This included 23 paired P. vivax samples from subjects who experienced recurrent P. vivax parasitemia following observed treatment with chloroquine and primaquine. METHODS Genomic DNA was extracted from whole blood samples collected from subjects. P. vivax DNA was enriched using selective whole genome amplification and whole genome sequencing. We used single nucleotide polymorphisms (SNPs) from the core P. vivax genome to determine characteristics of the parasite population using discriminant analysis of principal components, maximum likelihood estimation of individual ancestries, and phylogenetic analysis. We estimated the relatedness of the paired samples by calculating the number of segregating sites and using a hidden Markov model approach to estimate identity by descent. RESULTS We present a comprehensive dataset of population genetics of Plasmodium vivax in the Peruvian Amazonian. We define the parasite population structure in this region and demonstrate a novel method for distinguishing homologous relapses from reinfections or heterologous relapses with improved accuracy. The parasite population in this area was quite diverse with an estimated five subpopulations and evidence of a highly heterogeneous ancestry of some of the isolates, similar to previous analyses of P. vivax in this region. Pairwise comparison of recurrent infections determined that there were 12 homologous relapses and 3 likely heterologous relapses with highly related parasites. To the best of our knowledge, this is the first large-scale study to evaluate recurrent P. vivax infections using whole genome sequencing. CONCLUSIONS Whole genome sequencing is a high-resolution tool that can identify P. vivax homologous relapses with increased sensitivity, while also providing data about drug resistance and parasite population genetics. This information is important for evaluating the efficacy of known and novel antirelapse medications in endemic areas and thus advancing the campaign to eliminate malaria.
Collapse
Affiliation(s)
- Annie N Cowell
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
| | - Hugo O Valdivia
- U.S. Naval Medical Research No. 6, Venezuela Ave, Block 36, Bellavista, Callao, Peru
| | - Danett K Bishop
- U.S. Naval Medical Research No. 6, Venezuela Ave, Block 36, Bellavista, Callao, Peru
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| |
Collapse
|
16
|
Bourgard C, Albrecht L, Kayano ACAV, Sunnerhagen P, Costa FTM. Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics. Front Cell Infect Microbiol 2018; 8:34. [PMID: 29473024 PMCID: PMC5809496 DOI: 10.3389/fcimb.2018.00034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022] Open
Abstract
During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp. biology and host-parasite interactions. Among the several parasite species that cause human malaria, the neglected Plasmodium vivax presents great research challenges, as in vitro culturing is not yet feasible and functional assays are heavily limited. Therefore, there are gaps in our P. vivax biology knowledge that affect decisions for control policies aiming to eradicate vivax malaria in the near future. In this review, we provide a snapshot of key discoveries already achieved in P. vivax sequencing projects, focusing on developments, hurdles, and limitations currently faced by the research community, as well as perspectives on future vivax malaria research.
Collapse
Affiliation(s)
- Catarina Bourgard
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Letusa Albrecht
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil.,Laboratory of Regulation of Gene Expression, Instituto Carlos Chagas, Curitiba, Brazil
| | - Ana C A V Kayano
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| |
Collapse
|
17
|
Chen W, Huang Z, Wang W, Mao F, Guan L, Tang Y, Jiang H, Li J, Huang J, Jiang L, Zhu J. Discovery of new antimalarial agents: Second-generation dual inhibitors against FP-2 and PfDHFR via fragments assembely. Bioorg Med Chem 2017; 25:6467-6478. [DOI: 10.1016/j.bmc.2017.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/07/2017] [Accepted: 10/16/2017] [Indexed: 02/02/2023]
|
18
|
Armistead JS, Adams JH. Advancing Research Models and Technologies to Overcome Biological Barriers to Plasmodium vivax Control. Trends Parasitol 2017; 34:114-126. [PMID: 29153587 DOI: 10.1016/j.pt.2017.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 02/06/2023]
Abstract
Malaria prevalence has declined in the past 10 years, especially outside of sub-Saharan Africa. However, the proportion of cases due to Plasmodium vivax is increasing, accounting for up to 90-100% of the malaria burden in endemic regions. Nonetheless, investments in malaria research and control still prioritize Plasmodium falciparum while largely neglecting P. vivax. Specific biological features of P. vivax, particularly invasion of reticulocytes, occurrence of dormant liver forms of the parasite, and the potential for transmission of sexual-stage parasites prior to onset of clinical illness, promote its persistence and hinder development of research tools and interventions. This review discusses recent advances in P. vivax research, current knowledge of its unique biology, and proposes priorities for P. vivax research and control efforts.
Collapse
Affiliation(s)
- Jennifer S Armistead
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA.
| |
Collapse
|
19
|
de Oliveira TC, Rodrigues PT, Menezes MJ, Gonçalves-Lopes RM, Bastos MS, Lima NF, Barbosa S, Gerber AL, Loss de Morais G, Berná L, Phelan J, Robello C, de Vasconcelos ATR, Alves JMP, Ferreira MU. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. PLoS Negl Trop Dis 2017; 11:e0005824. [PMID: 28759591 PMCID: PMC5552344 DOI: 10.1371/journal.pntd.0005824] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/10/2017] [Accepted: 07/20/2017] [Indexed: 01/15/2023] Open
Abstract
Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data. Plasmodium vivax is the most common human malaria parasite in the Americas, but how and when this species arrived in the New World remains unclear. Here we describe high-quality whole-genome sequence data for nine P. vivax isolates from Brazil, a country that accounts for 37% of the malaria burden in this continent, and compare these data with additional publicly available P. vivax genomes from Brazil, Peru, Colombia, and Mexico. P. vivax populations from the New World were found to be as diverse as their counterparts from areas with substantially higher malaria transmission, such as Southeast Asia, and to carry several non-synonymous substitutions in candidate drug-resistance genes. Moreover, genome-wide patterns of linkage disequilibrium between pairs of polymorphic sites are consistent with very frequent outcrossing in these populations. Interestingly, local P. vivax is more polymorphic, with less between-population differentiation, than sympatric populations of P. falciparum, possibly as a result of different demographic histories of these two species in the Americas. We hypothesize that local P. vivax lineages originated from successive migratory waves and subsequent admixture between parasites from geographically diverse sites.
Collapse
Affiliation(s)
- Thais C. de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria José Menezes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Raquel M. Gonçalves-Lopes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Melissa S. Bastos
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nathália F. Lima
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Susana Barbosa
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandra L. Gerber
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Guilherme Loss de Morais
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Luisa Berná
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Robello
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Ana Tereza R. de Vasconcelos
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - João Marcelo P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
| |
Collapse
|
20
|
Shen HM, Chen SB, Wang Y, Xu B, Abe EM, Chen JH. Genome-wide scans for the identification of Plasmodium vivax genes under positive selection. Malar J 2017; 16:238. [PMID: 28587615 PMCID: PMC5461743 DOI: 10.1186/s12936-017-1882-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current trend of Plasmodium vivax cases imported from Southeast Asia into China has sharply increased recently, especially from the China-Myanmar border (CMB) area. High recombination rates of P. vivax populations associated with varied transmission intensity might cause distinct local selective pressures. The information on the genetic variability of P. vivax in this area is scant. Hence, this study assessed the genetic diversity of P. vivax genome sequence in CMB area and aimed to provide information on the positive selection of new gene loci. RESULTS This study reports a genome-wide survey of P. vivax in CMB area, using blood samples from local patients to identify population-specific selective processes. The result showed that considerable genetic diversity and mean pair-wise divergence among the sequenced P. vivax isolates were higher in some important gene families. Using the standardized integrated haplotype score (|iHS|) for all SNPs in chromosomal regions with SNPs above the top 1% distribution, it was observed that the top score locus involved 356 genes and most of them are associated with red blood cell invasion and immune evasion. The XP-EHH test was also applied and some important genes associated with anti-malarial drug resistance were observed in high positive scores list. This result suggests that P. vivax in CMB area is facing more pressure to survive than any other region and this has led to the strong positive selection of genes that are associated with host-parasite interactions. CONCLUSIONS This study suggests that greater genetic diversity in P. vivax from CMB area and positive selection signals in invasion and drug resistance genes are consistent with the history of drug use during malaria elimination programme in CMB area. Furthermore, this result also demonstrates that haplotype-based detecting selection can assist the genome-wide methods to identify the determinants of P. vivax diversity.
Collapse
Affiliation(s)
- Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Yue Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China.,Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, People's Republic of China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Eniola Michael Abe
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China.
| |
Collapse
|
21
|
Diez Benavente E, Ward Z, Chan W, Mohareb FR, Sutherland CJ, Roper C, Campino S, Clark TG. Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure. PLoS One 2017; 12:e0177134. [PMID: 28493919 PMCID: PMC5426636 DOI: 10.1371/journal.pone.0177134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/21/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Although Plasmodium vivax contributes to almost half of all malaria cases outside Africa, it has been relatively neglected compared to the more deadly P. falciparum. It is known that P. vivax populations possess high genetic diversity, differing geographically potentially due to different vector species, host genetics and environmental factors. RESULTS We analysed the high-quality genomic data for 46 P. vivax isolates spanning 10 countries across 4 continents. Using population genetic methods we identified hotspots of selection pressure, including the previously reported MRP1 and DHPS genes, both putative drug resistance loci. Extra copies and deletions in the promoter region of another drug resistance candidate, MDR1 gene, and duplications in the Duffy binding protein gene (PvDBP) potentially involved in erythrocyte invasion, were also identified. For surveillance applications, continental-informative markers were found in putative drug resistance loci, and we show that organellar polymorphisms could classify P. vivax populations across continents and differentiate between Plasmodia spp. CONCLUSIONS This study has shown that genomic diversity that lies within and between P. vivax populations can be used to elucidate potential drug resistance and invasion mechanisms, as well as facilitate the molecular barcoding of the parasite for surveillance applications.
Collapse
Affiliation(s)
- Ernest Diez Benavente
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Zoe Ward
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- The Bioinformatics Group, School of Water Energy and Environment, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Wilson Chan
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- Department of Pathology & Laboratory Medicine, Diagnostic & Scientific Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Fady R. Mohareb
- Department of Pathology & Laboratory Medicine, Diagnostic & Scientific Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Colin J. Sutherland
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Cally Roper
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Susana Campino
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Taane G. Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| |
Collapse
|
22
|
Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples. mBio 2017; 8:mBio.02257-16. [PMID: 28174312 PMCID: PMC5296604 DOI: 10.1128/mbio.02257-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens from clinical samples is a highly sensitive tool used to gain a deeper understanding of the biology, epidemiology, and drug resistance mechanisms of many infections. However, WGS of organisms which exhibit low densities in their hosts is challenging due to high levels of host genomic DNA (gDNA), which leads to very low coverage of the microbial genome. WGS of Plasmodium vivax, the most widely distributed form of malaria, is especially difficult because of low parasite densities and the lack of an ex vivo culture system. Current techniques used to enrich P. vivax DNA from clinical samples require significant resources or are not consistently effective. Here, we demonstrate that selective whole-genome amplification (SWGA) can enrich P. vivax gDNA from unprocessed human blood samples and dried blood spots for high-quality WGS, allowing genetic characterization of isolates that would otherwise have been prohibitively expensive or impossible to sequence. We achieved an average genome coverage of 24×, with up to 95% of the P. vivax core genome covered by ≥5 reads. The single-nucleotide polymorphism (SNP) characteristics and drug resistance mutations seen were consistent with those of other P. vivax sequences from a similar region in Peru, demonstrating that SWGA produces high-quality sequences for downstream analysis. SWGA is a robust tool that will enable efficient, cost-effective WGS of P. vivax isolates from clinical samples that can be applied to other neglected microbial pathogens. Malaria is a disease caused by Plasmodium parasites that caused 214 million symptomatic cases and 438,000 deaths in 2015. Plasmodium vivax is the most widely distributed species, causing the majority of malaria infections outside sub-Saharan Africa. Whole-genome sequencing (WGS) of Plasmodium parasites from clinical samples has revealed important insights into the epidemiology and mechanisms of drug resistance of malaria. However, WGS of P. vivax is challenging due to low parasite levels in humans and the lack of a routine system to culture the parasites. Selective whole-genome amplification (SWGA) preferentially amplifies the genomes of pathogens from mixtures of target and host gDNA. Here, we demonstrate that SWGA is a simple, robust method that can be used to enrich P. vivax genomic DNA (gDNA) from unprocessed human blood samples and dried blood spots for cost-effective, high-quality WGS.
Collapse
|
23
|
Auburn S, Barry AE. Dissecting malaria biology and epidemiology using population genetics and genomics. Int J Parasitol 2016; 47:77-85. [PMID: 27825828 DOI: 10.1016/j.ijpara.2016.08.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
Abstract
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches.
Collapse
Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia.
| |
Collapse
|
24
|
Metabolomic Profiling of the Malaria Box Reveals Antimalarial Target Pathways. Antimicrob Agents Chemother 2016; 60:6635-6649. [PMID: 27572391 DOI: 10.1128/aac.01224-16] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/16/2016] [Indexed: 12/11/2022] Open
Abstract
The threat of widespread drug resistance to frontline antimalarials has renewed the urgency for identifying inexpensive chemotherapeutic compounds that are effective against Plasmodium falciparum, the parasite species responsible for the greatest number of malaria-related deaths worldwide. To aid in the fight against malaria, a recent extensive screening campaign has generated thousands of lead compounds with low micromolar activity against blood stage parasites. A subset of these leads has been compiled by the Medicines for Malaria Venture (MMV) into a collection of structurally diverse compounds known as the MMV Malaria Box. Currently, little is known regarding the activity of these Malaria Box compounds on parasite metabolism during intraerythrocytic development, and a majority of the targets for these drugs have yet to be defined. Here we interrogated the in vitro metabolic effects of 189 drugs (including 169 of the drug-like compounds from the Malaria Box) using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention and offer a critical blueprint for selecting and advancing lead compounds as next-generation antimalarial drugs. Our results reveal several major classes of metabolic disruption, which allow us to predict the mode of action (MoA) for many of the Malaria Box compounds. We anticipate that future combination therapies will be greatly informed by these results, allowing for the selection of appropriate drug combinations that simultaneously target multiple metabolic pathways, with the aim of eliminating malaria and forestalling the expansion of drug-resistant parasites in the field.
Collapse
|
25
|
Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, Ben Mamoun C. Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions. Sci Rep 2016; 6:35284. [PMID: 27752055 PMCID: PMC5082761 DOI: 10.1038/srep35284] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/26/2016] [Indexed: 11/18/2022] Open
Abstract
Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution.
Collapse
Affiliation(s)
- Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Emmanuel Cornillot
- Institut de Biologie Computationnelle, IBC, Université de Montpellier, 860 rue St Priest, Bat 5 - CC05019, 34095 Montpellier, Cedex 5, France
- Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U896 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d’Aurelle, 34298 Montpellier, Cedex 5 France
| | - Carrie McCracken
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Sahar Usmani-Brown
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
- Yale School of Public Health and Yale School of Medicine, 60 College St., New Haven, Connecticut, CT 06520 USA
| | - Ankit Dwivedi
- Institut de Biologie Computationnelle, IBC, Université de Montpellier, 860 rue St Priest, Bat 5 - CC05019, 34095 Montpellier, Cedex 5, France
- Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U896 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d’Aurelle, 34298 Montpellier, Cedex 5 France
| | - Olukemi O. Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Hanzel T. Gotia
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Azan Z. Virji
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| | - Christelle Reynes
- Institut de Genomique Fonctionnelle, IGF - CNRS UMR 5203, 141 rue de la cardonille, 34094 Montpellier, Cedex 05, France
| | - Jacques Colinge
- Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U896 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d’Aurelle, 34298 Montpellier, Cedex 5 France
| | - Vidya Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| | - Lauren Lawres
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| | | | | | - Chris Hung
- Antigen Discovery Inc., Irvine, CA, 92618 USA
| | - Jana Brancato
- Yale School of Public Health and Yale School of Medicine, 60 College St., New Haven, Connecticut, CT 06520 USA
| | - Priti Kumari
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Kyle Tretina
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Marcus Chibucos
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Sandy Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Naomi Sengamalay
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Qi Su
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Roger Frutos
- Université de Montpellier, IES, UMR 5214, 860 rue de St Priest, Bt5, 34095 Montpellier, France
- CIRAD, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, 34398 Montpellier, France
| | | | - Peter J. Krause
- Yale School of Public Health and Yale School of Medicine, 60 College St., New Haven, Connecticut, CT 06520 USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| |
Collapse
|
26
|
Pearson RD, Amato R, Auburn S, Miotto O, Almagro-Garcia J, Amaratunga C, Suon S, Mao S, Noviyanti R, Trimarsanto H, Marfurt J, Anstey NM, William T, Boni MF, Dolecek C, Hien TT, White NJ, Michon P, Siba P, Tavul L, Harrison G, Barry A, Mueller I, Ferreira MU, Karunaweera N, Randrianarivelojosia M, Gao Q, Hubbart C, Hart L, Jeffery B, Drury E, Mead D, Kekre M, Campino S, Manske M, Cornelius VJ, MacInnis B, Rockett KA, Miles A, Rayner JC, Fairhurst RM, Nosten F, Price RN, Kwiatkowski DP. Genomic analysis of local variation and recent evolution in Plasmodium vivax. Nat Genet 2016; 48:959-964. [PMID: 27348299 PMCID: PMC4966634 DOI: 10.1038/ng.3599] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 05/27/2016] [Indexed: 01/12/2023]
Abstract
The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.
Collapse
Affiliation(s)
- Richard D Pearson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Roberto Amato
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Olivo Miotto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
| | - Jacob Almagro-Garcia
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - Seila Suon
- National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sivanna Mao
- Sampov Meas Referral Hospital, Pursat, Cambodia
| | - Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit and Queen Elizabeth Hospital Clinical Research Centre, Kota Kinabalu, Sabah, Malaysia
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tinh Tran Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
| | - Pascal Michon
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Faculty of Medicine and Health Sciences, Divine Word University, Madang, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Gabrielle Harrison
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Alyssa Barry
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivo Mueller
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nadira Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Sri Lanka
| | | | - Qi Gao
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu, People's Republic of China
| | - Christina Hubbart
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Lee Hart
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Eleanor Drury
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Mead
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Susana Campino
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Victoria J Cornelius
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Bronwyn MacInnis
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Kirk A Rockett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Alistair Miles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Julian C Rayner
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rick M Fairhurst
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - Francois Nosten
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
- Shoklo Malaria Research Unit, Mae Sot, Tak 63110, Thailand
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7LJ, UK
| | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| |
Collapse
|
27
|
Venkatesh A, Patel SK, Ray S, Shastri J, Chatterjee G, Kochar SK, Patankar S, Srivastava S. Proteomics ofPlasmodium vivaxmalaria: new insights, progress and potential. Expert Rev Proteomics 2016; 13:771-82. [DOI: 10.1080/14789450.2016.1210515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
28
|
Winter DJ, Pacheco MA, Vallejo AF, Schwartz RS, Arevalo-Herrera M, Herrera S, Cartwright RA, Escalante AA. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia. PLoS Negl Trop Dis 2015; 9:e0004252. [PMID: 26709695 PMCID: PMC4692395 DOI: 10.1371/journal.pntd.0004252] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/30/2015] [Indexed: 11/24/2022] Open
Abstract
Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. Although P. vivax is not as deadly as the more widely studied P. falciparum, it remains a pressing global health problem. Here we report the results of a whole-genome study of P. vivax from Cordóba, Colombia, in South America. This parasite is the most prevalent in this region. We show that the parasite population is genetically diverse, which is contrary to expectations from earlier studies from the Americas. We also find molecular evidence that resistance to an anti-malarial drug has arisen recently in this region. This selective sweep indicates that the parasite has been exposed to a drug that is not used as first-line treatment for this malaria parasite. In addition to extensive single nucleotide and microsatellite polymorphism, we report 18 new genetic loci that might be helpful for fine-scale studies of this species in the Americas.
Collapse
Affiliation(s)
- David J. Winter
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- * E-mail: (DJW); (AAE)
| | - M. Andreína Pacheco
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
| | | | - Rachel S. Schwartz
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Myriam Arevalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | | | - Reed A. Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- The School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Ananias A. Escalante
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (DJW); (AAE)
| |
Collapse
|