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Hu Y, Li Y, Brashear AM, Zeng W, Wu Z, Wang L, Wei H, Soe MT, Aung PL, Sattabongkot J, Kyaw MP, Yang Z, Zhao Y, Cui L, Cao Y. Plasmodium vivax populations in the western Greater Mekong Subregion evaluated using a genetic barcode. PLoS Negl Trop Dis 2024; 18:e0012299. [PMID: 38959285 PMCID: PMC11251639 DOI: 10.1371/journal.pntd.0012299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/16/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024] Open
Abstract
An improved understanding of the Plasmodium vivax populations in the Great Mekong Subregion (GMS) is needed to monitor the progress of malaria elimination. This study aimed to use a P. vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics and explore the gene flow among P. vivax parasite populations in the western GMS (China, Myanmar and Thailand). A total of 315 P. vivax patient samples collected in 2011 and 2018 from four regions of the western GMS were genotyped for 42 SNPs using the high-throughput MassARRAY SNP genotyping technology. Population genetic analysis was conducted to estimate the genetic diversity, effective population size, and population structure among the P. vivax populations. Overall, 291 samples were successfully genotyped at 39 SNPs. A significant difference was observed in the proportion of polyclonal infections among the five P. vivax populations (P = 0.0012, Pearson Chi-square test, χ2 = 18.1), with western Myanmar having the highest proportion (96.2%, 50/52) in 2018. Likewise, the average complexity of infection was also highest in western Myanmar (1.31) and lowest in northeast Myanmar (1.01) in 2018. The older samples from western China in 2011 had the highest pairwise nucleotide diversity (π, 0.388 ± 0.046), expected heterozygosity (He, 0.363 ± 0.02), and the largest effective population size. In comparison, in the neighboring northeast Myanmar, the more recent samples in 2018 showed the lowest values (π, 0.224 ± 0.036; He, 0.220 ± 0.026). Furthermore, the 2018 northeast Myanmar parasites showed high and moderate genetic differentiation from other populations with FST values of 0.162-0.252, whereas genetic differentiation among other populations was relatively low (FST ≤ 0.059). Principal component analysis, phylogeny, and STRUCTURE analysis showed that the P. vivax population in northeast Myanmar in 2018 substantially diverged from other populations. Although the 42 SNP barcode is a valuable tool for tracking parasite origins of worldwide parasite populations, a more extended barcode with additional SNPs is needed to distinguish the more related parasite populations in the western GMS.
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Affiliation(s)
- Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
- Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Awtum M. Brashear
- Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zifang Wu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Lin Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Haichao Wei
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Myat Thu Soe
- Myanmar Health Network Organization, Yangon, Myanmar
| | | | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Liwang Cui
- Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
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Kattenberg JH, Monsieurs P, De Meyer J, De Meulenaere K, Sauve E, de Oliveira TC, Ferreira MU, Gamboa D, Rosanas‐Urgell A. Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America. Ecol Evol 2024; 14:e11103. [PMID: 38529021 PMCID: PMC10961478 DOI: 10.1002/ece3.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility - crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.
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Affiliation(s)
| | - Pieter Monsieurs
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Julie De Meyer
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Present address:
Integrated Molecular Plant physiology Research (IMPRES) and Plants and Ecosystems (PLECO), Department of BiologyUniversity of AntwerpAntwerpBelgium
| | | | - Erin Sauve
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Thaís C. de Oliveira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical MedicineNova University of LisbonLisbonPortugal
| | - Dionicia Gamboa
- Instituto de Medicina Tropical “Alexander von Humboldt”Universidad Peruana Cayetano HerediaLimaPeru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e IngenieríaUniversidad Peruana Cayetano HerediaLimaPeru
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3
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Higgins M, Manko E, Ward D, Phelan JE, Nolder D, Sutherland CJ, Clark TG, Campino S. New reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri. Sci Rep 2024; 14:3843. [PMID: 38360879 PMCID: PMC10869833 DOI: 10.1038/s41598-024-54382-5] [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: 11/03/2023] [Accepted: 02/12/2024] [Indexed: 02/17/2024] Open
Abstract
Despite Plasmodium ovale curtisi (Poc) and wallikeri (Pow) being important human-infecting malaria parasites that are widespread across Africa and Asia, little is known about their genome diversity. Morphologically identical, Poc and Pow are indistinguishable and commonly misidentified. Recent rises in the incidence of Poc/Pow infections have renewed efforts to address fundamental knowledge gaps in their biology, and to develop diagnostic tools to understand their epidemiological dynamics and malaria burden. A major roadblock has been the incompleteness of available reference assemblies (PocGH01, PowCR01; ~ 33.5 Mbp). Here, we applied multiple sequencing platforms and advanced bioinformatics tools to generate new reference genomes, Poc221 (South Sudan; 36.0 Mbp) and Pow222 (Nigeria; 34.3 Mbp), with improved nuclear genome contiguity (> 4.2 Mbp), annotation and completeness (> 99% Plasmodium spp., single copy orthologs). Subsequent sequencing of 6 Poc and 15 Pow isolates from Africa revealed a total of 22,517 and 43,855 high-quality core genome SNPs, respectively. Genome-wide levels of nucleotide diversity were determined to be 2.98 × 10-4 (Poc) and 3.43 × 10-4 (Pow), comparable to estimates for other Plasmodium species. Overall, the new reference genomes provide a robust foundation for dissecting the biology of Poc/Pow, their population structure and evolution, and will contribute to uncovering the recombination barrier separating these species.
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Affiliation(s)
- Matthew Higgins
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Emilia Manko
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Daniel Ward
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Debbie Nolder
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- UK Health Security Agency, Malaria Reference Laboratory, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Colin J Sutherland
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- UK Health Security Agency, Malaria Reference Laboratory, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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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.
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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.
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Kundu P, Naskar D, McKie SJ, Dass S, Kanjee U, Introini V, Ferreira MU, Cicuta P, Duraisingh M, Deane JE, Rayner JC. The structure of a Plasmodium vivax Tryptophan Rich Antigen domain suggests a lipid binding function for a pan-Plasmodium multi-gene family. Nat Commun 2023; 14:5703. [PMID: 37709739 PMCID: PMC10502043 DOI: 10.1038/s41467-023-40885-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 08/10/2023] [Indexed: 09/16/2023] Open
Abstract
Tryptophan Rich Antigens (TRAgs) are encoded by a multi-gene family found in all Plasmodium species, but are significantly expanded in P. vivax and closely related parasites. We show that multiple P. vivax TRAgs are expressed on the merozoite surface and that one, PVP01_0000100 binds red blood cells with a strong preference for reticulocytes. Using X-ray crystallography, we solved the structure of the PVP01_0000100 C-terminal tryptophan rich domain, which defines the TRAg family, revealing a three-helical bundle that is conserved across Plasmodium and has structural homology with lipid-binding BAR domains involved in membrane remodelling. Biochemical assays confirm that the PVP01_0000100 C-terminal domain has lipid binding activity with preference for sulfatide, a glycosphingolipid present in the outer leaflet of plasma membranes. Deletion of the putative orthologue in P. knowlesi, PKNH_1300500, impacts invasion in reticulocytes, suggesting a role during this essential process. Together, this work defines an emerging molecular function for the Plasmodium TRAg family.
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Affiliation(s)
- Prasun Kundu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Deboki Naskar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Shannon J McKie
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Sheena Dass
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Viola Introini
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal
| | - Pietro Cicuta
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Manoj Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
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Yusuff SI, Tajudeen YA, Oladunjoye IO, Oladipo HJ, Bolarinwa OV, Popoola OT, Ahmed AF, Olana MD. The need to increase antimicrobial resistance surveillance among forcibly displaced persons (FDPs). Trop Dis Travel Med Vaccines 2023; 9:12. [PMID: 37653439 PMCID: PMC10472691 DOI: 10.1186/s40794-023-00198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/19/2023] [Indexed: 09/02/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to human health as 4.95 million deaths were associated with bacterial AMR in 2019 and is projected to reach 10 million by 2050. To mitigate AMR, surveillance is an essential tool for determining the burden of AMR and providing the necessary information for its control. However, the global AMR surveillance is inadequate and particularly limited among forcibly displaced persons (FDPs) despite having higher risks of harboring these pathogens. Predisposing factors among this group include poor living conditions, limited access to treatment and diagnostic tests, and inadequate trained health professionals in refugee camps. Strengthening AMR surveillance among FDPs would address the identified gaps and facilitate formulation and implementation of evidence-based policies on AMR control and prevention response. This article provides information on the growing population of FDPs, factors contributing to the AMR burden and AMR surveillance gaps in FDPs and highlighted recommendations for control.
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Affiliation(s)
- Sodiq Inaolaji Yusuff
- Department of Medicine, Faculty of Clinical Sciences, Obafemi Awolowo University, Ibadan-Ife Rd, Ife, 220101, Osun State, Nigeria
| | - Yusuf Amuda Tajudeen
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
- Department of Epidemiology and Medical Statistics, Faculty of Public Health, College of Medicine, University of Ibadan, P.M.B 5017 G.P.O, Ibadan, Oyo State, Nigeria
| | - Iyiola Olatunji Oladunjoye
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
| | - Habeebullah Jayeola Oladipo
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
- Faculty of Pharmaceutical Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
| | | | - Olalekan Tolulope Popoola
- Department of Public Health, Health Sciences Centre, University College, Dublin, 4 Stillorgan Rd, Belfield, Dublin 4, Ireland
| | - Abdulhakeem Funsho Ahmed
- Faculty of Health Sciences, Department of Public Health, Al-Hikmah University, Ilorin, 240281, Kwara State, Nigeria
- Institute of Basic and Applied Science, Department of Science Laboratory Technology, Kwara State Polytechnic, P.M.B 1375, Ilorin, Kwara State, Nigeria
| | - Matifan Dereje Olana
- Department of Medical Laboratory Sciences, Collage of Medicine and Health Sciences, Ambo University, Ambo, Ethiopia.
- Department of Microbiology, Immunology and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box 9086, Addis Ababa, Ethiopia.
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Dash R, Skillman KM, Pereira L, Mascarenhas A, Dass S, Walke J, Almeida A, Fernandes M, Gomes E, White J, Chery-Karschney L, Khandeparkar A, Rathod PK, Duraisingh MT, Kanjee U. Development of a Plasmodium vivax biobank for functional ex vivo assays. Malar J 2023; 22:250. [PMID: 37653486 PMCID: PMC10470152 DOI: 10.1186/s12936-023-04668-2] [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: 03/17/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Plasmodium vivax is the second most prevalent cause of malaria yet remains challenging to study due to the lack of a continuous in vitro culture system, highlighting the need to establish a biobank of clinical isolates with multiple freezes per sample for use in functional assays. Different methods for cryopreserving parasite isolates were compared and subsequently the most promising one was validated. Enrichment of early- and late-stage parasites and parasite maturation were quantified to facilitate assay planning. METHODS In order to compare cryopreservation protocols, nine clinical P. vivax isolates were frozen with four glycerolyte-based mixtures. Parasite recovery post thaw, post KCl-Percoll enrichment and in short-term in vitro culture was measured via slide microscopy. Enrichment of late-stage parasites by magnetic activated cell sorting (MACS) was measured. Short and long-term storage of parasites at either - 80 °C or liquid nitrogen were also compared. RESULTS Of the four cryopreservation mixtures, one mixture (glycerolyte:serum:RBC at a 2.5:1.5:1 ratio) resulted in improved parasite recovery and statistically significant (P < 0.05) enhancement in parasite survival in short-term in vitro culture. A parasite biobank was subsequently generated using this protocol resulting in a collection of 106 clinical isolates, each with 8 vials. The quality of the biobank was validated by measuring several factors from 47 thaws: the average reduction in parasitaemia post-thaw (25.3%); the average fold enrichment post KCl-Percoll (6.65-fold); and the average percent recovery of parasites (22.0%, measured from 30 isolates). During short-term in vitro culture, robust maturation of ring stage parasites to later stages (> 20% trophozoites, schizonts and gametocytes) was observed in 60.0% of isolates by 48 h. Enrichment of mature parasite stages via MACS showed good reproducibility, with an average of 30.0% post-MACS parasitaemia and an average of 5.30 × 105 parasites/vial. Finally, the effect of storage temperature was tested, and no large impacts from short-term (7 days) or long-term (7-10 years) storage at - 80 °C on parasite recovery, enrichment or viability was observed. CONCLUSIONS Here, an optimized freezing method for P. vivax clinical isolates is demonstrated as a template for the generation and validation of a parasite biobank for use in functional assays.
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Affiliation(s)
- Rashmi Dash
- Goa Medical College and Hospital, Bambolim, Goa, 403202, India
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Kristen M Skillman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ligia Pereira
- Goa Medical College and Hospital, Bambolim, Goa, 403202, India
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Anjali Mascarenhas
- Goa Medical College and Hospital, Bambolim, Goa, 403202, India
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Sheena Dass
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jayashri Walke
- Goa Medical College and Hospital, Bambolim, Goa, 403202, India
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Anvily Almeida
- Goa Medical College and Hospital, Bambolim, Goa, 403202, India
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Mezia Fernandes
- Goa Medical College and Hospital, Bambolim, Goa, 403202, India
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Edwin Gomes
- Goa Medical College and Hospital, Bambolim, Goa, 403202, India
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Laura Chery-Karschney
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | | | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
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8
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Dash R, Skillman KM, Pereira L, Mascarenhas A, Dass S, Walke J, Almeida A, Fernandes M, Gomes E, White J, Chery-Karschney L, Khandeparkar A, Rathod PK, Duraisingh MT, Kanjee U. Development of a Plasmodium vivax biobank for functional ex vivo assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533128. [PMID: 36993272 PMCID: PMC10055260 DOI: 10.1101/2023.03.17.533128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Plasmodium vivax is the second most prevalent cause of malaria yet remains challenging to study due to the lack of a continuous in vitro culture system, highlighting the need to establish a biobank of clinical isolates with multiple freezes per sample for use in functional assays. Different methods for cryopreserving parasite isolates were compared and subsequently the most promising one was validated. Enrichment of early- and late-stage parasites and parasite maturation were quantified to facilitate assay planning. Methods In order to compare cryopreservation protocols, nine clinical P. vivax isolates were frozen with four glycerolyte-based mixtures. Parasite recovery post thaw, post KCl-Percoll enrichment and in short-term in vitro culture was measured via slide microscopy. Enrichment of late-stage parasites by magnetic activated cell sorting (MACS) was measured. Short and long-term storage of parasites at either -80°C or liquid nitrogen were also compared. Results Of the four cryopreservation mixtures, one mixture (glycerolyte:serum:RBC at a 2.5:1.5:1 ratio) resulted in improved parasite recovery and statistically significant (P<0.05) enhancement in parasite survival in short-term in vitro culture. A parasite biobank was subsequently generated using this protocol resulting in a collection with 106 clinical isolates, each with 8 vials. The quality of the biobank was validated by measuring several factors from 47 thaws: the average reduction in parasitemia post-thaw (25.3%); the average fold enrichment post KCl-Percoll (6.65-fold); and the average percent recovery of parasites (22.0%, measured from 30 isolates). During short-term in vitro culture, robust maturation of ring stage parasites to later stages (>20% trophozoites, schizonts and gametocytes) was observed in 60.0% of isolates by 48 hours. Enrichment of mature parasite stages via MACS showed good reproducibility, with an average 30.0% post-MACS parasitemia and an average 5.30 × 10 5 parasites/vial. Finally, the effect of storage temperature was tested, and no large impacts from short-term (7 day) or long term (7 - 10 year) storage at -80°C on parasite recovery, enrichment or viability was observed. Conclusions Here, an optimized freezing method for P. vivax clinical isolates is demonstrated as a template for the generation and validation of a parasite biobank for use in functional assays.
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9
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Ibrahim A, Manko E, Dombrowski JG, Campos M, Benavente ED, Nolder D, Sutherland CJ, Nosten F, Fernandez D, Vélez-Tobón G, Castaño AT, Aguiar ACC, Pereira DB, da Silva Santos S, Suarez-Mutis M, Di Santi SM, Regina de Souza Baptista A, Dantas Machado RL, Marinho CR, Clark TG, Campino S. Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America. LANCET REGIONAL HEALTH. AMERICAS 2023; 18:100420. [PMID: 36844008 PMCID: PMC9950661 DOI: 10.1016/j.lana.2022.100420] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 01/03/2023]
Abstract
Background Brazil is a unique and understudied setting for malaria, with complex foci of transmission associated with human and environmental conditions. An understanding of the population genomic diversity of P. vivax parasites across Brazil can support malaria control strategies. Methods Through whole genome sequencing of P. vivax isolates across 7 Brazilian states, we use population genomic approaches to compare genetic diversity within country (n = 123), continent (6 countries, n = 315) and globally (26 countries, n = 885). Findings We confirm that South American isolates are distinct, have more ancestral populations than the other global regions, with differentiating mutations in genes under selective pressure linked to antimalarial drugs (pvmdr1, pvdhfr-ts) and mosquito vectors (pvcrmp3, pvP45/48, pvP47). We demonstrate Brazil as a distinct parasite population, with signals of selection including ABC transporter (PvABCI3) and PHIST exported proteins. Interpretation Brazil has a complex population structure, with evidence of P. simium infections and Amazonian parasites separating into multiple clusters. Overall, our work provides the first Brazil-wide analysis of P. vivax population structure and identifies important mutations, which can inform future research and control measures. Funding AI is funded by an MRC LiD PhD studentship. TGC is funded by the Medical Research Council (Grant no. MR/M01360X/1, MR/N010469/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1). SC is funded by Medical Research Council UK grants (MR/M01360X/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1) and Bloomsbury SET (ref. CCF17-7779). FN is funded by The Shloklo Malaria Research Unit - part of the Mahidol Oxford Research Unit, supported by the Wellcome Trust (Grant no. 220211). ARSB is funded by São Paulo Research Foundation - FAPESP (Grant no. 2002/09546-1). RLDM is funded by Brazilian National Council for Scientific and Technological Development - CNPq (Grant no. 302353/2003-8 and 471605/2011-5); CRFM is funded by FAPESP (Grant no. 2020/06747-4) and CNPq (Grant no. 302917/2019-5 and 408636/2018-1); JGD is funded by FAPESP fellowships (2016/13465-0 and 2019/12068-5) and CNPq (Grant no. 409216/2018-6).
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Affiliation(s)
- Amy Ibrahim
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Emilia Manko
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Jamille G. Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Mónica Campos
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Debbie Nolder
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Colin J. Sutherland
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research
Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak,
Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of
Clinical Medicine Research Building, University of Oxford Old Road Campus,
Oxford, UK
| | - Diana Fernandez
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | - Gabriel Vélez-Tobón
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | | | | | | | - Simone da Silva Santos
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | - Martha Suarez-Mutis
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | | | - Andrea Regina de Souza Baptista
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Ricardo Luiz Dantas Machado
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Claudio R.F. Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Taane G. Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Faculty of Epidemiology & Population Health, London School of Hygiene
& Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
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10
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Villena FE, Sanchez JF, Nolasco O, Braga G, Ricopa L, Barazorda K, Salas CJ, Lucas C, Lizewski SE, Joya CA, Gamboa D, Delgado-Ratto C, Valdivia HO. Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon. Sci Rep 2022; 12:16474. [PMID: 36182962 PMCID: PMC9526214 DOI: 10.1038/s41598-022-21028-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022] Open
Abstract
Malaria is a major health problem in Peru despite substantial progress achieved by the ongoing malaria elimination program. This study explored the population genetics of 63 Plasmodium falciparum and 170 P. vivax cases collected in the Peruvian Amazon Basin between 2015 and 2019. Microscopy and PCR were used for malaria detection and positive samples were genotyped at neutral and drug resistance-associated regions. The P. falciparum population exhibited a low nucleotide diversity (π = 0.02) whereas the P. vivax population presented a higher genetic diversity (π = 0.34). All P. falciparum samples (n = 63) carried chloroquine (CQ) resistant mutations on Pfcrt. Most P. falciparum samples (53 out of 54) carried sulfadoxine (SD) resistant mutations on Pfdhfr and Pfdhps. No evidence was found of artemisinin resistance mutations on kelch13. Population structure showed that a single cluster accounted for 93.4% of the P. falciparum samples whereas three clusters were found for P. vivax. Our study shows a low genetic diversity for both species with significant differences in genetic sub-structuring. The high prevalence of CQ-resistance mutations could be a result of indirect selection pressures driven by the P. vivax treatment scheme. These results could be useful for public health authorities to safeguard the progress that Peru has achieved towards malaria elimination.
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Affiliation(s)
| | - Juan F Sanchez
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Oscar Nolasco
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Greys Braga
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | | | | | - Carola J Salas
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Carmen Lucas
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Stephen E Lizewski
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Christie A Joya
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru.,Malaria Research Group (MaRCH), Global Health Institute, University of Antwerp, 2610, Antwerp, Belgium
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru.
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11
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
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12
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Humanized mice for investigating sustained Plasmodium vivax blood-stage infections and transmission. Nat Commun 2022; 13:4123. [PMID: 35840625 PMCID: PMC9287384 DOI: 10.1038/s41467-022-31864-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 07/07/2022] [Indexed: 01/13/2023] Open
Abstract
Plasmodium vivax is the most widespread human malaria parasite. Due to the presence of extravascular reservoirs and relapsing infections from dormant liver stages, P. vivax is particularly difficult to control and eliminate. Experimental research is hampered by the inability to maintain P. vivax cultures in vitro, due to its tropism for immature red blood cells (RBCs). Here, we describe a new humanized mice model that can support efficient human erythropoiesis and maintain long-lasting multiplication of inoculated cryopreserved P. vivax parasites and their sexual differentiation, including in bone marrow. Mature gametocytes were transmitted to Anopheles mosquitoes, which led to the formation of salivary gland sporozoites. Importantly, blood-stage P. vivax parasites were maintained after the secondary transfer of fresh or frozen infected bone marrow cells to naïve chimeras. This model provides a unique tool for investigating, in vivo, the biology of intraerythrocytic P. vivax.
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13
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Zhang X, Wei H, Zhang Y, Zhao Y, Wang L, Hu Y, Nguitragool W, Sattabongkot J, Adams J, Cui L, Cao Y, Wang Q. Genetic diversity of Plasmodium vivax reticulocyte binding protein 2b in global parasite populations. Parasit Vectors 2022; 15:205. [PMID: 35698238 PMCID: PMC9191549 DOI: 10.1186/s13071-022-05296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/23/2022] [Indexed: 11/19/2022] Open
Abstract
Background Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) plays a critical role in parasite invasion of reticulocytes by binding the transferrin receptor 1. PvRBP2b is a vaccine candidate based on the negative correlation between antibody titers against PvRBP2b recombinant proteins and parasitemia and risk of vivax malaria. The aim of this study was to analyze the genetic diversity of the PvRBP2b gene in the global P. vivax populations. Methods Near full-length PvRBP2b nucleotide sequences (190–8349 bp) were obtained from 88 P. vivax isolates collected from the China–Myanmar border (n = 44) and Thailand (n = 44). An additional 224 PvRBP2b sequences were retrieved from genome sequences from parasite populations worldwide. The genetic diversity, neutral selection, haplotype distribution and genetic differentiation of PvRBP2b were examined. Results The genetic diversity of PvRBP2b was distributed unevenly, with peak diversity found in the reticulocyte binding region in the N-terminus. Neutrality analysis suggested that this region is subjected to balancing selection or population bottlenecks. Several amino acid variants were found in all or nearly all P. vivax endemic regions. However, the critical residues responsible for reticulocyte binding were highly conserved. There was substantial population differentiation according to the geographical separation. The distribution of haplotypes in the reticulocyte binding region varied among regions; even the two major haplotypes Hap_6 and Hap_8 were found in only five populations. Conclusions Our data show considerable genetic variations of PvRBPb in global parasite populations. The geographic divergence may pose a challenge to PvRBP2b-based vaccine development. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05296-6.
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Affiliation(s)
- Xuexing Zhang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Haichao Wei
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Department of Blood Transfusion Medicine, General Hospital of Northern Theater Command, Shenyang, 110015, Liaoning, China
| | - Yangminghui Zhang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Lin Wang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Department of Blood Transfusion, Yantaishan Hospital, Yantai, 264000, Shandong, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Central Laboratory, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Wang Nguitragool
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - John Adams
- College of Public Health, Global Health Infectious Disease Research (GHIDR) Program, Tampa, FL, USA
| | - Liwang Cui
- College of Public Health, Global Health Infectious Disease Research (GHIDR) Program, Tampa, FL, USA.,Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL, 33612, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.
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14
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Johansen IC, Rodrigues PT, Tonini J, Vinetz J, Castro MC, Ferreira MU. Cohort profile: the Mâncio Lima cohort study of urban malaria in Amazonian Brazil. BMJ Open 2021; 11:e048073. [PMID: 34789490 PMCID: PMC8727682 DOI: 10.1136/bmjopen-2020-048073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
PURPOSE This population-based open cohort study aims to investigate biological and sociodemographic drivers of malaria transmission in the main urban hotspot of Amazonian Brazil. PARTICIPANTS Nearly 20% of the households in the northwestern town of Mâncio Lima were randomly selected and 2690 participants were enrolled since April 2018. Sociodemographic, housing quality, occupational, behavioural and morbidity information and travel histories were collected during consecutive study visits. Blood samples from participants>3 months old were used for malaria diagnosis and human genetic studies; samples from participants with laboratory-confirmed malaria have been cryopreserved for genetic and phenotypic characterisation of parasites. Serology was introduced in 2020 to measure the prevalence and longevity of SARS-CoV-2 IgG antibodies. FINDINGS TO DATE Malaria prevalence rates were low (up to 1.0% for Plasmodium vivax and 0.6% for P. falciparum) during five consecutive cross-sectional surveys between April-May 2018 and October-November 2020; 63% of infections diagnosed by microscopy were asymptomatic. Malaria risk is heterogeneously distributed, with 20% study participants contributing 86% of the overall burden of P. vivax infection. Adult males are at greatest risk of infection and human mobility across the urban-rural interface may contribute to sustained malaria transmission. Local P. vivax parasites are genetically diverse and fragmented into discrete inbred lineages that remain stable across space and time. FUTURE PLANS Two follow-up visits, with similar study protocols, are planned in 2021. We aim to identify high-risk individuals that fuel onwards malaria transmission and represent a priority target for more intensive and effective control interventions. TRIAL REGISTRATION NUMBER NCT03689036.
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Affiliation(s)
| | | | - Juliana Tonini
- Parasitology, University of Sao Paulo, Sao Paulo, Brazil
| | - Joseph Vinetz
- Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Marcia C Castro
- Global Health and Population, Harvard School of Public Health, Boston, Massachusetts, USA
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15
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de Oliveira TC, Rodrigues PT, Duarte AMRC, Rona LDP, Ferreira MU. Ongoing host-shift speciation in Plasmodium simium. Trends Parasitol 2021; 37:940-942. [PMID: 34535396 DOI: 10.1016/j.pt.2021.08.005] [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: 07/16/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022]
Abstract
Plasmodium simium, a malaria parasite that infects platyrrhine monkeys and humans in the New World, is nearly identical to Plasmodium vivax. Recent genomic comparative analyses of these sister species have identified elevated divergence in a gene that may underlie P. simium adaptation to non-human primates during its gradual speciation process.
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Affiliation(s)
- Thaís 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
| | - Ana Maria R C Duarte
- Laboratory of Biochemistry and Molecular Biology, Superintendency for the Control of Endemic Diseases (SUCEN), State Secretary of Health, São Paulo, Brazil; Laboratory of Protozoology, Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Luísa D P Rona
- Department of Cell Biology, Embryology, and Genetics, Federal University of Santa Catarina, Florianópolis, Brazil; National Council for Scientific and Technological Development, National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal.
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16
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Liu P, Shen L, Wang S, Qin P, Si Y, Pan M, Zeng W, Qin Y, Chen X, Zhang Y, Li C, Xiang Z, Menezes L, Huang Y, Cui L, Yang Z. Increasing proportions of relapsing parasite species among imported malaria in China's Guangxi Province from Western and Central Africa. Travel Med Infect Dis 2021; 43:102130. [PMID: 34166802 DOI: 10.1016/j.tmaid.2021.102130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Travel-related malaria in non-endemic areas returning from endemic areas presents important challenges to diagnosis and treatment. Imported malaria to newly malaria-free countries poses further threats of malaria re-introduction and potential resurgence. For those traveling to places with high Plasmodium falciparum prevalence, prophylaxis against this parasite is recommended, whereas causal prophylaxis against relapsing malaria is often overlooked. METHODS We analyzed a cluster of imported malaria among febrile patients in Shanglin County, Guangxi Province, China, who had recent travel histories to Western and Central Africa. Malaria was diagnosed by microscopy and subsequently confirmed by species- and subspecies-specific PCR. Plasmodium vivax was genotyped using a barcode consisting of 42 single nucleotide polymorphisms. RESULTS Investigations of 344 PCR-confirmed malaria cases revealed that in addition to Plasmodium falciparum being the major parasite species, the relapsing parasites Plasmodium ovale and P. vivax accounted for ~40% of these imported cases. Of the 114 P. ovale infections, 65.8% and 34.2% were P. ovale curtisi and P. ovale wallikeri, respectively, with the two subspecies having a ~2:1 ratio in both Western and Central Africa. Phylogenetic analysis of 14 P. vivax isolates using a genetic barcode demonstrated that 11 formed a distinct clade from P. vivax populations from Eastern Africa. CONCLUSION This study provides support for active P. vivax transmission in areas with the predominant Duffy-negative blood group. With relapsing malaria making a substantial proportion of the imported malaria, causal prophylaxis should be advocated to travelers with a travel destination to Western and Central Africa.
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Affiliation(s)
- Penglu Liu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Lijie Shen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Siqi Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Pien Qin
- Shanglin County People's Hospital, Shanglin, Guangxi, 530500, China
| | - Yu Si
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Maohua Pan
- Shanglin County People's Hospital, Shanglin, Guangxi, 530500, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Yucheng Qin
- Shanglin County People's Hospital, Shanglin, Guangxi, 530500, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Yanmei Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Cuiying Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China
| | - Lynette Menezes
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, MDC84, Tampa, FL, 33612, USA
| | - Yaming Huang
- Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, MDC84, Tampa, FL, 33612, USA.
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China.
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17
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Chaturvedi R, Chhibber-Goel J, Verma I, Gopinathan S, Parvez S, Sharma A. Geographical spread and structural basis of sulfadoxine-pyrimethamine drug-resistant malaria parasites. Int J Parasitol 2021; 51:505-525. [PMID: 33775670 DOI: 10.1016/j.ijpara.2020.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022]
Abstract
The global spread of sulfadoxine (Sdx, S) and pyrimethamine (Pyr, P) resistance is attributed to increasing number of mutations in DHPS and DHFR enzymes encoded by malaria parasites. The association between drug resistance mutations and SP efficacy is complex. Here we provide an overview of the geographical spread of SP resistance mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) encoded dhps and dhfr genes. In addition, we have collated the mutation data and mapped it on to the three-dimensional structures of DHPS and DHFR which have become available. Data from genomic databases and 286 studies were collated to provide a comprehensive landscape of mutational data from 2005 to 2019. Our analyses show that the Pyr-resistant double mutations are widespread in Pf/PvDHFR (P. falciparum ∼61% in Asia and the Middle East, and in the Indian sub-continent; in P. vivax ∼33% globally) with triple mutations prevailing in Africa (∼66%) and South America (∼33%). For PfDHPS, triple mutations dominate South America (∼44%), Asia and the Middle East (∼34%) and the Indian sub-continent (∼27%), while single mutations are widespread in Africa (∼45%). Contrary to the status for P. falciparum, Sdx-resistant single point mutations in PvDHPS dominate globally. Alarmingly, highly resistant quintuple and sextuple mutations are rising in Africa (PfDHFR-DHPS) and Asia (Pf/PvDHFR-DHPS). Structural analyses of DHFR and DHPS proteins in complexes with substrates/drugs have revealed that resistance mutations map proximal to Sdx and Pyr binding sites. Thus new studies can focus on discovery of novel inhibitors that target the non-substrate binding grooves in these two validated malaria parasite drug targets.
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Affiliation(s)
- Rini Chaturvedi
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ishika Verma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sreehari Gopinathan
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Suhel Parvez
- Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; National Institute of Malaria Research, Dwarka, New Delhi, India.
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18
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de Oliveira TC, Rodrigues PT, Early AM, Duarte AMRC, Buery JC, Bueno MG, Catão-Dias JL, Cerutti C, Rona LDP, Neafsey DE, Ferreira MU. Plasmodium simium: population genomics reveals the origin of a reverse zoonosis. J Infect Dis 2021; 224:1950-1961. [PMID: 33870436 DOI: 10.1093/infdis/jiab214] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/14/2021] [Indexed: 11/12/2022] Open
Abstract
The population history of Plasmodium simium, which causes malaria in sylvatic Neotropical monkeys and humans along the Atlantic Coast of Brazil, remains disputed. Genetically diverse P. vivax populations from various sources, including the lineages that founded the species P. simium, are thought to have arrived in the Americas in separate migratory waves. However, here we find a minimal genome-level differentiation between P. simium and present-day New World P. vivax isolates, consistent with their common geographic origin and subsequent divergence on this continent. The meagre genetic diversity in P. simium samples from humans and monkeys implies a recent transfer from humans to non-human primates - a unique example of malaria as a reverse zoonosis of public health significance. Likely genomic signatures of P. simium adaptation to new hosts include the deletion of >40% of a key erythrocyte invasion ligand, PvRBP2a, which may have favored more efficient simian host cell infection.
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Affiliation(s)
- Thaís 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
| | - Angela M Early
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ana Maria R C Duarte
- Laboratory of Biochemistry and Molecular Biology, Superintendency for the Control of Endemics (SUCEN), State Secretary of Health, São Paulo, Brazil.,Laboratory of Protozoology, Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Julyana C Buery
- Department of Social Medicine, Center for Health Sciences, Federal University of Espírito Santo, Vitória, Brazil
| | - Marina G Bueno
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.,Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - José L Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Crispim Cerutti
- Department of Social Medicine, Center for Health Sciences, Federal University of Espírito Santo, Vitória, Brazil
| | - Luísa D P Rona
- Department of Cell Biology, Embryology, and Genetics, Federal University of Santa Catarina, Florianópolis, Brazil.,National Council for Scientific and Technological Development, National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
| | - Daniel E Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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19
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Daron J, Boissière A, Boundenga L, Ngoubangoye B, Houze S, Arnathau C, Sidobre C, Trape JF, Durand P, Renaud F, Fontaine MC, Prugnolle F, Rougeron V. Population genomic evidence of Plasmodium vivax Southeast Asian origin. SCIENCE ADVANCES 2021; 7:7/18/eabc3713. [PMID: 33910900 PMCID: PMC8081369 DOI: 10.1126/sciadv.abc3713] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 03/10/2021] [Indexed: 05/15/2023]
Abstract
Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives (P. vivax-like) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of this hypothesis. Here, we extensively characterized the genomic variations of 447 human P. vivax strains and 19 ape P. vivax-like strains collected worldwide. Phylogenetic relationships between human and ape Plasmodium strains revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like By investigating various aspects of P. vivax genetic variation, we identified several notable geographical patterns in summary statistics in function of the increasing geographic distance from Southeast Asia, suggesting that P. vivax may have derived from a single area in Asia through serial founder effects.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
| | - Anne Boissière
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Larson Boundenga
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, 46 rue H. Huchard, 75877 Paris Cedex 18, France
| | - Celine Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Christine Sidobre
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
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20
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Ferreira MU, Nobrega de Sousa T, Rangel GW, Johansen IC, Corder RM, Ladeia-Andrade S, Gil JP. Monitoring Plasmodium vivax resistance to antimalarials: Persisting challenges and future directions. Int J Parasitol Drugs Drug Resist 2021; 15:9-24. [PMID: 33360105 PMCID: PMC7770540 DOI: 10.1016/j.ijpddr.2020.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 11/23/2022]
Abstract
Emerging antimalarial drug resistance may undermine current efforts to control and eliminate Plasmodium vivax, the most geographically widespread yet neglected human malaria parasite. Endemic countries are expected to assess regularly the therapeutic efficacy of antimalarial drugs in use in order to adjust their malaria treatment policies, but proper funding and trained human resources are often lacking to execute relatively complex and expensive clinical studies, ideally complemented by ex vivo assays of drug resistance. Here we review the challenges for assessing in vivo P. vivax responses to commonly used antimalarials, especially chloroquine and primaquine, in the presence of confounding factors such as variable drug absorption, metabolism and interaction, and the risk of new infections following successful radical cure. We introduce a simple modeling approach to quantify the relative contribution of relapses and new infections to recurring parasitemias in clinical studies of hypnozoitocides. Finally, we examine recent methodological advances that may render ex vivo assays more practical and widely used to confirm P. vivax drug resistance phenotypes in endemic settings and review current approaches to the development of robust genetic markers for monitoring chloroquine resistance in P. vivax populations.
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Affiliation(s)
- Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal.
| | - Tais Nobrega de Sousa
- Molecular Biology and Malaria Immunology Research Group, René Rachou Institute, Fiocruz, Belo Horizonte, Brazil
| | - Gabriel W Rangel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Igor C Johansen
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M Corder
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simone Ladeia-Andrade
- Laboratory of Parasitic Diseases, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - José Pedro Gil
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
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21
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Rolfe R, Kwobah C, Muro F, Ruwanpathirana A, Lyamuya F, Bodinayake C, Nagahawatte A, Piyasiri B, Sheng T, Bollinger J, Zhang C, Ostbye T, Ali S, Drew R, Kussin P, Anderson DJ, Woods CW, Watt MH, Mmbaga BT, Tillekeratne LG. Barriers to implementing antimicrobial stewardship programs in three low- and middle-income country tertiary care settings: findings from a multi-site qualitative study. Antimicrob Resist Infect Control 2021; 10:60. [PMID: 33766135 PMCID: PMC7993456 DOI: 10.1186/s13756-021-00929-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/19/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Antimicrobial resistance has been named as one of the top ten threats to public health in the world. Hospital-based antimicrobial stewardship programs (ASPs) can help reduce antimicrobial resistance. The purpose of this study was to determine perceived barriers to the development and implementation of ASPs in tertiary care centers in three low- and middle-income countries (LMICs). METHODS Interviews were conducted with 45 physicians at tertiary care hospitals in Sri Lanka (n = 22), Kenya (12), and Tanzania (11). Interviews assessed knowledge of antimicrobial resistance and ASPs, current antimicrobial prescribing practices, access to diagnostics that inform antimicrobial use, receptiveness to ASPs, and perceived barriers to implementing ASPs. Two independent reviewers coded the interviews using principles of applied thematic analysis, and comparisons of themes were made across the three sites. RESULTS Barriers to improving antimicrobial prescribing included prohibitively expensive antimicrobials, limited antimicrobial availability, resistance to changing current practices regarding antimicrobial prescribing, and limited diagnostic capabilities. The most frequent of these barriers in all three locations was limited drug availability. Many physicians in all three sites had not heard of ASPs before the interviews. Improved education was a suggested component of ASPs at all three sites. The creation of guidelines was also recommended, without prompting, by interviewees at all three sites. Although most participants felt microbiological results were helpful in tailoring antibiotic courses, some expressed distrust of laboratory culture results. Biomarkers like erythrocyte sedimentation rate and c-reactive protein were not felt to be specific enough to guide antimicrobial therapy. Despite limited or no prior knowledge of ASPs, most interviewees were receptive to implementing protocols that would include documentation and consultation with ASPs regarding antimicrobial prescribing. CONCLUSIONS Our study highlighted several important barriers to implementing ASPs that were shared between three tertiary care centers in LMICs. Improving drug availability, enhancing availability of and trust in microbiologic data, creating local guidelines, and providing education to physicians regarding antimicrobial prescribing are important steps that could be taken by ASPs in these facilities.
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Affiliation(s)
- Robert Rolfe
- Duke University, Durham, NC, USA.
- Duke Global Health Institute, Durham, NC, USA.
| | - Charles Kwobah
- Moi University/Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Florida Muro
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | | | - Furaha Lyamuya
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Champica Bodinayake
- Duke Global Health Institute, Durham, NC, USA
- University of Ruhuna, Galle, Sri Lanka
| | - Ajith Nagahawatte
- Duke Global Health Institute, Durham, NC, USA
- University of Ruhuna, Galle, Sri Lanka
| | | | | | | | - Chi Zhang
- Duke Global Health Institute, Durham, NC, USA
| | | | - Shamim Ali
- Moi University/Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Richard Drew
- Duke University, Durham, NC, USA
- Campbell University College of Pharmacy and Health Sciences, Buies Creek, NC, USA
| | | | - Deverick J Anderson
- Duke University, Durham, NC, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC, USA
| | - Christopher W Woods
- Duke University, Durham, NC, USA
- Duke Global Health Institute, Durham, NC, USA
| | | | - Blandina T Mmbaga
- Duke Global Health Institute, Durham, NC, USA
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - L Gayani Tillekeratne
- Duke University, Durham, NC, USA
- Duke Global Health Institute, Durham, NC, USA
- University of Ruhuna, Galle, Sri Lanka
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22
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Rosado J, White MT, Longley RJ, Lacerda M, Monteiro W, Brewster J, Sattabongkot J, Guzman-Guzman M, Llanos-Cuentas A, Vinetz JM, Gamboa D, Mueller I. Heterogeneity in response to serological exposure markers of recent Plasmodium vivax infections in contrasting epidemiological contexts. PLoS Negl Trop Dis 2021; 15:e0009165. [PMID: 33591976 PMCID: PMC7909627 DOI: 10.1371/journal.pntd.0009165] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/26/2021] [Accepted: 01/21/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Antibody responses as serological markers of Plasmodium vivax infection have been shown to correlate with exposure, but little is known about the other factors that affect antibody responses in naturally infected people from endemic settings. To address this question, we studied IgG responses to novel serological exposure markers (SEMs) of P. vivax in three settings with different transmission intensity. METHODOLOGY We validated a panel of 34 SEMs in a Peruvian cohort with up to three years' longitudinal follow-up using a multiplex platform and compared results to data from cohorts in Thailand and Brazil. Linear regression models were used to characterize the association between antibody responses and age, the number of detected blood-stage infections during follow-up, and time since previous infection. Receiver Operating Characteristic (ROC) analysis was used to test the performance of SEMs to identify P. vivax infections in the previous 9 months. PRINCIPAL FINDINGS Antibody titers were associated with age, the number of blood-stage infections, and time since previous P. vivax infection in all three study sites. The association between antibody titers and time since previous P. vivax infection was stronger in the low transmission settings of Thailand and Brazil compared to the higher transmission setting in Peru. Of the SEMs tested, antibody responses to RBP2b had the highest performance for classifying recent exposure in all sites, with area under the ROC curve (AUC) = 0.83 in Thailand, AUC = 0.79 in Brazil, and AUC = 0.68 in Peru. CONCLUSIONS In low transmission settings, P. vivax SEMs can accurately identify individuals with recent blood-stage infections. In higher transmission settings, the accuracy of this approach diminishes substantially. We recommend using P. vivax SEMs in low transmission settings pursuing malaria elimination, but they are likely to be less effective in high transmission settings focused on malaria control.
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Affiliation(s)
- Jason Rosado
- Unit of Malaria: Parasites and hosts, Institut Pasteur, Paris, France
- Sorbonne Université, ED 393, Paris, France
| | - Michael T. White
- Unit of Malaria: Parasites and hosts, Institut Pasteur, Paris, France
| | - Rhea J. Longley
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Australia
| | - Marcus Lacerda
- Instituto Leônidas & Maria Deane (Fiocruz), Manaus, Brazil
- Tropical Medicine Foundation Dr Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Wuelton Monteiro
- Tropical Medicine Foundation Dr Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Jessica Brewster
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Jetsumon Sattabongkot
- Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mitchel Guzman-Guzman
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ivo Mueller
- Unit of Malaria: Parasites and hosts, Institut Pasteur, Paris, France
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Australia
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23
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Villena FE, Maguiña JL, Santolalla ML, Pozo E, Salas CJ, Ampuero JS, Lescano AG, Bishop DK, Valdivia HO. Molecular surveillance of the Plasmodium vivax multidrug resistance 1 gene in Peru between 2006 and 2015. Malar J 2020; 19:450. [PMID: 33276776 PMCID: PMC7718670 DOI: 10.1186/s12936-020-03519-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 11/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high incidence of Plasmodium vivax infections associated with clinical severity and the emergence of chloroquine (CQ) resistance has posed a challenge to control efforts aimed at eliminating this disease. Despite conflicting evidence regarding the role of mutations of P. vivax multidrug resistance 1 gene (pvmdr1) in drug resistance, this gene can be a tool for molecular surveillance due to its variability and spatial patterns. METHODS Blood samples were collected from studies conducted between 2006 and 2015 in the Northern and Southern Amazon Basin and the North Coast of Peru. Thick and thin blood smears were prepared for malaria diagnosis by microscopy and PCR was performed for detection of P. vivax monoinfections. The pvmdr1 gene was subsequently sequenced and the genetic data was used for haplotype and diversity analysis. RESULTS A total of 550 positive P. vivax samples were sequenced; 445 from the Northern Amazon Basin, 48 from the Southern Amazon Basin and 57 from the North Coast. Eight non-synonymous mutations and three synonymous mutations were analysed in 4,395 bp of pvmdr1. Amino acid changes at positions 976F and 1076L were detected in the Northern Amazon Basin (12.8%) and the Southern Amazon Basin (4.2%) with fluctuations in the prevalence of both mutations in the Northern Amazon Basin during the course of the study that seemed to correspond with a malaria control programme implemented in the region. A total of 13 pvmdr1 haplotypes with non-synonymous mutations were estimated in Peru and an overall nucleotide diversity of π = 0.00054. The Northern Amazon Basin was the most diverse region (π = 0.00055) followed by the Southern Amazon and the North Coast (π = 0.00035 and π = 0.00014, respectively). CONCLUSION This study showed a high variability in the frequencies of the 976F and 1076L polymorphisms in the Northern Amazon Basin between 2006 and 2015. The low and heterogeneous diversity of pvmdr1 found in this study underscores the need for additional research that can elucidate the role of this gene on P. vivax drug resistance as well as in vitro and clinical data that can clarify the extend of CQ resistance in Peru.
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Affiliation(s)
- Fredy E Villena
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima, Peru.
| | - Jorge L Maguiña
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Meddly L Santolalla
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru.,Departamento de Parasitología, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Edwar Pozo
- Piura Sanitary Intelligence Unit, Piura Health Region, Piura, Peru
| | - Carola J Salas
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima, Peru
| | - Julia S Ampuero
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima, Peru
| | - Andres G Lescano
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Danett K Bishop
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima, Peru
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima, Peru
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24
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Almeida-de-Oliveira NK, de Abreu-Fernandes R, Lima-Cury L, de Lavigne AR, de Pina-Costa A, Perce-da-Silva DDS, Catanho M, Rossi AD, Brasil P, Tadeu Daniel-Ribeiro C, Ferreira-da-Cruz MDF. Balancing selection and high genetic diversity of Plasmodium vivax circumsporozoite central region in parasites from Brazilian Amazon and Rio de Janeiro Atlantic Forest. PLoS One 2020; 15:e0241426. [PMID: 33166298 PMCID: PMC7652573 DOI: 10.1371/journal.pone.0241426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/14/2020] [Indexed: 11/19/2022] Open
Abstract
Circumsporozoite protein (CSP) is the primary pre-erythrocytic vaccine target in Plasmodium species. Knowledge about their genetic diversity can help predict vaccine efficacy and the spread of novel parasite variants. Thus, we investigated pvcsp gene polymorphisms in 219 isolates (136 from Brazilian Amazon [BA], 71 from Rio de Janeiro Atlantic Forest [AF], and 12 from non-Brazilian countries [NB]). Forty-eight polymorphic sites were detected, 46 in the central repeat region (CR), and two in the C-terminal region. Also, the CR presents InDels and a variable number of repeats. All samples correspond to the VK210 variant, and 24 VK210 subtypes based on CR. Nucleotide diversity (π = 0.0135) generated a significant number of haplotypes (168) with low genetic differentiation between the Brazilian regions (Fst = 0.208). The haplotype network revealed similar distances among the BA and AF regions. The linkage disequilibrium indicates that recombination does not seem to be acting in diversity, reinforcing natural selection's role in accelerating adaptive evolution. The high diversity (low Fst) and polymorphism frequencies could be indicators of balancing selection. Although malaria in BA and AF have distinct vector species and different host immune pressures, consistent genetic signature was found in two regions. The immunodominant B-cell epitope mapped in the CR varies from seven to 19 repeats. The CR T-cell epitope is conserved only in 39 samples. Concerning to C-terminal region, the Th2R epitope presented nonsynonymous SNP only in 6% of Brazilian samples, and the Th3R epitope remained conserved in all studied regions. We conclude that, although the uneven distribution of alleles may jeopardize the deployment of vaccines directed to a specific variable locus, a unique vaccine formulation could protect populations in all Brazilian regions.
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Affiliation(s)
- Natália Ketrin Almeida-de-Oliveira
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Rebecca de Abreu-Fernandes
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Lidiane Lima-Cury
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Aline Rosa de Lavigne
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Anielle de Pina-Costa
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
- Centro Universitário Serra dos Órgãos (UNIFESO), Teresópolis, Rio de Janeiro, Brazil
| | - Daiana de Souza Perce-da-Silva
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, IOC, Fiocruz, Rio de Janeiro, Brazil
| | - Atila Duque Rossi
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Patrícia Brasil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
| | - Cláudio Tadeu Daniel-Ribeiro
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Maria de Fátima Ferreira-da-Cruz
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
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Ford A, Kepple D, Abagero BR, Connors J, Pearson R, Auburn S, Getachew S, Ford C, Gunalan K, Miller LH, Janies DA, Rayner JC, Yan G, Yewhalaw D, Lo E. Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes. PLoS Negl Trop Dis 2020; 14:e0008234. [PMID: 33044985 PMCID: PMC7581005 DOI: 10.1371/journal.pntd.0008234] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 10/22/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022] Open
Abstract
Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 123,711 SNPs were detected, of which 22.7% were nonsynonymous and 77.3% were synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (24,007 SNPs; 19.4% of total) and 10 (16,852 SNPs, 13.6% of total). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including merozoite surface protein 1 (MSP1) and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Two genes, MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and MSP3.11 on chromosome 10. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale. Plasmodium vivax is the most geographically widespread parasite species that causes malaria in humans. Although it occurs in Africa as a member of a mix of Plasmodium species, P. vivax is dominant in other parts of the world outside of Africa (e.g., Brazil). It was previously thought that most African populations were immune to P. vivax infections due to the absence of Duffy antigen chemokine receptor (DARC) gene expression required for erythrocyte invasion. However, several recent reports have indicated the emergence and potential spread of P. vivax across human populations in Africa. Compared to Southeast Asia and South America where P. vivax is highly endemic, data on polymorphisms in erythrocyte binding gene candidates of P. vivax from Africa is limited. Filling this knowlege gap is critical for identifying functional genes in erythrocyte invasion, biomarkers for tracking the P. vivax isolates from Africa, as well as potential gene targets for vaccine development. This paper examined the level of genetic polymorphisms in a panel of 43 potential erythrocyte binding protein genes based on whole genome sequences and described transmission patterns of P. vivax infections from different study sites in Ethiopia based on the genetic variants. Our analyses showed that chromosomes 9 and 10 of the P. vivax genomes isolated in Ethiopia had the most high-quality genetic polymorphisms. Among all erythrocyte binding protein gene candidates, the merozoite surface proteins 1 and merozoite surface protein 3 showed high levels of polymorphism. MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. The expansion of the Duffy binding protein and merozoite surface protein 3 gene copies was an independent process among the P. vivax lineages in Ethiopia. Various levels of gene flow were observed even at a smaller geographical scale. Our study provided baseline data for future comparison with P. vivax in Duffy negative individuals and help develop a panel of genetic markers that are informative at a micro-geographical scale.
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Affiliation(s)
- Anthony Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
| | - Daniel Kepple
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
| | - Beka Raya Abagero
- Tropical Infectious Disease Research Center, Jimma University, Ethiopia
| | - Jordan Connors
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Richard Pearson
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United States of America
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sisay Getachew
- College of Natural Sciences, Addis Ababa University, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Colby Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Louis H. Miller
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Julian C. Rayner
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 OXY, United Kingdom
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, United States of America
- * E-mail: (AF); (GY); (EL)
| | | | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
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de Oliveira TC, Corder RM, Early A, Rodrigues PT, Ladeia-Andrade S, Alves JMP, Neafsey DE, Ferreira MU. Population genomics reveals the expansion of highly inbred Plasmodium vivax lineages in the main malaria hotspot of Brazil. PLoS Negl Trop Dis 2020; 14:e0008808. [PMID: 33112884 PMCID: PMC7592762 DOI: 10.1371/journal.pntd.0008808] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/21/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plasmodium vivax is a neglected human malaria parasite that causes significant morbidity in the Americas, the Middle East, Asia, and the Western Pacific. Population genomic approaches remain little explored to map local and regional transmission pathways of P. vivax across the main endemic sites in the Americas, where great progress has been made towards malaria elimination over the past decades. METHODOLOGY/PRINCIPAL FINDINGS We analyze 38 patient-derived P. vivax genome sequences from Mâncio Lima (ML)-the Amazonian malaria hotspot next to the Brazil-Peru border-and 24 sequences from two other sites in Acre State, Brazil, a country that contributes 23% of malaria cases in the Americas. We show that the P. vivax population of ML is genetically diverse (π = 4.7 × 10-4), with a high polymorphism particularly in genes encoding proteins putatively involved in red blood cell invasion. Paradoxically, however, parasites display strong genome-wide linkage disequilibrium, being fragmented into discrete lineages that are remarkably stable across time and space, with only occasional recombination between them. Using identity-by-descent approaches, we identified a large cluster of closely related sequences that comprises 16 of 38 genomes sampled in ML over 26 months. Importantly, we found significant ancestry sharing between parasites at a large geographic distance, consistent with substantial gene flow between regional P. vivax populations. CONCLUSIONS/SIGNIFICANCE We have characterized the sustained expansion of highly inbred P. vivax lineages in a malaria hotspot that can seed regional transmission. Potential source populations in hotspots represent a priority target for malaria elimination in the Amazon.
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Affiliation(s)
- Thaís Crippa de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M. Corder
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Angela Early
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Departament of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simone Ladeia-Andrade
- Laboratory of Parasitic Diseases, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - João Marcelo P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel E. Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Departament of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Brashear AM, Huckaby AC, Fan Q, Dillard LJ, Hu Y, Li Y, Zhao Y, Wang Z, Cao Y, Miao J, Guler JL, Cui L. New Plasmodium vivax Genomes From the China-Myanmar Border. Front Microbiol 2020; 11:1930. [PMID: 32849480 PMCID: PMC7432439 DOI: 10.3389/fmicb.2020.01930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Plasmodium vivax is increasingly the dominant species of malaria in the Greater Mekong Subregion (GMS), which is pursuing regional malaria elimination. P. vivax lineages in the GMS are poorly characterized. Currently, P. vivax reference genomes are scarce due to difficulties in culturing the parasite and lack of high-quality samples. In addition, P. vivax is incredibly diverse, necessitating the procurement of reference genomes from different geographical regions. Here we present four new P. vivax draft genomes assembled de novo from clinical samples collected in the China-Myanmar border area. We demonstrate comparable length and content to existing genomes, with the majority of structural variation occurring around subtelomeric regions and exported proteins, which we corroborated with detection of copy number variations in these regions. We predicted peptides from all PIR gene subfamilies, except for PIR D. We confirmed that proteins classically labeled as PIR D family members are not identifiable by PIR motifs, and actually bear stronger resemblance to DUF (domain of unknown function) family DUF3671, potentially pointing to a new, closely related gene family. Further, phylogenetic analyses of MSP7 genes showed high variability within the MSP7-B family compared to MSP7-A and -C families, and the result was comparable to that from whole genome analyses. The new genome assemblies serve as a resource for studying P. vivax within the GMS.
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Affiliation(s)
- Awtum M. Brashear
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
| | - Adam C. Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Qi Fan
- Dalian Institute of Science and Technology, Dalian, China
| | - Luke J. Dillard
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Zenglei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
| | - Jennifer L. Guler
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
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Rougeron V, Elguero E, Arnathau C, Acuña Hidalgo B, Durand P, Houze S, Berry A, Zakeri S, Haque R, Shafiul Alam M, Nosten F, Severini C, Gebru Woldearegai T, Mordmüller B, Kremsner PG, González-Cerón L, Fontecha G, Gamboa D, Musset L, Legrand E, Noya O, Pumpaibool T, Harnyuttanakorn P, Lekweiry KM, Mohamad Albsheer M, Mahdi Abdel Hamid M, Boukary AOMS, Trape JF, Renaud F, Prugnolle F. Human Plasmodium vivax diversity, population structure and evolutionary origin. PLoS Negl Trop Dis 2020; 14:e0008072. [PMID: 32150544 PMCID: PMC7082039 DOI: 10.1371/journal.pntd.0008072] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 03/19/2020] [Accepted: 01/18/2020] [Indexed: 11/19/2022] Open
Abstract
More than 200 million malaria clinical cases are reported each year due to Plasmodium vivax, the most widespread Plasmodium species in the world. This species has been neglected and understudied for a long time, due to its lower mortality in comparison with Plasmodium falciparum. A renewed interest has emerged in the past decade with the discovery of antimalarial drug resistance and of severe and even fatal human cases. Nonetheless, today there are still significant gaps in our understanding of the population genetics and evolutionary history of P. vivax, particularly because of a lack of genetic data from Africa. To address these gaps, we genotyped 14 microsatellite loci in 834 samples obtained from 28 locations in 20 countries from around the world. We discuss the worldwide population genetic structure and diversity and the evolutionary origin of P. vivax in the world and its introduction into the Americas. This study demonstrates the importance of conducting genome-wide analyses of P. vivax in order to unravel its complex evolutionary history. Among the five Plasmodium species infecting humans, P. vivax is the most prevalent parasite outside Africa. To date, there has been less research on this species than for Plasmodium falciparum, a more lethal species, principally because of the lack of an in vitro culture system and also because P. vivax is considered relatively benign. Nevertheless, P. vivax is responsible for severe and incapacitating clinical symptoms with significant effects on human health. The emergence of new drug resistance and the discovery of severe and even fatal cases due to P. vivax question the benign status of P. vivax malaria. In recent years, there has been increased interest in characterizing the distribution of genetic variation in P. vivax. However, these studies either generated genetic information from a regional geographic scale or combine genetic datasets generated in different molecular platforms, which is known to generate biased results. In this study, we used a single genotyping platform to genotype 14 microsatellite markers in 834 samples of P. vivax obtained from 28 locations in 20 countries from around the world, including several populations from East and West Africa. We discuss the worldwide population genetic structure and the evolutionary origins of P. vivax, as well as its introduction into the Americas.
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Affiliation(s)
- Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
- * E-mail: ,
| | - Eric Elguero
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Céline Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Beatriz Acuña Hidalgo
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, Paris, France
| | - Antoine Berry
- Centre de Physiopathologie de Toulouse-Purpan (CPTP), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1043, CNRS UMR5282, Université de Toulouse Paul Sabatier, F-31300 Toulouse, France
- Service de Parasitologie-Mycologie, Institut Fédératif de Biologie, Centre Hospitalier Universitaire de Toulouse, F-31300 Toulouse, France
| | - Sedigheh Zakeri
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Rashidul Haque
- Emerging Infections & Parasitology Laboratory, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - Mohammad Shafiul Alam
- Emerging Infections & Parasitology Laboratory, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - François Nosten
- Centre for Tropical Medicine and Global Health,Oxford, United Kingdom
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Carlo Severini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Tamirat Gebru Woldearegai
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Medical Laboratory Sciences, College of Medical and Health Sciences, Haramaya University, Harar, Ethiopia
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | | | - Lilia González-Cerón
- Regional Centre of Research in Public Health, National Institute of Public Health, Tapachula, Chiapas, Mexico
| | - Gustavo Fontecha
- Microbiology Research Institute, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, AP, Lima, Peru
| | - Lise Musset
- Unit, Institut Pasteur de Guyane, BP6010, French Guiana
| | - Eric Legrand
- Malaria Genetic and Resistance Group, Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France
| | - Oscar Noya
- Centro para Estudios Sobre Malaria, Instituto de Altos Estudios en Salud “Dr. Arnoldo Gabaldón”, Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical, Universidad Central de Venezuela, Maracay, Caracas, Venezuela
| | - Tepanata Pumpaibool
- Biomedical Science, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Malaria Research Programme, College of Public Health Science, Chulalongkorn University, Bangkok, Thailand
| | - Pingchai Harnyuttanakorn
- Malaria Research Programme, College of Public Health Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Khadijetou Mint Lekweiry
- UR-Génomes et milieux, Faculté des Sciences et Techniques, Université de Nouakchott Al-Aasriya, Mauritania
| | - Musab Mohamad Albsheer
- Department of Parasitology and Medical Entomology, Medical Campus, University of Khartoum, Sudan
| | | | - Ali Ould Mohamed Salem Boukary
- UR-Génomes et milieux, Faculté des Sciences et Techniques, Université de Nouakchott Al-Aasriya, Mauritania
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
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Plasmodium vivax transcriptional profiling of low input cryopreserved isolates through the intraerythrocytic development cycle. PLoS Negl Trop Dis 2020; 14:e0008104. [PMID: 32119669 PMCID: PMC7067476 DOI: 10.1371/journal.pntd.0008104] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 03/12/2020] [Accepted: 01/30/2020] [Indexed: 11/19/2022] Open
Abstract
Approximately one-third of the global population is at risk of Plasmodium vivax infection, and an estimated 7.51 million cases were reported in 2017. Although, P. vivax research is currently limited by the lack of a robust continuous in vitro culture system for this parasite, recent work optimizing short-term ex vivo culture of P. vivax from cryopreserved isolates has facilitated quantitative assays on synchronous parasites. Pairing this improved culture system with low-input Smart-seq2 RNAseq library preparation, we sought to determine whether transcriptional profiling of P. vivax would provide insight into the differential survival of parasites in different culture media. To this end we probed the transcriptional signature of three different ex vivo P. vivax samples in four different culture media using only 1000 cells for each time point taken during the course of the intraerythrocytic development cycle (IDC). Using this strategy, we achieved similar quality transcriptional data to previously reported P. vivax transcriptomes. We found little effect with varying culture media on parasite transcriptional signatures, identified many novel gametocyte-specific genes from transcriptomes of FACS-isolated gametocytes, and determined invasion ligand expression in schizonts in biological isolates and across the IDC. In total, these data demonstrate the feasibility and utility of P. vivax RNAseq-based transcriptomic studies using minimal biomass input to maximize experimental capacity. Plasmodium vivax is the most prevalent malaria-causing parasite species outside of Sub-Saharan Africa and has many unique and poorly understood biological characteristics that make it particularly challenging to study and combat. Transcriptomic profiling of P. vivax under various conditions has the potential to unlock new experimental abilities and aid in elucidating biology and the development of clinical interventions. However, a lack of a robust in vitro culture system for this parasite has restricted transcriptomic studies to researchers with timely access to fresh human isolates from clinics, which often are in resource-poor settings, as well as nearby, well-equipped laboratories for sample processing. This study aimed to gain insight into the differential survival of P. vivax in various culture media from the parasites transcriptional signature in each media. By implementing low-input RNA library preparation strategies, this study obtains robust transcriptomic data at various parasite development stages and in different culture conditions from just 1000 FACS-purified, P. vivax-infected erythrocytes from viable cryopreserved patient isolates. With these data, we find culture media has little effect on transcriptional profile, we characterize invasion ligand expression across intraerythrocytic development and between clinical isolates, and we define the transcriptome of sexual, transmissible stages of the P. vivax parasite. These results highlight the establishment and utility of a powerful platform for studying the transcriptomic biology of this particularly challenging parasite.
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30
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria. PLoS Genet 2020; 16:e1008576. [PMID: 32053607 PMCID: PMC7043780 DOI: 10.1371/journal.pgen.1008576] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/26/2020] [Accepted: 12/19/2019] [Indexed: 11/19/2022] Open
Abstract
Although Plasmodium vivax parasites are the predominant cause of malaria outside of sub-Saharan Africa, they not always prioritised by elimination programmes. P. vivax is resilient and poses challenges through its ability to re-emerge from dormancy in the human liver. With observed growing drug-resistance and the increasing reports of life-threatening infections, new tools to inform elimination efforts are needed. In order to halt transmission, we need to better understand the dynamics of transmission, the movement of parasites, and the reservoirs of infection in order to design targeted interventions. The use of molecular genetics and epidemiology for tracking and studying malaria parasite populations has been applied successfully in P. falciparum species and here we sought to develop a molecular genetic tool for P. vivax. By assembling the largest set of P. vivax whole genome sequences (n = 433) spanning 17 countries, and applying a machine learning approach, we created a 71 SNP barcode with high predictive ability to identify geographic origin (91.4%). Further, due to the inclusion of markers for within population variability, the barcode may also distinguish local transmission networks. By using P. vivax data from a low-transmission setting in Malaysia, we demonstrate the potential ability to infer outbreak events. By characterising the barcoding SNP genotypes in P. vivax DNA sourced from UK travellers (n = 132) to ten malaria endemic countries predominantly not used in the barcode construction, we correctly predicted the geographic region of infection origin. Overall, the 71 SNP barcode outperforms previously published genotyping methods and when rolled-out within new portable platforms, is likely to be an invaluable tool for informing targeted interventions towards elimination of this resilient human malaria.
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Plasmodium Genomics and Genetics: New Insights into Malaria Pathogenesis, Drug Resistance, Epidemiology, and Evolution. Clin Microbiol Rev 2019; 32:32/4/e00019-19. [PMID: 31366610 DOI: 10.1128/cmr.00019-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protozoan Plasmodium parasites are the causative agents of malaria, a deadly disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild or severe symptoms, or fatal, depending on many factors such as parasite virulence and host immune status. Malaria can be treated with various drugs, with artemisinin-based combination therapies (ACTs) being the first-line choice. Recent advances in genetics and genomics of malaria parasites have contributed greatly to our understanding of parasite population dynamics, transmission, drug responses, and pathogenesis. However, knowledge gaps in parasite biology and host-parasite interactions still remain. Parasites resistant to multiple antimalarial drugs have emerged, while advanced clinical trials have shown partial efficacy for one available vaccine. Here we discuss genetic and genomic studies of Plasmodium biology, host-parasite interactions, population structures, mosquito infectivity, antigenic variation, and targets for treatment and immunization. Knowledge from these studies will advance our understanding of malaria pathogenesis, epidemiology, and evolution and will support work to discover and develop new medicines and vaccines.
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Verzier LH, Coyle R, Singh S, Sanderson T, Rayner JC. Plasmodium knowlesi as a model system for characterising Plasmodium vivax drug resistance candidate genes. PLoS Negl Trop Dis 2019; 13:e0007470. [PMID: 31158222 PMCID: PMC6564043 DOI: 10.1371/journal.pntd.0007470] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 06/13/2019] [Accepted: 05/15/2019] [Indexed: 12/29/2022] Open
Abstract
Plasmodium vivax causes the majority of malaria outside Africa, but is poorly understood at a cellular level partly due to technical difficulties in maintaining it in in vitro culture conditions. In the past decades, drug resistant P. vivax parasites have emerged, mainly in Southeast Asia, but while some molecular markers of resistance have been identified, none have so far been confirmed experimentally, which limits interpretation of the markers, and hence our ability to monitor and control the spread of resistance. Some of these potential markers have been identified through P. vivax genome-wide population genetic analyses, which highlighted genes under recent evolutionary selection in Southeast Asia, where chloroquine resistance is most prevalent. These genes could be involved in drug resistance, but no experimental proof currently exists to support this hypothesis. In this study, we used Plasmodium knowlesi, the most closely related species to P. vivax that can be cultured in human erythrocytes, as a model system to express P. vivax genes and test for their role in drug resistance. We adopted a strategy of episomal expression, and were able to express fourteen P. vivax genes, including two allelic variants of several hypothetical resistance genes. Their expression level and localisation were assessed, confirming cellular locations conjectured from orthologous species, and suggesting locations for several previously unlocalised proteins, including an apical location for PVX_101445. These findings establish P. knowlesi as a suitable model for P. vivax protein expression. We performed chloroquine and mefloquine drug assays, finding no significant differences in drug sensitivity: these results could be due to technical issues, or could indicate that these genes are not actually involved in drug resistance, despite being under positive selection pressure in Southeast Asia. These data confirm that in vitro P. knowlesi is a useful tool for studying P. vivax biology. Its close evolutionary relationship to P. vivax, high transfection efficiency, and the availability of markers for colocalisation, all make it a powerful model system. Our study is the first of its kind using P. knowlesi to study unknown P. vivax proteins and investigate drug resistance mechanisms.
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Affiliation(s)
- Lisa H. Verzier
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Rachael Coyle
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Shivani Singh
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Theo Sanderson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Julian C. Rayner
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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Monitoring the Efficacy of Chloroquine-Primaquine Therapy for Uncomplicated Plasmodium vivax Malaria in the Main Transmission Hot Spot of Brazil. Antimicrob Agents Chemother 2019; 63:AAC.01965-18. [PMID: 30782991 DOI: 10.1128/aac.01965-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/10/2019] [Indexed: 12/15/2022] Open
Abstract
Emerging Plasmodium vivax resistance to chloroquine (CQ) may undermine malaria elimination efforts in South America. CQ-resistant P. vivax has been found in the major port city of Manaus but not in the main malaria hot spots across the Amazon Basin of Brazil, where CQ is routinely coadministered with primaquine (PQ) for radical cure of vivax malaria. Here we randomly assigned 204 uncomplicated vivax malaria patients from Juruá Valley, northwestern Brazil, to receive either sequential (arm 1) or concomitant (arm 2) CQ-PQ treatment. Because PQ may synergize the blood schizontocidal effect of CQ and mask low-level CQ resistance, we monitored CQ-only efficacy in arm 1 subjects, who had PQ administered only at the end of the 28-day follow-up. We found adequate clinical and parasitological responses in all subjects assigned to arm 2. However, 2.2% of arm 1 patients had microscopy-detected parasite recrudescences at day 28. When PCR-detected parasitemias at day 28 were considered, response rates decreased to 92.1% and 98.8% in arms 1 and 2, respectively. Therapeutic CQ levels were documented in 6 of 8 recurrences, consistent with true CQ resistance in vivo In contrast, ex vivo assays provided no evidence of CQ resistance in 49 local P. vivax isolates analyzed. CQ-PQ coadministration was not found to potentiate the antirelapse efficacy of PQ over 180 days of surveillance; however, we suggest that larger studies are needed to examine whether and how CQ-PQ interactions, e.g., CQ-mediated inhibition of PQ metabolism, modulate radical cure efficacy in different P. vivax-infected populations. (This study has been registered at ClinicalTrials.gov under identifier NCT02691910.).
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Ferreira MU, Castro MC. Malaria Situation in Latin America and the Caribbean: Residual and Resurgent Transmission and Challenges for Control and Elimination. Methods Mol Biol 2019; 2013:57-70. [PMID: 31267493 DOI: 10.1007/978-1-4939-9550-9_4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Despite recent progress toward malaria elimination in Latin America and the Caribbean, with an overall 62% decrease in incidence between 2000 and 2015, malaria remains endemic to 21 countries and territories in the region, where 120 million people are exposed to some risk of infection. Here we review recent epidemiologic trends, highlight current challenges, and briefly discuss the relative role of traditional and novel strategies for better malaria control and elimination across the continent.
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Affiliation(s)
- Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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36
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Auburn S, Benavente ED, Miotto O, Pearson RD, Amato R, Grigg MJ, Barber BE, William T, Handayuni I, Marfurt J, Trimarsanto H, Noviyanti R, Sriprawat K, Nosten F, Campino S, Clark TG, Anstey NM, Kwiatkowski DP, Price RN. Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics. Nat Commun 2018; 9:2585. [PMID: 29968722 PMCID: PMC6030216 DOI: 10.1038/s41467-018-04965-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/01/2018] [Indexed: 01/13/2023] Open
Abstract
The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination.
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Affiliation(s)
- Sarah Auburn
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK
| | - Ernest D. Benavente
- 0000 0004 0425 469Xgrid.8991.9Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Olivo Miotto
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK ,0000 0004 1937 0490grid.10223.32Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, 10400 Thailand
| | - Richard D. Pearson
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK
| | - Roberto Amato
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK
| | - Matthew J. Grigg
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300 Kota Kinabalu Sabah, Malaysia
| | - Bridget E. Barber
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300 Kota Kinabalu Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300 Kota Kinabalu Sabah, Malaysia ,0000 0004 1772 8727grid.415560.3Clinical Research Centre, Queen Elizabeth Hospital, 88300 Kota Kinabalu Sabah, Malaysia ,Jesselton Medical Centre, 88300 Kota Kinabalu Sabah, Malaysia
| | - Irene Handayuni
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia
| | - Jutta Marfurt
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia
| | - Hidayat Trimarsanto
- 0000 0004 1795 0993grid.418754.bEijkman Institute for Molecular Biology, Jakarta, 10430 Indonesia ,0000 0001 0746 0534grid.432292.cAgency for Assessment and Application of Technology, Jl. MH Thamrin 8, Jakarta, 10340 Indonesia
| | - Rintis Noviyanti
- 0000 0004 1795 0993grid.418754.bEijkman Institute for Molecular Biology, Jakarta, 10430 Indonesia
| | - Kanlaya Sriprawat
- 0000 0004 1937 0490grid.10223.32Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot Tak, 63110 Thailand
| | - Francois Nosten
- 0000 0004 1937 0490grid.10223.32Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot Tak, 63110 Thailand ,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford Old Road Campus, Oxford, OX3 7LJ UK
| | - Susana Campino
- 0000 0004 0425 469Xgrid.8991.9Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Taane G. Clark
- 0000 0004 0425 469Xgrid.8991.9Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK ,0000 0004 0425 469Xgrid.8991.9Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Nicholas M. Anstey
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia
| | - Dominic P. Kwiatkowski
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK
| | - Ric N. Price
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford Old Road Campus, Oxford, OX3 7LJ UK
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37
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Obaldia N, Meibalan E, Sa JM, Ma S, Clark MA, Mejia P, Moraes Barros RR, Otero W, Ferreira MU, Mitchell JR, Milner DA, Huttenhower C, Wirth DF, Duraisingh MT, Wellems TE, Marti M. Bone Marrow Is a Major Parasite Reservoir in Plasmodium vivax Infection. mBio 2018; 9:e00625-18. [PMID: 29739900 PMCID: PMC5941073 DOI: 10.1128/mbio.00625-18] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 11/25/2022] Open
Abstract
Plasmodium vivax causes heavy burdens of disease across malarious regions worldwide. Mature P. vivax asexual and transmissive gametocyte stages occur in the blood circulation, and it is often assumed that accumulation/sequestration in tissues is not an important phase in their development. Here, we present a systematic study of P. vivax stage distributions in infected tissues of nonhuman primate (NHP) malaria models as well as in blood from human infections. In a comparative analysis of the transcriptomes of P. vivax and Plasmodium falciparum blood-stage parasites, we found a conserved cascade of stage-specific gene expression despite the greatly different gametocyte maturity times of these two species. Using this knowledge, we validated a set of conserved asexual- and gametocyte-stage markers both by quantitative real-time PCR and by antibody assays of peripheral blood samples from infected patients and NHP (Aotus sp.). Histological analyses of P. vivax parasites in organs of 13 infected NHP (Aotus and Saimiri species) demonstrated a major fraction of immature gametocytes in the parenchyma of the bone marrow, while asexual schizont forms were enriched to a somewhat lesser extent in this region of the bone marrow as well as in sinusoids of the liver. These findings suggest that the bone marrow is an important reservoir for gametocyte development and proliferation of malaria parasites.IMPORTANCEPlasmodium vivax malaria continues to cause major public health burdens worldwide. Yet, significant knowledge gaps in the basic biology and epidemiology of P. vivax malaria remain, largely due to limited available tools for research and diagnostics. Here, we present a systematic examination of tissue sequestration during P. vivax infection. Studies of nonhuman primates and malaria patients revealed enrichment of developing sexual stages (gametocytes) and mature replicative stages (schizonts) in the bone marrow and liver, relative to those present in peripheral blood. Identification of the bone marrow as a major P. vivax tissue reservoir has important implications for parasite diagnosis and treatment.
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Affiliation(s)
- Nicanor Obaldia
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
- Tropical Medicine Research, Panama City, Panama
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Elamaran Meibalan
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
- Center for Excellence in Vascular Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Juliana M Sa
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Siyuan Ma
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Martha A Clark
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Pedro Mejia
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Roberto R Moraes Barros
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - William Otero
- Tropical Medicine Research, Panama City, Panama
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - James R Mitchell
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Danny A Milner
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Matthias Marti
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
- Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom
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38
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Enhanced Ex Vivo Plasmodium vivax Intraerythrocytic Enrichment and Maturation for Rapid and Sensitive Parasite Growth Assays. Antimicrob Agents Chemother 2018; 62:AAC.02519-17. [PMID: 29378713 DOI: 10.1128/aac.02519-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 01/21/2018] [Indexed: 01/14/2023] Open
Abstract
Plasmodium vivax chloroquine resistance has been documented in nearly every region where this malaria-causing parasite is endemic. Unfortunately, P. vivax resistance surveillance and drug discovery are challenging due to the low parasitemias of patient isolates and poor parasite survival through ex vivo maturation that reduce the sensitivity and scalability of current P. vivax antimalarial assays. Using cryopreserved patient isolates from Brazil and fresh patient isolates from India, we established a robust enrichment method for P. vivax parasites. We next performed a medium screen for formulations that enhance ex vivo survival. Finally, we optimized an isotopic metabolic labeling assay for measuring P. vivax maturation and its sensitivity to antimalarials. A KCl Percoll density gradient enrichment method increased parasitemias from small-volume ex vivo isolates by an average of >40-fold. The use of Iscove's modified Dulbecco's medium for P. vivax ex vivo culture approximately doubled the parasite survival through maturation. Coupling these with [3H]hypoxanthine metabolic labeling permitted sensitive and robust measurements of parasite maturation, which was used to measure the sensitivities of Brazilian P. vivax isolates to chloroquine and several novel antimalarials. These techniques can be applied to rapidly and robustly assess the P. vivax isolate sensitivities to antimalarials for resistance surveillance and drug discovery.
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Lima NF, Gonçalves-Lopes RM, Kruize YCM, Yazdanbakhsh M, Ferreira MU. CD39 and immune regulation in a chronic helminth infection: The puzzling case of Mansonella ozzardi. PLoS Negl Trop Dis 2018; 12:e0006327. [PMID: 29505582 PMCID: PMC5854421 DOI: 10.1371/journal.pntd.0006327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 03/15/2018] [Accepted: 02/19/2018] [Indexed: 12/13/2022] Open
Abstract
Background Chronic helminth infections typically induce an immunoregulatory environment, with markedly reduced immune responses to both parasite-specific and unrelated bystander antigens. Here we tested whether these changes are also observed in human infections with Mansonella ozzardi, a neglected filarial nematode widely distributed across Latin America. Methods CD4+ T cell populations from microfilaremic (Fil+) and uninfected (Fil-) inhabitants in M. ozzardi-endemic riverine communities in Brazil were characterized by flow cytometry analysis. Plasma concentrations of a wide range of cytokines and chemokines were measured. We examined whether M. ozzardi infection is associated with suppressed in vitro lymphoproliferative and inflammatory cytokine responses upon stimulation with filarial antigen, unrelated antigens or mitogens. Principal findings/Conclusions Fil+ subjects had lower plasma levels of selected inflammatory cytokines, such as TNF-α, IL-8, and IL-6, than their Fil- counterparts. However, we found no evidence for attenuated T-cell responses to filarial antigens or co-endemic pathogens, such as malaria parasites and Toxoplasma gondii. CD4+ T cells expressing CD39, an ectonucleosidase involved in the generation of the anti-inflammatory molecule adenosine, were increased in frequency in Fil+ subjects, compared to uninfected controls. Significantly, such an expansion was directly proportional to microfilarial loads. Surprisingly, CD39 blocking with a neutralizing antibody suppressed antigen-driven lymphoproliferation in vitro, while decreasing inflammatory cytokine responses, in Fil+ and Fil- individuals. These findings suggest that circulating CD4+ CD39+ T cells comprise subsets with both regulatory and stimulatory roles that contribute to the immune homeostasis in chronic M. ozzardi infection. Helminth infections downregulate immunity and reduce host’s inflammatory responses, but the filarial nematode Mansonella ozzardi, which is widely distributed across Latin America, appears to represent an exception to this rule. We found similar lymphoproliferative responses to filarial and unrelated antigens and comparable regulatory cytokine responses in subjects harboring M. ozzardi microfilariae, compared to local uninfected controls. The proportion of CD4+ T cell subtypes expressing CD39 was significantly increased in infected subjects and correlated positively with their microfilarial density. However, antibody blocking of CD39, an ectonucleosidase involved in the synthesis of the immunosuppresive molecule adenosine, paradoxically reduced, rather than promoted, antigen-driven lymphoproliferation in vitro. We suggest that CD39+ CD4+ T cells circulating in microfilaremics comprise both regulatory and stimulatory cell subsets that are concomitantly expanded. The balance between these cell subsets with opposing regulatory functions may be crucial to maintain immune homeostasis during chronic M. ozzardi infections.
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Affiliation(s)
- Nathália F. Lima
- 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
| | - Yvonne C. M. Kruize
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
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40
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Rodrigues PT, Valdivia HO, de Oliveira TC, Alves JMP, Duarte AMRC, Cerutti-Junior C, Buery JC, Brito CFA, de Souza JC, Hirano ZMB, Bueno MG, Catão-Dias JL, Malafronte RS, Ladeia-Andrade S, Mita T, Santamaria AM, Calzada JE, Tantular IS, Kawamoto F, Raijmakers LRJ, Mueller I, Pacheco MA, Escalante AA, Felger I, Ferreira MU. Human migration and the spread of malaria parasites to the New World. Sci Rep 2018; 8:1993. [PMID: 29386521 PMCID: PMC5792595 DOI: 10.1038/s41598-018-19554-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/03/2018] [Indexed: 01/02/2023] Open
Abstract
We examined the mitogenomes of a large global collection of human malaria parasites to explore how and when Plasmodium falciparum and P. vivax entered the Americas. We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans. Importantly, mitochondrial lineages of the P. vivax-like species P. simium are shared by platyrrhine monkeys and humans in the Atlantic Forest ecosystem, but not across the Amazon, which most likely resulted from one or a few recent human-to-monkey transfers. While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax.
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Affiliation(s)
- Priscila T Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil.
| | - Hugo O Valdivia
- Laboratory of Immunology and Parasite Genomics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- U.S. Naval Medical Research Unit No. 6, Bellavista, Callao, Peru
| | - Thais C de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil
| | - João Marcelo P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil
| | - Ana Maria R C Duarte
- Laboratory of Biochemistry and Molecular Biology, Superintendency for the Control of Endemics (SUCEN), State Secretary of Health, São Paulo, Brazil
| | | | - Julyana C Buery
- Department of Social Medicine, Federal University of Espírito Santo, Vitória, Brazil
| | - Cristiana F A Brito
- Laboratory of Malaria, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil
| | - Júlio César de Souza
- Regional University of Blumenau, Blumenau, Blumenau, Brazil
- Center of Biological Research of Indaial, Indaial, Brazil
| | - Zelinda M B Hirano
- Regional University of Blumenau, Blumenau, Blumenau, Brazil
- Center of Biological Research of Indaial, Indaial, Brazil
| | - Marina G Bueno
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Luiz Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Rosely S Malafronte
- Laboratory of Protozoology, Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Simone Ladeia-Andrade
- Laboratory of Parasitic Diseases, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, Tokyo, Japan
| | - Ana Maria Santamaria
- Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama
| | - José E Calzada
- Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama
| | - Indah S Tantular
- Department of Parasitology, Faculty of Medicine, and Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Fumihiko Kawamoto
- Department of Social and Environmental Medicine, Institute of Scientific Research, Oita University, Oita, Japan
| | - Leonie R J Raijmakers
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Ivo Mueller
- Division of Population Health and Immunity, Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - M Andreina Pacheco
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Ananias A Escalante
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil.
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