1
|
Ohene-Adjei K, Asante KP, Akuffo KO, Tounaikok N, Asiamah M, Owiredu D, Manu AA, Danso-Appiah A. Malaria vaccine-related adverse events among children under 5 in sub-Saharan Africa: systematic review and meta-analysis protocol. BMJ Open 2023; 13:e076985. [PMID: 37793915 PMCID: PMC10551995 DOI: 10.1136/bmjopen-2023-076985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023] Open
Abstract
INTRODUCTION The RTS,S vaccine has been approved for use in children under 5 living in moderate to high malaria transmission areas. However, clinically important adverse events have been reported in countries in sub-Saharan Africa. This systematic review aims to assess the frequency, severity and clinical importance of vaccine-related adverse events. METHODS AND ANALYSIS This systematic review protocol has been prepared following robust methods and reported in line with the Preferred Reporting Items for Systematic reviews and Meta-Analyses for protocols guidelines. We will search PubMed, CINAHL, LILACS, Google Scholar, SCOPUS, WEB OF SCIENCE, Cochrane library, HINARI, African Journals Online, Trip Pro and TOXNET from 2000 to 30 September 2023, without language restrictions. We will also search conference proceedings, dissertations, World Bank Open Knowledge Repository, and WHO, PATH, UNICEF, Food and Drugs Authorities and European Medicines Agency databases, preprint repositories and reference lists of relevant studies for additional studies. Experts in the field will be contacted for unpublished or published studies missed by our searches. At least two reviewers will independently select studies and extract data using pretested tools and assess risk of bias in the included studies using the Cochrane risk of bias tool. Any disagreements will be resolved through discussion between the reviewers. Heterogeneity will be explored graphically, and statistically using the I2 statistic. We will conduct random-effects meta-analysis when heterogeneity is appreciable, and express dichotomous outcomes (serious adverse events, cerebral malaria and febrile convulsion) as risk ratio (RR) with their 95% CI. We will perform subgroup analysis to assess the impact of heterogeneity and sensitivity analyses to test the robustness of the effect estimates. The overall level of evidence will be assessed using Grading of Recommendations Assessment, Development and Evaluation. ETHICS AND DISSEMINATION Ethical approval is not required for a systematic review. The findings of this study will be disseminated through stakeholder forums, conferences and peer-review publications. PROSPERO REGISTRATION NUMBER CRD42021275155.
Collapse
Affiliation(s)
- Kennedy Ohene-Adjei
- Department of Epidemiology and Disease Control, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
- Tain District Health Directorate, Ghana Health Service, Tain, Ghana
| | - Kwaku Poku Asante
- Research and Development Division, Kintampo Health Research Centre, Ghana Health Service, Kintampo, Kintampo North Municipality, Bono East Region, Ghana
| | - Kwadwo Owusu Akuffo
- Department of Optometry and Visual Science, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Narcisse Tounaikok
- Centre for Evidence Synthesis and Policy, School of Public Health, University of Ghana, Accra, Ghana
- Department of Human and Animal Health, University of Emi Koussi, N'Djamena, Chad
| | - Morrison Asiamah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - David Owiredu
- Department of Epidemiology and Disease Control, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
- Centre for Evidence Synthesis and Policy, School of Public Health, University of Ghana, Accra, Ghana
| | - Alexander Ansah Manu
- Department of Epidemiology and Disease Control, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Anthony Danso-Appiah
- Department of Epidemiology and Disease Control, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana
- Centre for Evidence Synthesis and Policy, School of Public Health, University of Ghana, Accra, Ghana
| |
Collapse
|
2
|
Xu FF, Chen WQ, Liu W, Liu SS, Wang YX, Chen J, Cui J, Zhang X. Genetic structure of Spirometra mansoni (Cestoda: Diphyllobothriidae) populations in China revealed by a Target SSR-seq method. Parasit Vectors 2022; 15:485. [PMID: 36564786 PMCID: PMC9789593 DOI: 10.1186/s13071-022-05568-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In China, the plerocercoid of the cestode Spirometra mansoni is the main causative agent of human and animal sparganosis. However, the population genetic structure of this parasite remains unclear. In this study, we genotyped S. mansoni isolates with the aim to improve current knowledge on the evolution and population diversity of this cestode. METHODS We first screened 34 perfect simple sequence repeats (SSRs) using all available omic data and then constructed target sequencing technology (Target SSR-seq) based on the Illumina NovaSeq platform. Next, a series of STRUCTURE. clustering, principal component, analysis of molecular variance and TreeMix analyses were performed on 362 worm samples isolated from 12 different hosts in 16 geographical populations of China to identify the genetic structure. RESULTS A total of 170 alleles were detected. The whole population could be organized and was found to be derived from the admixture of two ancestral clusters. TreeMix analysis hinted that possible gene flow occurred from Guizhou (GZ) to Sichuan (SC), SC to Jaingxi (JX), SC to Hubei (HB), GZ to Yunnan (YN) and GZ to Jiangsu (JS). Both neighbor-joining clustering and principal coordinate analysis showed that isolates from intermediate hosts tend to cluster together, while parasites from definitive hosts revealed greater genetic differences. Generally, a S. mansoni population was observed to harbor high genetic diversity, moderate genetic differentiation and a little genetic exchange among geographical populations. CONCLUSIONS A Target SSR-seq genotyping method was successfully developed, and an in-depth view of genetic diversity and genetic relationship will have important implications for the prevention and control of sparganosis.
Collapse
Affiliation(s)
- Fang Fang Xu
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Wen Qing Chen
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Wei Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Sha Sha Liu
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Yi Xing Wang
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Jing Chen
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Jing Cui
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Xi Zhang
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| |
Collapse
|
3
|
Metchanun N, Borgemeister C, Amzati G, von Braun J, Nikolov M, Selvaraj P, Gerardin J. Modeling impact and cost-effectiveness of driving-Y gene drives for malaria elimination in the Democratic Republic of the Congo. Evol Appl 2022; 15:132-148. [PMID: 35126652 PMCID: PMC8792473 DOI: 10.1111/eva.13331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 11/15/2021] [Accepted: 11/29/2021] [Indexed: 12/17/2022] Open
Abstract
Malaria elimination will be challenging in countries that currently continue to bear high malaria burden. Sex-ratio-distorting gene drives, such as driving-Y, could play a role in an integrated elimination strategy if they can effectively suppress vector populations. Using a spatially explicit, agent-based model of malaria transmission in eight provinces spanning the range of transmission intensities across the Democratic Republic of the Congo, we predict the impact and cost-effectiveness of integrating driving-Y gene drive mosquitoes in malaria elimination strategies that include existing interventions such as insecticide-treated nets and case management of symptomatic malaria. Gene drive mosquitoes could eliminate malaria and were the most cost-effective intervention overall if the drive component was highly effective with at least 95% X-shredder efficiency at relatively low fertility cost, and associated cost of deployment below 7.17 $int per person per year. Suppression gene drive could be a cost-effective supplemental intervention for malaria elimination, but tight constraints on drive effectiveness and cost ceilings may limit its feasibility.
Collapse
Affiliation(s)
| | | | - Gaston Amzati
- Université Evangélique en AfriqueBukavuDemocratic Republic of the Congo
| | | | | | | | - Jaline Gerardin
- Institute for Disease ModelingBellevueWashingtonUSA
- Department of Preventive Medicine and Institute for Global HealthNorthwestern UniversityChicagoIllinoisUSA
| |
Collapse
|
4
|
Verity R, Aydemir O, Brazeau NF, Watson OJ, Hathaway NJ, Mwandagalirwa MK, Marsh PW, Thwai K, Fulton T, Denton M, Morgan AP, Parr JB, Tumwebaze PK, Conrad M, Rosenthal PJ, Ishengoma DS, Ngondi J, Gutman J, Mulenga M, Norris DE, Moss WJ, Mensah BA, Myers-Hansen JL, Ghansah A, Tshefu AK, Ghani AC, Meshnick SR, Bailey JA, Juliano JJ. The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC. Nat Commun 2020; 11:2107. [PMID: 32355199 DOI: 10.1038/s41467-020-15779-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/28/2020] [Indexed: 11/09/2022] Open
Abstract
The Democratic Republic of the Congo (DRC) harbors 11% of global malaria cases, yet little is known about the spatial and genetic structure of the parasite population in that country. We sequence 2537 Plasmodium falciparum infections, including a nationally representative population sample from DRC and samples from surrounding countries, using molecular inversion probes - a high-throughput genotyping tool. We identify an east-west divide in haplotypes known to confer resistance to chloroquine and sulfadoxine-pyrimethamine. Furthermore, we identify highly related parasites over large geographic distances, indicative of gene flow and migration. Our results are consistent with a background of isolation by distance combined with the effects of selection for antimalarial drug resistance. This study provides a high-resolution view of parasite genetic structure across a large country in Africa and provides a baseline to study how implementation programs may impact parasite populations. The genome of the malaria parasite Plasmodium falciparum contains a record of past evolutionary forces. Here, using 2537 parasite sequences from the Democratic Republic of the Congo, the authors demonstrate how drug pressure and human movement have shaped the present-day parasite population.
Collapse
|
5
|
Manda S, Haushona N, Bergquist R. A Scoping Review of Spatial Analysis Approaches Using Health Survey Data in Sub-Saharan Africa. Int J Environ Res Public Health 2020; 17:E3070. [PMID: 32354095 PMCID: PMC7246597 DOI: 10.3390/ijerph17093070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 01/03/2023]
Abstract
Spatial analysis has become an increasingly used analytic approach to describe and analyze spatial characteristics of disease burden, but the depth and coverage of its usage for health surveys data in Sub-Saharan Africa are not well known. The objective of this scoping review was to conduct an evaluation of studies using spatial statistics approaches for national health survey data in the SSA region. An organized literature search for studies related to spatial statistics and national health surveys was conducted through PMC, PubMed/Medline, Scopus, NLM Catalog, and Science Direct electronic databases. Of the 4,193 unique articles identified, 153 were included in the final review. Spatial smoothing and prediction methods were predominant (n = 108), followed by spatial description aggregation (n = 25), and spatial autocorrelation and clustering (n = 19). Bayesian statistics methods and lattice data modelling were predominant (n = 108). Most studies focused on malaria and fever (n = 47) followed by health services coverage (n = 38). Only fifteen studies employed nonstandard spatial analyses (e.g., spatial model assessment, joint spatial modelling, accounting for survey design). We recommend that for future spatial analysis using health survey data in the SSA region, there must be an improve recognition and awareness of the potential dangers of a naïve application of spatial statistical methods. We also recommend a wide range of applications using big health data and the future of data science for health systems to monitor and evaluate impacts that are not well understood at local levels.
Collapse
Affiliation(s)
- Samuel Manda
- Biostatistics Research Unit, South African Medical Research Council, Pretoria 0001, South Africa
- Department of Statistics, University of Pretoria, Pretoria 0002, South Africa
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg 3209, South Africa
| | - Ndamonaonghenda Haushona
- Biostatistics Research Unit, South African Medical Research Council, Pretoria 0001, South Africa
- Division of Epidemiology and Biostatistics, University of Stellenbosch, Cape Town 8000, South Africa
| | | |
Collapse
|
6
|
Li Y, Shetty AC, Lon C, Spring M, Saunders DL, Fukuda MM, Hien TT, Pukrittayakamee S, Fairhurst RM, Dondorp AM, Plowe CV, O’Connor TD, Takala-Harrison S, Stewart K. Detecting geospatial patterns of Plasmodium falciparum parasite migration in Cambodia using optimized estimated effective migration surfaces. Int J Health Geogr 2020; 19:13. [PMID: 32276636 PMCID: PMC7149848 DOI: 10.1186/s12942-020-00207-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/01/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Understanding the genetic structure of natural populations provides insight into the demographic and adaptive processes that have affected those populations. Such information, particularly when integrated with geospatial data, can have translational applications for a variety of fields, including public health. Estimated effective migration surfaces (EEMS) is an approach that allows visualization of the spatial patterns in genomic data to understand population structure and migration. In this study, we developed a workflow to optimize the resolution of spatial grids used to generate EEMS migration maps and applied this optimized workflow to estimate migration of Plasmodium falciparum in Cambodia and bordering regions of Thailand and Vietnam. METHODS The optimal density of EEMS grids was determined based on a new workflow created using density clustering to define genomic clusters and the spatial distance between genomic clusters. Topological skeletons were used to capture the spatial distribution for each genomic cluster and to determine the EEMS grid density; i.e., both genomic and spatial clustering were used to guide the optimization of EEMS grids. Model accuracy for migration estimates using the optimized workflow was tested and compared to grid resolutions selected without the optimized workflow. As a test case, the optimized workflow was applied to genomic data generated from P. falciparum sampled in Cambodia and bordering regions, and migration maps were compared to estimates of malaria endemicity, as well as geographic properties of the study area, as a means of validating observed migration patterns. RESULTS Optimized grids displayed both high model accuracy and reduced computing time compared to grid densities selected in an unguided manner. In addition, EEMS migration maps generated for P. falciparum using the optimized grid corresponded to estimates of malaria endemicity and geographic properties of the study region that might be expected to impact malaria parasite migration, supporting the validity of the observed migration patterns. CONCLUSIONS Optimized grids reduce spatial uncertainty in the EEMS contours that can result from user-defined parameters, such as the resolution of the spatial grid used in the model. This workflow will be useful to a broad range of EEMS users as it can be applied to analyses involving other organisms of interest and geographic areas.
Collapse
Affiliation(s)
- Yao Li
- Center for Geospatial Information Science, Department of Geographical Sciences, University of Maryland, College Park, 20742 MD USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Michele Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - David L. Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mark M. Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Arjen M. Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | | | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Kathleen Stewart
- Center for Geospatial Information Science, Department of Geographical Sciences, University of Maryland, College Park, 20742 MD USA
| |
Collapse
|
7
|
Nelson CS, Sumner KM, Freedman E, Saelens JW, Obala AA, Mangeni JN, Taylor SM, O'Meara WP. High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya. Nat Commun 2019; 10:5615. [PMID: 31819062 PMCID: PMC6901486 DOI: 10.1038/s41467-019-13578-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/14/2019] [Indexed: 01/03/2023] Open
Abstract
Novel interventions that leverage the heterogeneity of parasite transmission are needed to achieve malaria elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon next-generation sequencing of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From April 2013 to July 2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. Here, we evaluate genetic similarity between infected individuals using three indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly share haplotypes with their own household members. Furthermore, we observe robust temporal structuring of parasite genetic similarity and identify the unique molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures. Here, Nelson et al. use amplicon next-generation sequencing of two P. falciparum polymorphic gene regions to investigate the genetic similarity of parasite populations across time and space in a pediatric cohort in Kenya. They identify both micro- and macro-scale structuring of malaria parasites in this high-transmission setting, which could inform future intervention strategies.
Collapse
Affiliation(s)
- Cody S Nelson
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.
| | - Kelsey M Sumner
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Elizabeth Freedman
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Andrew A Obala
- School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Judith N Mangeni
- School of Nursing, Moi University College of Health Sciences, Eldoret, Kenya
| | - Steve M Taylor
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Wendy P O'Meara
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| |
Collapse
|
8
|
Deutsch-Feldman M, Aydemir O, Carrel M, Brazeau NF, Bhatt S, Bailey JA, Kashamuka M, Tshefu AK, Taylor SM, Juliano JJ, Meshnick SR, Verity R. The changing landscape of Plasmodium falciparum drug resistance in the Democratic Republic of Congo. BMC Infect Dis 2019; 19:872. [PMID: 31640574 PMCID: PMC6805465 DOI: 10.1186/s12879-019-4523-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Drug resistant malaria is a growing concern in the Democratic Republic of the Congo (DRC), where previous studies indicate that parasites resistant to sulfadoxine/pyrimethamine or chloroquine are spatially clustered. This study explores longitudinal changes in spatial patterns to understand how resistant malaria may be spreading within the DRC, using samples from nation-wide population-representative surveys. METHODS We selected 552 children with PCR-detectable Plasmodium falciparum infection and identified known variants in the pfdhps and pfcrt genes associated with resistance. We compared the proportion of mutant parasites in 2013 to those previously reported from adults in 2007, and identified risk factors for carrying a resistant allele using multivariate mixed-effects modeling. Finally, we fit a spatial-temporal model to the observed data, providing smooth allele frequency estimates over space and time. RESULTS The proportion of co-occurring pfdhps K540E/A581G mutations increased by 16% between 2007 and 2013. The spatial-temporal model suggests that the spatial range of the pfdhps double mutants expanded over time, while the prevalence and range of pfcrt mutations remained steady. CONCLUSIONS This study uses population-representative samples to describe the changing landscape of SP resistance within the DRC, and the persistence of chloroquine resistance. Vigilant molecular surveillance is critical for controlling the spread of resistance.
Collapse
Affiliation(s)
- Molly Deutsch-Feldman
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Margaret Carrel
- Department of Geographical & Sustainability Sciences, University of Iowa, Iowa City, IA, USA
| | - Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Samir Bhatt
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Melchior Kashamuka
- Ecole de Santé Publique, , Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Antoinette K Tshefu
- Ecole de Santé Publique, , Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Steve M Taylor
- Division of Infectious Diseases and Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.,Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Robert Verity
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| |
Collapse
|
9
|
Kozakiewicz CP, Burridge CP, Funk WC, VandeWoude S, Craft ME, Crooks KR, Ernest HB, Fountain‐Jones NM, Carver S. Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evol Appl 2018; 11:1763-1778. [PMID: 30459828 PMCID: PMC6231466 DOI: 10.1111/eva.12678] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/24/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free-living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host-vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross-disciplinary advances.
Collapse
Affiliation(s)
| | | | - W. Chris Funk
- Department of BiologyGraduate Degree Program in EcologyColorado State UniversityFort CollinsColorado
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColorado
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt. PaulMinnesota
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology LaboratoryDepartment of Veterinary SciencesUniversity of WyomingLaramieWyoming
| | | | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| |
Collapse
|
10
|
Aydemir O, Janko M, Hathaway NJ, Verity R, Mwandagalirwa MK, Tshefu AK, Tessema SK, Marsh PW, Tran A, Reimonn T, Ghani AC, Ghansah A, Juliano JJ, Greenhouse BR, Emch M, Meshnick SR, Bailey JA. Drug-Resistance and Population Structure of Plasmodium falciparum Across the Democratic Republic of Congo Using High-Throughput Molecular Inversion Probes. J Infect Dis 2018; 218:946-955. [PMID: 29718283 PMCID: PMC6093412 DOI: 10.1093/infdis/jiy223] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/26/2018] [Indexed: 11/21/2022] Open
Abstract
A better understanding of the drivers of the spread of malaria parasites and drug resistance across space and time is needed. These drivers can be elucidated using genetic tools. Here, a novel molecular inversion probe (MIP) panel targeting all major drug-resistance mutations and a set of microsatellites was used to genotype Plasmodium falciparum infections of 552 children from the 2013-2014 Demographic and Health Survey conducted in the Democratic Republic of the Congo (DRC). Microsatellite-based analysis of population structure suggests that parasites within the DRC form a homogeneous population. In contrast, sulfadoxine-resistance markers in dihydropteroate synthase show marked spatial structure with ongoing spread of double and triple mutants compared with 2007. These findings suggest that parasites in the DRC remain panmictic despite rapidly spreading antimalarial-resistance mutations. Moreover, highly multiplexed targeted sequencing using MIPs emerges as a cost-effective method for elucidating pathogen genetics in complex infections in large cohorts.
Collapse
Affiliation(s)
- Ozkan Aydemir
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester
| | - Mark Janko
- Department of Geography, University of North Carolina, Chapel Hill
| | - Nick J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester
| | - Robert Verity
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
| | | | - Antoinette K Tshefu
- Community Health, Kinshasa School of Public Health, School of Medicine, University of Kinshasa, Democratic Republic of Congo
| | | | - Patrick W Marsh
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester
| | - Alice Tran
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester
| | - Thomas Reimonn
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester
| | - Azra C Ghani
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute of Medical Research, Ghana
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill
- Division of Infectious Diseases, University of North Carolina, Chapel Hill
- Curriculum in Genetics and Microbiology, University of North Carolina, Chapel Hill
| | | | - Michael Emch
- Department of Geography, University of North Carolina, Chapel Hill
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester
| |
Collapse
|
11
|
|
12
|
Verity R, Hathaway NJ, Waltmann A, Doctor SM, Watson OJ, Patel JC, Mwandagalirwa K, Tshefu AK, Bailey JA, Ghani AC, Juliano JJ, Meshnick SR. Plasmodium falciparum genetic variation of var2csa in the Democratic Republic of the Congo. Malar J 2018; 17:46. [PMID: 29361940 PMCID: PMC5782373 DOI: 10.1186/s12936-018-2193-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Democratic Republic of the Congo (DRC) bears a high burden of malaria, which is exacerbated in pregnant women. The VAR2CSA protein plays a crucial role in pregnancy-associated malaria (PAM), and hence quantifying diversity at the var2csa locus in the DRC is important in understanding the basic epidemiology of PAM, and in developing a robust vaccine against PAM. METHODS Samples were taken from the 2013-14 Demographic and Health Survey conducted in the DRC, focusing on children under 5 years of age. A short subregion of the var2csa gene was sequenced in 115 spatial clusters, giving country-wide estimates of sequence polymorphism and spatial population structure. RESULTS Results indicate that var2csa is highly polymorphic, and that diversity is being maintained through balancing selection, however, there is no clear signal of phylogenetic or geographic structure to this diversity. Linear modelling demonstrates that the number of var2csa variants in a cluster correlates directly with cluster prevalence, but not with other epidemiological factors such as urbanicity. CONCLUSIONS Results suggest that the DRC fits within the global pattern of high var2csa diversity and little genetic differentiation between regions. A broad multivalent VAR2CSA vaccine candidate could benefit from targeting stable regions and common variants to address the substantial genetic diversity.
Collapse
Affiliation(s)
- Robert Verity
- Medical Research Council Centre for Outbreak Analysis & Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, MA, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts, Worcester, MA, USA
| | - Andreea Waltmann
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Stephanie M Doctor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Oliver J Watson
- Medical Research Council Centre for Outbreak Analysis & Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jaymin C Patel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Kashamuka Mwandagalirwa
- Kinshasa School of Public Health, Hôpital General Provincial de Reference de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Antoinette K Tshefu
- Community Health, Kinshasa School of Public Health, School of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, MA, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts, Worcester, MA, USA
| | - Azra C Ghani
- Medical Research Council Centre for Outbreak Analysis & Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA
- Curriculum in Genetics and Microbiology, University of North Carolina at Chapel Hill, 321 South Columbia Street, Chapel Hill, NC, 27516, USA
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
| |
Collapse
|
13
|
Miller RH, Hathaway NJ, Kharabora O, Mwandagalirwa K, Tshefu A, Meshnick SR, Taylor SM, Juliano JJ, Stewart VA, Bailey JA. A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity. Malar J 2017; 16:490. [PMID: 29246158 PMCID: PMC5732508 DOI: 10.1186/s12936-017-2137-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/06/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Humans living in regions with high falciparum malaria transmission intensity harbour multi-strain infections comprised of several genetically distinct malaria haplotypes. The number of distinct malaria parasite haplotypes identified from an infected human host at a given time is referred to as the complexity of infection (COI). In this study, an amplicon-based deep sequencing method targeting the Plasmodium falciparum apical membrane antigen 1 (pfama1) was utilized to (1) investigate the relationship between P. falciparum prevalence and COI, (2) to explore the population genetic structure of P. falciparum parasites from malaria asymptomatic individuals participating in the 2007 Demographic and Health Survey (DHS) in the Democratic Republic of Congo (DRC), and (3) to explore selection pressures on geospatially divergent parasite populations by comparing AMA1 amino acid frequencies in the DRC and Mali. RESULTS A total of 900 P. falciparum infections across 11 DRC provinces were examined. Deep sequencing of both individuals, for COI analysis, and pools of individuals, to examine population structure, identified 77 unique pfama1 haplotypes. The majority of individual infections (64.5%) contained polyclonal (COI > 1) malaria infections based on the presence of genetically distinct pfama1 haplotypes. A minimal correlation between COI and malaria prevalence as determined by sensitive real-time PCR was identified. Population genetic analyses revealed extensive haplotype diversity, the vast majority of which was shared across the sites. AMA1 amino acid frequencies were similar between parasite populations in the DRC and Mali. CONCLUSIONS Amplicon-based deep sequencing is a useful tool for the detection of multi-strain infections that can aid in the understanding of antigen heterogeneity of potential malaria vaccine candidates, population genetics of malaria parasites, and factors that influence complex, polyclonal malaria infections. While AMA1 and other diverse markers under balancing selection may perform well for understanding COI, they may offer little geographic or temporal discrimination between parasite populations.
Collapse
Affiliation(s)
- Robin H Miller
- Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD, USA
| | - Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts School of Medicine, 55 Lake Avenue North, Worcester, MA, USA
| | - Oksana Kharabora
- University of North Carolina School of Medicine, 101 Manning Drive, Chapel Hill, NC, USA
| | - Kashamuka Mwandagalirwa
- Ecole de Santé Publique, Université de Kinshasa, Commune de Lemba, P.O Box 11850, Kinshasa, Democratic Republic of Congo
| | - Antoinette Tshefu
- Ecole de Santé Publique, Université de Kinshasa, Commune de Lemba, P.O Box 11850, Kinshasa, Democratic Republic of Congo
| | - Steven R Meshnick
- University of North Carolina School of Medicine, 101 Manning Drive, Chapel Hill, NC, USA
| | - Steve M Taylor
- Division of Infectious Diseases and Duke Global Health Institute, Duke University Medical Center, 303 Research Drive, Durham, NC, USA
| | - Jonathan J Juliano
- University of North Carolina School of Medicine, 101 Manning Drive, Chapel Hill, NC, USA
| | - V Ann Stewart
- Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts School of Medicine, 55 Lake Avenue North, Worcester, MA, USA.
| |
Collapse
|
14
|
|