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Power RI, Doyle SR, Šlapeta J. Whole genome amplification and sequencing of individual Dirofilaria immitis microfilariae. Exp Parasitol 2024; 263-264:108806. [PMID: 39009178 DOI: 10.1016/j.exppara.2024.108806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/17/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
Abstract
Dirofilaria immitis is a filarial parasitic nematode of veterinary significance. With the emergence of drug-resistant isolates in the USA, it is imperative to determine the likelihood of resistance occurring in other regions of the world. One approach is to conduct population genetic studies across an extensive geographical range, and to sequence the genomes of individual worms to understand genome-wide genetic variation associated with resistance. The immature life stages of D. immitis found in the host blood are more accessible and less invasive to sample compared to extracting adult stages from the host heart. To assess the use of immature life stages for population genetic analyses, we have performed whole genome amplification and whole-genome sequencing on nine (n = 9) individual D. immitis microfilaria samples isolated from dog blood. On average, less than 1% of mapped reads aligned to each D. immitis genome (nuclear, mitochondrial, and Wolbachia endosymbiont). For the dog genome, an average of over 99% of mapped reads aligned to the nuclear genome and less than 1% aligned to the mitochondrial genome. The average coverage for all D. immitis genomes and the dog nuclear genome was less than 1, while the dog mitochondrial genome had an average coverage of 2.87. The overwhelming proportion of sequencing reads mapping to the dog host genome can be attributed to residual dog blood cells in the microfilariae samples. These results demonstrate the challenges of conducting genome-wide studies on individual immature parasite life stages, particularly in the presence of extraneous host DNA.
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Affiliation(s)
- Rosemonde I Power
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales, 2006, Australia
| | - Stephen R Doyle
- Wellcome Sanger Institute, Cambridgeshire, CB10 1SA, United Kingdom
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales, 2006, Australia; Sydney Infectious Diseases Institute, The University of Sydney, New South Wales, 2006, Australia.
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2
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Choi YJ, Fischer K, Méité A, Koudou BG, Fischer PU, Mitreva M. Distinguishing recrudescence from reinfection in lymphatic filariasis. EBioMedicine 2024; 105:105188. [PMID: 38848649 PMCID: PMC11200287 DOI: 10.1016/j.ebiom.2024.105188] [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: 11/14/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The Global Program to Eliminate Lymphatic Filariasis (GPELF) is the largest public health program based on mass drug administration (MDA). Despite decades of MDA, ongoing transmission in some countries remains a challenge. To optimise interventions, it is critical to differentiate between recrudescence and new infections. Since adult filariae are inaccessible in humans, deriving a method that relies on the offspring microfilariae (mf) is necessary. METHODS We developed a genome amplification and kinship analysis-based approach using Brugia malayi samples from gerbils, and applied it to analyse Wuchereria bancrofti mf from humans in Côte d'Ivoire. We examined the pre-treatment genetic diversity in 269 mf collected from 18 participants, and further analysed 1-year post-treatment samples of 74 mf from 4 participants. Hemizygosity of the male X-chromosome allowed for direct inference of haplotypes, facilitating robust maternal parentage inference. To enrich parasite DNA from samples contaminated with host DNA, a whole-exome capture panel was created for W. bancrofti. FINDINGS By reconstructing and temporally tracking sibling relationships across pre- and post-treatment samples, we differentiated between new and established maternal families, suggesting reinfection in one participant and recrudescence in three participants. The estimated number of reproductively active adult females ranged between 3 and 11 in the studied participants. Population structure analysis revealed genetically distinct parasites in Côte d'Ivoire compared to samples from other countries. Exome capture identified protein-coding variants with ∼95% genotype concordance rate. INTERPRETATION We have generated resources to facilitate the development of molecular genetic tools that can estimate adult worm burdens and monitor parasite populations, thus providing essential information for the successful implementation of GPELF. FUNDING This work was financially supported by the Bill and Melinda Gates Foundation (https://www.gatesfoundation.org) under grant OPP1201530 (Co-PIs PUF & Gary J. Weil). B. malayi parasite material was generated with support of the Foundation for Barnes Jewish Hospital (PUF). In addition, the development of computational methods was supported by the National Institutes of Health under grants AI144161 (MM) and AI146353 (MM). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Young-Jun Choi
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aboulaye Méité
- Programme National de la Lutte Contre la Schistosomiase, Les Geohelminthiases et la Filariose Lymphatique, Abidjan, Côte d'Ivoire
| | - Benjamin G Koudou
- Centre Suisse de Recherche Scientifique en Côte d'Ivoire, Abidjan, Côte d'Ivoire; Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Peter U Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
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3
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Crawford KE, Hedtke SM, Doyle SR, Kuesel AC, Armoo S, Osei-Atweneboana MY, Grant WN. Genome-based tools for onchocerciasis elimination: utility of the mitochondrial genome for delineating Onchocerca volvulus transmission zones. Int J Parasitol 2024; 54:171-183. [PMID: 37993016 DOI: 10.1016/j.ijpara.2023.11.002] [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: 05/03/2023] [Revised: 09/21/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
National programs in Africa have expanded their objectives from control of onchocerciasis (river blindness) as a public health problem to elimination of parasite transmission, motivated by the reduction of Onchocerca volvulus infection prevalence in many African meso- and hyperendemic areas due to mass drug administration of ivermectin (MDAi). Given the large, contiguous hypo-, meso-, and hyperendemic areas, sustainable elimination of onchocerciasis in sub-Saharan Africa requires delineation of geographic boundaries for parasite transmission zones, so that programs can consider the risk of parasite re-introduction through vector or human migration from areas with ongoing transmission when making decisions to stop MDAi. We propose that transmission zone boundaries can be delineated by characterising the parasite genetic population structure within and between potential zones. We analysed whole mitochondrial genome sequences of 189 O. volvulus adults to determine the pattern of genetic similarity across three West African countries: Ghana, Mali, and Côte d'Ivoire. Population genetic structure indicates that parasites from villages near the Pru, Daka, and Black Volta rivers in central Ghana belong to one parasite population, indicating that the assumption that river basins constitute individual transmission zones is not supported by the data. Parasites from Mali and Côte d'Ivoire are genetically distinct from those from Ghana. This research provides the basis for developing tools for elimination programs to delineate transmission zones, to estimate the risk of parasite re-introduction via vector or human movement when intervention is stopped in one area while transmission is ongoing in others, to identify the origin of infections detected post-treatment cessation, and to investigate whether persisting prevalence despite ongoing interventions in one area is due to parasites imported from others.
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Affiliation(s)
- Katie E Crawford
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Shannon M Hedtke
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia.
| | - Stephen R Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Annette C Kuesel
- UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Samuel Armoo
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Council for Scientific and Industrial Research, Council Close, Accra, Ghana
| | - Mike Y Osei-Atweneboana
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Council for Scientific and Industrial Research, Council Close, Accra, Ghana
| | - Warwick N Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia
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Otiti-Sengeri J, Sube KLL, Siewe Fodjo JN, Otabil KB, Colebunders R. Chorioretinitis among Immigrant and Travellers. Comment on Mansour et al. Presumed Onchocerciasis Chorioretinitis Spilling over into North America, Europe and Middle East. Diagnostics 2023, 13, 3626. Diagnostics (Basel) 2024; 14:478. [PMID: 38472950 DOI: 10.3390/diagnostics14050478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
We read, with interest, the paper by Mansour et al [...].
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Affiliation(s)
| | | | | | - Kenneth Bentum Otabil
- Department of Biological Science, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Robert Colebunders
- Global Health Institute, University of Antwerp, 2610 Antwerp, Belgium
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
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Gandasegui J, Power RI, Curry E, Lau DCW, O'Neill CM, Wolstenholme A, Prichard R, Šlapeta J, Doyle SR. Genome structure and population genomics of the canine heartworm Dirofilaria immitis. Int J Parasitol 2024; 54:89-98. [PMID: 37652224 DOI: 10.1016/j.ijpara.2023.07.006] [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: 04/24/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
The heartworm, Dirofilaria immitis, is a filarial parasitic nematode responsible for significant morbidity and mortality in wild and domesticated canids. Resistance to macrocyclic lactone drug prevention represents a significant threat to parasite control and has prompted investigations to understand the genetic determinants of resistance. This study aimed to improve the genomic resources of D. immitis to enable a more precise understanding of how genetic variation is distributed within and between parasite populations worldwide, which will inform the likelihood and rate by which parasites, and in turn, resistant alleles, might spread. We have guided the scaffolding of a recently published genome assembly for D. immitis (ICBAS_JMDir_1.0) using the chromosomal-scale reference genomes of Brugia malayi and Onchocerca volvulus, resulting in an 89.5 Mb assembly composed of four autosomal- and one sex-linked chromosomal-scale scaffolds representing 99.7% of the genome. Publicly available and new whole-genome sequencing data from 32 D. immitis samples from Australia, Italy and the USA were assessed using principal component analysis, nucleotide diversity (Pi) and absolute genetic divergence (Dxy) to characterise the global genetic structure and measure within- and between-population diversity. These population genetic analyses revealed broad-scale genetic structure among globally diverse samples and differences in genetic diversity between populations; however, fine-scale subpopulation analysis was limited and biased by differences between sample types. Finally, we mapped single nucleotide polymorphisms previously associated with macrocyclic lactone resistance in the new genome assembly, revealing the physical linkage of high-priority variants on chromosome 3, and determined their frequency in the studied populations. This new chromosomal assembly for D. immitis now allows for a more precise investigation of selection on genome-wide genetic variation and will enhance our understanding of parasite transmission and the spread of genetic variants responsible for resistance to treatment.
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Affiliation(s)
- Javier Gandasegui
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - University of Barcelona, Barcelona, Spain.
| | - Rosemonde I Power
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, Australia.
| | - Emily Curry
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, QC, Canada.
| | - Daisy Ching-Wai Lau
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, Australia.
| | - Connor M O'Neill
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.
| | - Adrian Wolstenholme
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.
| | - Roger Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, QC, Canada.
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, Australia.
| | - Stephen R Doyle
- Wellcome Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom.
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Stevens L, Martínez-Ugalde I, King E, Wagah M, Absolon D, Bancroft R, Gonzalez de la Rosa P, Hall JL, Kieninger M, Kloch A, Pelan S, Robertson E, Pedersen AB, Abreu-Goodger C, Buck AH, Blaxter M. Ancient diversity in host-parasite interaction genes in a model parasitic nematode. Nat Commun 2023; 14:7776. [PMID: 38012132 PMCID: PMC10682056 DOI: 10.1038/s41467-023-43556-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These interactions can lead to negative frequency-dependent selection, a form of balancing selection that is hypothesised to explain the high levels of polymorphism seen in many host immune and parasite antigen loci. Here, we sequence the genomes of several individuals of Heligmosomoides bakeri, a model parasite of house mice, and Heligmosomoides polygyrus, a closely related parasite of wood mice. Although H. bakeri is commonly referred to as H. polygyrus in the literature, their genomes show levels of divergence that are consistent with at least a million years of independent evolution. The genomes of both species contain hyper-divergent haplotypes that are enriched for proteins that interact with the host immune response. Many of these haplotypes originated prior to the divergence between H. bakeri and H. polygyrus, suggesting that they have been maintained by long-term balancing selection. Together, our results suggest that the selection pressures exerted by the host immune response have played a key role in shaping patterns of genetic diversity in the genomes of parasitic nematodes.
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Affiliation(s)
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
| | - Isaac Martínez-Ugalde
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Erna King
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Martin Wagah
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rowan Bancroft
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Jessica L Hall
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Elaine Robertson
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy B Pedersen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
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Choi YJ, Fischer K, Méité A, Koudou BG, Fischer PU, Mitreva M. Distinguishing recrudescence from reinfection in lymphatic filariasis: a genomics-based approach for monitoring worm burden. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.05.23297155. [PMID: 37986785 PMCID: PMC10659506 DOI: 10.1101/2023.11.05.23297155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background The Global Program to Eliminate Lymphatic Filariasis is the largest public health program based on mass drug administration (MDA). Despite decades of MDA, ongoing transmission in some countries remains a challenge. To optimize interventions, it is essential to differentiate between recrudescence (poor drug response and persistent infection) and new infections (ongoing transmission). Since adult filariae are inaccessible in humans, an approach that relies on genotyping the offspring microfilariae (mf) is required. Methods We utilized Brugia malayi adults and mf obtained from gerbils with a known pedigree to develop and validate our whole-genome amplification and kinship analysis approach. We then sequenced the genomes of Wuchereria bancrofti mf from infected humans from Côte d'Ivoire (CDI), characterized the population genetic diversity, and made inferences about the adult breeders. We developed a whole-exome capture panel for W. bancrofti to enrich parasite nuclear DNA from lower-quality samples contaminated with host DNA. Results We established a robust analysis pipeline using B. malayi adult and mf. We estimated the pre-treatment genetic diversity in W. bancrofti from 269 mf collected from 18 individuals, and further analyzed 1-year post-treatment samples of 74 mf from 4 individuals. By reconstructing and temporally tracking sibling relationships across pre- and post-treatment samples, we differentiated between new and established maternal families, suggesting reinfection in one subject and recrudescence in three subjects. Estimated reproductively active adult females ranged between 3 and 9 in the studied subjects. Hemizygosity of the male X-chromosome allowed for direct inference of haplotypes, facilitating robust maternal parentage inference, even when the genetic diversity was low. Population structure analysis revealed genetically distinct parasites among our CDI samples. Sequence composition and variant analysis of whole-exome libraries showed that the hybridization capture approach can effectively enrich parasite nuclear DNA and identify protein-coding variants with ∼95% genotype concordance rate. Conclusions We have generated resources to facilitate development of field-deployable genotyping tools that can estimate worm burdens and monitor parasite populations. These tools are essential for the success of lymphatic filariasis MDA programs. With further expansion of the databases to include geographically diverse samples, we will be able to spatially track parasite movement associated with host/vector migration.
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Hedtke SM, Kode A, Ukety TO, Mande JL, Abhafule GM, Raciu AA, Uvon CB, Jada SR, Hotterbeekx A, Siewe Fodjo JN, Mitreva M, Sebit W, Colebunders R, Grant WN, Kuesel AC. Procedure for Handling and Storage of Onchocerca volvulus Microfilariae Obtained from Skin Snips for Downstream Genetic Work. Trop Med Infect Dis 2023; 8:445. [PMID: 37755906 PMCID: PMC10536066 DOI: 10.3390/tropicalmed8090445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
WHO and endemic countries target elimination of transmission of Onchocerca volvulus, the parasite causing onchocerciasis. Population genetic analysis of O. volvulus may provide data to improve the evidence base for decisions on when, where, and for how long to deploy which interventions and post-intervention surveillance to achieve elimination. Development of necessary methods and tools requires parasites suitable for genetic analysis. Based on our experience with microfilariae obtained from different collaborators, we developed a microfilariae transfer procedure for large-scale studies in the Democratic Republic of Congo (DRC) comparing safety and efficacy of ivermectin, the mainstay of current onchocerciasis elimination strategies, and moxidectin, a new drug. This procedure is designed to increase the percentage of microfilariae in skin snips suitable for genetic analysis, improve assignment to metadata, and minimize time and materials needed by the researchers collecting the microfilariae. Among 664 microfilariae from South Sudan, 35.7% and 39.5% failed the mitochondrial and nuclear qPCR assay. Among the 576 microfilariae from DRC, 16.0% and 16.7% failed these assays, respectively. This difference may not only be related to the microfilariae transfer procedure but also to other factors, notably the ethanol concentration in the tubes in which microfilariae were stored (64% vs. ≥75%).
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Affiliation(s)
- Shannon M. Hedtke
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (W.N.G.)
| | - Anusha Kode
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (W.N.G.)
| | - Tony O. Ukety
- Centre de Recherche en Maladies Tropicales (CRMT), Bunia P.O. Box 143, Democratic Republic of the Congo; (T.O.U.); (J.L.M.); (G.M.A.); (A.A.R.); (C.B.U.)
| | - Jöel L. Mande
- Centre de Recherche en Maladies Tropicales (CRMT), Bunia P.O. Box 143, Democratic Republic of the Congo; (T.O.U.); (J.L.M.); (G.M.A.); (A.A.R.); (C.B.U.)
| | - Germain M. Abhafule
- Centre de Recherche en Maladies Tropicales (CRMT), Bunia P.O. Box 143, Democratic Republic of the Congo; (T.O.U.); (J.L.M.); (G.M.A.); (A.A.R.); (C.B.U.)
| | - Anuarite A. Raciu
- Centre de Recherche en Maladies Tropicales (CRMT), Bunia P.O. Box 143, Democratic Republic of the Congo; (T.O.U.); (J.L.M.); (G.M.A.); (A.A.R.); (C.B.U.)
| | - Claude B. Uvon
- Centre de Recherche en Maladies Tropicales (CRMT), Bunia P.O. Box 143, Democratic Republic of the Congo; (T.O.U.); (J.L.M.); (G.M.A.); (A.A.R.); (C.B.U.)
| | | | - An Hotterbeekx
- Global Health Institute, University of Antwerp, 2610 Antwerp, Belgium; (A.H.); (J.N.S.F.); (R.C.)
| | | | - Makedonka Mitreva
- Department of Medicine, Washington University in St. Louis and McDonnell Genome Institute, St. Louis, MO 63108, USA;
| | - Wilson Sebit
- National Public Health Laboratory, Juba P.O. Box 88, South Sudan;
| | - Robert Colebunders
- Global Health Institute, University of Antwerp, 2610 Antwerp, Belgium; (A.H.); (J.N.S.F.); (R.C.)
| | - Warwick N. Grant
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (W.N.G.)
| | - Annette C. Kuesel
- UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, CH-1211 Geneva, Switzerland;
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Hedtke SM, Choi YJ, Kode A, Chalasani GC, Sirwani N, Jada SR, Hotterbeekx A, Mandro M, Siewe Fodjo JN, Amambo GN, Abong RA, Wanji S, Kuesel AC, Colebunders R, Mitreva M, Grant WN. Assessing Onchocerca volvulus Intensity of Infection and Genetic Diversity Using Mitochondrial Genome Sequencing of Single Microfilariae Obtained before and after Ivermectin Treatment. Pathogens 2023; 12:971. [PMID: 37513818 PMCID: PMC10385737 DOI: 10.3390/pathogens12070971] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Onchocerciasis is a neglected tropical disease targeted for elimination using ivermectin mass administration. Ivermectin kills the microfilariae and temporarily arrests microfilariae production by the macrofilariae. We genotyped 436 microfilariae from 10 people each in Ituri, Democratic Republic of the Congo (DRC), and Maridi County, South Sudan, collected before and 4-5 months after ivermectin treatment. Population genetic analyses identified 52 and 103 mitochondrial DNA haplotypes among the microfilariae from DRC and South Sudan, respectively, with few haplotypes shared between people. The percentage of genotype-based correct assignment to person within DRC was ~88% and within South Sudan ~64%. Rarefaction and extrapolation analysis showed that the genetic diversity in DRC, and even more so in South Sudan, was captured incompletely. The results indicate that the per-person adult worm burden is likely higher in South Sudan than DRC. Analyses of haplotype data from a subsample (n = 4) did not discriminate genetically between pre- and post-treatment microfilariae, confirming that post-treatment microfilariae are not the result of new infections. With appropriate sampling, mitochondrial haplotype analysis could help monitor changes in the number of macrofilariae in a population as a result of treatment, identify cases of potential treatment failure, and detect new infections as an indicator of continuing transmission.
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Affiliation(s)
- Shannon M. Hedtke
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (G.C.C.); (N.S.); (W.N.G.)
| | - Young-Jun Choi
- Department of Medicine, Washington University in St. Louis and McDonnell Genome Institute, St. Louis, MO 63108, USA; (Y.-J.C.); (M.M.)
| | - Anusha Kode
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (G.C.C.); (N.S.); (W.N.G.)
| | - Gowtam C. Chalasani
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (G.C.C.); (N.S.); (W.N.G.)
| | - Neha Sirwani
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (G.C.C.); (N.S.); (W.N.G.)
| | | | - An Hotterbeekx
- Global Health Institute, University of Antwerp, Doornstraat 331, 2610 Antwerp, Belgium; (A.H.); (J.N.S.F.); (R.C.)
| | - Michel Mandro
- Provincial Health Division Ituri, Ministry of Health, Bunia P.O. Box 57, Democratic Republic of the Congo;
| | - Joseph N. Siewe Fodjo
- Global Health Institute, University of Antwerp, Doornstraat 331, 2610 Antwerp, Belgium; (A.H.); (J.N.S.F.); (R.C.)
| | - Glory Ngongeh Amambo
- Parasites and Vectors Research Unit, Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (G.N.A.); (R.A.A.); (S.W.)
| | - Raphael A. Abong
- Parasites and Vectors Research Unit, Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (G.N.A.); (R.A.A.); (S.W.)
- Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea P.O. Box 474, Cameroon
| | - Samuel Wanji
- Parasites and Vectors Research Unit, Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (G.N.A.); (R.A.A.); (S.W.)
- Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea P.O. Box 474, Cameroon
| | - Annette C. Kuesel
- UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, 1202 Geneva, Switzerland;
| | - Robert Colebunders
- Global Health Institute, University of Antwerp, Doornstraat 331, 2610 Antwerp, Belgium; (A.H.); (J.N.S.F.); (R.C.)
| | - Makedonka Mitreva
- Department of Medicine, Washington University in St. Louis and McDonnell Genome Institute, St. Louis, MO 63108, USA; (Y.-J.C.); (M.M.)
| | - Warwick N. Grant
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; (A.K.); (G.C.C.); (N.S.); (W.N.G.)
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10
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Thorn CS, Maness RW, Hulke JM, Delmore KE, Criscione CD. Population genomics of helminth parasites. J Helminthol 2023; 97:e29. [PMID: 36927601 DOI: 10.1017/s0022149x23000123] [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] [Indexed: 03/18/2023]
Abstract
Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.
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Affiliation(s)
- C S Thorn
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - R W Maness
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - J M Hulke
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - K E Delmore
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - C D Criscione
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
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11
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Otiti-Sengeri J, Omaido BA, Bhwana D, Nakanjako D, Missiru M, Muwonge M, Amaral LJ, Mmbando BP, Colebunders R. High Prevalence of Glaucoma among Patients in an Onchocerciasis Endemic Area (Mahenge, Tanzania). Pathogens 2022; 11:1046. [PMID: 36145478 PMCID: PMC9501165 DOI: 10.3390/pathogens11091046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
Onchocerciasis is known to cause skin lesions and blindness, but there is also epidemiological evidence that onchocerciasis is associated with epilepsy, including nodding syndrome. We carried out ocular exams in persons with epilepsy in Mahenge, an onchocerciasis endemic area with a high prevalence of epilepsy in Tanzania. We recruited 278 consecutive persons with epilepsy attending the epilepsy clinic at Mahenge hospital and satellite clinics in rural villages. They underwent a general physical and a detailed ocular examination and were tested for onchocerciasis Ov16 IgG4 antibodies. Glaucoma was defined by a raised intraocular pressure above 21 mmHg with evidence of typical glaucomatous disc changes in one or both eyes. Among the 278 participants, median age 27 (IQR 21-38) years, 55.4% were female; 151/210 (71.9%) (95% CI: 65.3-77.9) were Ov16 positive. The most frequent ophthalmic lesions were glaucoma (33.1%), vitreous opacities (6.5%) and cataracts (2.9%). In multivariate analysis, glaucoma (adjusted IRR = 1.46; 95% CI: 1.24-1.70) and age (adjusted IRR = 1.01; 95% CI: 1.01-1.02) were significantly associated with onchocerciasis. In conclusion, a high prevalence of glaucoma was observed among Ov16 positive persons with epilepsy. Persons with epilepsy with O. volvulus infection should undergo screening for glaucoma to prevent one of the causes of preventable blindness.
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Affiliation(s)
- Juliet Otiti-Sengeri
- Department of Ophthalmology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | - Blair Andrew Omaido
- Department of Ophthalmology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | - Dan Bhwana
- National Institute for Medical Research, Tanga Centre, Tanga P.O. Box 5004, Tanzania
| | - Damalie Nakanjako
- Department of Internal Medicine, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | - Malik Missiru
- Department of Ophthalmology, Mahenge District Hospital, Mahenge P.O. Box 4, Tanzania
| | - Musa Muwonge
- School of Medicine, Soroti University, Soroti P.O. Box 690, Uganda
| | - Luis-Jorge Amaral
- Global Health Institute, University of Antwerp, Kinsbergen Centrum, Doornstraat 331, 2610 Antwerp, Belgium
| | - Bruno P. Mmbando
- National Institute for Medical Research, Tanga Centre, Tanga P.O. Box 5004, Tanzania
| | - Robert Colebunders
- Global Health Institute, University of Antwerp, Kinsbergen Centrum, Doornstraat 331, 2610 Antwerp, Belgium
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12
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Doyle SR, Søe MJ, Nejsum P, Betson M, Cooper PJ, Peng L, Zhu XQ, Sanchez A, Matamoros G, Sandoval GAF, Cutillas C, Tchuenté LAT, Mekonnen Z, Ame SM, Namwanje H, Levecke B, Berriman M, Fredensborg BL, Kapel CMO. Population genomics of ancient and modern Trichuris trichiura. Nat Commun 2022; 13:3888. [PMID: 35794092 PMCID: PMC9259628 DOI: 10.1038/s41467-022-31487-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/17/2022] [Indexed: 11/14/2022] Open
Abstract
The neglected tropical disease trichuriasis is caused by the whipworm Trichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today, T. trichiura infects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.
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Affiliation(s)
| | - Martin Jensen Søe
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus N, Denmark
| | - Martha Betson
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Philip J Cooper
- Institute of Infection and Immunity, St George's University of London, London, UK
- School of Medicine, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Lifei Peng
- Department of Parasitology, School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, People's Republic of China
| | - Ana Sanchez
- Department of Health Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Gabriela Matamoros
- Microbiology Research Institute, Ciudad Universitaria, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | | | - Cristina Cutillas
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | | | - Zeleke Mekonnen
- Institute of Health, School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
| | - Shaali M Ame
- Public Health Laboratory Ivo de Carneri, Pemba, Tanzania
| | | | - Bruno Levecke
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | | | - Brian Lund Fredensborg
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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13
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McCann K, Grant W, Doyle SR. The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni. Wellcome Open Res 2021; 6:259. [PMID: 34796277 PMCID: PMC8564745 DOI: 10.12688/wellcomeopenres.17258.2] [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] [Accepted: 12/01/2021] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly and annotation of an individual female
Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus
Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite,
Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts.
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Affiliation(s)
- Kirsty McCann
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Warwick Grant
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Stephen R Doyle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
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14
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McCann K, Grant W, Doyle SR. The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni. Wellcome Open Res 2021; 6:259. [PMID: 34796277 PMCID: PMC8564745 DOI: 10.12688/wellcomeopenres.17258.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 09/02/2023] Open
Abstract
We present a genome assembly and annotation of an individual female Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite, Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts.
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Affiliation(s)
- Kirsty McCann
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Warwick Grant
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Australia
| | - Stephen R. Doyle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
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15
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Mattick J, Libro S, Bromley R, Chaicumpa W, Chung M, Cook D, Khan MB, Kumar N, Lau YL, Misra-Bhattacharya S, Rao R, Sadzewicz L, Saeung A, Shahab M, Sparklin BC, Steven A, Turner JD, Tallon LJ, Taylor MJ, Moorhead AR, Michalski M, Foster JM, Dunning Hotopp JC. X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes. PLoS Negl Trop Dis 2021; 15:e0009838. [PMID: 34705823 PMCID: PMC8575316 DOI: 10.1371/journal.pntd.0009838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/08/2021] [Accepted: 09/24/2021] [Indexed: 11/19/2022] Open
Abstract
The sequence diversity of natural and laboratory populations of Brugia pahangi and Brugia malayi was assessed with Illumina resequencing followed by mapping in order to identify single nucleotide variants and insertions/deletions. In natural and laboratory Brugia populations, there is a lack of sequence diversity on chromosome X relative to the autosomes (πX/πA = 0.2), which is lower than the expected (πX/πA = 0.75). A reduction in diversity is also observed in other filarial nematodes with neo-X chromosome fusions in the genera Onchocerca and Wuchereria, but not those without neo-X chromosome fusions in the genera Loa and Dirofilaria. In the species with neo-X chromosome fusions, chromosome X is abnormally large, containing a third of the genetic material such that a sizable portion of the genome is lacking sequence diversity. Such profound differences in genetic diversity can be consequential, having been associated with drug resistance and adaptability, with the potential to affect filarial eradication.
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Affiliation(s)
- John Mattick
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Silvia Libro
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Robin Bromley
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Matthew Chung
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Darren Cook
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Mohammad Behram Khan
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nikhil Kumar
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Ramakrishna Rao
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Lisa Sadzewicz
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Atiporn Saeung
- Center of Insect Vector Study, Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Mohd Shahab
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Benjamin C. Sparklin
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Andrew Steven
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Joseph D. Turner
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Luke J. Tallon
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Mark J. Taylor
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Andrew R. Moorhead
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Michelle Michalski
- University of Wisconsin Oshkosh, Oshkosh, Wisconsin, United States of America
| | - Jeremy M. Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Julie C. Dunning Hotopp
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
- Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland, United States of America
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16
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Cromwell EA, Osborne JCP, Unnasch TR, Basáñez MG, Gass KM, Barbre KA, Hill E, Johnson KB, Donkers KM, Shirude S, Schmidt CA, Adekanmbi V, Adetokunboh OO, Afarideh M, Ahmadpour E, Ahmed MB, Akalu TY, Al-Aly Z, Alanezi FM, Alanzi TM, Alipour V, Andrei CL, Ansari F, Ansha MG, Anvari D, Appiah SCY, Arabloo J, Arnold BF, Ausloos M, Ayanore MA, Baig AA, Banach M, Barac A, Bärnighausen TW, Bayati M, Bhattacharyya K, Bhutta ZA, Bibi S, Bijani A, Bohlouli S, Bohluli M, Brady OJ, Bragazzi NL, Butt ZA, Carvalho F, Chatterjee S, Chattu VK, Chattu SK, Cormier NM, Dahlawi SMA, Damiani G, Daoud F, Darwesh AM, Daryani A, Deribe K, Dharmaratne SD, Diaz D, Do HT, El Sayed Zaki M, El Tantawi M, Elemineh DA, Faraj A, Fasihi Harandi M, Fatahi Y, Feigin VL, Fernandes E, Foigt NA, Foroutan M, Franklin RC, Gubari MIM, Guido D, Guo Y, Haj-Mirzaian A, Hamagharib Abdullah K, Hamidi S, Herteliu C, de Hidru HD, Higazi TB, Hossain N, Hosseinzadeh M, Househ M, Ilesanmi OS, Ilic MD, Ilic IM, Iqbal U, Irvani SSN, Jha RP, Joukar F, Jozwiak JJ, Kabir Z, Kalankesh LR, Kalhor R, Karami Matin B, Karimi SE, Kasaeian A, Kavetskyy T, Kayode GA, Kazemi Karyani A, Kelbore AG, Keramati M, Khalilov R, Khan EA, Khan MNN, Khatab K, Khater MM, Kianipour N, Kibret KT, Kim YJ, Kosen S, Krohn KJ, Kusuma D, La Vecchia C, Lansingh VC, Lee PH, LeGrand KE, Li S, Longbottom J, Magdy Abd El Razek H, Magdy Abd El Razek M, Maleki A, Mamun AA, Manafi A, Manafi N, Mansournia MA, Martins-Melo FR, Mazidi M, McAlinden C, Meharie BG, Mendoza W, Mengesha EW, Mengistu DT, Mereta ST, Mestrovic T, Miller TR, Miri M, Moghadaszadeh M, Mohammadian-Hafshejani A, Mohammadpourhodki R, Mohammed S, Mohammed S, Moradi M, Moradzadeh R, Moraga P, Mosser JF, Naderi M, Nagarajan AJ, Naik G, Negoi I, Nguyen CT, Nguyen HLT, Nguyen TH, Nikbakhsh R, Oancea B, Olagunju TO, Olagunju AT, Omar Bali A, Onwujekwe OE, Pana A, Pourjafar H, Rahim F, Rahman MHU, Rathi P, Rawaf S, Rawaf DL, Rawassizadeh R, Resnikoff S, Reta MA, Rezapour A, Rubagotti E, Rubino S, Sadeghi E, Saghafipour A, Sajadi SM, Samy AM, Sarmiento-Suárez R, Sawhney M, Schipp MF, Shaheen AA, Shaikh MA, Shamsizadeh M, Sharafi K, Sheikh A, Shetty BSK, Shin JI, Shivakumar KM, Simonetti B, Singh JA, Skiadaresi E, Soheili A, Soltani S, Spurlock EE, Sufiyan MB, Tabuchi T, Tapak L, Thompson RL, Thomson AJ, Traini E, Tran BX, Ullah I, Ullah S, Uneke CJ, Unnikrishnan B, Uthman OA, Vinkeles Melchers NVS, Violante FS, Wolde HF, Wonde TE, Yamada T, Yaya S, Yazdi-Feyzabadi V, Yip P, Yonemoto N, Yousof HASA, Yu C, Yu Y, Yusefzadeh H, Zaki L, Zaman SB, Zamanian M, Zhang ZJ, Zhang Y, Ziapour A, Hay SI, Pigott DM. Predicting the environmental suitability for onchocerciasis in Africa as an aid to elimination planning. PLoS Negl Trop Dis 2021; 15:e0008824. [PMID: 34319976 PMCID: PMC8318275 DOI: 10.1371/journal.pntd.0008824] [Citation(s) in RCA: 6] [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: 05/08/2020] [Accepted: 05/13/2021] [Indexed: 11/19/2022] Open
Abstract
Recent evidence suggests that, in some foci, elimination of onchocerciasis from Africa may be feasible with mass drug administration (MDA) of ivermectin. To achieve continental elimination of transmission, mapping surveys will need to be conducted across all implementation units (IUs) for which endemicity status is currently unknown. Using boosted regression tree models with optimised hyperparameter selection, we estimated environmental suitability for onchocerciasis at the 5 × 5-km resolution across Africa. In order to classify IUs that include locations that are environmentally suitable, we used receiver operating characteristic (ROC) analysis to identify an optimal threshold for suitability concordant with locations where onchocerciasis has been previously detected. This threshold value was then used to classify IUs (more suitable or less suitable) based on the location within the IU with the largest mean prediction. Mean estimates of environmental suitability suggest large areas across West and Central Africa, as well as focal areas of East Africa, are suitable for onchocerciasis transmission, consistent with the presence of current control and elimination of transmission efforts. The ROC analysis identified a mean environmental suitability index of 0·71 as a threshold to classify based on the location with the largest mean prediction within the IU. Of the IUs considered for mapping surveys, 50·2% exceed this threshold for suitability in at least one 5 × 5-km location. The formidable scale of data collection required to map onchocerciasis endemicity across the African continent presents an opportunity to use spatial data to identify areas likely to be suitable for onchocerciasis transmission. National onchocerciasis elimination programmes may wish to consider prioritising these IUs for mapping surveys as human resources, laboratory capacity, and programmatic schedules may constrain survey implementation, and possibly delaying MDA initiation in areas that would ultimately qualify.
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Affiliation(s)
- Elizabeth A. Cromwell
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Joshua C. P. Osborne
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Thomas R. Unnasch
- GlobalHealth Infectious Disease, University of South Florida, Tampa, Florida, United States of America
| | - Maria-Gloria Basáñez
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Imperial College London, London, United Kingdom
| | - Katherine M. Gass
- Neglected Tropical Diseases Support Center, Task Force for Global Health, Decatur, Georgia, United States of America
| | - Kira A. Barbre
- Neglected Tropical Diseases Support Center, Task Force for Global Health, Decatur, Georgia, United States of America
| | - Elex Hill
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Kimberly B. Johnson
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Katie M. Donkers
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Shreya Shirude
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Chris A. Schmidt
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Victor Adekanmbi
- Population Health Sciences, King’s College London, London, England
| | - Olatunji O. Adetokunboh
- Centre of Excellence for Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - Mohsen Afarideh
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota, United States of America
- Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Ahmadpour
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Muktar Beshir Ahmed
- Department of Epidemiology, Jimma University, Jimma, Ethiopia
- Australian Center for Precision Health, University of South Australia, Adelaide, South Australia, Australia
| | | | - Ziyad Al-Aly
- John T. Milliken Department of Internal Medicine, Washington University in St. Louis, St. Louis, Montana, United States of America
- Clinical Epidemiology Center, Department of Veterans Affairs, St Louis, Montana, United States of America
| | | | - Turki M. Alanzi
- Health Information Management and Technology Department, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Vahid Alipour
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
- Health Economics Department, Iran University of Medical Sciences, Tehran, Iran
| | | | - Fereshteh Ansari
- Research Center for Evidence Based Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization (AREEO), Tehran, Iran
| | | | - Davood Anvari
- Department of Parasitology, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Parasitology, Iranshahr University of Medical Sciences, Iranshahr, Iran
| | - Seth Christopher Yaw Appiah
- Department of Sociology and Social Work, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Center for International Health, Ludwig Maximilians University, Munich, Germany
| | - Jalal Arabloo
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Benjamin F. Arnold
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Marcel Ausloos
- School of Business, University of Leicester, Leicester, United Kingdom
- Department of Statistics and Econometrics, Bucharest University of Economic Studies, Bucharest, Romania
| | - Martin Amogre Ayanore
- Department of Health Policy Planning and Management, University of Health and Allied Sciences, Ho, Ghana
| | - Atif Amin Baig
- Unit of Biochemistry, Sultan Zainal Abidin University (Universiti Sultan Zainal Abidin), Kuala Terengganu, Malaysia
| | - Maciej Banach
- Department of Hypertension, Medical University of Lodz, Lodz, Poland
- Polish Mothers’ Memorial Hospital Research Institute, Lodz, Poland
| | - Aleksandra Barac
- Clinic for Infectious and Tropical Diseases, Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Till Winfried Bärnighausen
- Heidelberg Institute of Global Health (HIGH), Heidelberg University, Heidelberg, Germany
- T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Mohsen Bayati
- Health Human Resources Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Krittika Bhattacharyya
- Department of Statistical and Computational Genomics, National Institute of Biomedical Genomics, Kalyani, India
- Department of Statistics, University of Calcutta, Kolkata, India
| | - Zulfiqar A. Bhutta
- Centre for Global Child Health, University of Toronto, Toronto, Ontario, Canada
- Centre of Excellence in Women & Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadia Bibi
- Institute of Soil and Environmental Sciences, University of Agriculture—Faisalabad, Faisalabad, Pakistan
| | - Ali Bijani
- Social Determinants of Health Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Somayeh Bohlouli
- Department of Veterinary Medicine, Islamic Azad University, Kermanshah, Iran
| | - Mahdi Bohluli
- Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences, Zanjan, Iran
- Department of Research and Innovation, Petanux Research GmBH, Bonn, Germany
| | - Oliver J. Brady
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Zahid A. Butt
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Ontario, Canada
- Al Shifa School of Public Health, Al Shifa Trust Eye Hospital, Rawalpindi, Pakistan
| | - Felix Carvalho
- Research Unit on Applied Molecular Biosciences (UCIBIO), University of Porto, Porto, Portugal
| | - Souranshu Chatterjee
- Department of Microbiology & Infection Control, Medanta Medicity, Gurugram, India
| | | | | | - Natalie Maria Cormier
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Saad M. A. Dahlawi
- Environmental Health Department, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Giovanni Damiani
- Clinical Dermatology, IRCCS Istituto Ortopedico Galeazzi, University of Milan, Milan, Italy
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Farah Daoud
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Aso Mohammad Darwesh
- Department of Information Technology, University of Human Development, Sulaymaniyah, Iraq
| | - Ahmad Daryani
- Toxoplasmosis Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Kebede Deribe
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, Brighton, United Kingdom
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Samath Dhamminda Dharmaratne
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Community Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Daniel Diaz
- Center of Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
- Faculty of Veterinary Medicine and Zootechnics, Autonomous University of Sinaloa, Culiacán Rosales, Mexico
| | - Hoa Thi Do
- Institute of Health Economics and Technology, Hanoi, Vietnam
| | - Maysaa El Sayed Zaki
- Reference Laboratory of Egyptian Universities Hospitals, Ministry of Higher Education and Research, Cairo, Egypt
| | - Maha El Tantawi
- Pediatric Dentistry and Dental Public Health Department, Alexandria University, Alexandria, Egypt
| | | | - Anwar Faraj
- Department of Political Science, University of Human Development, Sulaimaniyah, Iraq
| | - Majid Fasihi Harandi
- Department of Medical Parasitology, Kerman University of Medical Sciences, Kerman, Iran
| | - Yousef Fatahi
- Nanotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pharmaceutical Nanotechnology, Tehran University of Medical Sciences, Tehran, Iran
| | - Valery L. Feigin
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
- National Institute for Stroke and Applied Neurosciences, Auckland University of Technology, Auckland, New Zealand
- Research Center of Neurology, Moscow, Russia
| | - Eduarda Fernandes
- Associated Laboratory for Green Chemistry (LAQV), University of Porto, Porto, Portugal
| | - Nataliya A. Foigt
- Institute of Gerontology, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Masoud Foroutan
- Department of Medical Parasitology, Abadan Faculty of Medical Sciences, Abadan, Iran
| | - Richard Charles Franklin
- School of Public Health, Medical, and Veterinary Sciences, James Cook University, Douglas, Queensland, Australia
| | | | - Davide Guido
- Neurology, Public Health and Disability Unit, Carlo Besta Neurological Institute IRCCS (Fondazione IRCCS Istituto Neurologico Carlo Besta), Milan, Italy
| | - Yuming Guo
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Department of Epidemiology, Binzhou Medical University, Yantai City, China
| | - Arvin Haj-Mirzaian
- Department of Pharmacology, Tehran University of Medical Sciences, Tehran, Iran
- Obesity Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Samer Hamidi
- School of Health and Environmental Studies, Hamdan Bin Mohammed Smart University, Dubai, United Arab Emirates
| | - Claudiu Herteliu
- Department of Statistics and Econometrics, Bucharest University of Economic Studies, Bucharest, Romania
- School of Business, London South Bank University, London, United Kingdom
| | | | - Tarig B. Higazi
- Department of Biological Sciences, Ohio University, Zanesville, Ontario, United States of America
| | - Naznin Hossain
- Department of Pharmacology, Bangladesh Industrial Gases Limited, Tangail, Bangladesh
| | - Mehdi Hosseinzadeh
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- Department of Computer Science, University of Human Development, Sulaymaniyah, Iraq
| | - Mowafa Househ
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Olayinka Stephen Ilesanmi
- Department of Community Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Community Medicine, University College Hospital, Ibadan, Ibadan, Nigeria
| | - Milena D. Ilic
- Department of Epidemiology, University of Kragujevac, Kragujevac, Serbia
| | - Irena M. Ilic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Usman Iqbal
- College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Seyed Sina Naghibi Irvani
- Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Ira
| | - Ravi Prakash Jha
- Department of Community Medicine, Dr. Baba Saheb Ambedkar Medical College & Hospital, Delhi, India
- Department of Community Medicine, Banaras Hindu University, Varanasi, India
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Caspian Digestive Disease Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Jacek Jerzy Jozwiak
- Department of Family Medicine and Public Health, University of Opole, Opole, Poland
| | - Zubair Kabir
- School of Public Health, University College Cork, Cork, Ireland
| | - Leila R. Kalankesh
- School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rohollah Kalhor
- Institute for Prevention of Non-communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
- Health Services Management Department, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Behzad Karami Matin
- Research Center for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Salah Eddin Karimi
- Social Determinants of Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Kasaeian
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Iran University of Medical Sciences, Tehran, Iran
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Taras Kavetskyy
- Department of Applied Physics, The John Paul II Catholic University of Lublin, Lublin Voivodeship, Poland
- Department of Biology & Chemistry, Drohobych Ivan Franko State Pedagogical University, Drohobych, Ukraine
| | - Gbenga A. Kayode
- International Research Center of Excellence, Institute of Human Virology Nigeria, Abuja, Nigeria
- Julius Centre for Health Sciences and Primary Care, Utrecht University, Utrecht, Netherlands
| | - Ali Kazemi Karyani
- Research Center for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | | | - Rovshan Khalilov
- Department of Biophysics and Molecular Biology, Baku State University, Baku, Azerbaijan
- Institute of Radiation Problems, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Ejaz Ahmad Khan
- Department of Epidemiology and Biostatistics, Health Services Academy, Islamabad, Pakistan
| | - Md Nuruzzaman Nuruzzaman Khan
- Department of Population Sciences, Jatiya Kabi Kazi Nazrul Islam University, Mymensingh, Bangladesh
- Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Khaled Khatab
- Faculty of Health and Wellbeing, Sheffield Hallam University, Sheffield, United Kingdom
- College of Arts and Sciences, Ohio University, Zanesville, Ohio, United States of America
| | - Mona M. Khater
- Department of Medical Parasitology, Cairo University, Cairo, Egypt
| | - Neda Kianipour
- Department of Public Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Yun Jin Kim
- School of Traditional Chinese Medicine, Xiamen University Malaysia, Sepang, Malaysia
| | | | - Kris J. Krohn
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Dian Kusuma
- Imperial College Business School, Imperial College London, London, United Kingdom
- Faculty of Public Health, University of Indonesia, Depok, Indonesia
| | - Carlo La Vecchia
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Van Charles Lansingh
- Medical Director, HelpMeSee, New York, New York, United States of America
- General Director, Mexican Institute of Ophthalmology, Queretaro, Mexico
| | - Paul H. Lee
- School of Nursing, Hong Kong Polytechnic University, Hong Kong, China
| | - Kate E. LeGrand
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Shanshan Li
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Joshua Longbottom
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | | | - Afshin Maleki
- Environmental Health, Tehran University of Medical Sciences, Tehran, Iran
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Abdullah A. Mamun
- Institute for Social Science Research, The University of Queensland, Indooroopilly, Queensland, Australia
| | - Ali Manafi
- Plastic Surgery Department, Iran University of Medical Sciences, Tehran, Iran
| | - Navid Manafi
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- School of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mohammad Ali Mansournia
- Department of Epidemiology and Biostatistics, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohsen Mazidi
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Colm McAlinden
- Department of Ophthalmology, Singleton Hospital, Swansea, United Kingdom
| | | | - Walter Mendoza
- Peru Country Office, United Nations Population Fund (UNFPA), Lima, Peru
| | | | | | - Seid Tiku Mereta
- Department of Environmental Health Sciences and Technology, Jimma University, Jimma, Ethiopia
| | - Tomislav Mestrovic
- Clinical Microbiology and Parasitology Unit, Dr. Zora Profozic Polyclinic, Zagreb, Croatia
- University Centre Varazdin, University North, Varazdin, Croatia
| | - Ted R. Miller
- Pacific Institute for Research & Evaluation, Calverton, Maryland, United States of America
- School of Public Health, Curtin University, Perth, Australia
| | - Mohammad Miri
- Department of Environmental Health, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Non-communicable Diseases Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Masoud Moghadaszadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Reza Mohammadpourhodki
- Kashmar Center of Higher Health Education, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shafiu Mohammed
- Heidelberg Institute of Global Health (HIGH), Heidelberg University, Heidelberg, Germany
- Health Systems and Policy Research Unit, Ahmadu Bello University, Zaria, Nigeria
| | - Salahuddin Mohammed
- Department of Biomolecular Sciences, University of Mississippi, Oxford, Mississippi, United States of America
- Department of Pharmacy, Mizan-Tepi University, Mizan, Ethiopia
| | - Masoud Moradi
- Research Center for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Paula Moraga
- Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jonathan F. Mosser
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Mehdi Naderi
- Clinical Research Development Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ahamarshan Jayaraman Nagarajan
- Research and Analytics Department, Initiative for Financing Health and Human Development, Chennai, India
- Department of Research and Analytics, Bioinsilico Technologies, Chennai, India
| | - Gurudatta Naik
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ionut Negoi
- Department of General Surgery, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Department of General Surgery, Emergency Hospital of Bucharest, Bucharest, Romania
| | - Cuong Tat Nguyen
- Institute for Global Health Innovations, Duy Tan University, Hanoi, Vietnam
| | | | - Trang Huyen Nguyen
- Center of Excellence in Behavioral Medicine, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Rajan Nikbakhsh
- Obesity Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bogdan Oancea
- Administrative and Economic Sciences Department, University of Bucharest, Bucharest, Romania
| | - Tinuke O. Olagunju
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Andrew T. Olagunju
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
- Department of Psychiatry, University of Lagos, Lagos, Nigeria
| | - Ahmed Omar Bali
- Diplomacy and Public Relations Department, University of Human Development, Sulaimaniyah, Iraq
| | - Obinna E. Onwujekwe
- Department of Pharmacology and Therapeutics, University of Nigeria Nsukka, Enugu, Nigeria
| | - Adrian Pana
- Department of Statistics and Econometrics, Bucharest University of Economic Studies, Bucharest, Romania
- Department of Health Metrics, Center for Health Outcomes & Evaluation, Bucharest, Romania
| | - Hadi Pourjafar
- Department of Nutrition and Food Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Fakher Rahim
- Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Metabolomics and Genomics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hifz Ur Rahman
- Department of Community Medicine, Maharishi Markandeshwar Medical College & Hospital, Solan, India
| | - Priya Rathi
- Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Salman Rawaf
- Department of Primary Care and Public Health, Imperial College London, London, United Kingdom
- Academic Public Health England, Public Health England, London, United Kingdom
| | - David Laith Rawaf
- WHO Collaborating Centre for Public Health Education and Training, Imperial College London, London, United Kingdom
- University College London Hospitals, London, United Kingdom
| | - Reza Rawassizadeh
- Department of Computer Science, Boston University, Boston, Massachusetts, United States of America
| | - Serge Resnikoff
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
- Brien Holden Vision Institute, Sydney, Australia
| | - Melese Abate Reta
- Department of Medical Laboratory Science, Woldia University, Woldia, Ethiopia
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Aziz Rezapour
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Enrico Rubagotti
- Center for Research in Congenital Anomalies and Rare Diseases, ICESI University (Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras, Universidad Icesi), Cali, Colombia
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ehsan Sadeghi
- Research Center for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abedin Saghafipour
- Public Health, Ministry of Health and Medical Education, Qom, Iran
- Qom University of Medical Sciences, Qom, Iran
| | - S. Mohammad Sajadi
- Department of Phytochemistry, Soran University, Soran, Iraq
- Department of Nutrition, Cihan University, Erbil, Iraq
| | | | - Rodrigo Sarmiento-Suárez
- Department of Health and Society, Faculty of Medicine, University of Applied and Environmental Sciences, Bogota, Colombia
- National School of Public Health, Carlos III Health Institute, Madrid, Spain
| | - Monika Sawhney
- Department of Public Health Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Megan F. Schipp
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Amira A. Shaheen
- Public Health Division, An-Najah National University, Nablus, Palestine
| | | | - Morteza Shamsizadeh
- Faculty of Caring Science, Work Life, and Social Welfare, Faculty of Caring Science, Work Life and Social Welfare, University of Borås, Borås, Sweden, Borås, Sweden
| | - Kiomars Sharafi
- Research Center for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Aziz Sheikh
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, United Kingdom
- Division of General Internal Medicine, Harvard University, Boston, Massachusetts, United States of America
| | - B. Suresh Kumar Shetty
- Department of Forensic Medicine and Toxicology, Manipal Academy of Higher Education, Mangalore, India
| | - Jae Il Shin
- College of Medicine, Yonsei University, Seoul, South Korea
| | - K. M. Shivakumar
- Public Health Dentistry Department, Krishna Institute of Medical Sciences Deemed to be University, Karad, India
| | - Biagio Simonetti
- Department of Law, Economics, Management and Quantitative Methods, University of Sannio, Benevento, Italy
- WSB University in Gdańsk, Gdansk, Poland
| | - Jasvinder A. Singh
- School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Medicine Service, US Department of Veterans Affairs (VA), Birmingham, Alabama, United States of America
| | - Eirini Skiadaresi
- Department of Ophthalmology, Hywel Dda University Health Board, Llanelli, United Kingdom
| | - Amin Soheili
- Nursing Care Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Shahin Soltani
- Research Center for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Emma Elizabeth Spurlock
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | | | - Takahiro Tabuchi
- Cancer Control Center, Osaka International Cancer Institute, Osaka, Japan
| | - Leili Tapak
- Department of Biostatistics, Hamadan University of Medical Sciences, Hamadan, Iran
- Non-communicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Robert L. Thompson
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Alan J. Thomson
- Department of Global Health Research, Adaptive Knowledge Management, Victoria, British Columbia, Canada
| | - Eugenio Traini
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Bach Xuan Tran
- Department of Health Economics, Hanoi Medical University, Hanoi, Vietnam
| | - Irfan Ullah
- Department of Allied Health Sciences, Iqra National University, Peshawar, Pakistan
| | - Saif Ullah
- Institute of Soil and Environmental Sciences, University of Agriculture—Faisalabad, Faisalabad, Pakistan
| | - Chigozie Jesse Uneke
- Department of Medical Microbiology/Parasitology, Ebonyi State University, Abakaliki, Nigeria
| | | | - Olalekan A. Uthman
- Division of Health Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Francesco S. Violante
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Occupational Health Unit, Sant’Orsola Malpighi Hospital, Bologna, Italy
| | - Haileab Fekadu Wolde
- Department of Epidemiology and Biostatistics, University of Gondar, Gondar, Ethiopia
| | | | - Tomohide Yamada
- Department of Diabetes and Metabolic Diseases, University of Tokyo, Tokyo, Japan
| | - Sanni Yaya
- School of International Development and Global Studies, University of Ottawa, Ottawa, Ontario, Canada
- The George Institute for Global Health, University of Oxford, Oxford, United Kingdom
| | - Vahid Yazdi-Feyzabadi
- Health Services Management Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Health Management, Policy, and Economics, Kerman University of Medical Sciences, Kerman, Iran
| | - Paul Yip
- Centre for Suicide Research and Prevention, University of Hong Kong, Hong Kong, China
- Department of Social Work and Social Administration, University of Hong Kong, Hong Kong, China
| | - Naohiro Yonemoto
- Department of Neuropsychopharmacology, National Center of Neurology and Psychiatry, Kodaira, Japan
- Department of Public Health, Juntendo University, Tokyo, Japan
| | | | - Chuanhua Yu
- Department of Epidemiology and Biostatistics, Wuhan University, Wuhan, China
| | - Yong Yu
- School of Public Health and Management, Hubei University of Medicine, Shiyan, China
| | - Hasan Yusefzadeh
- Department of Health care Management and Economics, Urmia University of Medical Science, Urmia, Iran
| | - Leila Zaki
- Department of Parasitology and Entomology, Tarbiat Modares University, Tehran, Iran
| | - Sojib Bin Zaman
- The School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Maryam Zamanian
- Department of Epidemiology, Arak University of Medical Sciences, Arak, Iran
| | | | - Yunquan Zhang
- School of Public Health, Wuhan University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, China
| | - Arash Ziapour
- Department of Health Education and Health Promotion, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Simon I. Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David M. Pigott
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America
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Brattig NW, Cheke RA, Garms R. Onchocerciasis (river blindness) - more than a century of research and control. Acta Trop 2021; 218:105677. [PMID: 32857984 DOI: 10.1016/j.actatropica.2020.105677] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
This review summarises more than a century of research on onchocerciasis, also known as river blindness, and its control. River blindness is an infection caused by the tissue filaria Onchocerca volvulus affecting the skin, subcutaneous tissue and eyes and leading to blindness in a minority of infected persons. The parasite is transmitted by its intermediate hosts Simulium spp. which breed in rivers. Featured are history and milestones in onchocerciasis research and control, state-of-the-art data on the parasite, its endobacteria Wolbachia, on the vectors, previous and current prevalence of the infection, its diagnostics, the interaction between the parasite and its host, immune responses and the pathology of onchocerciasis. Detailed information is documented on the time course of control programmes in the afflicted countries in Africa and the Americas, a long road from previous programmes to current successes in control of the transmission of this infectious disease. By development, adjustment and optimization of the control measures, transmission by the vector has been interrupted in foci of countries in the Americas, in Uganda, in Sudan and elsewhere, followed by onchocerciasis eliminations. The current state and future perspectives for control, elimination and eradication within the next 20-30 years are described and discussed. This review contributes to a deeper comprehension of this disease by a tissue-dwelling filaria and it will be helpful in efforts to control and eliminate other filarial infections.
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Bennuru S, Oduro-Boateng G, Osigwe C, Del Valle P, Golden A, Ogawa GM, Cama V, Lustigman S, Nutman TB. Integrating Multiple Biomarkers to Increase Sensitivity for the Detection of Onchocerca volvulus Infection. J Infect Dis 2021; 221:1805-1815. [PMID: 31201416 DOI: 10.1093/infdis/jiz307] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/13/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Serological assessments for human onchocerciasis are based on IgG4 reactivity against the OV-16 antigen, with sensitivities of 60-80%. We have previously identified 7 novel proteins that could improve serodiagnosis. METHODS IgG4 responses to these 7 proteins were assessed by luciferase immunoprecipitation (LIPS) and enzyme-linked immunosorbent (ELISA) immunoassays. RESULTS OVOC10469 and OVOC3261 were identified as the most promising candidates by IgG4-based immunoassays with sensitivities of 53% for rOVOC10469 and 78% for rOVOC3261 while specificity for each was >99%. These 2 antigens in combination with OV-16 increased the sensitivity for patent infections to 94%. The kinetics of appearance of these IgG4 responses based on experimentally infected non-human primates indicated that they were microfilarial- driven. Further, the IgG4 responses to both OVOC10469 and OVOC3261 (as well as to OV-16) drop significantly (p<0.05) following successful treatment for onchocerciasis. A prototype lateral flow rapid diagnostic test to detect IgG4 to both Ov-16 and OVOC3261 was developed and tested demonstrating an overall 94% sensitivity. CONCLUSION The combined use of rOVOC3261 with OV-16 improved serologic assessment of O. volvulus infection, a current unmet need toward the goal of elimination of transmission of O. volvulus.
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Affiliation(s)
- Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Georgiette Oduro-Boateng
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Chinweoke Osigwe
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Priscilla Del Valle
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - Guilherme Maerschner Ogawa
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Vitaliano Cama
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Cheke RA, Little KE, Young S, Walker M, Basáñez MG. Taking the strain out of onchocerciasis? A reanalysis of blindness and transmission data does not support the existence of a savannah blinding strain of onchocerciasis in West Africa. ADVANCES IN PARASITOLOGY 2021; 112:1-50. [PMID: 34024357 DOI: 10.1016/bs.apar.2021.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Onchocerciasis (also known as 'river blindness'), is a neglected tropical disease (NTD) caused by the (Simulium-transmitted) filarial nematode Onchocerca volvulus. The occurrence of 'blinding' (savannah) and non-blinding (forest) parasite strains and the existence of corresponding, locally adapted Onchocerca-Simulium complexes were postulated to explain greater blindness prevalence in savannah than in forest foci. As a result, the World Health Organization (WHO) Onchocerciasis Control Programme in West Africa (OCP) focused anti-vectorial and anti-parasitic interventions in savannah endemic areas. In this paper, village-level data on blindness prevalence, microfilarial prevalence, and transmission intensity (measured by the annual transmission potential, the number of infective, L3, larvae per person per year) were extracted from 16 West-Central Africa-based publications, and analysed according to habitat (forest, forest-savannah mosaic, savannah) to test the dichotomous strain hypothesis in relation to blindness. When adjusting for sample size, there were no statistically significant differences in blindness prevalence between the habitats (one-way ANOVA, P=0.68, mean prevalence for forest=1.76±0.37 (SE); mosaic=1.49±0.38; savannah=1.89±0.26). The well-known relationship between blindness prevalence and annual transmission potential for savannah habitats was confirmed and shown to hold for (but not to be statistically different from) forest foci (excluding data from southern Côte d'Ivoire, in which blindness prevalence was significantly lower than in other West African forest communities, but which had been the focus of studies leading to the strain-blindness hypothesis that was accepted by OCP planners). We conclude that the evidence for a savannah blinding onchocerciasis strain in simple contrast with a non-blinding forest strain is equivocal. A re-appraisal of the strain hypothesis to explain patterns of ocular disease is needed to improve understanding of onchocerciasis epidemiology and disease burden estimates in the light of the WHO 2030 goals for onchocerciasis.
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Affiliation(s)
- Robert A Cheke
- Natural Resources Institute, Department of Agriculture, Health & Environment, University of Greenwich at Medway, Kent, United Kingdom; London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, United Kingdom
| | | | - Stephen Young
- Natural Resources Institute, Department of Agriculture, Health & Environment, University of Greenwich at Medway, Kent, United Kingdom
| | - Martin Walker
- London Centre for Neglected Tropical Disease Research, Department of Pathobiology and Populations Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Maria-Gloria Basáñez
- London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, United Kingdom; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, United Kingdom.
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20
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Myers KN, Conn D, Brown AMV. Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest. mSystems 2021; 6:e01048-20. [PMID: 33531407 PMCID: PMC7857533 DOI: 10.1128/msystems.01048-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.IMPORTANCE Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses. This study examined the hypothesis that the key to this symbiont's stable evolutionary association with its host is through provisioning nutrients that its host cannot make that may be lacking in the nematode's plant phloem diet, such as essential amino acids and several vitamins. The significance of our research is in demonstrating, using population genomics, the signatures of selective pressure on these hypothesized roles to ultimately learn how this independently evolved symbiont functionally mirrors symbionts of phloem-feeding insects.
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Affiliation(s)
- Kaitlyn N Myers
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Daniel Conn
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
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21
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Vanhamme L, Souopgui J, Ghogomu S, Ngale Njume F. The Functional Parasitic Worm Secretome: Mapping the Place of Onchocerca volvulus Excretory Secretory Products. Pathogens 2020; 9:pathogens9110975. [PMID: 33238479 PMCID: PMC7709020 DOI: 10.3390/pathogens9110975] [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: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 01/15/2023] Open
Abstract
Nematodes constitute a very successful phylum, especially in terms of parasitism. Inside their mammalian hosts, parasitic nematodes mainly dwell in the digestive tract (geohelminths) or in the vascular system (filariae). One of their main characteristics is their long sojourn inside the body where they are accessible to the immune system. Several strategies are used by parasites in order to counteract the immune attacks. One of them is the expression of molecules interfering with the function of the immune system. Excretory-secretory products (ESPs) pertain to this category. This is, however, not their only biological function, as they seem also involved in other mechanisms such as pathogenicity or parasitic cycle (molting, for example). We will mainly focus on filariae ESPs with an emphasis on data available regarding Onchocerca volvulus, but we will also refer to a few relevant/illustrative examples related to other worm categories when necessary (geohelminth nematodes, trematodes or cestodes). We first present Onchocerca volvulus, mainly focusing on the aspects of this organism that seem relevant when it comes to ESPs: life cycle, manifestations of the sickness, immunosuppression, diagnosis and treatment. We then elaborate on the function and use of ESPs in these aspects.
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Affiliation(s)
- Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
- Correspondence:
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
| | - Stephen Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, University of Buea, Buea P.O Box 63, Cameroon;
| | - Ferdinand Ngale Njume
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
- Molecular and Cell Biology Laboratory, Biotechnology Unit, University of Buea, Buea P.O Box 63, Cameroon;
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22
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Hedtke SM, Zendejas-Heredia PA, Graves PM, Sheridan S, Sheel M, Fuimaono SD, Lau CL, Grant WN. Genetic epidemiology of lymphatic filariasis in American Samoa after mass drug administration. Int J Parasitol 2020; 51:137-147. [PMID: 33166540 DOI: 10.1016/j.ijpara.2020.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022]
Abstract
Over 892 million people in 48 countries are at risk of infection by nematodes that cause lymphatic filariasis. As part of the Global Programme to Eliminate Lymphatic Filariasis, mass drug administration is distributed to communities until surveillance indicates infection rates are below target prevalence thresholds. In some countries, including American Samoa, lymphatic filariasis transmission persists despite years of mass drug administration and/or has resurged after cessation. Nothing is known about the population genetics of Wuchereria bancrofti worms in Polynesia, or whether local transmission is persisting and/or increasing due to inadequate mass drug administration coverage, expansion from residual hotspots, reintroduction from elsewhere, or a combination. We extracted DNA from microfilariae on blood slides collected during prevalence surveys in 2014 and 2016, comprising 31 pools of five microfilariae from 22 persons living in eight villages. We sequenced 1104 bp across three mitochondrial markers (ND4, COI, CYTB). We quantified parasite genetic differentiation using variant calls and estimated haplotypes using principal components analysis, F-statistics, and haplotype networks. Of the variants called, all but eight were shared across the main island of Tutuila, and three of those were from a previously described hotspot village, Fagali'i. Genotypic data did not support population genetic structure among regions or villages in 2016, although differences were observed between worms collected in Fagali'i in 2014 and those from 2016. Because estimated haplotype frequency varied between villages, these statistics suggested genetic differentiation, but were not consistent among villages. Finally, haplotype networks demonstrated American Samoan sequence clusters were related to previously published sequences from Papua New Guinea. These are, to our knowledge, the first reports of W. bancrofti genetic variation in Polynesia. The resurgent parasites circulating on the main island of American Samoa represent a single population. This study is the first step towards investigating how parasite population structure might inform strategies to manage resurgence and elimination of lymphatic filariasis.
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Affiliation(s)
- Shannon M Hedtke
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia.
| | - Patsy A Zendejas-Heredia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Patricia M Graves
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, Queensland, Australia
| | - Sarah Sheridan
- Department of Global Health, Research School of Population Health, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Meru Sheel
- National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Acton, Australian Capital Territory, Australia
| | | | - Colleen L Lau
- Department of Global Health, Research School of Population Health, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Warwick N Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
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23
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Easton A, Gao S, Lawton SP, Bennuru S, Khan A, Dahlstrom E, Oliveira RG, Kepha S, Porcella SF, Webster J, Anderson R, Grigg ME, Davis RE, Wang J, Nutman TB. Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans. eLife 2020; 9:e61562. [PMID: 33155980 PMCID: PMC7647404 DOI: 10.7554/elife.61562] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Human ascariasis is a major neglected tropical disease caused by the nematode Ascaris lumbricoides. We report a 296 megabase (Mb) reference-quality genome comprised of 17,902 protein-coding genes derived from a single, representative Ascaris worm. An additional 68 worms were collected from 60 human hosts in Kenyan villages where pig husbandry is rare. Notably, the majority of these worms (63/68) possessed mitochondrial genomes that clustered closer to the pig parasite Ascaris suum than to A. lumbricoides. Comparative phylogenomic analyses identified over 11 million nuclear-encoded SNPs but just two distinct genetic types that had recombined across the genomes analyzed. The nuclear genomes had extensive heterozygosity, and all samples existed as genetic mosaics with either A. suum-like or A. lumbricoides-like inheritance patterns supporting a highly interbred Ascaris species genetic complex. As no barriers appear to exist for anthroponotic transmission of these 'hybrid' worms, a one-health approach to control the spread of human ascariasis will be necessary.
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Affiliation(s)
- Alice Easton
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Shenghan Gao
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
| | - Scott P Lawton
- Epidemiology Research Unit (ERU) Department of Veterinary and Animal Sciences, Northern Faculty, Scotland’s Rural College (SRUC)InvernessUnited Kingdom
| | - Sasisekhar Bennuru
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Asis Khan
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Eric Dahlstrom
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Rita G Oliveira
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Stella Kepha
- London School of Tropical Medicine and HygieneLondonUnited Kingdom
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Joanne Webster
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
- Royal Veterinary College, University of London, Department of Pathobiology and Population SciencesHertfordshireUnited Kingdom
| | - Roy Anderson
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Michael E Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
- Department of Biochemistry and Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Thomas B Nutman
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
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24
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Large scale genome reconstructions illuminate Wolbachia evolution. Nat Commun 2020; 11:5235. [PMID: 33067437 PMCID: PMC7568565 DOI: 10.1038/s41467-020-19016-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our phylogenies based on both core-genome and gene content provide a robust reference for future studies, support new strains in model organisms, and reveal recent horizontal transfers amongst distantly related hosts. We find various instances of gene function gains and losses in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia-host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence. By greatly expanding the number of assembled genomes for Wolbachia (a group of intracellular bacteria) and constructing robust phylogenies, this study finds strong rate heterogeneity among Wolbachiapopulations and no support for synchronous divergence between Wolbachia and host mitochondria.
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25
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Konczal M, Przesmycka KJ, Mohammed RS, Phillips KP, Camara F, Chmielewski S, Hahn C, Guigo R, Cable J, Radwan J. Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis. Mol Ecol 2020; 29:1494-1507. [PMID: 32222008 DOI: 10.1111/mec.15421] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 03/05/2020] [Accepted: 03/19/2020] [Indexed: 12/30/2022]
Abstract
Determining the molecular basis of parasite adaptation to its host is an important component in understanding host-parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short- and long-term adaptive evolution in the eukaryotic parasite Gyrodactylus bullatarudis infecting Caribbean guppies (Poecilia reticulata), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyhelminthes, and by analysing resequenced samples from local Trinidadian populations. At the macroevolutionary timescale, we observed duplication of G-protein and serine proteases genes, which are probably important in host-parasite arms races. Serine protease also showed strong evidence of ongoing, diversifying selection at the microevolutionary timescale. Furthermore, our analyses revealed that a hybridization event, involving two divergent genomes, followed by recombination has dramatically affected the genetic composition of Trinidadian populations. The recombinant genotypes invaded Trinidad and replaced local parasites in all populations. We localized more than 300 genes in regions fixed in local populations for variants of different origin, possibly due to diversifying selection pressure from local host populations. In addition, around 70 genes were localized in regions identified as heterozygous in some, but not all, individuals. This pattern is consistent with a very recent spread of recombinant parasites. Overall, our results are consistent with the idea that recombination between divergent genomes can result in particularly successful parasites.
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Affiliation(s)
- Mateusz Konczal
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Karolina J Przesmycka
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Ryan S Mohammed
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies Zoology Museum, UWI, St. Augustine, Trinidad and Tobago
| | - Karl P Phillips
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland.,Marine Institute, Newport (Mayo), Ireland
| | - Francisco Camara
- Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sebastian Chmielewski
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | | | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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26
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Schultz DT, Eizenga JM, Corbett-Detig RB, Francis WR, Christianson LM, Haddock SH. Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii. PeerJ 2020; 8:e8356. [PMID: 32025367 PMCID: PMC6991124 DOI: 10.7717/peerj.8356] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/04/2019] [Indexed: 11/20/2022] Open
Abstract
To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.
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Affiliation(s)
- Darrin T. Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Jordan M. Eizenga
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Warren R. Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Steven H.D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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27
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Hedtke SM, Kuesel AC, Crawford KE, Graves PM, Boussinesq M, Lau CL, Boakye DA, Grant WN. Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions. Front Genet 2020; 10:1282. [PMID: 31998356 PMCID: PMC6964045 DOI: 10.3389/fgene.2019.01282] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022] Open
Abstract
Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Where program duration, treatment coverage, and compliance are sufficiently high, elimination is achievable for both parasites within defined geographic areas. However, transmission has re-emerged after apparent elimination in some areas, and in others has continued despite years of mass drug treatment. A critical question is whether this re-emergence and/or persistence of transmission is due to persistence of local parasites-i.e., the result of insufficient duration or drug coverage, poor parasite response to the drugs, or inadequate methods of assessment and/or criteria for determining when to stop treatment-or due to re-introduction of parasites via human or vector movement from another endemic area. We review recent genetics-based research exploring these questions in Onchocerca volvulus, the filarial nematode that causes onchocerciasis, and Wuchereria bancrofti, the major pathogen for lymphatic filariasis. We focus in particular on the combination of genomic epidemiology and genome-wide associations to delineate transmission zones and distinguish between local and introduced parasites as the source of resurgence or continuing transmission, and to identify genetic markers associated with parasite response to chemotherapy. Our ultimate goal is to assist elimination efforts by developing easy-to-use tools that incorporate genetic information about transmission and drug response for more effective mass drug distribution, surveillance strategies, and decisions on when to stop interventions to improve sustainability of elimination.
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Affiliation(s)
- Shannon M. Hedtke
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Annette C. Kuesel
- Unicef/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Katie E. Crawford
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Patricia M. Graves
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia
| | - Michel Boussinesq
- Unité Mixte Internationale 233 "TransVIHMI", Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Colleen L. Lau
- Department of Global Health, Research School of Population Health, Australian National University, Acton, ACT, Australia
| | - Daniel A. Boakye
- Parasitology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Warwick N. Grant
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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28
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Fauver JR, Martin J, Weil GJ, Mitreva M, Fischer PU. De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell. Sci Rep 2019; 9:19521. [PMID: 31863009 PMCID: PMC6925183 DOI: 10.1038/s41598-019-55908-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/28/2019] [Indexed: 11/15/2022] Open
Abstract
Filarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes are often discontinuous. Single molecule sequencing technologies can reduce the cost of genome sequencing and long reads produced from these devices can improve the contiguity and completeness of genome assemblies. In addition, these new technologies can make generation and analysis of large numbers of field isolates feasible. In this study, we assessed the performance of the Oxford Nanopore Technologies MinION for sequencing and assembling the genome of Brugia malayi, a human parasite widely used in filariasis research. Using data from a single MinION flowcell, a 90.3 Mb nuclear genome was assembled into 202 contigs with an N50 of 2.4 Mb. This assembly covered 96.9% of the well-defined B. malayi reference genome with 99.2% identity. The complete mitochondrial genome was obtained with individual reads and the nearly complete genome of the endosymbiotic bacteria Wolbachia was assembled alongside the nuclear genome. Long-read data from the MinION produced an assembly that approached the quality of a well-established reference genome using comparably fewer resources.
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Affiliation(s)
- Joseph R Fauver
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.
| | - John Martin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Gary J Weil
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Peter U Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
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The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nat Commun 2019; 10:4811. [PMID: 31641125 PMCID: PMC6805936 DOI: 10.1038/s41467-019-12695-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Haemonchus contortus is a haematophagous parasitic nematode of veterinary interest. We have performed a survey of its genome-wide diversity using single-worm whole genome sequencing of 223 individuals sampled from 19 isolates spanning five continents. We find an African origin for the species, together with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia. Strong selective sweeps surrounding the β-tubulin locus, a target of benzimidazole anthelmintic drug, are identified in independent populations. These sweeps are further supported by signals of diversifying selection enriched in genes involved in response to drugs and other anthelmintic-associated biological functions. We also identify some candidate genes that may play a role in ivermectin resistance. Finally, genetic signatures of climate-driven adaptation are described, revealing a gene acting as an epigenetic regulator and components of the dauer pathway. These results begin to define genetic adaptation to climate in a parasitic nematode. Based on single worm whole genome sequencing, the authors here characterise the global evolution of the gastrointestinal parasite Haemonchus contortus and identify genes that play a role in drug resistance as well as climate-driven adaptations involving an epigenetic regulator.
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Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
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Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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Abstract
PURPOSE OF REVIEW With increasing international travel and mass global population migration, clinicians in nonendemic countries must be familiar with imported neglected tropical diseases including onchocerciasis, which is commonly known as 'river blindness'. RECENT FINDINGS Imported onchocerciasis manifests differently in travelers compared with migrants from endemic areas and is likely underdiagnosed in both groups. Recent clinical studies confirm that eosinophilia is not a sensitive marker for Onchocerca volvulus, with one-third of patients having a normal eosinophil count. Novel diagnostics measuring antibodies to multiple recombinant O. volvulus antigens maintain a high sensitivity while improving specificity compared with conventional pan-filarial serologic testing. A 6-week course of doxycycline has macrofilaricidal activity through Wolbachia depletion and may be useful in nonendemic areas in addition to standard serial ivermectin. SUMMARY Recent studies characterizing distinct clinical presentations in travelers and migrants may enable clinicians to better recognize imported onchocerciasis. Although novel diagnostics have improved specificity, most remain restricted to tropical disease reference laboratories and to date there is no marker of cure. Prolonged doxycycline treatment may reduce the need for serial ivermectin, though more potent short-course macrofilaricidal drugs are being developed.
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Affiliation(s)
| | - Thomas B. Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Al-Khafaji AM, Clegg SR, Pinder AC, Luu L, Hansford KM, Seelig F, Dinnis RE, Margos G, Medlock JM, Feil EJ, Darby AC, McGarry JW, Gilbert L, Plantard O, Sassera D, Makepeace BL. Multi-locus sequence typing of Ixodes ricinus and its symbiont Candidatus Midichloria mitochondrii across Europe reveals evidence of local co-cladogenesis in Scotland. Ticks Tick Borne Dis 2018; 10:52-62. [PMID: 30197267 DOI: 10.1016/j.ttbdis.2018.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/17/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023]
Abstract
Ticks have relatively complex microbiomes, but only a small proportion of the bacterial symbionts recorded from ticks are vertically transmitted. Moreover, co-cladogenesis between ticks and their symbionts, indicating an intimate relationship over evolutionary history driven by a mutualistic association, is the exception rather than the rule. One of the most widespread tick symbionts is Candidatus Midichloria, which has been detected in all of the major tick genera of medical and veterinary importance. In some species of Ixodes, such as the sheep tick Ixodes ricinus (infected with Candidatus Midichloria mitochondrii), the symbiont is fixed in wild adult female ticks, suggesting an obligate mutualism. However, almost no information is available on genetic variation in Candidatus M. mitochondrii or possible co-cladogenesis with its host across its geographic range. Here, we report the first survey of Candidatus M. mitochondrii in I. ricinus in Great Britain and a multi-locus sequence typing (MLST) analysis of tick and symbiont between British ticks and those collected in continental Europe. We show that while the prevalence of the symbiont in nymphs collected in England is similar to that reported from the continent, a higher prevalence in nymphs and adult males is apparent in Wales. In general, Candidatus M. mitochondrii exhibits very low levels of sequence diversity, although a consistent signal of host-symbiont coevolution was apparent in Scotland. Moreover, the tick MLST scheme revealed that Scottish specimens form a clade that is partially separated from other British ticks, with almost no contribution of continental sequence types in this north-westerly border of the tick's natural range. The low diversity of Candidatus M. mitochondrii, in contrast with previously reported high rates of polymorphism in I. ricinus mitogenomes, suggests that the symbiont may have swept across Europe recently via a horizontal, rather than vertical, transmission route.
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Affiliation(s)
- Alaa M Al-Khafaji
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK; College of Veterinary Medicine, University of Al-Qadisiyah, Diwaniyah 58001, Qadisiyyah Province, Iraq
| | - Simon R Clegg
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK; School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK
| | - Alice C Pinder
- Institute of Veterinary Science, University of Liverpool, 401 Great Newton Street, Liverpool L3 5RP, UK
| | - Lisa Luu
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Kayleigh M Hansford
- Medical Entomology and Zoonoses Ecology, Public Health England, Manor Farm Road, Porton Down, Salisbury SP4 0JG, UK
| | - Frederik Seelig
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Ruth E Dinnis
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Gabriele Margos
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Jolyon M Medlock
- Medical Entomology and Zoonoses Ecology, Public Health England, Manor Farm Road, Porton Down, Salisbury SP4 0JG, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK
| | - John W McGarry
- Institute of Veterinary Science, University of Liverpool, 401 Great Newton Street, Liverpool L3 5RP, UK
| | - Lucy Gilbert
- Ecological Sciences Group, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Olivier Plantard
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France
| | - Davide Sassera
- Department of Biology & Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Benjamin L Makepeace
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK.
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Multi-locus phylogenetics of the Midichloria endosymbionts reveals variable specificity of association with ticks. Parasitology 2018; 145:1969-1978. [PMID: 29779502 DOI: 10.1017/s0031182018000793] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Candidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria-tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes. Using this method, multi-locus phylogenetic analyses revealed the structuring of a wide Midichloria genetic diversity into three distinct lineages associated with ticks. Overall, two distinct evolutionary strategies are obvious depending on lineage: two Midichloria lineages are generalists with infections acquired through horizontal transfers between distantly related tick species but one other Midichloria lineage rather show a high specificity degree to the Ixodes tick genus. This pattern suggests a capacity of certain Midichloria strains to maintain infections in only limited range of related tick species. These different infection strategies of Midichloria highlight an unexpected variability in their dependency to their tick hosts. We further conjecture that this pattern is also likely to indicate variability in their effects on ticks.
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Abstract
Helminth.net ( www.helminth.net ) is a web-based resource that was launched in 2000 as simply " Nematode.net " to host and investigate gene sequences from nematode genomes. Over the years it has evolved to become the moniker for a collection of databases: Nematode.net and Trematode.net . These databases host information for 73 nematode (roundworms) and 17 trematode (flatworms) species and serve as backbone for a number of tools that allow users to query slices of the data for multifactorial combinations of species-omics properties. Recent focus has been on inclusion of gene and protein expression data, population genomics and cross-kingdom interactions (metagenomics datasets). This chapter describes the website, the available tools and some of the new features.
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Affiliation(s)
- John Martin
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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Bennuru S, O'Connell EM, Drame PM, Nutman TB. Mining Filarial Genomes for Diagnostic and Therapeutic Targets. Trends Parasitol 2017; 34:80-90. [PMID: 29031509 DOI: 10.1016/j.pt.2017.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/12/2017] [Accepted: 09/20/2017] [Indexed: 02/04/2023]
Abstract
Filarial infections of humans cause some of the most important neglected tropical diseases. The global efforts for eliminating filarial infections by mass drug administration programs may require additional tools (safe macrofilaricidal drugs, vaccines, and diagnostic biomarkers). The accurate and sensitive detection of viable parasites is essential for diagnosis and for surveillance programs. Current community-wide treatment modalities do not kill the adult filarial worms effectively; hence, there is a need to identify and develop safe macrofilaricidal drugs. High-throughput sequencing, mass spectroscopy methods and advances in computational biology have greatly accelerated the discovery process. Here, we describe post-genomic developments toward the identification of diagnostic biomarkers and drug targets for the filarial infection of humans.
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Affiliation(s)
- Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Elise M O'Connell
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Papa M Drame
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Norice-Tra CT, Ribeiro J, Bennuru S, Fay MP, Tyagi R, Mitreva M, Nutman TB. Insights Into Onchocerca volvulus Population Biology Through Multilocus Immunophenotyping. J Infect Dis 2017; 216:736-743. [PMID: 28934436 DOI: 10.1093/infdis/jix394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/03/2017] [Indexed: 11/13/2022] Open
Abstract
We have developed a serologically based immunophenotyping approach to study Onchocerca volvulus (Ov) population diversity. Using genomic sequence data and polymerase chain reaction-based genotyping, we identified nonsynonymous single-nucleotide polymorphisms (SNPs) in the genes of 16 major immunogenic Ov proteins: Ov-CHI-1/Ov-CHI-2, Ov16, Ov-FAR-1, Ov-CPI-1, Ov-B20, Ov-ASP-1, Ov-TMY-1, OvSOD1, OvGST1, Ov-CAL-1, M3/M4, Ov-RAL-1, Ov-RAL-2, Ov-ALT-1, Ov-FBA-1, and Ov-B8. We assessed the immunoreactivity of onchocerciasis patient sera (n = 152) from the Americas, West Africa, Central Africa, and East Africa against peptides derived from 10 of these proteins containing SNPs. Statistically significant variation in immunoreactivity among the regions was seen in SNP-containing peptides derived from 8 of 10 proteins tested: OVOC1192(1-15), OVOC9988(28-42), OVOC9225(320-334), OVOC7453(22-36), OVOC11517(14-28), OVOC3177(283-297), OVOC7911(594-608), and OVOC12628(174-188). Our data show that differences in immunoreactivity to variant antigenic peptides may be used to characterize Ov populations, thereby elucidating features of Ov population biology previously inaccessible because of the limited availability of parasite material.
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Affiliation(s)
| | | | | | - Michael P Fay
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - Makedonka Mitreva
- McDonnell Genome Institute.,Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
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Doyle SR, Bourguinat C, Nana-Djeunga HC, Kengne-Ouafo JA, Pion SDS, Bopda J, Kamgno J, Wanji S, Che H, Kuesel AC, Walker M, Basáñez MG, Boakye DA, Osei-Atweneboana MY, Boussinesq M, Prichard RK, Grant WN. Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity. PLoS Negl Trop Dis 2017; 11:e0005816. [PMID: 28746337 PMCID: PMC5546710 DOI: 10.1371/journal.pntd.0005816] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/07/2017] [Accepted: 07/19/2017] [Indexed: 12/30/2022] Open
Abstract
Background Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana—exposed to more than a decade of regular ivermectin treatment—have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread. Methodology/Principal findings Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR. Conclusions/Significance This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations. Onchocerciasis is a human parasitic disease endemic across large areas of Sub-Saharan Africa, where more than 99% of the estimated 100 million people globally at-risk live. The microfilarial stage of Onchocerca volvulus causes pathologies ranging from mild itching to visual impairment and ultimately, irreversible blindness. Mass administration of ivermectin kills microfilariae and has an anti-fecundity effect on adult worms by temporarily inhibiting the development in utero and/or release into the skin of new microfilariae, thereby reducing morbidity and transmission. Phenotypic and genetic changes in some parasite populations that have undergone multiple ivermectin treatments in Cameroon and Ghana have raised concern that sub-optimal response to ivermectin's anti-fecundity effect may increase in frequency, reducing the impact of ivermectin-based control measures. We used next generation sequencing of small pools of parasites to define genome-wide genetic differences between phenotypically characterised good and sub-optimal responder parasites from Cameroon and Ghana, and identified multiple regions of the genome that differentiated the response types. These regions were largely different between parasites from these two countries but revealed common molecular pathways that might be involved in determining the extent of response to ivermectin's anti-fecundity effect. These data reveal a more complex than previously described pattern of genetic diversity among O. volvulus populations that differ in their geography and response to ivermectin treatment.
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Affiliation(s)
- Stephen R. Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- * E-mail: (SRD); (RKP); (WNG)
| | - Catherine Bourguinat
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
| | - Hugues C. Nana-Djeunga
- Parasitology and Ecology Laboratory, Department of Animal Biology and Physiology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
| | - Jonas A. Kengne-Ouafo
- Research Foundation in Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Sébastien D. S. Pion
- Institut de Recherche pour le Développement (IRD), IRD UMI 233 TransVIHMI – Université Montpellier – INSERM U1175, Montpellier, France
| | - Jean Bopda
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Joseph Kamgno
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Samuel Wanji
- Research Foundation in Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Hua Che
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
| | - Annette C. Kuesel
- UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (WHO/TDR), World Health Organization, Geneva, Switzerland
| | - Martin Walker
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, United Kingdom
| | - Maria-Gloria Basáñez
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, United Kingdom
| | - Daniel A. Boakye
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mike Y. Osei-Atweneboana
- Department of Environmental Biology and Health Water Research Institute, Council for Scientific and Industrial Research (CSIR), Accra, Ghana
| | - Michel Boussinesq
- Institut de Recherche pour le Développement (IRD), IRD UMI 233 TransVIHMI – Université Montpellier – INSERM U1175, Montpellier, France
| | - Roger K. Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
- * E-mail: (SRD); (RKP); (WNG)
| | - Warwick N. Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
- * E-mail: (SRD); (RKP); (WNG)
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Wit J, Gilleard JS. Resequencing Helminth Genomes for Population and Genetic Studies. Trends Parasitol 2017; 33:388-399. [DOI: 10.1016/j.pt.2017.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
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Affiliation(s)
- Sara Lustigman
- Molecular Parasitology, New York Blood Center, New York, NY, United States of America
- * E-mail:
| | - Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, United States of America
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, United States of America
- College of Global Public Health, New York University, New York, NY, United States of America
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Murdoch ME, Murdoch IE, Evans J, Yahaya H, Njepuome N, Cousens S, Jones BR, Abiose A. Pre-control relationship of onchocercal skin disease with onchocercal infection in Guinea Savanna, Northern Nigeria. PLoS Negl Trop Dis 2017; 11:e0005489. [PMID: 28355223 PMCID: PMC5386293 DOI: 10.1371/journal.pntd.0005489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/10/2017] [Accepted: 03/13/2017] [Indexed: 01/22/2023] Open
Abstract
Background Onchocerca volvulus infection can result in blindness, itching and skin lesions. Previous research concentrated on blindness. Methods A clinical classification system of the cutaneous changes in onchocerciasis was used for the first time in this study within the context of an early ivermectin drug trial in the savanna region of Kaduna State, northern Nigeria. Skin examinations were performed in 6,790 individuals aged 5+ years in endemic communities and 1,343 individuals in nonendemic communities. Results / Discussion There was increased risk for all forms of onchocercal skin disease in endemic communities with the most common finding being the presence of nodules (1,438 individuals, 21.2%), followed by atrophy (367, 6.1% of those < 50 years), acute papular onchodermatitis, APOD (233, 3.4%), depigmentation (216, 3.2%) and chronic papular onchodermatitis, CPOD (155, 2.3%). A further 645 individuals (9.5%) complained of pruritus but had completely normal skin. APOD was more common in males whereas atrophy, hanging groin and nodules were more common in females. After controlling for age and sex, microfilarial positivity was a risk factor for CPOD, depigmentation, hanging groin and nodules (OR 1.54, p = 0.046; OR 2.29, p = 0.002; OR 2.18, p = 0.002 and OR 3.80, p <0.001 respectively). Comparable results were found using presence of nodules as the marker for infection. Microfilarial load showed similar, though weaker, results. A total of 2621(38.6%) endemic residents had itching with normal skin, or had one or more types of onchocercal skin disease including nodules, which may be considered as a composite index of the overall prevalence of onchocercal skin disease. Conclusion Significant levels of onchocercal skin disease were documented in this savanna area, which subsequently resulted in a reassessment of the true burden of skin disease in onchocerciasis. This paper represents the first detailed report of the association of onchocercal skin disease with markers for onchocercal infection. Onchocerciasis is a tropical parasitic infection caused by the nematode worm Onchocerca volvulus. The disease mainly occurs across tropical Africa and infection can result in blindness, debilitating itching and a variety of skin changes. Initial research concentrated mainly on the problem of blindness. A number of studies on onchocercal skin disease were performed but were difficult to interpret and compare because of the use of inconsistent terminology. Within the setting of one of the early trials of ivermectin in a savanna area of northern Nigeria, where there were known high rates of onchocercal blindness, we used a novel clinical classification of the skin changes in onchocerciasis. We identified significant levels of itching and various forms of onchocercal skin disease within these endemic communities. A positive skin-snip result proved to be a significant risk factor for the presence of chronic papular onchodermatitis (CPOD), depigmentation, hanging groin and onchocercal nodules. Comparable results were found when the presence of nodules was used as the marker for infection and similar, though weaker odds ratios were found with microfilarial load per se. The findings triggered a reassessment of the true burden of skin disease in onchocerciasis. It is the first detailed report of the association between onchocercal skin disease and markers of infection.
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Affiliation(s)
- Michele E. Murdoch
- St. John's Institute of Dermatology, London, United Kingdom
- Department of Dermatology, Watford General Hospital, West Herts Hospitals NHS Trust, Watford, Herts., United Kingdom
- * E-mail:
| | - Ian E. Murdoch
- Department of Ophthalmology, Ahmadu Bello University Hospital, Kaduna, Nigeria
- International Centre for Eye Health, Institute of Ophthalmology, London, United Kingdom
| | - Jennifer Evans
- Department of Ophthalmology, Ahmadu Bello University Hospital, Kaduna, Nigeria
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Haliru Yahaya
- Department of Medicine, Ahmadu Bello University Teaching Hospital, Kaduna, Nigeria
| | - Ngozi Njepuome
- Department of Medicine, Ahmadu Bello University Teaching Hospital, Kaduna, Nigeria
| | - Simon Cousens
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Barrie R. Jones
- Department of Ophthalmology, Ahmadu Bello University Hospital, Kaduna, Nigeria
- International Centre for Eye Health, Institute of Ophthalmology, London, United Kingdom
| | - Adenike Abiose
- Department of Ophthalmology, Ahmadu Bello University Hospital, Kaduna, Nigeria
- National Eye Centre, Kaduna, Nigeria
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Cheke RA. Factors affecting onchocerciasis transmission: lessons for infection control. Expert Rev Anti Infect Ther 2017; 15:377-386. [PMID: 28117596 DOI: 10.1080/14787210.2017.1286980] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Onchocerca volvulus infects in excess of 15 million people. The vectors are Simulium blackflies, varieties of which differ in their ecologies, behavior and vectorial abilities. Control of the vectors and mass administrations of ivermectin have succeeded in reducing prevalences with elimination achieved in some foci, particularly in Central and southern America. In Africa, progress towards elimination has been less successful. Areas covered: Even with community directed treatment with ivermectin (CDTI), control has been difficult in African areas with initial prevalences in excess of 55%, especially if only annual treatments are dispensed. This is partly attributable to insufficient coverage, but the appearance of incipiently resistant non-responding parasites and lack of attention to vector biology in modeling and planning outcomes of intervention programmes have also played their parts, with recrudescence now appearing in some treated areas. Expert commentary: The biology of onchocerciasis is complex involving different vectors with differing abilities to transmit parasites, diverse pathologies related to geographical and parasite variations and endosymbionts in both parasite and vector. Modeling to predict epidemiological and control outcomes is addressing this complexity but more attention needs to be given to the vectors' roles to further understanding of where and when control measures will succeed.
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Affiliation(s)
- Robert A Cheke
- a Agriculture, Health and Environment Department, Natural Resources Institute , University of Greenwich at Medway , Kent , UK.,b Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus) , Imperial College London , London , UK
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