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Pilling OA, Sundararaman SA, Brisson D, Beiting DP. Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment. PLoS Pathog 2024; 20:e1012418. [PMID: 39264872 PMCID: PMC11392400 DOI: 10.1371/journal.ppat.1012418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens.
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Affiliation(s)
- Olivia A Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sesh A Sundararaman
- Department of Pediatrics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Pennsylvania, United States of America
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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2
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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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3
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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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Shrestha H, McCulloch K, Chisholm RH, Armoo SK, Veriegh F, Sirwani N, Crawford KE, Osei-Atweneboana MY, Grant WN, Hedtke SM. Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination. Mol Ecol 2024; 33:e17357. [PMID: 38683054 DOI: 10.1111/mec.17357] [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: 11/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024]
Abstract
We present a framework for identifying when conditions are favourable for transmission of vector-borne diseases between communities by incorporating predicted disease prevalence mapping with landscape analysis of sociological, environmental and host/parasite genetic data. We explored the relationship between environmental features and gene flow of a filarial parasite of humans, Onchocerca volvulus, and its vector, blackflies in the genus Simulium. We generated a baseline microfilarial prevalence map from point estimates from 47 locations in the ecological transition separating the savannah and forest in Ghana, where transmission of O. volvulus persists despite onchocerciasis control efforts. We generated movement suitability maps based on environmental correlates with mitochondrial population structure of 164 parasites from 15 communities and 93 vectors from only four sampling sites, and compared these to the baseline prevalence map. Parasite genetic distance between sampling locations was significantly associated with elevation (r = .793, p = .005) and soil moisture (r = .507, p = .002), while vector genetic distance was associated with soil moisture (r = .788, p = .0417) and precipitation (r = .835, p = .0417). The correlation between baseline prevalence and parasite resistance surface maps was stronger than that between prevalence and vector resistance surface maps. The centre of the study area had high prevalence and suitability for parasite and vector gene flow, potentially contributing to persistent transmission and suggesting the importance of re-evaluating transmission zone boundaries. With suitably dense sampling, this framework can help delineate transmission zones for onchocerciasis and would be translatable to other vector-borne diseases.
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Affiliation(s)
- Himal Shrestha
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Karen McCulloch
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Rebecca H Chisholm
- Department of Mathematical and Physical Sciences, La Trobe University, Bundoora, Victoria, Australia
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Samuel K Armoo
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Accra, Ghana
| | - Francis Veriegh
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Accra, Ghana
| | - Neha Sirwani
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Katie E Crawford
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | | | - Warwick N Grant
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Shannon M Hedtke
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
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Rehmann CT, Ralph PL, Kern AD. Evaluating evidence for co-geography in the Anopheles-Plasmodium host-parasite system. G3 (BETHESDA, MD.) 2024; 14:jkae008. [PMID: 38230808 PMCID: PMC10917517 DOI: 10.1093/g3journal/jkae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/08/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
The often tight association between parasites and their hosts means that under certain scenarios, the evolutionary histories of the two species can become closely coupled both through time and across space. Using spatial genetic inference, we identify a potential signal of common dispersal patterns in the Anopheles gambiae and Plasmodium falciparum host-parasite system as seen through a between-species correlation of the differences between geographic sampling location and geographic location predicted from the genome. This correlation may be due to coupled dispersal dynamics between host and parasite but may also reflect statistical artifacts due to uneven spatial distribution of sampling locations. Using continuous-space population genetics simulations, we investigate the degree to which uneven distribution of sampling locations leads to bias in prediction of spatial location from genetic data and implement methods to counter this effect. We demonstrate that while algorithmic bias presents a problem in inference from spatio-genetic data, the correlation structure between A. gambiae and P. falciparum predictions cannot be attributed to spatial bias alone and is thus likely a genetic signal of co-dispersal in a host-parasite system.
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Affiliation(s)
- Clara T Rehmann
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene 97403, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene 97403, USA
- Department of Mathematics, University of Oregon, Eugene 97403, USA
| | - Andrew D Kern
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene 97403, USA
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Lehmann T, Kouam C, Woo J, Diallo M, Wilkerson R, Linton YM. The African mosquito-borne diseasosome: geographical patterns, range expansion and future disease emergence. Proc Biol Sci 2023; 290:20231581. [PMID: 38018102 PMCID: PMC10685135 DOI: 10.1098/rspb.2023.1581] [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: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Mosquito-borne diseases (MBDs) threaten public health and food security globally. We provide the first biogeographic description of the African mosquito fauna (677 species) and the 151 mosquito-borne pathogens (MBPs) they transmit. While mosquito species richness agrees with expectations based on Africa's land surface, African arboviruses and mammalian plasmodia are more speciose than expected. Species assemblages of mosquitoes and MBPs similarly separate sub-Saharan Africa from North Africa, and those in West and Central Africa from eastern and southern Africa. Similarities between mosquitoes and MBPs in diversity and range size suggest that mosquitoes are key in delimiting the range of MBPs. With approximately 25% endemicity, approximately 50% occupying one to three countries and less than 5% occupying greater than 25 countries, the ranges of mosquitoes and MBPs are surprisingly small, suggesting that most MBPs are transmitted by a single mosquito species. Exceptionally widespread mosquito species feed on people and livestock, and most are high-altitude-windborne migrants. Likewise, widespread MBPs are transmitted among people or livestock by widespread mosquitoes, suggesting that adapting to people or livestock and to widespread mosquito species promote range expansion in MBPs. Range size may predict range expansion and emergence risk. We highlight key knowledge gaps that impede prediction and mitigation of future emergence of local and global MBDs.
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Affiliation(s)
- Tovi Lehmann
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Cedric Kouam
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Joshua Woo
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Mawlouth Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar, Senegal
| | - Richard Wilkerson
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History, Washington, DC, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History, Washington, DC, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
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7
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Rehmann CT, Ralph PL, Kern AD. Evaluating evidence for co-geography in the Anopheles-Plasmodium host-parasite system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549405. [PMID: 37503196 PMCID: PMC10370088 DOI: 10.1101/2023.07.17.549405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The often tight association between parasites and their hosts means that under certain scenarios, the evolutionary histories of the two species can become closely coupled both through time and across space. Using spatial genetic inference, we identify a potential signal of common dispersal patterns in the Anopheles gambiae and Plasmodium falciparum host-parasite system as seen through a between-species correlation of the differences between geographic sampling location and geographic location predicted from the genome. This correlation may be due to coupled dispersal dynamics between host and parasite, but may also reflect statistical artifacts due to uneven spatial distribution of sampling locations. Using continuous-space population genetics simulations, we investigate the degree to which uneven distribution of sampling locations leads to bias in prediction of spatial location from genetic data and implement methods to counter this effect. We demonstrate that while algorithmic bias presents a problem in inference from spatio-genetic data, the correlation structure between A. gambiae and P. falciparum predictions cannot be attributed to spatial bias alone, and is thus likely a genetic signal of co-dispersal in a host-parasite system.
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Affiliation(s)
- Clara T Rehmann
- University of Oregon, Institute of Ecology and Evolution and Department of Biology
| | - Peter L Ralph
- University of Oregon, Institute of Ecology and Evolution and Department of Biology
- University of Oregon, Department of Mathematics
| | - Andrew D Kern
- University of Oregon, Institute of Ecology and Evolution and Department of Biology
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8
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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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Dwivedi-Yu JA, Oppler ZJ, Mitchell MW, Song YS, Brisson D. A fast machine-learning-guided primer design pipeline for selective whole genome amplification. PLoS Comput Biol 2023; 19:e1010137. [PMID: 37068103 PMCID: PMC10138271 DOI: 10.1371/journal.pcbi.1010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 04/27/2023] [Accepted: 03/23/2023] [Indexed: 04/18/2023] Open
Abstract
Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales-precisely the scales at which these processes occur-microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluation strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluate the novel swga2.0 pipeline by designing primer sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.
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Affiliation(s)
- Jane A. Dwivedi-Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Facebook AI Research, 1 Rathbone Square, London, England
| | - Zachary J. Oppler
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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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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Schmeller DS, Urbach D, Bates K, Catalan J, Cogălniceanu D, Fisher MC, Friesen J, Füreder L, Gaube V, Haver M, Jacobsen D, Le Roux G, Lin YP, Loyau A, Machate O, Mayer A, Palomo I, Plutzar C, Sentenac H, Sommaruga R, Tiberti R, Ripple WJ. Scientists' warning of threats to mountains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158611. [PMID: 36087665 DOI: 10.1016/j.scitotenv.2022.158611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/04/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Mountains are an essential component of the global life-support system. They are characterized by a rugged, heterogenous landscape with rapidly changing environmental conditions providing myriad ecological niches over relatively small spatial scales. Although montane species are well adapted to life at extremes, they are highly vulnerable to human derived ecosystem threats. Here we build on the manifesto 'World Scientists' Warning to Humanity', issued by the Alliance of World Scientists, to outline the major threats to mountain ecosystems. We highlight climate change as the greatest threat to mountain ecosystems, which are more impacted than their lowland counterparts. We further discuss the cascade of "knock-on" effects of climate change such as increased UV radiation, altered hydrological cycles, and altered pollution profiles; highlighting the biological and socio-economic consequences. Finally, we present how intensified use of mountains leads to overexploitation and abstraction of water, driving changes in carbon stock, reducing biodiversity, and impacting ecosystem functioning. These perturbations can provide opportunities for invasive species, parasites and pathogens to colonize these fragile habitats, driving further changes and losses of micro- and macro-biodiversity, as well further impacting ecosystem services. Ultimately, imbalances in the normal functioning of mountain ecosystems will lead to changes in vital biological, biochemical, and chemical processes, critically reducing ecosystem health with widespread repercussions for animal and human wellbeing. Developing tools in species/habitat conservation and future restoration is therefore essential if we are to effectively mitigate against the declining health of mountains.
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Affiliation(s)
| | - Davnah Urbach
- Global Mountain Biodiversity Assessment, Institute of Plant Sciences, University of Bern, Bern, Switzerland.
| | - Kieran Bates
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK; Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.
| | - Jordi Catalan
- CREAF Campus UAB, Edifici C, Cerdanyola Del Valles, Spain; CSIC, Campus UAB, Cerdanyola Del Valles, Spain.
| | - Dan Cogălniceanu
- Ovidius University Constanţa, Faculty of Natural Sciences and Agricultural Sciences, Al. Universităţii 1, 900470 Constanţa, Romania
| | - Matthew C Fisher
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
| | - Jan Friesen
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Leopold Füreder
- Department of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
| | - Veronika Gaube
- University of Natural Resources and Life Sciences, Vienna, Department of Economics and Social Sciences, Institute of Social Ecology (SEC), Schottenfeldgasse 29, Austria.
| | - Marilen Haver
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Dean Jacobsen
- Freshwater Biological Section, Dept. Biology, University of Copenhagen, Denmark.
| | - Gael Le Roux
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
| | - Adeline Loyau
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Oliver Machate
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Andreas Mayer
- University of Natural Resources and Life Sciences, Vienna, Department of Economics and Social Sciences, Institute of Social Ecology (SEC), Schottenfeldgasse 29, Austria.
| | - Ignacio Palomo
- Univ. Grenoble-Alpes, IRD, CNRS, Grenoble INP*, IGE, 38000 Grenoble, France.
| | - Christoph Plutzar
- University of Natural Resources and Life Sciences, Vienna, Department of Economics and Social Sciences, Institute of Social Ecology (SEC), Schottenfeldgasse 29, Austria.
| | - Hugo Sentenac
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Ruben Sommaruga
- Department of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
| | - Rocco Tiberti
- Department of Earth and Environmental Sciences - DSTA, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
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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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Greene SE, Fischer K, Choi YJ, Curtis KC, Budge PJ, Mitreva M, King CL, Fischer PU, Weil GJ. Characterization of a novel microfilarial antigen for diagnosis of Wuchereria bancrofti infections. PLoS Negl Trop Dis 2022; 16:e0010407. [PMID: 35604906 PMCID: PMC9126377 DOI: 10.1371/journal.pntd.0010407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Background Lymphatic filariasis (LF) is a neglected tropical disease caused by the filarial nematodes Wuchereria bancrofti, Brugia malayi and Brugia timori. The Global Program to Eliminate LF uses mass drug administration (MDA) of anti-filarial drugs that clear microfilariae (Mf) from blood to interrupt transmission by mosquitos. New diagnostic tools are needed to assess the impact of MDA on bancroftian filariasis, because available serologic tests can remain positive after successful treatment. Methodology/Principal findings We identified Wb-bhp-1, which encodes a W. bancrofti homologue of BmR1, the B. malayi protein used in the Brugia Rapid antibody test for brugian filariasis. Wb-bhp-1 has a single exon that encodes a 16.3 kD protein (Wb-Bhp-1) with 45% amino acid identity to BmR1. Immunohistology shows that anti-Wb-Bhp-1 antibodies primarily bind to Mf. Plasma from 124 of 224 (55%) microfilaremic individuals had IgG4 antibodies to Wb-Bhp-1 by ELISA. Serologic reactivity to Wb-Bhp-1 varied widely with samples from different regions (sensitivity range 32–92%), with 77% sensitivity for 116 samples collected from microfilaremic individuals outside of sub-Saharan Africa. This variable sensitivity highlights the importance of validating new diagnostic tests for parasitic diseases with samples from different geographical regions. Individuals with higher Mf counts were more likely to have anti-Wb-Bhp-1 antibodies. Cross-reactivity was observed with a minority of plasma samples from people with onchocerciasis (17%) or loiasis (10%). We also identified, cloned and characterized BmR1 homologues from O. volvulus and L. loa that have 41% and 38% identity to BmR1, respectively. However, antibody assays with these antigens were not sensitive for onchocerciasis or loiasis. Conclusions Wb-Bhp-1 is a novel antigen that is useful for serologic diagnosis of bancroftian filariasis. Additional studies are needed to assess the value of this antigen for monitoring the success of filariasis elimination programs. Lymphatic filariasis (LF) is a highly disabling and stigmatizing disease caused by parasitic worms that are transmitted by mosquitoes. There is a coordinated global effort to eliminate LF based on mass drug administration (MDA) of donated anti-filarial medications. Improved methods are needed to determine when transmission of the infection has been interrupted in previously endemic areas so that MDA can be safely stopped. This paper reports the discovery and characterization of a novel W. bancrofti antigen, Wb-Bhp-1, which is a homologue of the Brugia malayi protein used in antibody tests to monitor filariasis elimination in areas of Asia where LF is caused by Brugia species. We show that a test for IgG4 antibodies to Wb-Bhp-1 was fairly specific for W. bancrofti infection. However, the sensitivity of this test varied by the geographic origin of the samples. Sensitivity was highest for samples collected in the Indo-Pacific region and lowest for samples collected in Côte d’Ivoire. Geographic differences in the parasite or the human immune responses to infection may account for this variability. This range in sensitivity highlights the importance of validating new diagnostic tests for parasitic diseases with samples from different geographical regions.
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MESH Headings
- Animals
- Antibodies, Helminth/analysis
- Antibodies, Helminth/genetics
- Antibodies, Helminth/immunology
- Antigens, Helminth/analysis
- Antigens, Helminth/genetics
- Antigens, Helminth/immunology
- Brugia malayi
- Cross Reactions
- Elephantiasis, Filarial/diagnosis
- Elephantiasis, Filarial/genetics
- Elephantiasis, Filarial/immunology
- Elephantiasis, Filarial/parasitology
- Filariasis/diagnosis
- Filariasis/genetics
- Filariasis/immunology
- Filariasis/parasitology
- Humans
- Loiasis/diagnosis
- Loiasis/immunology
- Microfilariae/immunology
- Onchocerciasis/diagnosis
- Onchocerciasis/immunology
- Serologic Tests
- Wuchereria bancrofti/genetics
- Wuchereria bancrofti/immunology
- Wuchereria bancrofti/isolation & purification
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Affiliation(s)
- Sarah E. Greene
- Infectious Diseases Division, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Young-Jun Choi
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Kurt C. Curtis
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Philip J. Budge
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Makedonka Mitreva
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Christopher L. King
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University and Veterans Affairs Research Service, Cleveland, Ohio, United States of America
| | - Peter U. Fischer
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Gary J. Weil
- Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
- * E-mail:
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14
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Adjobimey T, Hoerauf A. Distinct N-Linked Immunoglobulin G Glycosylation Patterns Are Associated With Chronic Pathology and Asymptomatic Infections in Human Lymphatic Filariasis. Front Immunol 2022; 13:790895. [PMID: 35401511 PMCID: PMC8992374 DOI: 10.3389/fimmu.2022.790895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/03/2022] [Indexed: 12/12/2022] Open
Abstract
Lymphatic filariasis presents a complex spectrum of clinical manifestations ranging from asymptomatic microfilariaemic (MF+) to chronic pathology (CP), including lymphedema and elephantiasis. Emerging evidence suggests a link between the physiopathology of filarial infections and antibody properties. Post-translational glycosylation has been shown to play a key role in the modulation of antibodies’ effector functions. Here, we investigated the link between total IgG-N-glycosylation patterns and the physiopathology of human lymphatic filariasis using UPLC-FLD/ESI-MS comparison of N-glycan profiles of total IgG purified from endemic normals (EN), MF+, and CP patients. We detected a total of 19 glycans released from all IgG samples. Strikingly, agalactosylated glycan residues were more prominent in EN, whereas sialylation and bisecting GlcNac correlated with asymptomatic infections. While IgG from all three clinical groups expressed high levels of fucosylated residues, significantly lower expressions of afucosylated IgG were seen in MF+ individuals compared to EN and CP. Our data reveal distinct N-linked IgG glycan profiles in EN, MF+, and CP and suggest that IgG galactosylation and sialylation are associated with chronic pathology, whereas agalactosylation correlates with putative immunity. The results also indicate a role for sialylation, fucosylation, and bisecting GlcNac in immune tolerance to the parasite. These findings highlight the link between N-glycosylation and the physiopathology of lymphatic filariasis and open new research avenues for next-generation therapeutic formulations against infectious diseases.
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Affiliation(s)
- Tomabu Adjobimey
- Institute of Medical Microbiology, Immunology and Parasitology Institut for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany.,Faculté des Sciences et Techniques (FAST), Université d'Abomey Calavi, Abomey Calavi, Benin
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology Institut for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany.,Bonn-Cologne Site, German Center for Infectious Disease Research Deutsches Zentrum für Infektionsforschung (DZIF), Bonn, Germany
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15
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Platt RN, Le Clec'h W, Chevalier FD, McDew‐White M, LoVerde PT, Ramiro de Assis R, Oliveira G, Kinung'hi S, Djirmay AG, Steinauer ML, Gouvras A, Rabone M, Allan F, Webster BL, Webster JP, Emery AM, Rollinson D, Anderson TJC. Genomic analysis of a parasite invasion: Colonization of the Americas by the blood fluke Schistosoma mansoni. Mol Ecol 2022; 31:2242-2263. [PMID: 35152493 PMCID: PMC9305930 DOI: 10.1111/mec.16395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 11/29/2022]
Abstract
Schistosoma mansoni, a snail-borne, blood fluke that infects humans, was introduced into the Americas from Africa during the Trans-Atlantic slave trade. As this parasite shows strong specificity to the snail intermediate host, we expected that adaptation to South American Biomphalaria spp. snails would result in population bottlenecks and strong signatures of selection. We scored 475,081 single nucleotide variants in 143 S. mansoni from the Americas (Brazil, Guadeloupe and Puerto Rico) and Africa (Cameroon, Niger, Senegal, Tanzania, and Uganda), and used these data to ask: (i) Was there a population bottleneck during colonization? (ii) Can we identify signatures of selection associated with colonization? (iii) What were the source populations for colonizing parasites? We found a 2.4- to 2.9-fold reduction in diversity and much slower decay in linkage disequilibrium (LD) in parasites from East to West Africa. However, we observed similar nuclear diversity and LD in West Africa and Brazil, suggesting no strong bottlenecks and limited barriers to colonization. We identified five genome regions showing selection in the Americas, compared with three in West Africa and none in East Africa, which we speculate may reflect adaptation during colonization. Finally, we infer that unsampled populations from central African regions between Benin and Angola, with contributions from Niger, are probably the major source(s) for Brazilian S. mansoni. The absence of a bottleneck suggests that this is a rare case of a serendipitous invasion, where S. mansoni parasites were pre-adapted to the Americas and able to establish with relative ease.
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Affiliation(s)
- Roy N. Platt
- Texas Biomedical Research InstituteSan AntonioTexasUSA
| | | | | | | | | | | | - Guilherme Oliveira
- Centro de Pesquisas René Rachou—Fiocruz/MGBelo HorizonteBrazil
- Instituto Tecnológico ValeBelémBrazil
| | | | - Amadou Garba Djirmay
- Réseau International Schistosomiases Environnemental Aménagement et Lutte (RISEAL)NiameyNiger
| | | | | | | | - Fiona Allan
- Department of Pathobiology and Population SciencesRoyal Veterinary College, Centre for Emerging, Endemic and Exotic DiseasesUniversity of LondonHertfordshireUK
- London Centre for Neglected Tropical Disease Research, Imperial College LondonSchool of Public HealthLondonUK
| | - Bonnie L. Webster
- Natural History MuseumLondonUK
- London Centre for Neglected Tropical Disease Research, Imperial College LondonSchool of Public HealthLondonUK
| | - Joanne P. Webster
- Department of Pathobiology and Population SciencesRoyal Veterinary College, Centre for Emerging, Endemic and Exotic DiseasesUniversity of LondonHertfordshireUK
- London Centre for Neglected Tropical Disease Research, Imperial College LondonSchool of Public HealthLondonUK
| | - Aidan M. Emery
- Natural History MuseumLondonUK
- London Centre for Neglected Tropical Disease Research, Imperial College LondonSchool of Public HealthLondonUK
| | - David Rollinson
- Natural History MuseumLondonUK
- London Centre for Neglected Tropical Disease Research, Imperial College LondonSchool of Public HealthLondonUK
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16
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Das NC, Sen Gupta PS, Biswal S, Patra R, Rana MK, Mukherjee S. In-silico evidences on filarial cystatin as a putative ligand of human TLR4. J Biomol Struct Dyn 2021; 40:8808-8824. [PMID: 33955317 DOI: 10.1080/07391102.2021.1918252] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cystatin is a small molecular weight immunomodulatory protein of filarial parasite that plays a pivotal role in downregulating the host immune response to prolong the survival of the parasite inside the host body. Hitherto, this protein is familiar as an inhibitor of human proteases. However, growing evidences on the role of cystatin in regulating inflammatory homeostasis prompted us to investigate the molecular reasons behind the explicit anti-inflammatory trait of this protein. We have explored molecular docking and molecular dynamics simulation approaches to explore the interaction of cystatin of Wuchereria bancrofti (causative parasite of human filariasis) with human Toll-like receptors (TLRs). TLRs are the most crucial component of frontline host defence against pathogenic infections including filarial infection. Our in-silico data clearly revealed that cystatin strongly interacts with the extracellular domain of TLR4 (binding energy=-93.5 ± 10 kJ/mol) and this biophysical interaction is mediated by hydrogen bonding and hydrophobic interaction. Molecular dynamics simulation analysis revealed excellent stability of the cystatin-TLR4 complex. Taken together, our data indicated that cystatin appears to be a ligand of TLR4 and we hypothesize that cystatin-TLR4 interaction most likely to play a key role in activating the alternative activation pathways to establish an anti-inflammatory milieu. Thus, the study provokes the development of chemotherapeutics and/or vaccines for targeting the cystatin-TLR4 interaction to disrupt the pathological attributes of human lymphatic filariasis. Our findings are expected to provide a novel dimension to the existing knowledge on filarial immunopathogenesis and it will encourage the scientific communities for experimental validation of the present investigation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Parth Sarthi Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha, India
| | - Satyaranjan Biswal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha, India
| | - Ritwik Patra
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha, India
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
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17
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Senanayake KS, Söderberg J, Põlajev A, Malmberg M, Karunanayake EH, Tennekoon KH, Samarakoon SR, Bongcam-Rudloff E, Niazi A. The Genome of Setaria digitata: A Cattle Nematode Closely Related to Human Filarial Parasites. Genome Biol Evol 2020; 12:3971-3976. [PMID: 32022853 PMCID: PMC7061230 DOI: 10.1093/gbe/evaa017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2020] [Indexed: 01/25/2023] Open
Abstract
Here we present the draft genome sequence of Setaria digitata, a parasitic nematode affecting cattle. Due to its similarity to Wuchereria bancrofti, the parasitic nematode that causes lymphatic filariasis in humans, S. digitata has been used as a model organism at the genomic level to find drug targets which can be used for the development of novel drugs and/or vaccines for human filariasis. Setaria digitata causes cerebrospinal nematodiasis in goats, sheep, and horses posing a serious threat to livestock in developing countries. The genome sequence of S. digitata will assist in finding candidate genes to use as drug targets in both S. digitata and W. bancrofti. The assembled draft genome is ∼90 Mb long and contains 8,974 genomic scaffolds with a G+C content of 31.73%.
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Affiliation(s)
- Kanchana S Senanayake
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Sri Lanka
| | - Jonas Söderberg
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Aleksei Põlajev
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maja Malmberg
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Eric H Karunanayake
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Sri Lanka
| | - Kamani H Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Sri Lanka
| | - Sameera R Samarakoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Sri Lanka
| | - Erik Bongcam-Rudloff
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Adnan Niazi
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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18
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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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19
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Abstract
The global spread of parasites is unquestionably linked with human activities. Migration in all its different forms played a major role in the introduction of parasites into new areas. In ancient times, mass migrations were the main causes for the spread of parasites while in the recent past and present, emigration, immigration, displacement, external and internal migration, and labor migration were the reasons for the dispersal of parasites. With the advent of seagoing ships, long-distance trading became another important mode of spreading parasites. This review summarizes the spread of parasites using notable examples. In addition, the different hypotheses explaining the arrival of Plasmodium vivax and soil-transmitted helminths in pre-Columbian America are also discussed.
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Affiliation(s)
- Dietmar Steverding
- Bob Champion Research and Education Building, Norwich Medical School, University of East Anglia , Norwich, UK
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20
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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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21
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Nowak RM, Jastrzębski JP, Kuśmirek W, Sałamatin R, Rydzanicz M, Sobczyk-Kopcioł A, Sulima-Celińska A, Paukszto Ł, Makowczenko KG, Płoski R, Tkach VV, Basałaj K, Młocicki D. Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta. Sci Data 2019; 6:302. [PMID: 31796747 PMCID: PMC6890685 DOI: 10.1038/s41597-019-0311-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/04/2019] [Indexed: 01/26/2023] Open
Abstract
Despite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.
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Affiliation(s)
- Robert M Nowak
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.
| | | | - Wiktor Kuśmirek
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Rusłan Sałamatin
- Department of General Biology and Parasitology, Medical University of Warsaw, Warsaw, Poland
- Department of Parasitology and Vector-Borne Diseases, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
| | | | | | - Anna Sulima-Celińska
- Department of General Biology and Parasitology, Medical University of Warsaw, Warsaw, Poland
| | | | | | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Vasyl V Tkach
- Department of Biology, University of North Dakota, Grand Forks, USA
| | - Katarzyna Basałaj
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Warsaw, Poland
| | - Daniel Młocicki
- Department of General Biology and Parasitology, Medical University of Warsaw, Warsaw, Poland.
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Warsaw, Poland.
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22
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Doyle SR, Sankaranarayanan G, Allan F, Berger D, Jimenez Castro PD, Collins JB, Crellen T, Duque-Correa MA, Ellis P, Jaleta TG, Laing R, Maitland K, McCarthy C, Moundai T, Softley B, Thiele E, Ouakou PT, Tushabe JV, Webster JP, Weiss AJ, Lok J, Devaney E, Kaplan RM, Cotton JA, Berriman M, Holroyd N. Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing. Front Genet 2019; 10:826. [PMID: 31616465 PMCID: PMC6764475 DOI: 10.3389/fgene.2019.00826] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023] Open
Abstract
Whole-genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications. Although late-stage juvenile and adult parasites typically produce sufficient DNA for molecular analyses, these parasitic stages are almost always inaccessible in the live host; immature life stages found in the environment for which samples can be collected non-invasively offer a potential alternative; however, these samples typically yield very low quantities of DNA, can be environmentally resistant, and are susceptible to contamination, often from bacterial or host DNA. Here, we have tested five low-input DNA extraction protocols together with a low-input sequencing library protocol to assess the feasibility of whole-genome sequencing of individual immature helminth samples. These approaches do not use whole-genome amplification, a common but costly approach to increase the yield of low-input samples. We first tested individual parasites from two species spotted onto FTA cards-egg and L1 stages of Haemonchus contortus and miracidia of Schistosoma mansoni-before further testing on an additional five species-Ancylostoma caninum, Ascaridia dissimilis, Dirofilaria immitis, Strongyloides stercoralis, and Trichuris muris-with an optimal protocol. A sixth species-Dracunculus medinensis-was included for comparison. Whole-genome sequencing followed by analyses to determine the proportion of on- and off-target mapping revealed successful sample preparations for six of the eight species tested with variation both between species and between different life stages from some species described. These results demonstrate the feasibility of whole-genome sequencing of individual parasites, and highlight a new avenue toward generating sensitive, specific, and information-rich data for the diagnosis and surveillance of helminths.
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Affiliation(s)
- Stephen R. Doyle
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Fiona Allan
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Duncan Berger
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Pablo D. Jimenez Castro
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Grupo de Parasitologia Veterinaria, Universidad Nacional de Colombia, Bogotá, Colombia
| | - James Bryant Collins
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Thomas Crellen
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Peter Ellis
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Tegegn G. Jaleta
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Catherine McCarthy
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Ben Softley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Elizabeth Thiele
- Department of Biology, Vassar College, Poughkeepsie, NY, United States
| | | | - John Vianney Tushabe
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Joanne P. Webster
- Centre for Emerging, Endemic and Exotic Diseases, Department of Pathology and Population Sciences, Royal Veterinary College, University of London, Herts, United Kingdom
| | - Adam J. Weiss
- Guinea Worm Eradication Program, The Carter Center, Atlanta, GA, United States
| | - James Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ray M. Kaplan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - James A. Cotton
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Matthew Berriman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Nancy Holroyd
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
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