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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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2
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Nikolakis ZL, Adams RH, Wade KJ, Lund AJ, Carlton EJ, Castoe TA, Pollock DD. Prospects for genomic surveillance for selection in schistosome parasites. FRONTIERS IN EPIDEMIOLOGY 2022; 2:932021. [PMID: 38455290 PMCID: PMC10910990 DOI: 10.3389/fepid.2022.932021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/12/2022] [Indexed: 03/09/2024]
Abstract
Schistosomiasis is a neglected tropical disease caused by multiple parasitic Schistosoma species, and which impacts over 200 million people globally, mainly in low- and middle-income countries. Genomic surveillance to detect evidence for natural selection in schistosome populations represents an emerging and promising approach to identify and interpret schistosome responses to ongoing control efforts or other environmental factors. Here we review how genomic variation is used to detect selection, how these approaches have been applied to schistosomes, and how future studies to detect selection may be improved. We discuss the theory of genomic analyses to detect selection, identify experimental designs for such analyses, and review studies that have applied these approaches to schistosomes. We then consider the biological characteristics of schistosomes that are expected to respond to selection, particularly those that may be impacted by control programs. Examples include drug resistance, host specificity, and life history traits, and we review our current understanding of specific genes that underlie them in schistosomes. We also discuss how inherent features of schistosome reproduction and demography pose substantial challenges for effective identification of these traits and their genomic bases. We conclude by discussing how genomic surveillance for selection should be designed to improve understanding of schistosome biology, and how the parasite changes in response to selection.
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Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Richard H. Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, United States
| | - Kristen J. Wade
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Andrea J. Lund
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO, United States
| | - Elizabeth J. Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO, United States
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
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3
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Vianney TJ, Berger DJ, Doyle SR, Sankaranarayanan G, Serubanja J, Nakawungu PK, Besigye F, Sanya RE, Holroyd N, Allan F, Webb EL, Elliott AM, Berriman M, Cotton JA. Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities. PLoS Negl Trop Dis 2022; 16:e0010188. [PMID: 35981002 PMCID: PMC9426917 DOI: 10.1371/journal.pntd.0010188] [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: 01/31/2022] [Revised: 08/30/2022] [Accepted: 07/05/2022] [Indexed: 12/23/2022] Open
Abstract
Populations within schistosomiasis control areas, especially those in Africa, are recommended to receive regular mass drug administration (MDA) with praziquantel (PZQ) as the main strategy for controlling the disease. The impact of PZQ treatment on schistosome genetics remains poorly understood, and is limited by a lack of high-resolution genetic data on the population structure of parasites within these control areas. We generated whole-genome sequence data from 174 individual miracidia collected from both children and adults from fishing communities on islands in Lake Victoria in Uganda that had received either annual or quarterly MDA with PZQ over four years, including samples collected immediately before and four weeks after treatment. Genome variation within and between samples was characterised and we investigated genomic signatures of natural selection acting on these populations that could be due to PZQ treatment. The parasite population on these islands was more diverse than found in nearby villages on the lake shore. We saw little or no genetic differentiation between villages, or between the groups of villages with different treatment intensity, but slightly higher genetic diversity within the pre-treatment compared to post-treatment parasite populations. We identified classes of genes significantly enriched within regions of the genome with evidence of recent positive selection among post-treatment and intensively treated parasite populations. The differential selection observed in post-treatment and pre-treatment parasite populations could be linked to any reduced susceptibility of parasites to praziquantel treatment.
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Affiliation(s)
- Tushabe John Vianney
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Duncan J. Berger
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Stephen R. Doyle
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Joel Serubanja
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Prossy Kabuubi Nakawungu
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Fred Besigye
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Richard E. Sanya
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Health and Systems for Health Unit, African Population and Health Research Center, Nairobi, Kenya
| | - Nancy Holroyd
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Fiona Allan
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Emily L. Webb
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Alison M. Elliott
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Berriman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - James A. Cotton
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
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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: 1] [Impact Index Per Article: 0.5] [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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5
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Lund AJ, Wade KJ, Nikolakis ZL, Ivey KN, Perry BW, Pike HNC, Paull SH, Liu Y, Castoe TA, Pollock DD, Carlton EJ. Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination. eLife 2022; 11:79320. [PMID: 36040013 PMCID: PMC9427098 DOI: 10.7554/elife.79320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.
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Affiliation(s)
- Andrea J Lund
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Kristen J Wade
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Zachary L Nikolakis
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Kathleen N Ivey
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Blair W Perry
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Hamish NC Pike
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Sara H Paull
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Yang Liu
- Sichuan Centers for Disease Control and PreventionChengduChina
| | - Todd A Castoe
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - David D Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Elizabeth J Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
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6
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Rogers MJ, McManus DP, Muhi S, Gordon CA. Membrane Technology for Rapid Point-of-Care Diagnostics for Parasitic Neglected Tropical Diseases. Clin Microbiol Rev 2021; 34:e0032920. [PMID: 34378956 PMCID: PMC8404699 DOI: 10.1128/cmr.00329-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Parasitic neglected tropical diseases (NTDs) affect over one billion people worldwide, with individuals from communities in low-socioeconomic areas being most at risk and suffering the most. Disease management programs are hindered by the lack of infrastructure and resources for clinical sample collection, storage, and transport and a dearth of sensitive diagnostic methods that are inexpensive as well as accurate. Many diagnostic tests and tools have been developed for the parasitic NTDs, but the collection and storage of clinical samples for molecular and immunological diagnosis can be expensive due to storage, transport, and reagent costs, making these procedures untenable in most areas of endemicity. The application of membrane technology, which involves the use of specific membranes for either sample collection and storage or diagnostic procedures, can streamline this process, allowing for long-term sample storage at room temperature. Membrane technology can be used in serology-based diagnostic assays and for nucleic acid purification prior to molecular analysis. This facilitates the development of relatively simple and rapid procedures, although some of these methods, mainly due to costs, lack accessibility in low-socioeconomic regions of endemicity. New immunological procedures and nucleic acid storage, purification, and diagnostics protocols that are simple, rapid, accurate, and cost-effective must be developed as countries progress control efforts toward the elimination of the parasitic NTDs.
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Affiliation(s)
- Madeleine J. Rogers
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen Muhi
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Catherine A. Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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7
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Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts. Sci Rep 2021; 11:6884. [PMID: 33767307 PMCID: PMC7994584 DOI: 10.1038/s41598-021-86287-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
Schistosomiasis persists in Asian regions despite aggressive elimination measures. To identify factors enabling continued parasite transmission, we performed reduced representation genome sequencing on Schistosoma japonicum miracidia collected across multiple years from transmission hotspots in Sichuan, China. We discovered strong geographic structure, suggesting that local, rather than imported, reservoirs are key sources of persistent infections in the region. At the village level, parasites collected after referral for praziquantel treatment are closely related to local pre-treatment populations. Schistosomes within villages are also highly related, suggesting that only a few parasites from a limited number of hosts drive re-infection. The close familial relationships among miracidia from different human hosts also implicate short transmission routes among humans. At the individual host level, genetic evidence indicates that multiple humans retained infections following referral for treatment. Our findings suggest that end-game schistosomiasis control measures should focus on completely extirpating local parasite reservoirs and confirming successful treatment of infected human hosts.
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8
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Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Mol Genet Genomics 2021; 296:457-471. [PMID: 33469716 DOI: 10.1007/s00438-020-01756-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.
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9
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Nikolakis ZL, Hales NR, Perry BW, Schield DR, Timm LE, Liu Y, Zhong B, Kechris KJ, Carlton EJ, Pollock DD, Castoe TA. Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum). PLoS Negl Trop Dis 2021; 15:e0009020. [PMID: 33406094 PMCID: PMC7815185 DOI: 10.1371/journal.pntd.0009020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/19/2021] [Accepted: 11/30/2020] [Indexed: 02/05/2023] Open
Abstract
Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia. As an example, we sequenced whole genomes of 22 miracidia from 11 human hosts representing two villages in rural Sichuan, China, and used these data to evaluate patterns of relatedness and genetic diversity. We also down-sampled our dataset to test how lower coverage sequencing could increase the cost effectiveness of WGS while maintaining power to accurately infer relatedness. Collectively, our results illustrate that population-level WGS datasets are attainable for individual miracidia and represent a powerful tool for ultimately providing insight into overall genetic diversity, parasite relatedness, and transmission patterns for better design and evaluation of disease control efforts.
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Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Nicole R. Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Blair W. Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Drew R. Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Laura E. Timm
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Yang Liu
- Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People’s Republic of China
| | - Bo Zhong
- Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People’s Republic of China
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, Colorado, United States of America
| | - Elizabeth J. Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, Colorado, United States of America
| | - David D. Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
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10
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Abstract
While disease and outbreaks are mainly clonal for bacteria and other asexually reproducing organisms, sexual reproduction in schistosomes and other helminths usually results in unique individuals. For sexually reproducing organisms, the traits conserved in clones will instead be conserved in the group of organisms that tends to breed together, the population. While the same tools are applied to characterize DNA, how results are interpreted can be quite different at times (see another article in this collection, http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.AME-0002-2018). It is difficult to know what the real effect any control program has on the parasite population without assessing the health of this population, how they respond to the control measure, and how they recover, if they do. This review, part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, concentrates on one approach using pooled samples to study schistosome populations and shows how this and other approaches have contributed to our understanding of this parasite family's biology and epidemiology. *This article is part of a curated collection.
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11
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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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de Medeiros BAS, Farrell BD. Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci. PeerJ 2018; 6:e5089. [PMID: 30038852 PMCID: PMC6054070 DOI: 10.7717/peerj.5089] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/05/2018] [Indexed: 12/18/2022] Open
Abstract
Whole-genome amplification by multiple displacement amplification (MDA) is a promising technique to enable the use of samples with only limited amount of DNA for the construction of RAD-seq libraries. Previous work has shown that, when the amount of DNA used in the MDA reaction is large, double-digest RAD-seq (ddRAD) libraries prepared with amplified genomic DNA result in data that are indistinguishable from libraries prepared directly from genomic DNA. Based on this observation, here we evaluate the quality of ddRAD libraries prepared from MDA-amplified genomic DNA when the amount of input genomic DNA and the coverage obtained for samples is variable. By simultaneously preparing libraries for five species of weevils (Coleoptera, Curculionidae), we also evaluate the likelihood that potential contaminants will be encountered in the assembled dataset. Overall, our results indicate that MDA may not be able to rescue all samples with small amounts of DNA, but it does produce ddRAD libraries adequate for studies of phylogeography and population genetics even when conditions are not optimal. We find that MDA makes it harder to predict the number of loci that will be obtained for a given sequencing effort, with some samples behaving like traditional libraries and others yielding fewer loci than expected. This seems to be caused both by stochastic and deterministic effects during amplification. Further, the reduction in loci is stronger in libraries with lower amounts of template DNA for the MDA reaction. Even though a few samples exhibit substantial levels of contamination in raw reads, the effect is very small in the final dataset, suggesting that filters imposed during dataset assembly are important in removing contamination. Importantly, samples with strong signs of contamination and biases in heterozygosity were also those with fewer loci shared in the final dataset, suggesting that stringent filtering of samples with significant amounts of missing data is important when assembling data derived from MDA-amplified genomic DNA. Overall, we find that the combination of MDA and ddRAD results in high-quality datasets for population genetics as long as the sequence data is properly filtered during assembly.
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Affiliation(s)
- Bruno A S de Medeiros
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Brian D Farrell
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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Abstract
Adult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.
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Shortt JA, Card DC, Schield DR, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD. Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia. PLoS Negl Trop Dis 2017; 11:e0005292. [PMID: 28107347 PMCID: PMC5287463 DOI: 10.1371/journal.pntd.0005292] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 02/01/2017] [Accepted: 12/29/2016] [Indexed: 11/18/2022] Open
Abstract
Background In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies. Methodology/Principal Findings We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq) to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample. Conclusions/Significance This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species and other parasitic helminthes. Schistosomiasis is a devastating tropical disease that affects more than 200 million people worldwide. Over the past several decades, transmission control strategies implemented in China have reduced the prevalence and morbidity of Schistosoma japonicum in many areas. Infections still persist, however, and it is therefore of great interest to determine the sources of recurring infections. Genetic analysis is a promising means to achieve this. Towards this aim, we conducted a pilot study to assess the feasibility of using high-throughput sequencing to assess the geographic distribution of schistosome genetic variants. Because DNA yields from miracidia, the most easily accessible life stage, are insufficient for high throughput sequencing, we first employed whole genome amplification to obtain sufficient quantities of DNA. We then employed a technique that reproducibly sequences the same fraction of a genome across numerous samples. We successfully sequenced 6-year old S. japonicum samples from Sichuan Province, China, easily and economically identifying tens of thousands of variable loci, a sufficient number to discriminate fine-scale population structure. Further population sampling will help answer important questions concerning the persistence of infections, the sources of new infections, and whether parasite populations have undergone incipient evolution of drug resistance.
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Affiliation(s)
- Jonathan A. Shortt
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Daren C. Card
- Department of Biology, University of Texas Arlington, Arlington, TX, United States of America
| | - Drew R. Schield
- Department of Biology, University of Texas Arlington, Arlington, TX, United States of America
| | - Yang Liu
- Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People’s Republic of China
| | - Bo Zhong
- Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People’s Republic of China
| | - Todd A. Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX, United States of America
| | - Elizabeth J. Carlton
- Department of Environmental and Occupational Health, University of Colorado, Colorado School of Public Health, Aurora, CO, United States of America
| | - David D. Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America
- * E-mail:
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