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Ilík V, Schwarz EM, Nosková E, Pafčo B. Hookworm genomics: dusk or dawn? Trends Parasitol 2024; 40:452-465. [PMID: 38677925 DOI: 10.1016/j.pt.2024.04.003] [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: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
Hookworms are parasites, closely related to the model nematode Caenorhabditis elegans, that are a major economic and health burden worldwide. Primarily three hookworm species (Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum) infect humans. Another 100 hookworm species from 19 genera infect primates, ruminants, and carnivores. Genetic data exist for only seven of these species. Genome sequences are available from only four of these species in two genera, leaving 96 others (particularly those parasitizing wildlife) without any genomic data. The most recent hookworm genomes were published 5 years ago, leaving the field in a dusk. However, assembling genomes from single hookworms may bring a new dawn. Here we summarize advances, challenges, and opportunities for studying these neglected but important parasitic nematodes.
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Affiliation(s)
- Vladislav Ilík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eva Nosková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
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2
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Crawford KE, Hedtke SM, Doyle SR, Kuesel AC, Armoo S, Osei-Atweneboana MY, Grant WN. Genome-based tools for onchocerciasis elimination: utility of the mitochondrial genome for delineating Onchocerca volvulus transmission zones. Int J Parasitol 2024; 54:171-183. [PMID: 37993016 DOI: 10.1016/j.ijpara.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/21/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
National programs in Africa have expanded their objectives from control of onchocerciasis (river blindness) as a public health problem to elimination of parasite transmission, motivated by the reduction of Onchocerca volvulus infection prevalence in many African meso- and hyperendemic areas due to mass drug administration of ivermectin (MDAi). Given the large, contiguous hypo-, meso-, and hyperendemic areas, sustainable elimination of onchocerciasis in sub-Saharan Africa requires delineation of geographic boundaries for parasite transmission zones, so that programs can consider the risk of parasite re-introduction through vector or human migration from areas with ongoing transmission when making decisions to stop MDAi. We propose that transmission zone boundaries can be delineated by characterising the parasite genetic population structure within and between potential zones. We analysed whole mitochondrial genome sequences of 189 O. volvulus adults to determine the pattern of genetic similarity across three West African countries: Ghana, Mali, and Côte d'Ivoire. Population genetic structure indicates that parasites from villages near the Pru, Daka, and Black Volta rivers in central Ghana belong to one parasite population, indicating that the assumption that river basins constitute individual transmission zones is not supported by the data. Parasites from Mali and Côte d'Ivoire are genetically distinct from those from Ghana. This research provides the basis for developing tools for elimination programs to delineate transmission zones, to estimate the risk of parasite re-introduction via vector or human movement when intervention is stopped in one area while transmission is ongoing in others, to identify the origin of infections detected post-treatment cessation, and to investigate whether persisting prevalence despite ongoing interventions in one area is due to parasites imported from others.
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Affiliation(s)
- Katie E Crawford
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Shannon M Hedtke
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia.
| | - Stephen R Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Annette C Kuesel
- UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Samuel Armoo
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Council for Scientific and Industrial Research, Council Close, Accra, Ghana
| | - Mike Y Osei-Atweneboana
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Council for Scientific and Industrial Research, Council Close, Accra, Ghana
| | - Warwick N Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia
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3
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Lee YC, Ke HM, Liu YC, Lee HH, Wang MC, Tseng YC, Kikuchi T, Tsai IJ. Single-worm long-read sequencing reveals genome diversity in free-living nematodes. Nucleic Acids Res 2023; 51:8035-8047. [PMID: 37526286 PMCID: PMC10450198 DOI: 10.1093/nar/gkad647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
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Affiliation(s)
- Yi-Chien Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Min-Chen Wang
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Yung-Che Tseng
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
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4
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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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Papaiakovou M, Fraija-Fernández N, James K, Briscoe AG, Hall A, Jenkins TP, Dunn J, Levecke B, Mekonnen Z, Cools P, Doyle SR, Cantacessi C, Littlewood DTJ. Evaluation of genome skimming to detect and characterise human and livestock helminths. Int J Parasitol 2023; 53:69-79. [PMID: 36641060 DOI: 10.1016/j.ijpara.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023]
Abstract
The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples.
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Affiliation(s)
- Marina Papaiakovou
- Natural History Museum, Cromwell Road, London, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Natalia Fraija-Fernández
- Natural History Museum, Cromwell Road, London, UK; Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain
| | - Katherine James
- Natural History Museum, Cromwell Road, London, UK; Interdisciplinary Computing and Complex BioSystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew G Briscoe
- Natural History Museum, Cromwell Road, London, UK; NatureMetrics, Surrey Research Park, Guildford, UK
| | - Andie Hall
- Natural History Museum, Cromwell Road, London, UK
| | - Timothy P Jenkins
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Dunn
- Department of Infectious Disease Epidemiology, Imperial College, London W2 1PG, UK
| | - Bruno Levecke
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | - Zeleke Mekonnen
- Jimma University Institute of Health (JUIH), Jimma, Ethiopia
| | - Piet Cools
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | | | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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6
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Molecular diagnostics for gastrointestinal helminths in equids: Past, present and future. Vet Parasitol 2023; 313:109851. [PMID: 36521296 DOI: 10.1016/j.vetpar.2022.109851] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
This review is aimed to (i) appraise the literature on the use of molecular techniques for the detection, quantification and differentiation of gastrointestinal helminths (GIH) of equids, (ii) identify the knowledge gaps and, (iii) discuss diagnostic prospects in equine parasitology. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews, we retrieved 54 studies (horses: 50/54; donkeys and zebras: 4/54) from four databases. Polymerase chain reaction (PCR) was employed in all of the studies whereas PCR amplicons were sequenced in only 18 of them. Other techniques used (including modifications of PCR) were reverse line blot, quantitative (q)PCR, restriction fragment length polymorphism, nested-PCR, PCR-directed next-generation sequencing, Southern blotting, single strand conformation polymorphism, PCR-enzyme linked immunosorbent assay, matrix-assisted laser desorption/ionisation-time of flight and random amplification of polymorphic DNA. Most of the studies (53/54) used nuclear ribosomal RNA (including the internal transcribed spacers, intergenic spacer, 5.8 S, 18 S, 28 S and 12 S) as target loci while cytochrome c oxidase subunit 1 and random genomic regions were targeted in only three and one studies, respectively. Overall, to date, the majority of molecular studies have focused on the diagnosis and identification of GIHs of equids (i.e. species of Anoplocephala, Craterostomum, cyathostomins, Oesophagodontus, Parascaris, Strongylus, Strongyloides and Triodontophorus), with a recent shift towards investigations on anthelmintic resistance and the use of high-throughput nemabiome metabarcoding. With the increasing reports of anthelmintic resistance in equid GIHs, it is crucial to develop and apply techniques such as advanced metabarcoding for surveillance of parasite populations in order to gain detailed insights into their diversity and sustainable control. To the best of our knowledge, this is the first systematic review that evaluates molecular investigations published on the diagnosis and quantification of equid GIHs and provides useful insights into important knowledge gaps and future research directions in equid molecular parasitology.
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Doyle SR, Laing R, Bartley D, Morrison A, Holroyd N, Maitland K, Antonopoulos A, Chaudhry U, Flis I, Howell S, McIntyre J, Gilleard JS, Tait A, Mable B, Kaplan R, Sargison N, Britton C, Berriman M, Devaney E, Cotton JA. Genomic landscape of drug response reveals mediators of anthelmintic resistance. Cell Rep 2022; 41:111522. [PMID: 36261007 PMCID: PMC9597552 DOI: 10.1016/j.celrep.2022.111522] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/11/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
Like other pathogens, parasitic helminths can rapidly evolve resistance to drug treatment. Understanding the genetic basis of anthelmintic drug resistance in parasitic nematodes is key to tracking its spread and improving the efficacy and sustainability of parasite control. Here, we use an in vivo genetic cross between drug-susceptible and multi-drug-resistant strains of Haemonchus contortus in a natural host-parasite system to simultaneously map resistance loci for the three major classes of anthelmintics. This approach identifies new alleles for resistance to benzimidazoles and levamisole and implicates the transcription factor cky-1 in ivermectin resistance. This gene is within a locus under selection in ivermectin-resistant populations worldwide; expression analyses and functional validation using knockdown experiments support that cky-1 is associated with ivermectin survival. Our work demonstrates the feasibility of high-resolution forward genetics in a parasitic nematode and identifies variants for the development of molecular diagnostics to combat drug resistance in the field.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK.
| | - David Bartley
- Moredun Research Institute, Penicuik, Midlothian EH26 0PZ, UK
| | - Alison Morrison
- Moredun Research Institute, Penicuik, Midlothian EH26 0PZ, UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Alistair Antonopoulos
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Ilona Flis
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Sue Howell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Jennifer McIntyre
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary T2N 1N4, Canada
| | - Andy Tait
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Barbara Mable
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Ray Kaplan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Neil Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Collette Britton
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - James A Cotton
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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Doyle SR. Improving helminth genome resources in the post-genomic era. Trends Parasitol 2022; 38:831-840. [PMID: 35810065 DOI: 10.1016/j.pt.2022.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 01/02/2023]
Abstract
Rapid advancement in high-throughput sequencing and analytical approaches has seen a steady increase in the generation of genomic resources for helminth parasites. Now, helminth genomes and their annotations are a cornerstone of numerous efforts to compare genetic and transcriptomic variation, from single cells to populations of globally distributed parasites, to genome modifications to understand gene function. Our understanding of helminths is increasingly reliant on these genomic resources, which are primarily static once published and vary widely in quality and completeness between species. This article seeks to highlight the cause and effect of this variation and argues for the continued improvement of these genomic resources - even after their publication - which is necessary to provide a more accurate and complete understanding of the biology of these important pathogens.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
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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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Ranaraja DMAE, Mahakapuge TAN, Thilakarathne DS, Dharmasuriya JYC, Rajapakse RPVJ. Hepatic trematode Platynosomum sp. (Dicrocoeliidae) from a domestic cat in Colombo, Sri Lanka: Case report and molecular identification. Vet Parasitol Reg Stud Reports 2022; 34:100762. [PMID: 36041797 DOI: 10.1016/j.vprsr.2022.100762] [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: 10/18/2021] [Revised: 05/29/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Platynosomum is a digenean trematode causing hepatobiliary disease in cats in tropical and subtropical regions. The presence of Platynosomum species in Sri Lanka has not been previously reported or investigated. In the current study, we report a clinical case of a cat suffering from hepatic and biliary complications. Fine-needle aspiration of the biliary extract revealed a large number of parasite eggs, and the morphological and molecular identification of eggs was carried out. Molecular phylogenetics was performed using the nuclear ribosomal Internal Transcribed Spacer 2 (ITS2) and a portion of a mitochondrially encoded gene; Cytochrome C Oxidase subunit 1 (COX1). Through a combination of history, clinical signs, blood reports, ultrasound scanning, light microscopy of eggs from biliary aspirate and molecular studies, the disease was confirmed as parasitism caused by a Platynosomum like species. The Platynosomum species in Sri Lanka is phylogenetically related to Platynosomum illiciens reported from Costa Rica, Central America. This case emphasizes the importance of future studies in Sri Lanka regarding the prevalence and distribution of Platynosomum among cat populations. Further, the inclusion of feline platynosomiasis in the differential diagnoses list for hepatobiliary diseases is required.
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Affiliation(s)
| | - Thilini Anupama Nanayakkarawasam Mahakapuge
- Division of Veterinary Parasitology, Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Dulari Samanthika Thilakarathne
- Division of Veterinary Parasitology, Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
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Berger DJ, Léger E, Sankaranarayanan G, Sène M, Diouf ND, Rabone M, Emery A, Allan F, Cotton JA, Berriman M, Webster JP. Genomic evidence of contemporary hybridization between Schistosoma species. PLoS Pathog 2022; 18:e1010706. [PMID: 35939508 PMCID: PMC9387932 DOI: 10.1371/journal.ppat.1010706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/18/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022] Open
Abstract
Hybridization between different species of parasites is increasingly being recognised as a major public and veterinary health concern at the interface of infectious diseases biology, evolution, epidemiology and ultimately control. Recent research has revealed that viable hybrids and introgressed lineages between Schistosoma spp. are prevalent across Africa and beyond, including those with zoonotic potential. However, it remains unclear whether these hybrid lineages represent recent hybridization events, suggesting hybridization is ongoing, and/or whether they represent introgressed lineages derived from ancient hybridization events. In human schistosomiasis, investigation is hampered by the inaccessibility of adult-stage worms due to their intravascular location, an issue which can be circumvented by post-mortem of livestock at abattoirs for Schistosoma spp. of known zoonotic potential. To characterise the composition of naturally-occurring schistosome hybrids, we performed whole-genome sequencing of 21 natural livestock infective schistosome isolates. To facilitate this, we also assembled a de novo chromosomal-scale draft assembly of Schistosoma curassoni. Genomic analyses identified isolates of S. bovis, S. curassoni and hybrids between the two species, all of which were early generation hybrids with multiple generations found within the same host. These results show that hybridization is an ongoing process within natural populations with the potential to further challenge elimination efforts against schistosomiasis. Schistosomiasis is a chronic and debilitating major neglected tropical disease affecting both humans and livestock. Increasingly, zoonotic spillover of livestock infections, facilitated by hybridization between different Schistosoma species, is increasingly being recognised as a risk to human health. Multiple surveys conducted within endemic regions have found a high prevalence of these hybrid lineages. However, it is often unclear whether these lineages are derived from recent hybridization events, suggesting hybridization is ongoing and may be linked to anthropogenic environmental change, or simply indicators of introgression from ancient hybridization events. To understand the origin and evolution of these hybrid lineages, we produced a chromosomal-scale assembly of Schistosoma curassoni and performed whole-genome sequencing of 21 natural livestock-infective S. curassoni, S. bovis and hybridized schistosome isolates, including multi-stage sampling from the same hosts. Our analyses exclusively identified early generation hybrid lineages, including multiple unrelated generations within the same hosts, suggesting that these hybrids are viable and derived from multiple independent hybridization events.
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Affiliation(s)
- Duncan J. Berger
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Royal Veterinary College, University of London, London, United Kingdom
- * E-mail: (DB); (EL); (MB); (JPW)
| | - Elsa Léger
- Royal Veterinary College, University of London, London, United Kingdom
- London Centre for Neglected Tropical Diseases Research, Imperial College Faculty of Medicine, London, United Kingdom
- * E-mail: (DB); (EL); (MB); (JPW)
| | | | - Mariama Sène
- Unité de Formation et de Recherche des Sciences Agronomiques, d’Aquaculture et de Technologies Alimentaires, Université Gaston Berger, Saint-Louis, Senegal
| | - Nicolas D. Diouf
- Unité de Formation et de Recherche des Sciences Agronomiques, d’Aquaculture et de Technologies Alimentaires, Université Gaston Berger, Saint-Louis, Senegal
| | - Muriel Rabone
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London, United Kingdom
| | - Aidan Emery
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London, United Kingdom
| | - Fiona Allan
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London, United Kingdom
- Pelagic Ecology Research Group, Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - James A. Cotton
- Wellcome Sanger Institute, Hinxton, United Kingdom
- London Centre for Neglected Tropical Diseases Research, Imperial College Faculty of Medicine, London, United Kingdom
| | - Matthew Berriman
- Wellcome Sanger Institute, Hinxton, United Kingdom
- London Centre for Neglected Tropical Diseases Research, Imperial College Faculty of Medicine, London, United Kingdom
- * E-mail: (DB); (EL); (MB); (JPW)
| | - Joanne P. Webster
- Royal Veterinary College, University of London, London, United Kingdom
- London Centre for Neglected Tropical Diseases Research, Imperial College Faculty of Medicine, London, United Kingdom
- * E-mail: (DB); (EL); (MB); (JPW)
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12
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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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13
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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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14
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Chan AHE, Saralamba N, Saralamba S, Ruangsittichai J, Chaisiri K, Limpanont Y, Charoennitiwat V, Thaenkham U. Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes. Sci Rep 2022; 12:9947. [PMID: 35705676 PMCID: PMC9200835 DOI: 10.1038/s41598-022-14176-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies.
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Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sompob Saralamba
- Mathematical and Economic Modelling (MAEMOD), Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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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: 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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16
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Papaiakovou M, Littlewood DTJ, Doyle SR, Gasser RB, Cantacessi C. Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics. Parasit Vectors 2022; 15:118. [PMID: 35365192 PMCID: PMC8973539 DOI: 10.1186/s13071-022-05225-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.
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Affiliation(s)
- Marina Papaiakovou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | | | | | - Robin B. Gasser
- Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
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17
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Assessment of three DNA extraction kits for the absolute quantification of strongyle nematode eggs in faecal samples. Acta Vet Scand 2022; 64:5. [PMID: 35139862 PMCID: PMC8826664 DOI: 10.1186/s13028-022-00624-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Haemonchus contortus is one of the most pathogenic gastrointestinal nematodes of small ruminants. The current diagnostic approach for the detection of this species relies on coproscopic methods, which both have low sensitivity and are time consuming. Methods employing detection through DNA amplification, such as droplet digital polymerase chain reaction (ddPCR), offer an advantageous approach to the diagnosis of H. contortus. However, DNA extraction protocols need to be constantly updated for the optimal retrieval of diagnostically usable template. Here, we describe the evaluation of three genomic DNA extraction kits for the detection and quantification of H. contortus ITS2 amplicon DNA from faecal samples, using droplet digital PCR. Results DNA samples, extracted from faecal material with the Nucleospin DNA Stool kit, produced the highest amounts of ITS2 amplicon copies and had the lowest coefficient of variation across different dilutions and sample types (fresh or frozen) out of the tested kits (Nucleospin DNA Stool, E.Z.N.A.® Stool DNA Kit and QIAamp Fast DNA Stool Mini Kit). Furthermore, the protocol of this kit has the fewest number of steps and the price of DNA extraction per sample is reasonable (2.77 €). Conclusions The Nucleospin DNA Stool kit is an attractive option for the detection and quantification of H. contortus DNA in faecal samples of small ruminants in a diagnostic setting.
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18
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Mkandawire TT, Grencis RK, Berriman M, Duque-Correa MA. Hatching of parasitic nematode eggs: a crucial step determining infection. Trends Parasitol 2022; 38:174-187. [PMID: 34538735 DOI: 10.1016/j.pt.2021.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022]
Abstract
Although hatching from eggs is fundamental for nematode biology it remains poorly understood. For animal-parasitic nematodes in particular, advancement has been slow since the 1980s. Understanding such a crucial life-cycle process would greatly improve the tractability of parasitic nematodes as experimental systems, advance fundamental knowledge, and enable translational research. Here, we review the role of eggs in the nematode life cycle and the current knowledge on the hatching cascade, including the different inducing and contributing factors, and highlight specific areas of the field that remain unknown. We examine how these knowledge gaps could be addressed and discuss their potential impact and application in nematode parasite research, treatment, and control.
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Affiliation(s)
| | - Richard K Grencis
- The Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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19
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Costa IN, Bosqui LR, Corral MA, Costa-Cruz JM, Gryschek RCB, de Paula FM. Diagnosis of human strongyloidiasis: Application in clinical practice. Acta Trop 2021; 223:106081. [PMID: 34364894 DOI: 10.1016/j.actatropica.2021.106081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/08/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022]
Abstract
This review considers the advantages and disadvantages of parasitological techniques, methods of detecting antibodies and antigens, as well as molecular biology techniques in the diagnosis of human strongyloidiasis. In addition, it elucidates the potential of different techniques for rapid and effective detection of clinical cases, thus enabling early treatment and preventing fatal consequences of this helminthiasis.
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20
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Sloan S, Jenvey CJ, Piedrafita D, Preston S, Stear MJ. Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes. BMC Biotechnol 2021; 21:35. [PMID: 34001079 PMCID: PMC8130168 DOI: 10.1186/s12896-021-00695-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time. Results 11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45–11.5 ng/μL, and on Qubit™ ranged between undetectable – 0.962 ng/μL. Median A260/280 ranged between 0.505–3.925, and median A260/230 ranged − 0.005 – 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity. Conclusions A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00695-6.
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Affiliation(s)
- S Sloan
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia.
| | - C J Jenvey
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
| | - D Piedrafita
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - S Preston
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - M J Stear
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
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21
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Rashid M, Rashid MI, Ali Q. An accurate, rapid and simple loop-mediated isothermal amplification method for Explanatum explanatum detection in animals. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2021; 12:377-381. [PMID: 34815851 PMCID: PMC8576162 DOI: 10.30466/vrf.2020.111872.2657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/05/2020] [Indexed: 11/01/2022]
Abstract
Paramphistomosis is an infectious disease caused by the liver flukes and it is associated with heavy loss of ruminant's population. Explanatum explanatum is a digenetic trematode commonly affecting domesticated ruminants. The available methods for pathogen detection are laborious and expensive and offer limited specificity; thus, considered not suitable for post mortem pathogen detection, surveillance and prevalence studies. New detection techniques offering simplicity, specificity and rapidity are absolutely needed. We have designed a loop-mediated isothermal amplification (LAMP) based polymerase chain reaction method, targeting a sequence of the explanatum species, using a primer pair from the internal transcribed spacer-2 region. The DNA from adult flukes belonging to explanatum species was isolated from infected livers and used to optimize the LAMP assay. The specificity and sensitivity of the LAMP assay were evaluated and found highly efficient in species-specific DNA detection with the sensitivity to detect 50.00 pg DNA in a 25.00 µL reaction mix. The procedure has the potential to be adapted for stool samples for field detection and disease surveillance/prevalence in rural and unprivileged areas.
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Affiliation(s)
- Muhammad Rashid
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan;,Correspondence Muhammad Rashid. PhD, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan. E-mail:
| | - Muhammad Imran Rashid
- Department of Parasitology, Faculty of Veterinary Science, University of Veterinary and Animal Sciences, Lahore, Pakistan.
| | - Qasim Ali
- Department of Parasitology, Faculty of Veterinary Science, University of Veterinary and Animal Sciences, Lahore, Pakistan.
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22
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Kotze AC, Gilleard JS, Doyle SR, Prichard RK. Challenges and opportunities for the adoption of molecular diagnostics for anthelmintic resistance. Int J Parasitol Drugs Drug Resist 2020; 14:264-273. [PMID: 33307336 PMCID: PMC7726450 DOI: 10.1016/j.ijpddr.2020.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Anthelmintic resistance is a significant threat to livestock production systems worldwide and is emerging as an important issue in companion animal parasite management. It is also an emerging concern for the control of human soil-transmitted helminths and filaria. An important aspect of managing anthelmintic resistance is the ability to utilise diagnostic tests to detect its emergence at an early stage. In host-parasite systems where resistance is already widespread, diagnostics have a potentially important role in determining those drugs that remain the most effective. The development of molecular diagnostics for anthelmintic resistance is one focus of the Consortium for Anthelmintic Resistance and Susceptibility (CARS) group. The present paper reflects discussions of this issue that occurred at the most recent meeting of the group in Wisconsin, USA, in July 2019. We compare molecular resistance diagnostics with in vivo and in vitro phenotypic methods, and highlight the advantages and disadvantages of each. We assess whether our knowledge on the identity of molecular markers for resistance towards the different drug classes is sufficient to provide some expectation that molecular tests for field use may be available in the short-to-medium term. We describe some practical aspects of such tests and how our current capabilities compare to the requirements of an 'ideal' test. Finally, we describe examples of drug class/parasite species interactions that provide the best opportunity for commercial use of molecular tests in the near future. We argue that while such prototype tests may not satisfy the requirements of an 'ideal' test, their potential to provide significant advances over currently-used phenotypic methods warrants their development as field diagnostics.
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Affiliation(s)
- Andrew C. Kotze
- CSIRO Agriculture and Food, St. Lucia, Brisbane, 4072, QLD, Australia,Corresponding author. , CSIRO Agriculture and Food, St. Lucia, Brisbane, 4072, QLD, Australia.
| | - John S. Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Stephen R. Doyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Roger K. Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, QC, H9X 3V9, Canada
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23
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Webster JP, Neves MI, Webster BL, Pennance T, Rabone M, Gouvras AN, Allan F, Walker M, Rollinson D. Parasite Population Genetic Contributions to the Schistosomiasis Consortium for Operational Research and Evaluation within Sub-Saharan Africa. Am J Trop Med Hyg 2020; 103:80-91. [PMID: 32400355 PMCID: PMC7351308 DOI: 10.4269/ajtmh.19-0827] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Analyses of the population genetic structure of schistosomes under the "Schistosomiasis Consortium for Operational Research and Evaluation" (SCORE) contrasting treatment pressure scenarios in Tanzania, Niger, and Zanzibar were performed to provide supplementary critical information with which to evaluate the impact of these large-scale control activities and guide how activities could be adjusted. We predicted that population genetic analyses would reveal information on a range of important parameters including, but not exclusive to, recruitment and transmission of genotypes, occurrence of hybridization events, differences in reproductive mode, and degrees of inbreeding, and hence, the evolutionary potential, and responses of parasite populations under contrasting treatment pressures. Key findings revealed that naturally high levels of gene flow and mixing of the parasite populations between neighboring sites were likely to dilute any effects imposed by the SCORE treatment arms. Furthermore, significant inherent differences in parasite fecundity were observed, independent of current treatment arm, but potentially of major impact in terms of maintaining high levels of ongoing transmission in persistent "biological hotspot" sites. Within Niger, naturally occurring Schistosoma haematobium/Schistosoma bovis viable hybrids were found to be abundant, often occurring in significantly higher proportions than that of single-species S. haematobium infections. By examining parasite population genetic structures across hosts, treatment regimens, and the spatial landscape, our results to date illustrate key transmission processes over and above that which could be achieved through standard parasitological monitoring of prevalence and intensity alone, as well as adding to our understanding of Schistosoma spp. life history strategies in general.
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Affiliation(s)
- Joanne P Webster
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom.,Department of Pathobiology and Population Sciences, Centre for Emerging, Endemic and Exotic Diseases (CEEED), Royal Veterinary College, University of London, Hawkshead Campus, Herts, United Kingdom
| | - Maria Inês Neves
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom.,Department of Pathobiology and Population Sciences, Centre for Emerging, Endemic and Exotic Diseases (CEEED), Royal Veterinary College, University of London, Hawkshead Campus, Herts, United Kingdom
| | - Bonnie L Webster
- Department of Life Sciences, Wolfson Wellcome Biomedical Laboratories, The Natural History Museum, London, United Kingdom.,London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom
| | - Tom Pennance
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.,Department of Life Sciences, Wolfson Wellcome Biomedical Laboratories, The Natural History Museum, London, United Kingdom.,London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom
| | - Muriel Rabone
- Department of Life Sciences, Wolfson Wellcome Biomedical Laboratories, The Natural History Museum, London, United Kingdom.,London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom
| | - Anouk N Gouvras
- Department of Life Sciences, Wolfson Wellcome Biomedical Laboratories, The Natural History Museum, London, United Kingdom.,London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom
| | - Fiona Allan
- Department of Life Sciences, Wolfson Wellcome Biomedical Laboratories, The Natural History Museum, London, United Kingdom.,London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom
| | - Martin Walker
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom.,Department of Pathobiology and Population Sciences, Centre for Emerging, Endemic and Exotic Diseases (CEEED), Royal Veterinary College, University of London, Hawkshead Campus, Herts, United Kingdom
| | - David Rollinson
- Department of Life Sciences, Wolfson Wellcome Biomedical Laboratories, The Natural History Museum, London, United Kingdom.,London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College Faculty of Medicine, London, United Kingdom
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