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Charrier E, Chen R, Thundathil N, Gilleard JS. A set of nematode rRNA cistron databases and a primer assessment tool to enable more flexible and comprehensive metabarcoding. Mol Ecol Resour 2024; 24:e13965. [PMID: 38733216 DOI: 10.1111/1755-0998.13965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/25/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
The ITS-2-rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free-living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS-1 intergenic spacer and the region spanning ITS-1_5.8S_ITS-2. These databases comprise 2645, 254, 13,461 and 10,107 unique full-length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS-1 database includes the largest number of unique full-length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short-read or long-read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum.
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Affiliation(s)
- Eléonore Charrier
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - Rebecca Chen
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - Noelle Thundathil
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - John S Gilleard
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
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2
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Byrne O, Gangotia D, Crowley J, Zintl A, Kiser L, Boxall O, McSweeney D, O'Neill F, Dunne S, Lamb BR, Walshe N, Mulcahy G. Molecular species determination of cyathostomins from horses in Ireland. Vet Parasitol 2024; 328:110168. [PMID: 38547830 DOI: 10.1016/j.vetpar.2024.110168] [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: 12/14/2023] [Revised: 03/09/2024] [Accepted: 03/09/2024] [Indexed: 05/18/2024]
Abstract
Cyathostomins are globally important equine parasites, responsible for both chronic and acute pathogenic effects. The occurrence of mixed infections with numerous cyathostomin species hinders our understanding of parasite epidemiology, host-parasite dynamics, and species pathogenicity. There have been few studies of cyathostomin species occurring in horses in Ireland, where temperate climatic conditions with year-round rainfall provide suitable conditions for infection of grazing animals with bursate nematodes. Here, we amplified and sequenced the ITS-2 region of adult worms harvested at post-mortem from eleven adult horses between August 2018 and June 2020, and recorded species prevalence and abundance of worms recovered from the caecum, right ventral colon and left dorsal colon, using both BLAST and IDTAXA for taxonomic attribution. Phylogenetic relationships and community composition were also recorded and compared with other relevant studies, including a global meta-analysis. Overall, our results agree with previous studies that there does not seem to be a major difference in cyathostomin species occurrence in equids in different geographical regions. We confirmed the results of other workers in relation to the difficulties in discriminating between Cylicostephanus calicatus and Coronocyclus coronatus on the basis of ITS-2 sequences.
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Affiliation(s)
- Orla Byrne
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
| | - Disha Gangotia
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - John Crowley
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Annetta Zintl
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Liam Kiser
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Olivia Boxall
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Daniel McSweeney
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Fiona O'Neill
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stacey Dunne
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Breanna Rose Lamb
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Nicola Walshe
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Grace Mulcahy
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland
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3
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Abbas G, Ghafar A, McConnell E, Beasley A, Bauquier J, Wilkes EJA, El-Hage C, Carrigan P, Cudmore L, Hurley J, Gauci CG, Beveridge I, Ling E, Jacobson C, Stevenson MA, Nielsen MK, Hughes KJ, Jabbar A. A national survey of anthelmintic resistance in ascarid and strongylid nematodes in Australian Thoroughbred horses. Int J Parasitol Drugs Drug Resist 2024; 24:100517. [PMID: 38064906 PMCID: PMC10757041 DOI: 10.1016/j.ijpddr.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/19/2023] [Accepted: 11/19/2023] [Indexed: 01/02/2024]
Abstract
This study quantified the extent of anthelmintic resistance (AR) in ascarid and strongylid nematodes against commonly used anthelmintics in Australian Thoroughbred horses. Faecal egg count reduction tests (FECRTs, n = 86) and egg reappearance period (ERP) tests were conducted on 22 farms across Australia. Faecal egg counts (FECs) were determined using the modified McMaster technique, and percent faecal egg count reduction (%FECR) was calculated using the Bayesian hierarchical model and hybrid Frequentist/Bayesian analysis method. The results were interpreted using old (published in 1992) and new (2023) research guidelines of the World Association for the Advancement of Veterinary Parasitology (WAAVP). The species composition of strongylid nematodes was detected utilising a DNA-metabarcoding method using pre- and post-treatment samples. Resistance was observed in strongylid nematodes to commonly used single-active and combination anthelmintics, including ivermectin (IVM %FECR range: 82%-92%; 95% lower credible interval (LCI) range: 80%-90%), abamectin (ABM: 73%-92%; 65%-88%), moxidectin (MOX: 89%-91%; 84%-89%), oxfendazole (OFZ: 0%-56%; 0%-31%) and its combination with pyrantel (OFZ + PYR: 0%-82%; 0%-78%). Resistance in Parascaris spp. was observed to IVM (10%-43%; 0%-36%), ABM (0%; 0%) and MOX (0%; 0%). When the new thresholds recommended by the WAAVP were used, AR was detected in six additional FECRTs for strongylids and three more tests for Parascaris spp., introducing resistance to OFZ and OFZ + PYR in the latter. Shortened ERPs (4-6 weeks) of strongylids were observed in 31 FECRTs in which AR was not detected at 2 weeks post-treatment for all the anthelmintics tested. Among cyathostomins, Cylicocyclus nassatus, Cylicostephanus longibursatus and Coronocyclus coronatus were the most prevalent species at 2 weeks post-treatment, whereas the main species appearing at five weeks following treatments with macrocyclic lactones were Cylicocyclus nassatus, Cylicostephanus longibursatus and Cylicocyclus ashworthi. After treatment with OFZ + PYR, the latter three, plus Coronocyclus coronatus and Cyathostomum catinatum, were detected at 5 weeks post-treatment. Overall, the study highlights the prevalence of AR in both ascarids and strongylid nematodes against commonly used anthelmintic products to control worms in Australian horses. The results indicate that ML combination products provided acceptable efficacy at 2 weeks. However, ERP calculations suggest that products work less effectively than previously measured. It is suggested to regularly monitor the efficacy of the anthelmintics and consider changing the worm control practices to better manage worms and AR in Australian horses.
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Affiliation(s)
- Ghazanfar Abbas
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Abdul Ghafar
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Emma McConnell
- Centre for Animal Production and Health, Murdoch University, Murdoch, Western Australia, Australia
| | - Anne Beasley
- School of Agriculture and Food Sustainability, University of Queensland, Gatton, Queensland 4343, Australia
| | - Jenni Bauquier
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | | | - Charles El-Hage
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Peter Carrigan
- Scone Equine Hospital, Scone, New South Wales 2337, Australia
| | - Lucy Cudmore
- Scone Equine Hospital, Scone, New South Wales 2337, Australia
| | - John Hurley
- Swettenham Stud, Nagambie, Victoria 3608, Australia
| | - Charles G Gauci
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Ian Beveridge
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Elysia Ling
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Caroline Jacobson
- Centre for Animal Production and Health, Murdoch University, Murdoch, Western Australia, Australia
| | - Mark A Stevenson
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Martin K Nielsen
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Kristopher J Hughes
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Abdul Jabbar
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia.
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Mason B, Cervena B, Frias L, Goossens B, Hasegawa H, Keuk K, Langgeng A, Majewski K, Matsumoto T, Matsuura K, Mendonça R, Okamoto M, Peter S, Petrzelkova KJ, Sipangkui S, Xu Z, Pafco B, MacIntosh AJ. Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates. Parasitology 2024; 151:514-522. [PMID: 38629119 PMCID: PMC11106507 DOI: 10.1017/s0031182024000386] [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: 01/12/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.
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Affiliation(s)
- Bethan Mason
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Barbora Cervena
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Liesbeth Frias
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Benoit Goossens
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Hideo Hasegawa
- Department of Biomedicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Kenneth Keuk
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Abdullah Langgeng
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Kasia Majewski
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Japan
| | - Keiko Matsuura
- Department of Biomedicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Renata Mendonça
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Centre for Functional Ecology – Science for People & the Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Munehiro Okamoto
- Center for the Evolutionary Origins of Human Behavior (EHUB), Kyoto University, Kyoto, Japan
| | - Steve Peter
- Kulliyah of Science, Department of Biotechnology, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Klara J. Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Liberec Zoo, Liberec, Czech Republic
| | | | - Zhihong Xu
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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Malsa J, Boudesocque-Delaye L, Wimel L, Auclair-Ronzaud J, Dumont B, Mach N, Reigner F, Guégnard F, Chereau A, Serreau D, Théry-Koné I, Sallé G, Fleurance G. Chicory (Cichorium intybus) reduces cyathostomin egg excretion and larval development in grazing horses. Int J Parasitol Drugs Drug Resist 2024; 24:100523. [PMID: 38368671 PMCID: PMC10884488 DOI: 10.1016/j.ijpddr.2024.100523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/20/2024]
Abstract
Cyathostomins are the most prevalent parasitic nematodes of grazing horses. They are responsible for colic and diarrhea in their hosts. After several decades of exposure to synthetic anthelmintics, they have evolved to become resistant to most compounds. In addition, the drug-associated environmental side-effects question their use in the field. Alternative control strategies, like bioactive forages, are needed to face these challenges. Among these, chicory (Cichorium intybus, Puna II cultivar (cv.)) is known to convey anthelmintic compounds and may control cyathostomins in grazing horses. To challenge this hypothesis, we measured fecal egg counts and the rate of larval development in 20 naturally infected young saddle horses (2-year-old) grazing either (i) a pasture sown with chicory (n = 10) or (ii) a mesophile grassland (n = 10) at the same stocking rate (2.4 livestock unit (LU)/ha). The grazing period lasted 45 days to prevent horse reinfection. Horses in the chicory group mostly grazed chicory (89% of the bites), while those of the control group grazed mainly grasses (73%). Cyathostomins egg excretion decreased in both groups throughout the experiment. Accounting for this trajectory, the fecal egg count reduction (FECR) measured in individuals grazing chicory relative to control individuals increased from 72.9% at day 16 to 85.5% at the end of the study. In addition, larval development in feces from horses grazed on chicory was reduced by more than 60% from d31 compared to control individuals. Using a metabarcoding approach, we also evidenced a significant decrease in cyathostomin species abundance in horses grazing chicory. Chicory extract enriched in sesquiterpenes lactones was tested on two cyathostomins isolates. The estimated IC50 was high (1 and 3.4 mg/ml) and varied according to the pyrantel sensitivity status of the worm isolate. We conclude that the grazing of chicory (cv. Puna II) by horses is a promising strategy for reducing cyathostomin egg excretion and larval development that may contribute to lower the reliance on synthetic anthelmintics. The underpinning modes of action remain to be explored further.
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Affiliation(s)
- Joshua Malsa
- INRAE, Université de Tours, UMR 1282 Infectiologie et Santé Publique, Nouzilly, France.
| | | | - Laurence Wimel
- Institut Français Du Cheval et de L'équitation, Plateau Technique de Chamberet, Chamberet, France
| | - Juliette Auclair-Ronzaud
- Institut Français Du Cheval et de L'équitation, Plateau Technique de Chamberet, Chamberet, France
| | - Bertrand Dumont
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR 1213 Herbivores, Saint-Genès-Champanelle, France
| | - Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, Cedex 3, 31076, France
| | - Fabrice Reigner
- INRAE, Unité Expérimentale de Physiologie Animale de L'Orfrasière, Nouzilly, France
| | - Fabrice Guégnard
- INRAE, Université de Tours, UMR 1282 Infectiologie et Santé Publique, Nouzilly, France
| | - Angélique Chereau
- INRAE, Université de Tours, UMR 1282 Infectiologie et Santé Publique, Nouzilly, France
| | - Delphine Serreau
- INRAE, Université de Tours, UMR 1282 Infectiologie et Santé Publique, Nouzilly, France
| | - Isabelle Théry-Koné
- Université de Tours, EA 7502 Synthèse et Isolement de Molécules Bioactives, Tours, France
| | - Guillaume Sallé
- INRAE, Université de Tours, UMR 1282 Infectiologie et Santé Publique, Nouzilly, France
| | - Géraldine Fleurance
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR 1213 Herbivores, Saint-Genès-Champanelle, France; Institut Français Du Cheval et de L'équitation, Pôle Développement, Innovation et Recherche, Saint-Genès-Champanelle, France
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Hamad MH, Islam SI, Jitsamai W, Chinkangsadarn T, Naraporn D, Ouisuwan S, Taweethavonsawat P. Metabarcoding study to reveal the structural community of strongylid nematodes in domesticated horses in Thailand. BMC Vet Res 2024; 20:70. [PMID: 38395874 PMCID: PMC10893705 DOI: 10.1186/s12917-024-03934-y] [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: 10/05/2023] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Mixed strongylid infections significantly impact equine health and performance. Traditional microscopy-based methods exhibit limitations in accurately identifying strongylid species. Nemabiome deep amplicon sequencing approach previously succeeded in describing the strongylid communities in livestock including equids. However, there are no available studies that describe the structural communities of strongylid parasites in horses in Thailand. Therefore, this study was undertaken encompassing the ITS-2 rDNA metabarcoding assay to characterize strongylid species within horse fecal samples collected from a cohort of yearlings at the largest domesticated stud farm in Thailand. In addition, to investigate the capability of ITS-2 rDNA in assessing the phylogenetic relationships among the identified strongylid species. RESULTS The study identified 14 strongylid species in the examined equine populations, each with varying prevalence. Notably, Cylicocyclus nassatus and Cylicostephanus longibursatus were identified as the predominant species, with Strongylus spp. conspicuously absent. The phylogenetic analysis of 207 amplicon sequence variants (ASVs) displayed a complex relationship among the investigated cyathostomin species, with some species are positioned across multiple clades, demonstrating close associations with various species and genera. CONCLUSION The ITS-2 nemabiome sequencing technique provided a detailed picture of horse strongylid parasite species in the studied population. This establishes a foundation for future investigations into the resistance status of these parasites and enables efforts to mitigate their impact.
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Affiliation(s)
- Mohamed H Hamad
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44511, Egypt
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sk Injamamul Islam
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanarit Jitsamai
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Teerapol Chinkangsadarn
- Department of Surgery, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Darm Naraporn
- Horse Farm and Laboratory Animal Breeding Center, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Hua-Hin, Prachuap Khiri Khan Province, 77110, Thailand
| | - Suraseha Ouisuwan
- Horse Farm and Laboratory Animal Breeding Center, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Hua-Hin, Prachuap Khiri Khan Province, 77110, Thailand
| | - Piyanan Taweethavonsawat
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Biomarkers in Animals Parasitology Research Unit, Chulalongkorn University, Bangkok, 10330, Thailand.
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Hamad MH, Islam SI, Jitsamai W, Chinkangsadarn T, Naraporn D, Ouisuwan S, Taweethavonsawat P. Patterns of Equine Small Strongyle Species Infection after Ivermectin Intervention in Thailand: Egg Reappearance Period and Nemabiome Metabarcoding Approach. Animals (Basel) 2024; 14:574. [PMID: 38396542 PMCID: PMC10886017 DOI: 10.3390/ani14040574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The indiscriminate use of anthelmintics to control parasitic nematodes in horses has led to the emergence of anthelmintic resistance worldwide. However, there are no data available on using ivermectin for treating strongyle infections within domesticated horses in Thailand. Therefore, this study aimed to use the fecal egg count reduction (FECR) test to determine the strongylid egg reappearance period (ERP). Additionally, the nemabiome metabarcoding approach is incorporated to study patterns of strongyle species infection following ivermectin treatment. The study results indicate that, although ivermectin effectively eliminated adult strongyle parasites within two weeks post-treatment, the ERP was shortened to 6 weeks post-treatment with a mean FECR of 70.4% (95% CI 46.1-84.0). This potentially indicates a recent change in drug performance. In addition, nemabiome metabarcoding revealed that strongyle species have different levels of susceptibility in response to anthelmintic drugs. The reduction in ERP was associated with the early reappearance of specific species, dominated by Cylicostephanus longibursatus and Cylicocyclus nassatus, indicating the lower susceptibility of these species. In contrast, Poteriostomum imparidentatum, Triodontophorus nipponicus, and Triodontophorus serratus were not found post-treatment, indicating the high level of susceptibility of these species. This information is vital for comprehending the factors contributing to the emergence of resistance and for devising strategies to manage and control strongyle infections in horses.
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Affiliation(s)
- Mohamed H. Hamad
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (M.H.H.); (S.I.I.)
- Department of Animal Infectious Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sk Injamamul Islam
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (M.H.H.); (S.I.I.)
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wanarit Jitsamai
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand;
| | - Teerapol Chinkangsadarn
- Department of Surgery, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Darm Naraporn
- Horse Farm and Laboratory Animal Breeding Center, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Hua-Hin 77110, Thailand; (D.N.); (S.O.)
| | - Suraseha Ouisuwan
- Horse Farm and Laboratory Animal Breeding Center, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Hua-Hin 77110, Thailand; (D.N.); (S.O.)
| | - Piyanan Taweethavonsawat
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Biomarkers in Animals Parasitology Research Unit, Chulalongkorn University, Bangkok 10330, Thailand
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8
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Halvarsson P, Grandi G, Hägglund S, Höglund J. Gastrointestinal parasite community structure in horses after the introduction of selective anthelmintic treatment strategies. Vet Parasitol 2024; 326:110111. [PMID: 38218052 DOI: 10.1016/j.vetpar.2023.110111] [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: 10/26/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/15/2024]
Abstract
A relatively new method to study the species richness and diversity of nematode parasites in grazing animals is to perform deep sequencing on composite samples containing a mixture of parasites. In this work, we compared species composition of strongyles in two groups of horses as a function of egg count and age, based on a DNA barcoding approach. Faecal egg counts and larval cultures were obtained from nearly 300 horses, i.e., domestic horses (n = 167) and trotters (n = 130) sampled nationwide. The second internal transcribed spacer region (ITS2) of strongyle nematodes in the larval cultures was first amplified using barcoded universal primers and then sequenced on the PacBio platform. Subsequently, bioinformatic sequence analysis was performed using SCATA to assign operational taxonomic units (OTU). Finally, species occurrence and composition were assessed using R. ITS2 sequences were found in the majority (89%) of larval samples. Sequencing yielded an average of 140 (26 to 503) reads per sample. The OTUs were assigned to 28 different taxa, of which all but three could be identified as species. The average relative abundance of the seven most abundant species (all Cyathostominae) accounted for 87% of the combined data set. The three species with the highest prevalence in both horse groups were Cyathostomum catinatum, Cylicocyclus nassatus and Cylicostephanus calicatus, and they were frequently found in different combinations with other species regardless of horse group. Interestingly, this result is largely consistent with a previous Swedish study based on morphological analysis of adult worms. In addition, two migratory strongylids (Strongylus vulgaris and S. edentatus) occurred in few domestic horses and trotters. Except for C. minutus and C. nassatus, which decreased with age, and C. catinatum and S. vulgaris, which increased, no specific trends were observed with respect to horse age. Taken together, these results are broadly consistent with data obtained before the introduction of selective targeted treatment in Sweden in 2007. All in all, our results suggest that this treatment strategy has not led to a significant change in strongyle nematode community structure in Swedish horses. The study also confirms that nemabiome analysis in combination with diversity index analysis is an objective method to study strongyle communities in horses.
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Affiliation(s)
- Peter Halvarsson
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, Uppsala, Sweden
| | - Giulio Grandi
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, Uppsala, Sweden
| | | | - Johan Höglund
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, Uppsala, Sweden.
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9
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Huggins LG, Atapattu U, Young ND, Traub RJ, Colella V. Development and validation of a long-read metabarcoding platform for the detection of filarial worm pathogens of animals and humans. BMC Microbiol 2024; 24:28. [PMID: 38245715 PMCID: PMC10799534 DOI: 10.1186/s12866-023-03159-3] [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: 10/30/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Filarial worms are important vector-borne pathogens of a large range of animal hosts, including humans, and are responsible for numerous debilitating neglected tropical diseases such as, lymphatic filariasis caused by Wuchereria bancrofti and Brugia spp., as well as loiasis caused by Loa loa. Moreover, some emerging or difficult-to-eliminate filarioid pathogens are zoonotic using animals like canines as reservoir hosts, for example Dirofilaria sp. 'hongkongensis'. Diagnosis of filariasis through commonly available methods, like microscopy, can be challenging as microfilaremia may wane below the limit of detection. In contrast, conventional PCR methods are more sensitive and specific but may show limited ability to detect coinfections as well as emerging and/or novel pathogens. Use of deep-sequencing technologies obviate these challenges, providing sensitive detection of entire parasite communities, whilst also being better suited for the characterisation of rare or novel pathogens. Therefore, we developed a novel long-read metabarcoding assay for deep-sequencing the filarial nematode cytochrome c oxidase subunit I gene on Oxford Nanopore Technologies' (ONT) MinION™ sequencer. We assessed the overall performance of our assay using kappa statistics to compare it to commonly used diagnostic methods for filarial worm detection, such as conventional PCR (cPCR) with Sanger sequencing and the microscopy-based modified Knott's test (MKT). RESULTS We confirmed our metabarcoding assay can characterise filarial parasites from a diverse range of genera, including, Breinlia, Brugia, Cercopithifilaria, Dipetalonema, Dirofilaria, Onchocerca, Setaria, Stephanofilaria and Wuchereria. We demonstrated proof-of-concept for this assay by using blood samples from Sri Lankan dogs, whereby we identified infections with the filarioids Acanthocheilonema reconditum, Brugia sp. Sri Lanka genotype and zoonotic Dirofilaria sp. 'hongkongensis'. When compared to traditionally used diagnostics, such as the MKT and cPCR with Sanger sequencing, we identified an additional filarioid species and over 15% more mono- and coinfections. CONCLUSIONS Our developed metabarcoding assay may show broad applicability for the metabarcoding and diagnosis of the full spectrum of filarioids from a wide range of animal hosts, including mammals and vectors, whilst the utilisation of ONT' small and portable MinION™ means that such methods could be deployed for field use.
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Affiliation(s)
- Lucas G Huggins
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia.
| | - Ushani Atapattu
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Neil D Young
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Rebecca J Traub
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Vito Colella
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
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10
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Owens LA, Friant S, Martorelli Di Genova B, Knoll LJ, Contreras M, Noya-Alarcon O, Dominguez-Bello MG, Goldberg TL. VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages. Nat Commun 2024; 15:402. [PMID: 38195557 PMCID: PMC10776621 DOI: 10.1038/s41467-023-44521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.
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Affiliation(s)
- Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| | - Sagan Friant
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bruno Martorelli Di Genova
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, The University of Vermont, Burlington, VT, USA
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
| | - Oscar Noya-Alarcon
- Centro Amazónico de Investigación y Control de Enfermedades Tropicales-CAICET, Puerto Ayacucho, Amazonas, Venezuela
| | - Maria G Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University-New Brunswick, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
- Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA
- Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Abbas G, Ghafar A, Beasley A, Stevenson MA, Bauquier J, Koehler AV, Wilkes EJA, McConnell E, El-Hage C, Carrigan P, Cudmore L, Hurley J, Gauci CG, Beveridge I, Jacobson C, Nielsen MK, Hughes KJ, Jabbar A. Understanding temporal and spatial distribution of intestinal nematodes of horses using faecal egg counts and DNA metabarcoding. Vet Parasitol 2024; 325:110094. [PMID: 38091893 DOI: 10.1016/j.vetpar.2023.110094] [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: 11/01/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/25/2023]
Abstract
This study reports the spatial and temporal distribution of ascarid and strongylid nematodes in Thoroughbred horses by age category across different climatic zones in Australia over an 18-month period. Faecal samples (n = 2046) from individual horses were analysed using the modified McMaster technique for faecal egg counts (FECs). Strongylids were identified using PCR-directed next-generation sequencing of the second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA. Yearlings had the highest prevalence (82%) of strongyle eggs followed by weanlings (79%), foals (58%), wet mares (49%) and dry mares (46%). For Parascaris spp., foals had the highest prevalence (35%) followed by weanlings (21%) and yearlings (10%). The highest mean FECs for Parascaris spp. were observed in foals (525 eggs per gram [EPG] of faeces) while those for strongyles were in yearlings (962 EPG). Among horses that were classified as adults at the time of sampling, 77% (860 of 1119) of mares were low (i.e., <250 EPG) strongyle egg-shedders. Mean strongyle FEC counts were highest in the Mediterranean (818 EPG) followed by summer (599 EPG), winter (442 EPG), and non-seasonal (413 EPG) rainfall zones. Twenty-six nematode species were detected, with Cylicostephanus longibursatus (26.5%), Cylicocyclus nassatus (23.7%) and Coronocyclus coronatus (20.5%) being the most frequently detected species. Their richness and relative abundance varied with horse age, season and climatic zone. In addition, Strongylus equinus and Triodontophorus spp. (T. brevicauda and T. serratus) were also detected. This comprehensive study elucidates spatial (climatic zone) and temporal (i.e., seasonal) trends in prevalence and burdens of intestinal nematodes in Australian horses using non-invasive conventional and molecular methods. The information presented in this study is crucial for developing integrated management strategies to control horse parasites in farmed horses.
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Affiliation(s)
- Ghazanfar Abbas
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Abdul Ghafar
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Anne Beasley
- School of Agriculture and Food Sustainability, University of Queensland, Gatton, Queensland 4343, Australia
| | - Mark A Stevenson
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Jenni Bauquier
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Anson V Koehler
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | | | - Emma McConnell
- Centre for Animal Production and Health, Murdoch University, Murdoch, Western Australia, Australia
| | - Charles El-Hage
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Peter Carrigan
- Scone Equine Hospital, Scone, New South Wales 2337, Australia
| | - Lucy Cudmore
- Scone Equine Hospital, Scone, New South Wales 2337, Australia
| | - John Hurley
- Swettenham Stud, Nagambie, Victoria 3608, Australia
| | - Charles G Gauci
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Ian Beveridge
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia
| | - Caroline Jacobson
- Centre for Animal Production and Health, Murdoch University, Murdoch, Western Australia, Australia
| | - Martin K Nielsen
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Kristopher J Hughes
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Abdul Jabbar
- Melbourne Veterinary School, The University of Melbourne, Werribee, Victoria 3030, Australia.
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12
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Lobanov VA, Konecsni KA, Scandrett WB, Jenkins EJ. Identification of Trichinella taxa by ITS-1 amplicon next-generation sequencing with an improved resolution for detecting underrepresented genotypes in mixed natural infections. Parasit Vectors 2023; 16:466. [PMID: 38129932 PMCID: PMC10734138 DOI: 10.1186/s13071-023-06035-1] [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: 07/06/2023] [Accepted: 10/29/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Amplicon-based next-generation sequencing (NGS) has rapidly gained popularity as a powerful method for delineating taxa in complex communities, including helminths. Here, we applied this approach to identify species and genotypes of zoonotic nematodes of the Trichinella genus. A known limitation of the current multiplex PCR (mPCR) assay recommended by the International Commission on Trichinellosis is that it does not differentiate Trichinella nativa from T. chanchalensis. METHODS The new assay entails deep sequencing of an amplified variable fragment of the ribosomal cistron's (rDNA) internal transcribed spacer 1 using the Illumina platform. The assay was evaluated using first-stage larvae (L1) of select laboratory strains of various Trichinella taxa mixed in known proportions and then validated using archived L1 from 109 wildlife hosts. The species/genotypes of these L1 isolates from wildlife were previously determined using mPCR. RESULTS NGS data analysis for Trichinella laboratory strains selected as representative of North American fauna revealed a sequence representation bias. Trichinella pseudospiralis, a non-encapsulated species, was the most underrepresented when mixed with T. spiralis, T. murrelli, T. nativa and Trichinella T6 in equal quantities. However, five L1 of T. pseudospiralis were readily revealed by NGS in a mix with 2000 L1 of T. nativa (1:400 ratio). From naturally infected wildlife, all Trichinella taxa revealed by mPCR were also identified by NGS in 103 of 107 (96.3%) samples amplified on both assays. NGS identified additional taxa in 11 (10.3%) samples, whereas additional taxa were revealed by mPCR in only four (3.7%) samples. Most isolates comprised single or mixed infections of T. nativa and Trichinella T6. On NGS, T. chanchalensis (T13) was detected in combination with Trichinella T6 in a wolverine (Gulo gulo) and in combination with T. nativa and Trichinella T6 in a marten (Martes americana) from the Northwest Territories, Canada. CONCLUSIONS This new NGS assay demonstrates strong potential as a single assay for identifying all recognised Trichinella taxa as well as improved sensitivity for detecting under-represented and novel genotypes in mixed infections. In addition, we report a new host record for T. chanchalensis in American marten.
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Affiliation(s)
- Vladislav A Lobanov
- Center for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, Saskatoon, SK, Canada.
| | - Kelly A Konecsni
- Center for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, Saskatoon, SK, Canada
| | - W Brad Scandrett
- Center for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, Saskatoon, SK, Canada
| | - Emily J Jenkins
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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13
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Hedberg Alm Y, Halvarsson P, Martin F, Osterman-Lind E, Törngren V, Tydén E. Demonstration of reduced efficacy against cyathostomins without change in species composition after pyrantel embonate treatment in Swedish equine establishments. Int J Parasitol Drugs Drug Resist 2023; 23:78-86. [PMID: 37979235 PMCID: PMC10690405 DOI: 10.1016/j.ijpddr.2023.11.003] [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: 08/26/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023]
Abstract
Consisting of approximately 50 different species, the cyathostomin parasites are ubiquitous in grazing horses. Co-infection with several species is common, and large burdens can cause the fatal disease of larval cyathostominosis. Due to intense anthelmintic drug use, cyathostomin resistance has developed to all available anthelmintic drug groups. Resistance to the anthelmintic drug pyrantel (PYR) has been documented in over 90% of studies published over the past two decades. In Sweden, a study performed in the early 2000s only confirmed resistance in 4.5% of farms. Further, prescription-only administration of equine anthelmintic drugs was enforced in Sweden in 2007. However, it is unknown if this conservative drug use has maintained PYR efficacy in cyathostomins. The aim of the present study was to investigate the effect of PYR on cyathostomin infection in Sweden using fecal egg count reduction tests (FECRTs). Further, the effect of PYR treatment on cyathostomin species composition was studied using metabarcoding. Sixteen farms with at least six horses excreting a minimum of 100 eggs per gram feces were included. Using the current World Association for the Advancement of Veterinary Parasitology (WAAVP) guidelines, PYR resistance was demonstrated in nine of farms, with seven farms showing full susceptibility. Farms with low biosecurity measures had significantly lower efficacy of PYR treatment. The most common cyathostomin species were Cylicocyclus nassatus, Cyathostomum catinatum, Cylicostephanus longibursatus, Cys. calicatus, Cys. goldi, Cys. minutus, Coronocyclus coronatus and Cya. pateratum, accounting for 97% of all sequence reads prior to treatment. Of these, Cyc. nassatus and Cya. catinatum had the highest occurrence, accounting for 68% of all sequence reads prior to PYR treatment. Treatment did not significantly affect the species composition. The results highlight the importance of drug efficacy testing when using PYR to treat cyathostomin infection, even when selective anthelmintic treatment and thus low treatment intensity, is used on the farm.
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Affiliation(s)
- Ylva Hedberg Alm
- Department of Biomedical Science and Veterinary Public Health, Parasitology Unit, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
| | - Peter Halvarsson
- Department of Biomedical Science and Veterinary Public Health, Parasitology Unit, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Frida Martin
- Department of Biomedical Science and Veterinary Public Health, Parasitology Unit, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Eva Osterman-Lind
- Department of Microbiology, Section for Parasitology, National Veterinary Institute (SVA), SE-751 89, Uppsala, Sweden
| | - Vendela Törngren
- Department of Biomedical Science and Veterinary Public Health, Parasitology Unit, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Eva Tydén
- Department of Biomedical Science and Veterinary Public Health, Parasitology Unit, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
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14
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Halvarsson P, Tydén E. The complete ITS2 barcoding region for Strongylus vulgaris and Strongylus edentatus. Vet Res Commun 2023; 47:1767-1771. [PMID: 36598645 PMCID: PMC10485102 DOI: 10.1007/s11259-022-10067-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Gastrointestinal nematode parasites are of major concern for horses, where Strongylus vulgaris is considered the most pathogenic among the Strongylus species. Diagnosis of S. vulgaris infections can be determined with next generation sequencing techniques, which are inherently dependent on reference sequences. The best marker for parasitic nematodes is internal transcribed spacer 2 (ITS2) and we provide the first complete ITS2 sequences from five morphologically identified S. vulgaris and additional sequences from two S. edentatus. These sequences have high similarity to already published partial sequences and amplicon sequence variants (ASV) based on next generation sequencing (NGS). The ITS2 sequences from S. vulgaris matched available partial ITS2 sequences and the full ASVs, whereas the S. edentatus sequence matched another complete sequence. We also compare Sanger sequencing and NGS methods and conclude that the ITS2 variation is better represented with NGS methods. Based on this, we recommend that further sequencing of morphologically identified specimens of various species should be performed with NGS cover the intraspecific variation in the ITS2.
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Affiliation(s)
- Peter Halvarsson
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 750 05, Uppsala, Sweden.
| | - Eva Tydén
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 750 05, Uppsala, Sweden
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15
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Kaplan RM, Denwood MJ, Nielsen MK, Thamsborg SM, Torgerson PR, Gilleard JS, Dobson RJ, Vercruysse J, Levecke B. World Association for the Advancement of Veterinary Parasitology (W.A.A.V.P.) guideline for diagnosing anthelmintic resistance using the faecal egg count reduction test in ruminants, horses and swine. Vet Parasitol 2023; 318:109936. [PMID: 37121092 DOI: 10.1016/j.vetpar.2023.109936] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
The faecal egg count reduction test (FECRT) remains the method of choice for establishing the efficacy of anthelmintic compounds in the field, including the diagnosis of anthelmintic resistance. We present a guideline for improving the standardization and performance of the FECRT that has four sections. In the first section, we address the major issues relevant to experimental design, choice of faecal egg count (FEC) method, statistical analysis, and interpretation of the FECRT results. In the second section, we make a series of general recommendations that are applicable across all animals addressed in this guideline. In the third section, we provide separate guidance details for cattle, small ruminants (sheep and goats), horses and pigs to address the issues that are specific to the different animal types. Finally, we provide overviews of the specific details required to conduct an FECRT for each of the different host species. To address the issues of statistical power vs. practicality, we also provide two separate options for each animal species; (i) a version designed to detect small changes in efficacy that is intended for use in scientific studies, and (ii) a less resource-intensive version intended for routine use by veterinarians and livestock owners to detect larger changes in efficacy. Compared to the previous FECRT recommendations, four important differences are noted. First, it is now generally recommended to perform the FECRT based on pre- and post-treatment FEC of the same animals (paired study design), rather than on post-treatment FEC of both treated and untreated (control) animals (unpaired study design). Second, instead of requiring a minimum mean FEC (expressed in eggs per gram (EPG)) of the group to be tested, the new requirement is for a minimum total number of eggs to be counted under the microscope (cumulative number of eggs counted before the application of a conversion factor). Third, we provide flexibility in the required size of the treatment group by presenting three separate options that depend on the (expected) number of eggs counted. Finally, these guidelines address all major livestock species, and the thresholds for defining reduced efficacy are adapted and aligned to host species, anthelmintic drug and parasite species. In conclusion, these new guidelines provide improved methodology and standardization of the FECRT for all major livestock species.
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Affiliation(s)
- Ray M Kaplan
- Pathobiology Department, School of Veterinary Medicine, St. George's University, W.I., Grenada.
| | - Matthew J Denwood
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Martin K Nielsen
- Maxwell H. Gluck Equine Research Center, University of Kentucky, KY, USA
| | - Stig M Thamsborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Paul R Torgerson
- Section of Epidemiology, Vetsuisse Faculty, University of Zürich, Switzerland
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
| | - Robert J Dobson
- School of Veterinary and Life Sciences, Murdoch University, Australia
| | - Jozef Vercruysse
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | - Bruno Levecke
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
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16
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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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17
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Boisseau M, Dhorne-Pollet S, Bars-Cortina D, Courtot É, Serreau D, Annonay G, Lluch J, Gesbert A, Reigner F, Sallé G, Mach N. Species interactions, stability, and resilience of the gut microbiota - Helminth assemblage in horses. iScience 2023; 26:106044. [PMID: 36818309 PMCID: PMC9929684 DOI: 10.1016/j.isci.2023.106044] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/16/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The nature and strength of interactions entertained among helminths and their host gut microbiota remain largely unexplored. Using 40 naturally infected Welsh ponies, we tracked the gut microbiota-cyathostomin temporal dynamics and stability before and following anthelmintic treatment and the associated host blood transcriptomic response. High shedders harbored 14 species of cyathostomins, dominated by Cylicocyclus nassatus. They exhibited a highly diverse and temporal dynamic gut microbiota, with butyrate-producing Clostridia likely driving the ecosystem steadiness and host tolerance toward cyathostomins infection. However, anthelmintic administration sharply bent the microbial community. It disrupted the ecosystem stability and the time-dependent network of interactions, affecting longer term microbial resilience. These observations highlight how anthelmintic treatments alter the triangular relationship of parasite, host, and gut microbiota and open new perspectives for adding nutritional intervention to current parasite management strategies.
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Affiliation(s)
- Michel Boisseau
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France,IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France
| | - Sophie Dhorne-Pollet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - David Bars-Cortina
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Élise Courtot
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
| | - Delphine Serreau
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
| | - Gwenolah Annonay
- INRAE, US UMR 1426, Genomic platform, 31326 Castanet-Tolosan, France
| | - Jérôme Lluch
- INRAE, US UMR 1426, Genomic platform, 31326 Castanet-Tolosan, France
| | - Amandine Gesbert
- INRAE, UE Physiologie Animale de l’Orfrasière, 37380 Nouzilly, France
| | - Fabrice Reigner
- INRAE, UE Physiologie Animale de l’Orfrasière, 37380 Nouzilly, France
| | - Guillaume Sallé
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France,Corresponding author
| | - Núria Mach
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France,IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France,Corresponding author
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Davey ML, Kamenova S, Fossøy F, Solberg EJ, Davidson R, Mysterud A, Rolandsen CM. Faecal metabarcoding provides improved detection and taxonomic resolution for non-invasive monitoring of gastrointestinal nematode parasites in wild moose populations. Parasit Vectors 2023; 16:19. [PMID: 36653864 PMCID: PMC9847159 DOI: 10.1186/s13071-022-05644-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Although wild ungulate populations are heavily monitored throughout Europe, we understand little of how parasites affect population dynamics, and there is no systematic, long-term monitoring of parasite diversity and parasite loads. Such monitoring is in part hampered by a lack of time- and cost-effective assay methodologies with high sensitivity and good taxonomic resolution. DNA metabarcoding has been successfully used to characterize the parasitic nemabiome with high taxonomic resolution in a variety of wild and domestic hosts. However, in order to implement this technique in large-scale, potentially non-invasive monitoring of gastrointestinal parasitic nematodes (GIN), protocol optimization is required to maximize biodiversity detection, whilst maintaining time- and cost-effectiveness. METHODS Faecal samples were collected from a wild moose population and GIN communities were characterized and quantified using both parasitological techniques (egg and larva counting) and DNA metabarcoding of the ITS2 region of rDNA. Three different isolation methods were compared that differed in the volume of starting material and cell lysis method. RESULTS Similar nematode faunas were recovered from all samples using both parasitological and metabarcoding methods, and the approaches were largely congruent. However, metabarcoding assays showed better taxonomic resolution and slightly higher sensitivity than egg and larvae counts. The metabarcoding was not strictly quantitative, but the proportion of target nematode sequences recovered was correlated with the parasitologically determined parasite load. Species detection rates in the metabarcoding assays were maximized using a DNA isolation method that included mechanical cell disruption and maximized the starting material volume. CONCLUSIONS DNA metabarcoding is a promising technique for the non-invasive, large-scale monitoring of parasitic GINs in wild ungulate populations, owing to its high taxonomic resolution, increased assay sensitivity, and time- and cost-effectiveness. Although metabarcoding is not a strictly quantitative method, it may nonetheless be possible to create a management- and conservation-relevant index for the host parasite load from this data. To optimize the detection rates and time- and cost-effectiveness of metabarcoding assays, we recommend choosing a DNA isolation method that involves mechanical cell disruption and maximizes the starting material volume.
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Affiliation(s)
- Marie L. Davey
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Stefaniya Kamenova
- grid.5510.10000 0004 1936 8921University of Oslo, Oslo, Norway ,grid.19477.3c0000 0004 0607 975XNorwegian University of Life Sciences, Ås, Norway
| | - Frode Fossøy
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Erling J. Solberg
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Rebecca Davidson
- grid.410549.d0000 0000 9542 2193Norwegian Veterinary Institute, Tromsø, Norway
| | - Atle Mysterud
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway ,grid.5510.10000 0004 1936 8921University of Oslo, Oslo, Norway
| | - Christer M. Rolandsen
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
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19
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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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Courtot É, Boisseau M, Dhorne-Pollet S, Serreau D, Gesbert A, Reigner F, Basiaga M, Kuzmina T, Lluch J, Annonay G, Kuchly C, Diekmann I, Krücken J, von Samson-Himmelstjerna G, Mach N, Sallé G. Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing. PeerJ 2023; 11:e15124. [PMID: 37070089 PMCID: PMC10105562 DOI: 10.7717/peerj.15124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/03/2023] [Indexed: 04/19/2023] Open
Abstract
Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.
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Affiliation(s)
- Élise Courtot
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Michel Boisseau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | | | - Delphine Serreau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Amandine Gesbert
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | - Fabrice Reigner
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | | | - Tetiana Kuzmina
- Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Slovak Republic
| | - Jérôme Lluch
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Gwenolah Annonay
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Claire Kuchly
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Irina Diekmann
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Nuria Mach
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Guillaume Sallé
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
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21
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Sargison N, Chambers A, Chaudhry U, Costa Júnior L, Doyle SR, Ehimiyein A, Evans M, Jennings A, Kelly R, Sargison F, Sinclair M, Zahid O. Faecal egg counts and nemabiome metabarcoding highlight the genomic complexity of equine cyathostomin communities and provide insight into their dynamics in a Scottish native pony herd. Int J Parasitol 2022; 52:763-774. [PMID: 36208676 DOI: 10.1016/j.ijpara.2022.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 11/05/2022]
Abstract
Understanding the composition of gastrointestinal nematode communities may help to mitigate or exploit parasite adaptations within their host. We have used nemabiome deep amplicon sequencing of internal transcribed spacer-2 (ITS-2) ribosomal DNA to describe the temporal and host species composition of gastrointestinal nematode communities following sampling of six Scottish ponies across 57 months. In the absence of parasite control, each horse showed seasonal trends of increases and decreases in faecal egg counts, consistent with the epidemiology of equine strongylid parasites, however, the composition of parasites within individuals changed over time. Sixteen presumptive strongylid species were identified in each of the horses, 13 of which were distributed in a complex clade together with small numbers of amplicon sequences which could not be classified beyond the Cyathostominae subfamily level. Egg shedding of seven trichostrongylid species, which had previously been identified in co-grazed Soay sheep, was identified during the early spring. Faecal egg counts and the percentage of amplicon sequences assigned to each gastrointestinal nematode species were combined to describe their relative abundance across both host and time. Significant differences in species diversity between horses and between months were observed, being greatest from March to May and least from October to December. The magnitude of the individual horse effect varied between months and, conversely, the magnitude of the seasonal effect varied between individual horses. The most abundant gastrointestinal nematode in each of the horses was Cylicostephanus longibursatus (46.6% overall), while the abundance of the other strongylid species varied between horses and relative to each other. Patent C. longibursatus infections over the winter months might represent a genetic adaptation towards longer adult worm survival, or a lower rate of developmental arrest in the autumn. This study provides insight into highly complex phylogenetic relationships between closely related cyathostomin species; and describes the dynamics of egg shedding and pasture contamination of co-infecting equine gastrointestinal nematode communities. The results could be applied to determine how climatic and management factors affect the equilibrium between hosts and their parasites, and to inform the development of sustainable gastrointestinal nematode control strategies for different host species.
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Affiliation(s)
- Neil Sargison
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK.
| | - Alex Chambers
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Umer Chaudhry
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Livio Costa Júnior
- Federal University of Maranhão, Pathology Department, São Luís, Maranhão, Brazil
| | - Stephen R Doyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ajoke Ehimiyein
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Mike Evans
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Amy Jennings
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Rob Kelly
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Fiona Sargison
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | | | - Osama Zahid
- University of Edinburgh, Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
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22
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Nielsen MK, Steuer AE, Anderson HP, Gavriliuc S, Carpenter AB, Redman EM, Gilleard JS, Reinemeyer CR, Poissant J. Shortened egg reappearance periods of equine cyathostomins following ivermectin or moxidectin treatment: morphological and molecular investigation of efficacy and species composition. Int J Parasitol 2022; 52:787-798. [PMID: 36244428 DOI: 10.1016/j.ijpara.2022.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/05/2022]
Abstract
Macrocyclic lactones have been the most widely used drugs for equine parasite control during the past four decades. Unlike ivermectin, moxidectin exhibits efficacy against encysted cyathostomin larvae, and is reported to have persistent efficacy with substantially longer egg reappearance periods. However, shortened egg reappearance periods have been reported recently for both macrocyclic lactones, and these findings have raised several questions: (i) are egg reappearance period patterns different after ivermectin or moxidectin treatment? (ii) Are shortened egg reappearance periods associated with certain cyathostomin species or stages? (iii) How does moxidectin's larvicidal efficacy affect egg reappearance period? To address these questions, 36 horses at pasture, aged 2-5 years old, were randomly allocated to three treatment groups: 1, moxidectin; 2, ivermectin; and 3, untreated control. Strongylid fecal egg counts were measured on a weekly basis, and the egg reappearance period was 5 weeks for both compounds. Strongylid worm counts were determined for all horses: 18 were necropsied at 2 weeks post-treatment (PT), and the remaining 18 at 5 weeks PT. Worms were identified to species morphologically and by internal transcribed spacer-2 (ITS-2) rDNA metabarcoding. Moxidectin and ivermectin were 99.9% and 99.7% efficacious against adults at 2 weeks post treatment, whereas the respective efficacies against luminal L4s were 84.3% and 69.7%. At 5 weeks PT, adulticidal efficacy was 88.3% and 57.6% for moxidectin and ivermectin, respectively, while the efficacy against luminal L4s was 0% for both drugs. Moxidectin reduced early L3 counts by 18.1% and 8.0% at 2 or 5 weeks, while the efficacies against late L3s and mucosal L4s were 60.4% and 21.2% at the same intervals, respectively. The luminal L4s surviving ivermectin treatment were predominantly Cylicocyclus (Cyc.) insigne. The ITS-2 rDNA metabarcoding was in good agreement with morphologic species estimates but suggested differential activity between moxidectin and ivermectin for several species, most notably Cyc. insigne and Cylicocyclus nassatus. This study was a comprehensive investigation of current macrocyclic lactone efficacy patterns and provided important insight into potential mechanisms behind shortened egg reappearance periods.
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Affiliation(s)
- Martin K Nielsen
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA.
| | - Ashley E Steuer
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Haley P Anderson
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Stefan Gavriliuc
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Alyssa B Carpenter
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Elizabeth M Redman
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Jocelyn Poissant
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
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Rinaldi L, Krücken J, Martinez-Valladares M, Pepe P, Maurelli MP, de Queiroz C, Castilla Gómez de Agüero V, Wang T, Cringoli G, Charlier J, Gilleard JS, von Samson-Himmelstjerna G. Advances in diagnosis of gastrointestinal nematodes in livestock and companion animals. ADVANCES IN PARASITOLOGY 2022; 118:85-176. [PMID: 36088084 DOI: 10.1016/bs.apar.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Diagnosis of gastrointestinal nematodes in livestock and companion animals has been neglected for years and there has been an historical underinvestment in the development and improvement of diagnostic tools, undermining the undoubted utility of surveillance and control programmes. However, a new impetus by the scientific community and the quickening pace of technological innovations, are promoting a renaissance of interest in developing diagnostic capacity for nematode infections in veterinary parasitology. A cross-cutting priority for diagnostic tools is the development of pen-side tests and associated decision support tools that rapidly inform on the levels of infection and morbidity. This includes development of scalable, parasite detection using artificial intelligence for automated counting of parasitic elements and research towards establishing biomarkers using innovative molecular and proteomic methods. The aim of this review is to assess the state-of-the-art in the diagnosis of helminth infections in livestock and companion animals and presents the current advances of diagnostic methods for intestinal parasites harnessing (i) automated methods for copromicroscopy based on artificial intelligence, (ii) immunodiagnosis, and (iii) molecular- and proteome-based approaches. Regardless of the method used, multiple factors need to be considered before diagnostics test results can be interpreted in terms of control decisions. Guidelines on how to apply diagnostics and how to interpret test results in different animal species are increasingly requested and some were recently made available in veterinary parasitology for the different domestic species.
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Affiliation(s)
- Laura Rinaldi
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy.
| | - J Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
| | - M Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - P Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - M P Maurelli
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - C de Queiroz
- Faculty of Veterinary Medicine, 3331 Hospital Drive, Host-Parasite Interactions (HPI) Program University of Calgary, Calgary, Alberta, Canada; Faculty of Veterinary Medicine, St Georges University, Grenada
| | - V Castilla Gómez de Agüero
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - T Wang
- Kreavet, Kruibeke, Belgium
| | - Giuseppe Cringoli
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | | | - J S Gilleard
- Faculty of Veterinary Medicine, 3331 Hospital Drive, Host-Parasite Interactions (HPI) Program University of Calgary, Calgary, Alberta, Canada
| | - G von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
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24
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Smith MA, Carpenter AB, Nielsen MK. Precision of cyathostomin luminal worm counts: Investigation of storage duration and fixative. Vet Parasitol 2022; 309:109773. [DOI: 10.1016/j.vetpar.2022.109773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/22/2022] [Accepted: 07/30/2022] [Indexed: 10/16/2022]
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25
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Baltrušis P, Halvarsson P, Höglund J. Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis. Parasit Vectors 2022; 15:290. [PMID: 35953825 PMCID: PMC9373329 DOI: 10.1186/s13071-022-05399-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Next-generation sequencing (NGS) has provided an alternative strategy to study the composition of nematode communities with increased resolution and sensitivity. However, the handling and processing of gigabytes worth of amplicon sequence data produced by an NGS platform is still a major hurdle, limiting the use and adoption of faster and more convenient analysis software. Methods In total 32 paired, fecal samples from Swedish sheep flocks were cultured and the larvae subsequently harvested subjected to internal transcribed spacer 2 (ITS2) amplicon sequencing using the PacBio platform. Samples were analyzed with three different bioinformatic pipelines, i.e. the DADA2, Mothur and SCATA pipelines, to determine species composition and richness. Results For the the major species tested in this study (Haemonchus contortus, Teladorsagia circumcinta and Trichostrongylus colubriformis) neither relative abundances nor species diversity differed significantly between the three pipelines, effectively showing that all three analysis pipelines, although different in their approaches, yield nearly identical outcomes. In addition, the samples analyzed here had especially high frequencies of H. contortus (90–95% across the three pipelines) both before and after sample treatment, followed by T. circumcinta (3.5–4%). This shows that H. contortus is the parasite of primary importance in contemporary Swedish sheep farms struggling with anthelmintic resistance. Finally, although on average a significant reduction in egg counts was achieved post-treatment, no significant shifts in major species relative frequencies occurred, indicating highly rigid community structures at sheep farms where anthelmintic resistance has been reported. Conclusions The findings presented here further contribute to the development and application of NGS technology to study nemabiome compositions in sheep, in addition to expanding our understanding about the most recent changes in parasite species abundances from Swedish sheep farms struggling with anthelmintic resistance. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05399-0.
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Affiliation(s)
- Paulius Baltrušis
- Section for Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Peter Halvarsson
- Section for Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Höglund
- Section for Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Effect of sainfoin ( Onobrychis viciifolia) on cyathostomin eggs excretion, larval development, larval community structure, and efficacy of ivermectin treatment in horses. Parasitology 2022; 149:1439-1449. [PMID: 35929352 PMCID: PMC10090777 DOI: 10.1017/s0031182022000853] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Alternative strategies to chemical anthelmintics are needed for the sustainable control of equine strongylids. Bioactive forages like sainfoin (Onobrychis viciifolia) could contribute to reducing drug use, with the first hints of in vitro activity against cyathostomin free-living stages observed in the past. We analysed the effect of a sainfoin-rich diet on cyathostomin population and the efficacy of oral ivermectin treatment. Two groups of 10 naturally infected horses were enrolled in a 78-day experimental trial. Following a 1-week adaptation period, they were either fed with dehydrated sainfoin pellets (70% of their diet dry matter) or with alfalfa pellets (control group) for 21-days. No difference was found between the average fecal egg counts (FECs) of the two groups, but a significantly lower increase in larval development rate was observed for the sainfoin group, at the end of the trial. Quantification of cyathostomin species abundances with an ITS-2-based metabarcoding approach revealed that the sainfoin diet did not affect the nemabiome structure compared to the control diet. Following oral ivermectin treatment of all horses on day 21, the drug concentration was lower in horses fed with sainfoin, and cyathostomin eggs reappeared earlier in that group. Our results demonstrated that short-term consumption of a sainfoin-rich diet does not decrease cyathostomin FEC but seems to slightly reduce larval development. Consumption of dehydrated sainfoin pellets also negatively affected ivermectin pharmacokinetics, underscoring the need to monitor horse feeding regimes when assessing ivermectin efficacy in the field.
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Titcomb GC, Pansu J, Hutchinson MC, Tombak KJ, Hansen CB, Baker CCM, Kartzinel TR, Young HS, Pringle RM. Large-herbivore nemabiomes: patterns of parasite diversity and sharing. Proc Biol Sci 2022; 289:20212702. [PMID: 35538775 PMCID: PMC9091847 DOI: 10.1098/rspb.2021.2702] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Amidst global shifts in the distribution and abundance of wildlife and livestock, we have only a rudimentary understanding of ungulate parasite communities and parasite-sharing patterns. We used qPCR and DNA metabarcoding of fecal samples to characterize gastrointestinal nematode (Strongylida) community composition and sharing among 17 sympatric species of wild and domestic large mammalian herbivore in central Kenya. We tested a suite of hypothesis-driven predictions about the role of host traits and phylogenetic relatedness in describing parasite infections. Host species identity explained 27-53% of individual variation in parasite prevalence, richness, community composition and phylogenetic diversity. Host and parasite phylogenies were congruent, host gut morphology predicted parasite community composition and prevalence, and hosts with low evolutionary distinctiveness were centrally positioned in the parasite-sharing network. We found no evidence that host body size, social-group size or feeding height were correlated with parasite composition. Our results highlight the interwoven evolutionary and ecological histories of large herbivores and their gastrointestinal nematodes and suggest that host identity, phylogeny and gut architecture-a phylogenetically conserved trait related to parasite habitat-are the overriding influences on parasite communities. These findings have implications for wildlife management and conservation as wild herbivores are increasingly replaced by livestock.
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Affiliation(s)
- Georgia C. Titcomb
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA,Mpala Research Centre, Nanyuki, Kenya
| | - Johan Pansu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA,ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Matthew C. Hutchinson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Kaia J. Tombak
- Mpala Research Centre, Nanyuki, Kenya,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA,Department of Anthropology, Hunter College of the City University of New York, New York, NY, USA
| | - Christina B. Hansen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Christopher C. M. Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA,US Army ERDC Cold Regions Research and Engineering Laboratory, Hanover, NH, USA
| | - Tyler R. Kartzinel
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA,Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, USA,Institute at Brown for Environment and Society, Brown University, Providence, RI, USA
| | - Hillary S. Young
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA,Mpala Research Centre, Nanyuki, Kenya
| | - Robert M. Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
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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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Nielsen MK, von Samson-Himmelstjerna G, Kuzmina TA, van Doorn DC, Meana A, Rehbein S, Elliott T, Reinemeyer CR. World association for the advancement of veterinary parasitology (WAAVP): Third edition of guideline for evaluating the efficacy of equine anthelmintics. Vet Parasitol 2022; 303:109676. [DOI: 10.1016/j.vetpar.2022.109676] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 11/15/2022]
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Tombak KJ, Hansen CB, Kinsella JM, Pansu J, Pringle RM, Rubenstein DI. The gastrointestinal nematodes of plains and Grevy's zebras: Phylogenetic relationships and host specificity. Int J Parasitol Parasites Wildl 2021; 16:228-235. [PMID: 34712556 PMCID: PMC8529100 DOI: 10.1016/j.ijppaw.2021.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023]
Abstract
Equids are chronically infected with parasitic strongyle nematodes. There is a rich literature on horse strongyles, but they are difficult to identify morphologically and genetic studies on strongyles infecting other equid species are few, hampering studies of host specificity. We sequenced expelled worms from two sympatric zebra species in central Kenya to expand the strongyle phylogeny and used DNA metabarcoding on faecal samples to genetically characterize zebra nemabiomes for the first time. We generated sequences for several species new to public genetic reference databases, all of which are typical strongyles in wild zebras (i.e., the three species of Cylindropharynx and Cyathostomum montgomeryi), and identified their closest relatives. We also discovered an apparent fungus infecting a quarter of the expelled Crossocephalus viviparus worms, a hyperabundant nematode species in the family Atractidae, hinting at the possibility that zebra host-parasite dynamics may involve a zebra-fungus mutualism. The two zebra species had similar nemabiomes; we found a complete overlap in the list of nematode species they carry and very similar prevalence (i.e., proportion of hosts infected) for the different nematode species. Our study suggests limited host-specificity in zebra strongyles and high potential for transmission between the plains zebra and the endangered Grevy's zebra.
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Affiliation(s)
- Kaia J. Tombak
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Ave, New York, NY, USA, 10065
- Corresponding author. Department of Anthropology, Hunter College of the City University of New York, 695 Park Ave, New York, NY, 10065, USA.
| | - Christina B. Hansen
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
| | | | - Johan Pansu
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Robert M. Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
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Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding. Parasit Vectors 2021; 14:422. [PMID: 34419166 PMCID: PMC8380370 DOI: 10.1186/s13071-021-04935-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Background Gastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations. Conventional monitoring of gastrointestinal parasitic nematodes in wild populations involves morphological identification of eggs, larvae, and adults from faeces or intestinal samples. Adult worms are typically required for species-level identification, meaning intestinal material from dead animals is needed to characterize the nematode community with high taxonomic resolution. DNA metabarcoding of environmental samples is increasingly used for time- and cost-effective, high-throughput biodiversity monitoring of small-bodied organisms, including parasite communities. Here, we evaluate the potential of DNA metabarcoding of faeces and soil samples for non-invasive monitoring of gastrointestinal parasitic nematode communities in a wild ruminant population. Methods Faeces and intestines were collected from a population of wild reindeer, and soil was collected both from areas showing signs of animal congregation, as well as areas with no signs of animal activity. Gastrointestinal parasitic nematode faunas were characterized using traditional morphological methods that involve flotation and sedimentation steps to concentrate nematode biomass, as well as using DNA metabarcoding. DNA metabarcoding was conducted on bulk samples, in addition to samples having undergone sedimentation and flotation treatments. Results DNA metabarcoding and morphological approaches were largely congruent, recovering similar nematode faunas from all samples. However, metabarcoding provided higher-resolution taxonomic data than morphological identification in both faeces and soil samples. Although concentration of nematode biomass by sedimentation or flotation prior to DNA metabarcoding reduced non-target amplification and increased the diversity of sequence variants recovered from each sample, the pretreatments did not improve species detection rates in soil and faeces samples. Conclusions DNA metabarcoding of bulk faeces samples is a non-invasive, time- and cost-effective method for assessing parasitic nematode populations that provides data with comparable taxonomic resolution to morphological methods that depend on parasitological investigations of dead animals. The successful detection of parasitic gastrointestinal nematodes from soils demonstrates the utility of this approach for mapping distribution and occurrences of the free-living stages of gastrointestinal parasitic nematodes. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04935-8.
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