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Miller ML, Rota C, Welsh A. Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review. Parasit Vectors 2024; 17:311. [PMID: 39030625 DOI: 10.1186/s13071-024-06388-1] [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: 02/24/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol. METHODS We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process. RESULTS We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups. CONCLUSIONS Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
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Affiliation(s)
- Madison L Miller
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.
| | - Christopher Rota
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Amy Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
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Ilík V, Schwarz EM, Nosková E, Pafčo B. Hookworm genomics: dusk or dawn? Trends Parasitol 2024; 40:452-465. [PMID: 38677925 DOI: 10.1016/j.pt.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
Hookworms are parasites, closely related to the model nematode Caenorhabditis elegans, that are a major economic and health burden worldwide. Primarily three hookworm species (Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum) infect humans. Another 100 hookworm species from 19 genera infect primates, ruminants, and carnivores. Genetic data exist for only seven of these species. Genome sequences are available from only four of these species in two genera, leaving 96 others (particularly those parasitizing wildlife) without any genomic data. The most recent hookworm genomes were published 5 years ago, leaving the field in a dusk. However, assembling genomes from single hookworms may bring a new dawn. Here we summarize advances, challenges, and opportunities for studying these neglected but important parasitic nematodes.
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Affiliation(s)
- Vladislav Ilík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eva Nosková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
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Zahid O, Butler M, Hopker A, Freeman E, Costa Júnior LM, Chaudhry U, Sargison N. Nemabiome metabarcoding shows a high prevalence of Haemonchus contortus and predominance of Camelostrongylus mentulatus in alpaca herds in the northern UK. Parasitol Res 2024; 123:201. [PMID: 38698272 PMCID: PMC11065920 DOI: 10.1007/s00436-024-08226-w] [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: 03/02/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Gastrointestinal nematodes (GINs) are a common threat faced by pastoral livestock. Since their major introduction to the UK in the early 1990s, South American camelids have been cograzed with sheep, horses, and other livestock, allowing exposure to a range of GIN species. However, there have been no molecular-based studies to investigate the GIN populations present in these camelids. In the current study, we sampled nine alpaca herds from northern England and southern Scotland and used high-throughput metabarcoded sequencing to describe their GIN species composition. A total of 71 amplicon sequence variants (ASVs) were identified representing eight known GIN species. Haemonchus contortus was the most prevalent species found in almost all herds in significant proportions. The identification of H. contortus in other livestock species is unusual in the northern UK, implying that alpacas may be suitable hosts and potential reservoirs for infection in other hosts. In addition, the camelid-adapted GIN species Camelostrongylus mentulatus was identified predominantly in herds with higher faecal egg counts. These findings highlight the value of applying advanced molecular methods, such as nemabiome metabarcoding to describe the dynamics of gastrointestinal nematode infections in novel situations. The results provide a strong base for further studies involving cograzing animals to confirm the potential role of alpacas in transmitting GIN species between hosts.
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Affiliation(s)
- Osama Zahid
- Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, University of Edinburgh, Midlothian, EH25 9RG, UK.
| | - Meghan Butler
- Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
- Current Address: Galedin Veterinary, Kelso, TD5 7BH, UK
| | - Andy Hopker
- Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Emily Freeman
- Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Livio M Costa Júnior
- Pathology Department, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
- School of Veterinary Medicine, St. George's University, St. George's Grenada, West Indies, Grenada
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, GU2 7AL, UK
| | - Neil Sargison
- Royal (Dick) School of Veterinary Studies and Roslin Institute, Easter Bush Veterinary Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
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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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Francis EK, Šlapeta J. The proof is in the poo-ding: Benefits of the longitudinal molecular surveillance of drug resistance demonstrated in a New South Wales cattle herd. Vet Parasitol 2024; 327:110145. [PMID: 38382382 DOI: 10.1016/j.vetpar.2024.110145] [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: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/23/2024]
Abstract
Our understanding of anthelmintic resistance in the gastrointestinal nematodes of Australian cattle relies exclusively on small-scale phenotypic reports utilising traditional faecal egg count reduction tests. This approach is not readily scalable to establish the national prevalence of resistance, nor is it conducive of routine longitudinal surveillance for the emergence of resistance in its early stages. This study introduces the benefits of applying mixed amplicon metabarcoding longitudinally for timely and cost-efficient molecular surveillance of multiple anthelmintic resistance mutations, as they emerge on farms. Using opportunistically collected faecal samples from a cattle herd in central west New South Wales (2019-2023), we detected the early emergence of Haemonchus spp. levamisole-resistant S168T shortly after levamisole introduction, while benzimidazole-resistant allele frequencies remained constant. Additionally, we observed the possible spill-over of resistant Haemonchus contortus from sheep, along with variations in faecal burdens and species diversity influenced by climate stochasticity and host immunity. This study emphasises the power of molecular diagnostics for farm-level anthelmintic resistance management, providing essential evidence to support its integration into routine surveillance programmes.
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Affiliation(s)
- Emily Kate Francis
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia.
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia; The University of Sydney Institute for Infectious Diseases, The University of Sydney, New South Wales 2006, Australia
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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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Pafčo B, Nosková E, Ilík V, Anettová L, Červená B, Kreisinger J, Pšenková I, Václavek P, Vyhlídalová T, Ježková J, Malát K, Mihalca AD, Modrý D. First insight into strongylid nematode diversity and anthelmintic treatment effectiveness in beef cattle in the Czech Republic explored by HTS metagenomics. Vet Parasitol Reg Stud Reports 2024; 47:100961. [PMID: 38199682 DOI: 10.1016/j.vprsr.2023.100961] [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: 05/04/2023] [Revised: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Parasitic diseases and mitigation of their effects play an important role in the health management of grazing livestock worldwide, with gastrointestinal strongylid nematodes being of prominent importance. These helminths typically occur in complex communities, often composed of species from numerous strongylid genera. Detecting the full diversity of strongylid species in non-invasively collected faecal samples is nearly impossible using conventional methods. In contrast, high-throughput amplicon sequencing (HTS) can effectively identify co-occurring species. During the four-year project, we collected and analysed faecal samples from beef cattle on >120 farms throughout the Czech Republic. Strongylids were the predominant nematodes, detected in 56% of the samples, but at a low level of infection. The apparent limitations in identifying strongylid taxa prompted this pilot study on a representative group of samples testing positive for strongylids using ITS-2 metabarcoding. The most widespread genera parasitizing Czech cattle were Ostertagia (O. ostertagi) and Oesophagostomum spp., followed by Trichostrongylus and Cooperia, while Bunostomum, Nematodirus and Chabertia were present only in a minority. As comparative material, 21 samples of cattle from the Danube Delta in Romania were used, which, in contrast, were dominated by Haemonchus placei. Finally, the effect of ivermectin treatment was tested at two Czech farms. After treatment with the anthelmintic, there was a shift in the strongylid communities, with a dominance of Cooperia and Ostertagia.
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Affiliation(s)
- Barbora Pafčo
- CEITEC VETUNI, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 00 Brno, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00 Brno, Czech Republic.
| | - Eva Nosková
- CEITEC VETUNI, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 00 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Vladislav Ilík
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lucia Anettová
- CEITEC VETUNI, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 00 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Barbora Červená
- CEITEC VETUNI, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 00 Brno, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00 Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Ilona Pšenková
- CEITEC VETUNI, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 00 Brno, Czech Republic
| | - Petr Václavek
- State Veterinary Institute Jihlava, Rantířovská 93/20, 586 01 Jihlava, Czech Republic
| | - Tereza Vyhlídalová
- State Veterinary Institute Jihlava, Rantířovská 93/20, 586 01 Jihlava, Czech Republic
| | - Jana Ježková
- State Veterinary Institute Jihlava, Rantířovská 93/20, 586 01 Jihlava, Czech Republic
| | - Kamil Malát
- Czech Beef Breeders Association, Těšnov 65/17, 110 00 Prague, Czech Republic
| | - Andrei D Mihalca
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Calea Mănăștur 3-5, 400372 Cluj-Napoca, Romania
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
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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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10
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Ilík V, Kreisinger J, Modrý D, Schwarz EM, Tagg N, Mbohli D, Nkombou IC, Petrželková KJ, Pafčo B. High diversity and sharing of strongylid nematodes in humans and great apes co-habiting an unprotected area in Cameroon. PLoS Negl Trop Dis 2023; 17:e0011499. [PMID: 37624869 PMCID: PMC10484444 DOI: 10.1371/journal.pntd.0011499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 09/07/2023] [Accepted: 07/03/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid increases in human populations and environmental changes of past decades have led to changes in rates of contact and spatial overlap with wildlife. Together with other historical, social and environmental processes, this has significantly contributed to pathogen transmission in both directions, especially between humans and non-human primates, whose close phylogenetic relationship facilitates cross-infections. Using high-throughput amplicon sequencing, we studied strongylid communities in sympatric western lowland gorillas, central chimpanzees and humans co-occurring in an unprotected area in the northern periphery of the Dja Faunal Reserve, Cameroon. At the genus level, we classified 65 strongylid ITS-2 amplicon sequencing variants (ASVs) in humans and great apes. Great apes exhibited higher strongylid diversity than humans. Necator and Oesophagostomum were the most prevalent genera, and we commonly observed mixed infections of more than one strongylid species. Human strongylid communities were dominated by the human hookworm N. americanus, while great apes were mainly infected with N. gorillae, O. stephanostomum and trichostrongylids. We were also able to detect rare strongylid taxa (such as Ancylostoma and Ternidens). We detected eight ASVs shared between humans and great apes (four N. americanus variants, two N. gorillae variants, one O. stephanostomum type I and one Trichostrongylus sp. type II variant). Our results show that knowledge of strongylid communities in primates, including humans, is still limited. Sharing the same habitat, especially outside protected areas (where access to the forest is not restricted), can enable mutual parasite exchange and can even override host phylogeny or conserved patterns. Such studies are critical for assessing the threats posed to all hosts by increasing human-wildlife spatial overlap. In this study, the term "contact" refers to physical contact, while "spatial overlap" refers to environmental contact.
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Affiliation(s)
- Vladislav Ilík
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Erich Marquard Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Nikki Tagg
- Centre for Research and Conservation/KMDA, Antwerp, Belgium
| | - Donald Mbohli
- Association de la Protection des Grands Singes, Yaoundé, Cameroon
| | | | - Klára Judita Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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11
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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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12
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Štarhová Serbina L, Gajski D, Pafčo B, Zurek L, Malenovský I, Nováková E, Schuler H, Dittmer J. Microbiome of pear psyllids: A tale about closely related species sharing their endosymbionts. Environ Microbiol 2022; 24:5788-5808. [PMID: 36054322 PMCID: PMC10086859 DOI: 10.1111/1462-2920.16180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/20/2022] [Indexed: 01/12/2023]
Abstract
Psyllids are phloem-feeding insects that can transmit plant pathogens such as phytoplasmas, intracellular bacteria causing numerous plant diseases worldwide. Their microbiomes are essential for insect physiology and may also influence the capacity of vectors to transmit pathogens. Using 16S rRNA gene metabarcoding, we compared the microbiomes of three sympatric psyllid species associated with pear trees in Central Europe. All three species are able to transmit 'Candidatus Phytoplasma pyri', albeit with different efficiencies. Our results revealed potential relationships between insect biology and microbiome composition that varied during psyllid ontogeny and between generations in Cacopsylla pyri and C. pyricola, as well as between localities in C. pyri. In contrast, no variations related to psyllid life cycle and geography were detected in C. pyrisuga. In addition to the primary endosymbiont Carsonella ruddii, we detected another highly abundant endosymbiont (unclassified Enterobacteriaceae). C. pyri and C. pyricola shared the same taxon of Enterobacteriaceae which is related to endosymbionts harboured by other psyllid species from various families. In contrast, C. pyrisuga carried a different Enterobacteriaceae taxon related to the genus Sodalis. Our study provides new insights into host-symbiont interactions in psyllids and highlights the importance of host biology and geography in shaping microbiome structure.
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Affiliation(s)
- Liliya Štarhová Serbina
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Domagoj Gajski
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ludek Zurek
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.,Department of Microbiology, Nutrition and Dietetics/CINeZ, Czech University of Life Sciences, Prague, Czech Republic
| | - Igor Malenovský
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Nováková
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Jessica Dittmer
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Université d'Angers, Institut Agro, INRAE, IRHS, SFR Quasav, Angers, France
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13
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Petrželková K, Samaš P, Romportl D, Uwamahoro C, Červená B, Pafčo B, Prokopová T, Cameira R, Granjon A, Shapiro A, Bahizi M, Nziza J, Noheri J, Syaluha E, Eckardt W, Ndagijimana F, Šlapeta J, Modrý D, Gilardi K, Muvunyi R, Uwingeli P, Mudakikwa A, Mapilanga J, Kalonji A, Hickey J, Cranfield M. Ecological drivers of helminth infection patterns in the Virunga Massif mountain gorilla population. Int J Parasitol Parasites Wildl 2022; 17:174-184. [PMID: 35145846 PMCID: PMC8802862 DOI: 10.1016/j.ijppaw.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 01/16/2023]
Abstract
The Virunga Massif mountain gorilla population has been periodically monitored since the early 1970s, with gradually increasing effort. The population declined drastically in the 1970s, but the numbers stabilized in the 1980s. Since then, the population has been steadily increasing within their limited habitat fragment that is surrounded by a dense human population. We examined fecal samples collected during the Virunga 2015-2016 surveys in monitored and unmonitored gorilla groups and quantified strongylid and tapeworm infections using egg counts per gram to determine environmental and host factors that shape these helminth infections. We showed that higher strongylid infections were present in gorilla groups with smaller size of the 500-m buffered minimum-convex polygon (MCP) of detected nest sites per gorilla group, but in higher gorilla densities and inhabiting vegetation types occurring at higher elevations with higher precipitation and lower temperatures. On the contrary, the impact of monitoring (habituation) was minor, detected in tapeworms and only when in the interaction with environmental variables and MCP area. Our results suggest that the Virunga mountain gorilla population may be partially regulated by strongylid nematodes at higher gorilla densities. New health challenges are probably emerging among mountain gorillas because of the success of conservation efforts, as manifested by significant increases in gorilla numbers in recent decades, but few possibilities for the population expansion due to limited amounts of habitat.
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Affiliation(s)
- K.J. Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
- Liberec Zoo, Liberec, Czech Republic
| | - P. Samaš
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - D. Romportl
- Department of Physical Geography and Geoecology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | - B. Červená
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
| | - B. Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - T. Prokopová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
| | - R. Cameira
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
| | - A.C. Granjon
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - A. Shapiro
- Here + There Mapping Solutions, Berlin, Germany
| | - M. Bahizi
- Gorilla Doctors (MGVP, Inc.), Davis, CA, USA
| | - J. Nziza
- Gorilla Doctors (MGVP, Inc.), Davis, CA, USA
| | - J.B. Noheri
- Gorilla Doctors (MGVP, Inc.), Davis, CA, USA
| | | | - W. Eckardt
- Dian Fossey Gorilla Fund, Musanze, Rwanda
| | | | - J. Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia
| | - D. Modrý
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Veterinary Sciences/CINeZ, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - K. Gilardi
- Gorilla Doctors (MGVP, Inc.), Davis, CA, USA
- School of Veterinary Medicine, University of California, Davis, CA, USA
| | - R. Muvunyi
- Rwanda Development Board, Kigali, Rwanda
| | | | | | - J. Mapilanga
- Institut Congolais pour la Conservation de la Nature, Kinshasa, Congo
| | - A. Kalonji
- Institut Congolais pour la Conservation de la Nature, Parc National de Kahuzi Biega, Bukavu, Congo
| | - J.R. Hickey
- International Gorilla Conservation Programme, Kigali, Rwanda
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14
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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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15
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Schmiedová L, Tomášek O, Pinkasová H, Albrecht T, Kreisinger J. Variation in diet composition and its relation to gut microbiota in a passerine bird. Sci Rep 2022; 12:3787. [PMID: 35260644 PMCID: PMC8904835 DOI: 10.1038/s41598-022-07672-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/17/2022] [Indexed: 12/04/2022] Open
Abstract
Quality and quantity of food items consumed has a crucial effect on phenotypes. In addition to direct effects mediated by nutrient resources, an individual’s diet can also affect the phenotype indirectly by altering its gut microbiota, a potent modulator of physiological, immunity and cognitive functions. However, most of our knowledge of diet-microbiota interactions is based on mammalian species, whereas little is still known about these effects in other vertebrates. We developed a metabarcoding procedure based on cytochrome c oxidase I high-throughput amplicon sequencing and applied it to describe diet composition in breeding colonies of an insectivorous bird, the barn swallow (Hirundo rustica). To identify putative diet-microbiota associations, we integrated the resulting diet profiles with an existing dataset for faecal microbiota in the same individual. Consistent with previous studies based on macroscopic analysis of diet composition, we found that Diptera, Hemiptera, Coleoptera and Hymenoptera were the dominant dietary components in our population. We revealed pronounced variation in diet consumed during the breeding season, along with significant differences between nearby breeding colonies. In addition, we found no difference in diet composition between adults and juveniles. Finally, our data revealed a correlation between diet and faecal microbiota composition, even after statistical control for environmental factors affecting both diet and microbiota variation. Our study suggests that variation in diet induce slight but significant microbiota changes in a non-mammalian host relying on a narrow spectrum of items consumed.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic.
| | - Oldřich Tomášek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Hana Pinkasová
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic. .,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Sciences, Charles University, Vinicna 7 CZ-128 44, Prague 2, Czech Republic
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16
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Francis EK, Šlapeta J. A new diagnostic approach to fast-track and increase the accessibility of gastrointestinal nematode identification from faeces: FECPAK G2 egg nemabiome metabarcoding. Int J Parasitol 2022; 52:331-342. [PMID: 35218762 DOI: 10.1016/j.ijpara.2022.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 01/20/2022] [Indexed: 12/17/2022]
Abstract
Effective gastrointestinal nematode (GIN) management in livestock industries is becoming increasingly difficult due to the rise of anthelmintic resistance and changes in the temporal and geographical distribution of major GINs. Underpinning the response to these challenges is the need for a fast-tracked diagnostic identification technique, making it easier for livestock producers to make informed GIN management decisions. The traditional 'gold-standard' approach, larval culture followed by morphological differentiation, is laborious and potentially inaccurate. We developed a new diagnostic approach to identify GINs that integrates a remote-location digital faecal egg count platform, FECPAKG2, with internal transcribed spacer 2 (ITS2) nemabiome metabarcoding. The technique involves a quick and simple protocol to harvest concentrated strongyle eggs from the FECPAKG2 cassette utilising a repurposed pipette tip, followed by DNA isolation and Illumina next generation amplicon sequencing. The GIN compositions and alpha diversity generated by our FECPAKG2 egg nemabiome metabarcoding approach was not significantly different to traditional morphological larval differentiation and nemabiome metabarcoding of larval and faecal samples. We demonstrated that storing FECPAKG2 harvested eggs in either DNA isolation lysis buffer or 80% ethanol (v/v) had no impact on GIN identification outcomes for at least 60 days; enabling the transport of biological samples from their remote origins to a molecular diagnostic facility for nemabiome metabarcoding, in the absence of a cold chain. We discovered that sustained GIN egg embryonation in the lysis buffer storage solution lead to higher yields of DNA compared with ethanol-stored GIN eggs or faeces with GIN eggs. Taking advantage of an already well-established platform such as FECPAKG2, and providing the livestock producers that use it with the option to identify GINs in their samples and contribute to large-scale GIN distribution and/or anthelmintic resistance surveys, is an important future direction for the FECPAKG2 egg nemabiome metabarcoding approach.
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Affiliation(s)
- Emily Kate Francis
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, New South Wales, 2006, Australia
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, New South Wales, 2006, Australia.
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17
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Shift from morphological to recent advanced molecular approaches for the identification of nematodes. Genomics 2022; 114:110295. [DOI: 10.1016/j.ygeno.2022.110295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
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18
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Abstract
AbstractObserving and quantifying primate behavior in the wild is challenging. Human presence affects primate behavior and habituation of new, especially terrestrial, individuals is a time-intensive process that carries with it ethical and health concerns, especially during the recent pandemic when primates are at even greater risk than usual. As a result, wildlife researchers, including primatologists, have increasingly turned to new technologies to answer questions and provide important data related to primate conservation. Tools and methods should be chosen carefully to maximize and improve the data that will be used to answer the research questions. We review here the role of four indirect methods—camera traps, acoustic monitoring, drones, and portable field labs—and improvements in machine learning that offer rapid, reliable means of combing through large datasets that these methods generate. We describe key applications and limitations of each tool in primate conservation, and where we anticipate primate conservation technology moving forward in the coming years.
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19
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Shutt-Phillips K, Pafčo B, Heistermann M, Kasim A, Petrželková KJ, Profousová-Pšenková I, Modrý D, Todd A, Fuh T, Dicky JF, Bopalanzognako JB, Setchell JM. Fecal glucocorticoids and gastrointestinal parasite infections in wild western lowland gorillas (Gorilla gorilla gorilla) involved in ecotourism. Gen Comp Endocrinol 2021; 312:113859. [PMID: 34298054 DOI: 10.1016/j.ygcen.2021.113859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/13/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
Wildlife ecotourism can offer a source of revenue which benefits local development and conservation simultaneously. However, habituation of wildlife for ecotourism can cause long-term elevation of glucocorticoid hormones, which may suppress immune function and increase an animal's vulnerability to disease. We have previously shown that western lowland gorillas (Gorilla gorilla gorilla) undergoing habituation in Dzanga-Sangha Protected Areas, Central African Republic, have higher fecal glucocorticoid metabolite (FGCM) levels than both habituated and unhabituated gorillas. Here, we tested the relationship between FGCM levels and strongylid infections in the same gorillas. If high FGCM levels suppress the immune system, we predicted that FGCM levels will be positively associated with strongylid egg counts and that gorillas undergoing habituation will have the highest strongylid egg counts, relative to both habituated and unhabituated gorillas. We collected fecal samples over 12 months in two habituated gorilla groups, one group undergoing habituation and completely unhabituated gorillas. We established FGCM levels and fecal egg counts of Necator/Oesophagostomum spp. and Mammomonogamus sp. Controlling for seasonal variation and age-sex category in strongylid infections we found no significant relationship between FGCMs and Nectator/Oesophagostomum spp. or Mammomonogamus sp. egg counts in a within group comparison in either a habituated group or a group undergoing habituation. However, across groups, egg counts of Nectator/Oesophagostomum spp. were lowest in unhabituated animals and highest in the group undergoing habituation, matching the differences in FGCM levels among these gorilla groups. Our findings partially support the hypothesis that elevated glucocorticoids reduce a host's ability to control the extent of parasitic infections, and show the importance of non-invasive monitoring of endocrine function and parasite infection in individuals exposed to human pressure including habituation process and ecotourism.
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Affiliation(s)
- Kathryn Shutt-Phillips
- Department of Anthropology, Durham University, Durham, UK; UN Environment Programme World Conservation Monitoring Center, Cambridge, UK
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Czech Republic.
| | | | - Adetayo Kasim
- Wolfson Research Institute for Health and Wellbeing, Durham University Queen's Campus University Boulevard, Thornaby, UK
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic; Liberec Zoo, Liberec, Czech Republic.
| | | | - David Modrý
- Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences, Prague, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Terence Fuh
- WWF-CAR, BP 1053 Bangui, Central African Republic
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20
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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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Čížková D, Ďureje Ľ, Piálek J, Kreisinger J. Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death. Heredity (Edinb) 2021; 127:141-150. [PMID: 34045683 PMCID: PMC8322053 DOI: 10.1038/s41437-021-00445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.
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Affiliation(s)
- Dagmar Čížková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- grid.4491.80000 0004 1937 116XFaculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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Sirima C, Bizet C, Hamou H, Červená B, Lemarcis T, Esteban A, Peeters M, Mpoudi Ngole E, Mombo IM, Liégeois F, Petrželková KJ, Boussinesq M, Locatelli S. Soil-transmitted helminth infections in free-ranging non-human primates from Cameroon and Gabon. Parasit Vectors 2021; 14:354. [PMID: 34225777 PMCID: PMC8259424 DOI: 10.1186/s13071-021-04855-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zoonotic diseases are a serious threat to both public health and animal conservation. Most non-human primates (NHP) are facing the threat of forest loss and fragmentation and are increasingly living in closer spatial proximity to humans. Humans are infected with soil-transmitted helminths (STH) at a high prevalence, and bidirectional infection with NHP has been observed. The aim of this study was to determine the prevalence, genetic diversity, distribution and presence of co-infections of STH in free-ranging gorillas, chimpanzees and other NHP species, and to determine the potential role of these NHP as reservoir hosts contributing to the environmental sustenance of zoonotic nematode infections in forested areas of Cameroon and Gabon. METHODS A total of 315 faecal samples from six species of NHPs were analysed. We performed PCR amplification, sequencing and maximum likelihood analysis of DNA fragments of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA to detect the presence and determine the genetic diversity of Oesophagostomum spp., Necator spp. and Trichuris spp., and of targeted DNA fragments of the internal transcribed spacer 1 (ITS1) to detect the presence of Ascaris spp. RESULTS Necator spp. infections were most common in gorillas (35 of 65 individuals), but also present in chimpanzees (100 of 222 individuals) and in one of four samples from greater spot-nosed monkeys. These clustered with previously described type II and III Necator spp. Gorillas were also the most infected NHP with Oesophagostomum (51/65 individuals), followed by chimpanzees (157/222 individuals), mandrills (8/12 samples) and mangabeys (7/12 samples), with O. stephanostomum being the most prevalent species. Oesophagostomum bifurcum was detected in chimpanzees and a red-capped mangabey, and a non-classified Oesophagostomum species was detected in a mandrill and a red-capped mangabey. In addition, Ternidens deminutus was detected in samples from one chimpanzee and three greater spot-nosed monkeys. A significant relative overabundance of co-infections with Necator and Oesophagostomum was observed in chimpanzees and gorillas. Trichuris sp. was detected at low prevalence in a gorilla, a chimpanzee and a greater spot-nosed monkey. No Ascaris was observed in any of the samples analysed. CONCLUSIONS Our results on STH prevalence and genetic diversity in NHP from Cameroon and Gabon corroborate those obtained from other wild NHP populations in other African countries. Future research should focus on better identifying, at a molecular level, the species of Necator and Oesophagostomum infecting NHP and determining how human populations may be affected by increased proximity resulting from encroachment into sylvatic STH reservoir habitats.
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Affiliation(s)
- C. Sirima
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
| | - C. Bizet
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
| | - H. Hamou
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
| | - B. Červená
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - T. Lemarcis
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
| | - A. Esteban
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
| | - M. Peeters
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
| | - E. Mpoudi Ngole
- Projet Prévention du Sida Au Cameroun (PRESICA) and Virology Laboratory IMPM/IRD, Yaoundé, Cameroon
| | - I. M. Mombo
- Centre Interdisciplinaire de Recherches Médicales de Franceville, BP 769, Franceville, Gabon
| | - F. Liégeois
- Present Address: Institut de Recherche Pour Le Développement (IRD), Maladies Infectieuses Et Vecteurs : Écologie, Génétique, Évolution et Contrôle (MIVEGEC), IRD 224-CNRS 5290–University of Montpellier, Montpellier, France
| | - K. J. Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - M. Boussinesq
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
| | - S. Locatelli
- Institut de Recherche Pour Le Développement (IRD), UMI 233-TransVIHMI-INSERM U1175–University of Montpellier, Montpellier, France
- Present Address: Institut de Recherche Pour Le Développement (IRD), Maladies Infectieuses Et Vecteurs : Écologie, Génétique, Évolution et Contrôle (MIVEGEC), IRD 224-CNRS 5290–University of Montpellier, Montpellier, France
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Petrželková KJ, Uwamahoro C, Pafčo B, Červená B, Samaš P, Mudakikwa A, Muvunyi R, Uwingeli P, Gilardi K, Nziza J, Noheri JB, Eckardt W, Ndagijimana F, Ssebide B, Okwirokello R, Nizeyimana F, Syaluha EK, Nzayisenga G, Flores Girón L, Bahizi M, Ntwari AE, Lukusa JP, Tumushime JC, Mangura D, Mapilanga J, Kalonji A, Aruho R, Stryková A, Tehlarová Z, Cameira R, Lowenstine L, Šlapeta J, Romportl D, Ferrari N, Cranfield M, Modrý D. Heterogeneity in patterns of helminth infections across populations of mountain gorillas (Gorilla beringei beringei). Sci Rep 2021; 11:10869. [PMID: 34035316 PMCID: PMC8149636 DOI: 10.1038/s41598-021-89283-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/20/2021] [Indexed: 02/04/2023] Open
Abstract
Conservation efforts have led to the recovery of the endangered mountain gorilla populations. Due to their limited potential for spatial expansion, population densities increased, which may alter the epidemiology of infectious diseases. Recently, clinical gastrointestinal illnesses linked to helminth infections have been recorded in both gorilla populations. To understand drivers and patterns of helminth infections we quantified strongylid and tapeworm infections across both Virunga Massif and Bwindi populations using fecal egg counts. We assessed the impact of age, sex, group size, season and spatial differences used as a proxy, which reflects observed variation in the occurrence of gastrointestinal problems, vegetation types, gorilla subpopulation growth and associated social structure on helminth infections. We revealed striking geographic differences in strongylid infections with higher egg counts mostly in areas with high occurrences of gastrointestinal disease. Increased helminth egg counts were also associated with decreasing group size in some areas. Observed spatial differences may reflect mutual effects of variations in subpopulation growth rates, gorilla social structure, and vegetation associated with altitude across mountain gorilla habitat. Helminth infection intensities in Virunga gorillas were lowest in the youngest and the oldest animals. Elucidating parasite infection patterns of endangered species with low genetic diversity is crucial for their conservation management.
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Affiliation(s)
- Klara J. Petrželková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic ,grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, Ceske Budejovice, Czech Republic ,Liberec Zoo, Liberec, Czech Republic
| | | | - Barbora Pafčo
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic
| | - Barbora Červená
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic ,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Peter Samaš
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic
| | - Antoine Mudakikwa
- grid.508147.f0000 0000 9490 3868Rwanda Development Board, Kigali, Rwanda
| | - Richard Muvunyi
- grid.508147.f0000 0000 9490 3868Rwanda Development Board, Kigali, Rwanda
| | - Prosper Uwingeli
- grid.508147.f0000 0000 9490 3868Rwanda Development Board, Kigali, Rwanda
| | | | - Julius Nziza
- grid.508041.8Gorilla Doctors (MGVP, Inc.), Davis, CA USA
| | | | | | | | - Benard Ssebide
- grid.508041.8Gorilla Doctors (MGVP, Inc.), Davis, CA USA
| | | | | | | | | | - Luis Flores Girón
- Centre de Recherche en Sciences Naturelles de Lwiro, Lwiro, Democratic Republic of Congo ,Lwiro Primate Rehabilitation Center, Democratic Republic of Congo and Ivan Carter Wildlife Conservation Alliance, Orlando, FL USA
| | - Méthode Bahizi
- grid.508041.8Gorilla Doctors (MGVP, Inc.), Davis, CA USA
| | | | | | | | - Damien Mangura
- grid.508041.8Gorilla Doctors (MGVP, Inc.), Davis, CA USA
| | - Jeff Mapilanga
- Institut Congolais pour la Conservation de la Nature, Kinshasa, Democratic Republic of Congo
| | - Arthur Kalonji
- Institut Congolais pour la Conservation de la Nature, Parc National de Kahuzi Biega, Bukavu, Democratic Republic of Congo
| | - Robert Aruho
- grid.463699.7Uganda Wildlife Authority, Kampala, Uganda
| | - Anna Stryková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Zuzana Tehlarová
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic
| | - Rita Cameira
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic ,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Linda Lowenstine
- grid.27860.3b0000 0004 1936 9684School of Veterinary Medicine, University of California Davis, Davis, CA USA
| | - Jan Šlapeta
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - Dušan Romportl
- grid.4491.80000 0004 1937 116XDepartment of Physical Geography and Geoecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nicola Ferrari
- grid.4708.b0000 0004 1757 2822Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy ,grid.4708.b0000 0004 1757 2822Research Center Epidemiology and Molecular Surveillance of Infections ‘‘EpiSoMI’’, Università degli Studi di Milano, Milan, Italy
| | | | - David Modrý
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, Ceske Budejovice, Czech Republic ,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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25
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Yalcindag E, Stuart P, Hasegawa H, Streit A, Doležalová J, Morrogh-Bernard H, Cheyne SM, Nurcahyo W, Foitová I. Genetic characterization of nodular worm infections in Asian Apes. Sci Rep 2021; 11:7226. [PMID: 33790353 PMCID: PMC8012698 DOI: 10.1038/s41598-021-86518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
Parasitic nematodes of Oesophagostomum spp., commonly known, as 'nodular worms' are emerging as the most widely distributed and prevalent zoonotic nematodes. Oesophagostomum infections are well documented in African non-human primates; however, the taxonomy, distribution and transmission of Oesophagostomum in Asian non-human primates are not adequately studied. To better understand which Oesophagostomum species infect Asian non-human primates and determine their phylogeny we analysed 55 faecal samples from 50 orangutan and 5 gibbon individuals from Borneo and Sumatra. Both microscopy and molecular results revealed that semi-wild animals had higher Oesophagostomum infection prevalence than free ranging animals. Based on sequence genotyping analysis targeting the Internal transcribed spacer 2 of rDNA, we report for the first time the presence of O. aculeatum in Sumatran apes. Population genetic analysis shows that there is significant genetic differentiation between Bornean and Sumatran O. aculeatum populations. Our results clearly reveal that O. aculeatum in free-ranging animals have a higher genetic variation than those in semi-wild animals, demonstrating that O. aculeatum is circulating naturally in wildlife and zoonotic transmission is possible. Further studies should be conducted to better understand the epidemiology and dynamics of Oesophagostomum transmission between humans, non-human primates and other wild species and livestock in Southeast Asia.
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Affiliation(s)
- Erhan Yalcindag
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Peter Stuart
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- Department of Biological and Pharmaceutical Sciences, Munster Technological University, Tralee, Co. Kerry, Ireland
| | - Hideo Hasegawa
- Department of Biomedicine, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama, Yufu, Oita, 879-5593, Japan
| | - Adrian Streit
- Department Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Jana Doležalová
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Palackého tř. 1, Brno, Czech Republic
| | - Helen Morrogh-Bernard
- Borneo Nature Foundation, Palangkaraya, Central Kalimantan, Indonesia
- Department of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK
| | - Susan M Cheyne
- Department of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK
| | - Wisnu Nurcahyo
- Department of Parasitology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Ivona Foitová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
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Building food networks from molecular data: Bayesian or fixed-number thresholds for including links. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Flaherty BR, Barratt J, Lane M, Talundzic E, Bradbury RS. Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing. MICROBIOME 2021; 9:1. [PMID: 33388088 PMCID: PMC7778815 DOI: 10.1186/s40168-020-00939-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/14/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest obstacle to this has been the genetic diversity of parasitic agents, which include helminths, protozoa, arthropods, and some acanthocephalans. Meanwhile, universal amplification of conserved loci from all parasites without amplifying host DNA has proven challenging. Pan-eukaryotic PCRs preferentially amplify the more abundant host DNA, obscuring parasite-derived reads following TADS. Flaherty et al. (2018) described a pan-parasitic TADS method involving amplification of eukaryotic 18S rDNA regions possessing restriction sites only in vertebrates. Using this method, host DNA in total DNA extracts could be selectively digested prior to PCR using restriction enzymes, thereby increasing the number of parasite-derived reads obtained following NGS. This approach showed promise though was only as sensitive as conventional PCR. RESULTS Here, we expand on this work by designing a second set of pan-eukaryotic primers flanking the priming sites already described, enabling nested PCR amplification of the established 18S rDNA target. This nested approach facilitated introduction of a second restriction digestion between the first and second PCR, reducing the proportional mass of amplifiable host-derived DNA while increasing the number of PCR amplification cycles. We applied this method to blood specimens containing Babesia, Plasmodium, various kinetoplastids, and filarial nematodes and confirmed its limit of detection (LOD) to be approximately 10-fold lower than previously described, falling within the range of most qPCR methods. CONCLUSIONS The assay detects and differentiates the major malaria parasites of humans, along with several other clinically important blood parasites. This represents an important step towards a TADS-based universal parasite diagnostic (UPDx) test with a sufficient LOD for routine applications. Video Abstract.
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Affiliation(s)
- Briana R Flaherty
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
| | - Meredith Lane
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Synergy America Inc., Duluth, GA, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard S Bradbury
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
- School of Health and Life Sciences, Federation University, Ballarat, Australia.
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28
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Poissant J, Gavriliuc S, Bellaw J, Redman EM, Avramenko RW, Robinson D, Workentine ML, Shury TK, Jenkins EJ, McLoughlin PD, Nielsen MK, Gilleard JS. A repeatable and quantitative DNA metabarcoding assay to characterize mixed strongyle infections in horses. Int J Parasitol 2020; 51:183-192. [PMID: 33242465 DOI: 10.1016/j.ijpara.2020.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/29/2020] [Accepted: 09/03/2020] [Indexed: 01/04/2023]
Abstract
Horses are ubiquitously infected by a diversity of gastro-intestinal parasitic helminths. Of particular importance are nematodes of the family Strongylidae, which can significantly impact horse health and performance. However, knowledge about equine strongyles remains limited due to our inability to identify most species non-invasively using traditional morphological techniques. We developed a new internal transcribed spacer 2 (ITS2) DNA metabarcoding 'nemabiome' assay to characterise mixed strongyle infections in horses and assessed its performance by applying it to pools of infective larvae from fecal samples from an experimental herd in Kentucky, USA and two feral horse populations from Sable Island and Alberta, Canada. In addition to reporting the detection of 33 different species with high confidence, we illustrate the assay's repeatability by comparing results generated from aliquots from the same fecal samples and from individual horses sampled repeatedly over multiple days or months. We also validate the quantitative potential of the assay by demonstrating that the proportion of amplicon reads assigned to different species scales linearly with the number of larvae present. This new tool significantly improves equine strongyle diagnostics, presenting opportunities for research on species-specific anthelmintic resistance and the causes and consequences of variation in mixed infections.
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Affiliation(s)
- Jocelyn Poissant
- Department of Ecosystem and Public Health, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6, Canada.
| | - Stefan Gavriliuc
- Department of Ecosystem and Public Health, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6, Canada
| | - Jennifer Bellaw
- 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, Host-Parasite Interactions (HPI) Program, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6, Canada
| | - Russell W Avramenko
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6, Canada
| | - David Robinson
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6, Canada
| | - Matthew L Workentine
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6, Canada
| | - Todd K Shury
- Parks Canada Agency, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Emily J Jenkins
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus drive, Saskatoon, SK S7N 5B4, Canada
| | - Philip D McLoughlin
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Martin K Nielsen
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6, Canada
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29
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Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study. Sci Rep 2020; 10:13246. [PMID: 32764739 PMCID: PMC7413396 DOI: 10.1038/s41598-020-70249-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
Animal-associated microbiota is expected to impose crucial effects on the host's fitness-related performance, including reproduction. Most research to date has focused on interactions between the host with its gut microbiota; however, there remain considerable gaps in knowledge regarding microbial consortia in other organs, including interspecific divergence, temporal stability, variation drivers, and their effects on the host. To fill these gaps, we examined oral and vaginal microbiota composition in four free-living mouse species of the genus Apodemus, each varying in the degree of female promiscuity. To assess temporal stability and microbiota resistance to environmental change, we exposed one of the species, Apodemus uralensis, to standardized captive conditions and analyzed longitudinal changes in its microbiota structure. Our results revealed the existence of a "core" oral microbiota that was not only shared among all four species but also persisted almost unchanged in captivity. On the other hand, vaginal microbiota appears to be more plastic in captive conditions and less species-specific in comparison with oral microbiota. This study is amongst the first to describe oral microbiota dynamics. Furthermore, the vaginal microbiota results are especially surprising in light of the well-known role of stable vaginal microbiota as a defense against pathogens. The results indicate the existence of diverse mechanisms that shape each microbiota. On the other hand, our data provides somewhat ambiguous support for the systematic effect of phylogeny and social system on both oral and vaginal microbiota structures.
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30
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Schneider-Crease I, Beehner JC, Bergman TJ, Gomery MA, Koklic L, Lu A, Snyder-Mackler N. Ecology eclipses phylogeny as a major driver of nematode parasite community structure in a graminivorous primate. Funct Ecol 2020; 34:1898-1906. [PMID: 33071424 DOI: 10.1111/1365-2435.13603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the relative strength of ecology and phylogeny in shaping parasite communities can inform parasite control and wildlife conservation initiatives while contributing to the study of host species evolution.We tested the relative strengths of phylogeny and ecology in driving parasite community structure in a host whose ecology diverges significantly from that of its closest phylogenetic relatives.We characterized the gastrointestinal (GI) parasite community of wild geladas (Theropithecus gelada), primates that are closely related to baboons but specialized to graminovory in the Ethiopian Highlands.Geladas exhibited very constrained GI parasite communities: only two genera (Oesophagostomum and Trichostrongylus) were identified across 303 samples. This is far below the diversity reported for baboons (Papio spp.) and at the low end of the range of domestic grazers (e.g., Bos taurus, Ovis aries) inhabiting the same region and ecological niche.Using deep amplicon sequencing, we identified 15 amplicon sequence variants (ASVs) within the two genera, seven of which matched to Oesophagostomum sp., seven to Trichostrongylus sp., and one to T. vitrinus.Population was an important predictor of ASV richness. Geladas in the most ecologically disturbed area of the national park exhibited ~4x higher ASV richness than geladas at a less disturbed location within the park.In this system, ecology was a stronger predictor of parasite community structure than phylogeny, with geladas sharing more elements of their parasite communities with other grazers in the same area than with closely related sister taxa.
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Affiliation(s)
- India Schneider-Crease
- Department of Psychology, University of Washington, Seattle, Washington, 98195.,Department of Anthropology, Stony Brook University, Stony Brook, New York, 11794.,Simien Mountains Gelada Research Project, Sankaber, Ethiopia.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, 85281
| | - Jacinta C Beehner
- Simien Mountains Gelada Research Project, Sankaber, Ethiopia.,Department of Anthropology, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Psychology, University of Michigan, Ann Arbor, Michigan, 48109
| | - Thore J Bergman
- Simien Mountains Gelada Research Project, Sankaber, Ethiopia.,Department of Psychology, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Ecology and Evolution, University of Michigan, Ann Arbor, Michigan, 48109
| | - Megan A Gomery
- Simien Mountains Gelada Research Project, Sankaber, Ethiopia
| | - Lia Koklic
- Department of Psychology, University of Washington, Seattle, Washington, 98195
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, New York, 11794.,Simien Mountains Gelada Research Project, Sankaber, Ethiopia
| | - Noah Snyder-Mackler
- Department of Psychology, University of Washington, Seattle, Washington, 98195.,Simien Mountains Gelada Research Project, Sankaber, Ethiopia.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, 85281.,Center for Studies in Demography and Ecology, University of Washington, Seattle, Washington, 98195.,Washington National Primate Research Center, University of Washington, Seattle, Washington, 98195
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31
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Knot IE, Zouganelis GD, Weedall GD, Wich SA, Rae R. DNA Barcoding of Nematodes Using the MinION. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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32
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Schenk J, Geisen S, Kleinboelting N, Traunspurger W. Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.46704] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microscopic organisms are the dominant and most diverse organisms on Earth. Nematodes, as part of this microscopic diversity, are by far the most abundant animals and their diversity is equally high. Molecular metabarcoding is often applied to study the diversity of microorganisms, but has yet to become the standard to determine nematode communities. As such, the information metabarcoding provides, such as in terms of species coverage, taxonomic resolution and especially if sequence reads can be linked to the abundance or biomass of nematodes in a sample, has yet to be determined. Here, we applied metabarcoding using three primer sets located within ribosomal rRNA gene regions to target assembled mock-communities consisting of 18 different nematode species that we established in 9 different compositions. We determined abundances and biomass of all species added to examine if relative sequence abundance or biomass can be linked to relative sequence reads. We found that nematode communities are not equally represented by the three different primer sets and we found that relative read abundances almost perfectly correlated positively with relative species biomass for two of the primer sets. This strong biomass-read number correlation suggests that metabarcoding reads can reveal biomass information even amongst more complex nematode communities as present in the environment and possibly can be transferred to better study other groups of organisms. This biomass-read link is of particular importance for more reliably assessing nutrient flow through food-webs, as well as adjusting biogeochemical models through user-friendly and easily obtainable metabarcoding data.
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33
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Pafčo B, Kreisinger J, Čížková D, Pšenková-Profousová I, Shutt-Phillips K, Todd A, Fuh T, Petrželková KJ, Modrý D. Genetic diversity of primate strongylid nematodes: Do sympatric nonhuman primates and humans share their strongylid worms? Mol Ecol 2019; 28:4786-4797. [PMID: 31573713 DOI: 10.1111/mec.15257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022]
Abstract
The close phylogenetic relationship between humans and nonhuman primates (NHPs) can result in a high potential for pathogen exchange. In recent decades, NHP and human interactions have become more frequent due to increasing habitat encroachment and ecotourism. Strongylid communities, which include members of several genera, are typically found in NHPs. Using optimized high-throughput sequencing for strain-level identification of primate strongylids, we studied the structure of strongylid communities in NHPs and humans co-habiting a tropical forest ecosystem in the Central African Republic. General taxonomic assignment of 85 ITS-2 haplotypes indicated that the studied primates harbour at least nine genera of strongylid nematodes, with Oesophagostomum and Necator being the most prevalent. We detected both host-specific and shared strongylid haplotypes. Skin-penetrating Necator gorillaehaplotypes were shared between humans and gorillas but Necator americanus were much more restricted to humans. Strongylid communities of local hunter-gatherers employed as trackers were more similar to those of gorillas compared to their relatives, who spent more time in villages. This was due to lower abundance of human-origin N. americanus in both gorillas and trackers. Habituated gorillas or those under habituation did not show larger overlap of strongylids with humans compared to unhabituated. We concluded that the occurrence of the human-specific strongylids in gorillas does not increase with direct contact between gorillas and humans due to the habituation. Overall, our results indicate that the degree of habitat sharing between hosts, together with mode of parasite transmission, are important factors for parasite spillover among primates.
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Affiliation(s)
- Barbora Pafčo
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Dagmar Čížková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ilona Pšenková-Profousová
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic
| | | | | | | | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Central European Institute for Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
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34
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Sympatric western lowland gorillas, central chimpanzees and humans are infected with different trichomonads. Parasitology 2019; 147:225-230. [PMID: 31559930 DOI: 10.1017/s0031182019001343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We investigated intestinal trichomonads in western lowland gorillas, central chimpanzees and humans cohabiting the forest ecosystem of Dzanga-Sangha Protected Area in Central African Republic, using the internal transcribed spacer (ITS) region and SSU rRNA gene sequences. Trichomonads belonging to the genus Tetratrichomonas were detected in 23% of the faecal samples and in all host species. Different hosts were infected with different genotypes of Tetratrichomonas. In chimpanzees, we detected tetratrichomonads from 'novel lineage 2', which was previously reported mostly in captive and wild chimpanzees. In gorillas, we found two different genotypes of Tetratrichomonas. The ITS region sequences of the more frequent genotype were identical to the sequence found in a faecal sample of a wild western lowland gorilla from Cameroon. Sequences of the second genotype from gorillas were almost identical to sequences previously obtained from an anorexic French woman. We provide the first report of the presence of intestinal tetratrichomonads in asymptomatic, apparently healthy humans. Human tetratrichomonads belonged to the lineage 7, which was previously reported in domestic and wild pigs and a domestic horse. Our findings suggest that the ecology and spatial overlap among hominids in the tropical forest ecosystem has not resulted in exchange of intestinal trichomonads among these hosts.
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35
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Bradbury RS. Ternidens deminutus Revisited: A Review of Human Infections with the False Hookworm. Trop Med Infect Dis 2019; 4:tropicalmed4030106. [PMID: 31323820 PMCID: PMC6789545 DOI: 10.3390/tropicalmed4030106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 11/16/2022] Open
Abstract
Ternidens deminutus, the false hookworm of humans and non-human primates, represents a truly neglected intestinal helminth infection. The similarity of the eggs of this nematode to those of hookworm both presents a diagnostic challenge and a potential confounder in prevalence surveys of soil transmitted helminths (STH) in regions where T. deminutus is found. The helminth infects non-human primates throughout Africa and Asia, but reports of human infection are almost exclusively found in eastern and southern Africa. Historically, an infection prevalence up to 87% has been reported from some parts of Zimbabwe. Scarce reports of ternidensiasis have also been made in individuals in Suriname and one from Thailand. Little work has been performed on this parasite since the 1970s and it not known why human infection has not been reported more widely or what the current prevalence in humans from historically endemic areas is. This review serves to revisit this enigmatic parasite and provide detail to a modern audience of parasitologists on its history, clinical presentation, geographic distribution, life cycle, biology, morphology, diagnosis and treatment.
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Affiliation(s)
- Richard S Bradbury
- Slovak Tropical Institute, St. Elizabeth University, 81101 Bratislava, Slovakia.
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36
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Vlčková K, Pafčo B, Petrželková KJ, Modrý D, Todd A, Yeoman CJ, Torralba M, Wilson BA, Stumpf RM, White BA, Nelson KE, Leigh SR, Gomez A. Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas. Front Microbiol 2018; 9:1202. [PMID: 29963018 PMCID: PMC6013710 DOI: 10.3389/fmicb.2018.01202] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Relationships between gastrointestinal parasites (GIPs) and the gastrointestinal microbiome (GIM) are widely discussed topics across mammalian species due to their possible impact on the host's health. GIPs may change the environment determining alterations in GIM composition. We evaluated the associations between GIP infections and fecal microbiome composition in two habituated and two unhabituated groups of wild western lowland gorillas (Gorilla g. gorilla) from Dzanga Sangha Protected Areas, Central African Republic. We examined 43 fecal samples for GIPs and quantified strongylid nematodes. We characterized fecal microbiome composition through 454 pyrosequencing of the V1-V3 region of the bacterial 16S rRNA gene. Entamoeba spp. infections were associated with significant differences in abundances of bacterial taxa that likely play important roles in nutrition and metabolism for the host, besides being characteristic members of the gorilla gut microbiome. We did not observe any relationships between relative abundances of several bacterial taxa and strongylid egg counts. Based on our findings, we suggest that there is a significant relationship between fecal microbiome and Entamoeba infection in wild gorillas. This study contributes to the overall knowledge about factors involved in modulating GIM communities in great apes.
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Affiliation(s)
- Klára Vlčková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Barbora Pafčo
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia.,Liberec Zoo, Liberec, Czechia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia.,Central European Institute for Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Angelique Todd
- WWF, Dzanga Sangha Protected Areas, Bangui, Central African Republic
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, United States
| | | | - Brenda A Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rebecca M Stumpf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Bryan A White
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Karen E Nelson
- J. Craig Venter Institute, Rockville, MD, United States.,J. Craig Venter Institute, La Jolla, CA, United States
| | - Steven R Leigh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Anthropology, University of Colorado at Boulder, Boulder, CO, United States
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St Paul, MN, United States
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