ArticleParasitology research2020
Untargeted metagenomics shows a reliable performance for synchronous detection of parasites.
Article in Parasitology research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- Molecular epidemiology of Dientamoeba fragilis coinfections with Blastocystis sp. and Giardia duodenalis in symptomatic patients from Valencia, Spain.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Gastrointestinal parasites of red and roe deer investigated via metagenomics and histology.Parasites & vectors · 2026Article
- Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.BMC microbiology · 2026Article
- Next-Gen intestinal parasite detection: Leveraging metataxonomics for improved diagnosis of intestinal protists and helminths.PloS one · 2026Article
- Metagenomics enables the first detection ofFrontiers in systems biology · 2025Article
- Subtype Distribution ofMicroorganisms · 2024Article
- Parasite effects on receivers in animal communication: Hidden impacts on behavior, ecology, and evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Field survey and molecular characterization of apicomplexan parasites in small mammals from military camps in Afghanistan.Parasitology research · 2023Article
- Investigation of Parasitic Infection in Crocodile Lizards (Animals : an open access journal from MDPI · 2022Article
- The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept.Nutrients · 2022Review
- Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal.Microbiome · 2022Article
- Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR.Microorganisms · 2021Article
- Meta-Ribosomalomics: RNA Sequencing Is an Unbiased Method for Parasite Detection of Different Sample Types.Frontiers in microbiology · 2021Article
- In action-an early warning system for the detection of unexpected or novel pathogens.Virus evolution · 2021Article
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Authors and funding
5 authors.
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Abstract
Shotgun metagenomics with high-throughput sequencing (HTS) techniques is increasingly used for pathogen identification and characterization. While many studies apply targeted amplicon sequencing, here we used untargeted metagenomics to simultaneously identify protists and helminths in pre-diagnosed faecal and tissue samples. The approach starts from RNA and operates without an amplification step, therefore allowing the detection of all eukaryotes, including pathogens, since it circumvents the bias typically observed in amplicon-based HTS approaches. The generated metagenomics datasets were analysed using the RIEMS tool for initial taxonomic read assignment. Mapping analyses against ribosomal reference sequences were subsequently applied to extract 18S rRNA sequences abundantly present in the sequence datasets. The original diagnosis, which was based on microscopy and/or PCR, could be confirmed in nearly all cases using ribosomal RNA metagenomics. In addition to the pre-diagnosed taxa, we detected other intestinal eukaryotic parasites of uncertain pathogenicity (of the genera Dientamoeba, Entamoeba, Endolimax, Hymenolepis) that are often excluded from routine diagnostic protocols. The study clearly demonstrates the applicability of untargeted RNA metagenomics for the parallel detection of parasites.
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