Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples

International Journal for Parasitology
Claudia WylezichD Höper

Abstract

Efficient and reliable identification of emerging pathogens is crucial for the design and implementation of timely and proportionate control strategies. This is difficult if the pathogen is so far unknown or only distantly related with known pathogens. Diagnostic metagenomics - an undirected, broad and sensitive method for the efficient identification of pathogens - was frequently used for virus and bacteria detection, but seldom applied to parasite identification. Here, metagenomics datasets prepared from swine faeces using an unbiased sample processing approach with RNA serving as starting material were re-analysed with respect to parasite detection. The taxonomic identification tool RIEMS, used for initial detection, provided basic hints on potential pathogens contained in the datasets. The suspected parasites/intestinal protists (Blastocystis, Entamoeba, Iodamoeba, Neobalantidium, Tetratrichomonas) were verified using subsequently applied reference mapping analyses on the base of rRNA sequences. Nearly full-length gene sequences could be extracted from the RNA-derived datasets. In the case of Blastocystis, subtyping was possible with subtype (ST)15 discovered for the first known time in swine faeces. Using RIEMS, some of th...Continue Reading

Citations

Jun 28, 2020·Parasitology Research·Claudia WylezichDirk Höper
Oct 14, 2020·Research in Veterinary Science·Josephine S Y HublinMonica Santin
Jan 28, 2021·Animal Microbiome·Yuliaxis Ramayo-CaldasMaria Ballester
Dec 3, 2020·International Journal of Environmental Research and Public Health·Noppon PoprukDuangdao Palasuwan
Jun 3, 2021·Microorganisms·Christen Rune StensvoldHenrik Vedel Nielsen
Jul 20, 2021·Frontiers in Microbiology·Frits F J FranssenMark W J van Passel
Aug 28, 2021·Microorganisms·Simona GabrielliSimonetta Mattiucci

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