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Article

Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR

1
Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
2
Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic
3
Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Bygning 221, DK-2800 Kongens Lyngby, Denmark
4
Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
*
Author to whom correspondence should be addressed.
Academic Editor: O. Roger Anderson
Microorganisms 2021, 9(6), 1189; https://doi.org/10.3390/microorganisms9061189
Received: 11 May 2021 / Revised: 26 May 2021 / Accepted: 27 May 2021 / Published: 31 May 2021
(This article belongs to the Special Issue Evolution and Genetic Diversity of Gut Protozoan Parasites)
Several parasite species are shared between humans and pigs. We explored the application of next-generation sequencing-based metabarcoding supplemented with real-time PCR to fecal DNAs from 259 samples from 116 pigs in Denmark to detect and differentiate single-celled intestinal parasites of zoonotic relevance. Enterocytozoon bieneusi, Balantioides coli, and Giardia duodenalis were observed in 34/37 (92%), 148/259 (57%), and 86/259 (33%) samples, respectively. Entamoeba polecki ST1, E. polecki ST3, and Entamoeba hartmanni were detected in 104/259 (40%), 161/259 (62%), and 8/259 (3%) samples, respectively. Metabarcoding and real-time PCR detected Cryptosporidium in 90/259 (35%) and 239/259 (92%) of the samples, respectively, with Cryptosporidium suis and Cryptosporidium scrofarum observed in nearly equal proportions. Blastocystis subtypes 1, 3, 5, and 15 were found in 72 (28%), 6 (2%), 176 (68%), and 36 (14%) of 259 samples, respectively. Iodamoeba was identified in 1/259 samples (<1%), while none of 37 tested samples was positive for Dientamoeba fragilis. Our results illustrate how metabarcoding exemplifies a ‘one-fits-many’ approach to detecting intestinal single-celled parasites in feces supplemented with real-time PCR for selected parasites. Using metabarcoding with pathogen-specific assays may help detect emerging and previously underdetected pathogens and further elucidate the role of micro-eukaryotic parasites in human and animal health and disease. View Full-Text
Keywords: metabarcoding; next-generation sequencing; zoonotic infections; parasite; parasitology; host specificity; genetic diversity; DNA; PCR metabarcoding; next-generation sequencing; zoonotic infections; parasite; parasitology; host specificity; genetic diversity; DNA; PCR
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MDPI and ACS Style

Stensvold, C.R.; Jirků-Pomajbíková, K.; Tams, K.W.; Jokelainen, P.; Berg, R.P.K.D.; Marving, E.; Petersen, R.F.; Andersen, L.O.; Angen, Ø.; Nielsen, H.V. Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR. Microorganisms 2021, 9, 1189. https://doi.org/10.3390/microorganisms9061189

AMA Style

Stensvold CR, Jirků-Pomajbíková K, Tams KW, Jokelainen P, Berg RPKD, Marving E, Petersen RF, Andersen LO, Angen Ø, Nielsen HV. Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR. Microorganisms. 2021; 9(6):1189. https://doi.org/10.3390/microorganisms9061189

Chicago/Turabian Style

Stensvold, Christen R.; Jirků-Pomajbíková, Kateřina; Tams, Katrine W.; Jokelainen, Pikka; Berg, Rebecca P.K.D.; Marving, Ellinor; Petersen, Randi F.; Andersen, Lee O.; Angen, Øystein; Nielsen, Henrik V. 2021. "Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR" Microorganisms 9, no. 6: 1189. https://doi.org/10.3390/microorganisms9061189

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