| Summary: | 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. <i>Enterocytozoon bieneusi</i>, <i>Balantioides coli</i>, and <i>Giardia duodenalis</i> were observed in 34/37 (92%), 148/259 (57%), and 86/259 (33%) samples, respectively. <i>Entamoeba polecki</i> ST1, <i>E. polecki</i> ST3, and <i>Entamoeba hartmanni</i> were detected in 104/259 (40%), 161/259 (62%), and 8/259 (3%) samples, respectively. Metabarcoding and real-time PCR detected <i>Cryptosporidium</i> in 90/259 (35%) and 239/259 (92%) of the samples, respectively, with <i>Cryptosporidium suis</i> and <i>Cryptosporidium scrofarum</i> observed in nearly equal proportions. <i>Blastocystis</i> subtypes 1, 3, 5, and 15 were found in 72 (28%), 6 (2%), 176 (68%), and 36 (14%) of 259 samples, respectively. <i>Iodamoeba</i> was identified in 1/259 samples (<1%), while none of 37 tested samples was positive for <i>Dientamoeba fragilis</i>. 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.
|
|---|