Nucleotide polymorphism in Fasciola species rDNA unit (F. hepatica, F. gigantica, hybrid and co-infection)

To demonstrate presence of F. hepatica and F. gigantica DNA as well as co-infection/Fasciola-hybrid signatures within field faecal samples we used PCR primer pairs that specifically target key ITS1 rDNA and LSU rDNA SNPs within approximately 200 nt long amplicons. Sequencing using Illumina NGS platform was used to quantitatively evaluate the SNPs. The ability of the NGS approach to detect degree of mixtures of DNA we tested it using manually isolated and mixed F. hepatica and F. gigantica eggs. The quantitative Illumina amplicon sequencing of ITS1 rDNA and LSU rDNA enables rapid surveillance of large number of animals for presence of Fasciola species, their co-infection or presence of F. hepatica/F. gigantica-hybrids, and relies only on faecal samples.