ITS-2 rDNA and beta-tubulin isoform 1 gene amplicon metabarcoding "nemabiome" from faeces of Cambodian dogs
We carried out three separate PCR assays on 100 DNA samples isolated from dog faeces and metabarcoded for Illumina Next Generation Sequencing (NGS), with resulting amplicon sequence variants (ASVs) classified to hookworm and other parasite species. We successfully amplified and identified hookworm ITS-2 DNA in 59% of the dog faeces samples belonging to Ancylostoma ceylanicum, Ancylostoma caninum, Ancylostoma braziliense and Necatar americanus. The beta-tubulin sequencing detected two non-target parasites of dogs, Spirometra cf. mansoni and Opisthorchis viverrini. Only benzimidazole susceptible SNPs across A. ceylanicum, A. caninum, and N. americanus beta-tubulin sequences.