NGS-based detection and differentiation of Entamoeba in Algerian wildlife and domestic animals

This study investigated the distribution and genetic diversity of Entamoeba in 217 faecal samples from mammals, birds, rodents, reptiles, amphibians, fish, and invertebrates sampled across Algeria. By next-generation sequencing (NGS)-based metabarcoding of SSU rDNA, an overall positivity rate of 13 % (n = 29/217) was observed, with positive cases limited to five host families: Bovidae, Camelidae, Equidae, Cervidae, and Caviidae, all of which are herbivores. From the 34 established cluster consensus sequences, we identified one species: Entamoeba bovis, two ribosomal lineages (RL1 and RL8), three conditional lineages (CL3, CL4, and CL10), and one already described sequence type, SQT-A, expanding on the known host range of previously identified Entamoeba. Also, nine novel sequences types (SQT-K to SQT-S) were proposed. Massive genetic diversity was observed, with mixed infections detected in all positive samples. Phylogenetic analyses revealed both generalist and host-specific clusters. Significant genetic similarities between the taxa identified in this study and those previously documented in hosts from Greenland were documented. We observed that herbivores are infected by multiple Entamoeba taxa, a pattern also reported in previous studies. This study highlights the power of molecular tools such as NGS and metabarcoding in deciphering complex Entamoeba co-infections, providing valuable insights into host-parasite interactions.