Prevalence and genetic characterisation of Giardia duodenalis in river water and riverbed sediment using next-generation sequencing

Giardia duodenalis has been reported in different sources such as water, human stools, animal stools, vegetable farms and markets and soil of public places. However, different assemblages of G.duodenalis harboured in riverbed sediments have not yet been investigated. Thus, in this study, we quantified and genetically characterised G.duodenalis harboured in the water column and the riverbed sediment of the Apies River to cross this frontier of the unknown in freshwater sediment. Enumeration of G.duodenalis cysts was performed by epifluorescence microscopy observation and quantitative polymerase chain reaction (qPCR). Genetic characterisation was achieved by next-generation sequencing (NGS) using the {beta}-giardin gene and bioinformatics analysis of the NGS data. Results obtained through epifluorescence microscopy revealed a prevalence rate of 87% (140/160) of G.duodenalis cysts in river water, which was higher than that observed in riverbed sediments (78%, 125/160). However, the qPCR assay showed that gene copies of G.duodenalis, which ranged between3.27 log10 and 7.26 log10 copies/L in re-suspended riverbed sediments, and between 0.49 log10 and 3.95 log10 copies/L in river water Genetic characterisation revealed six and seven assemblages in river water (A, B, C, D, E and F) and riverbed sediment (A, B, C, D, E, F and G), respectively. Both matrices carried similar sub-assemblages belonging to assemblages A (AI, AII and AIII) and B (BI, BII, BIII, BIV and BV), whereas riverbed sediment carried an additional sub-assemblage BX belonging to the assemblage B. The present genetic characterisation results suggest that Apies River water and its bed sediment harbour considerable quantities of G.duodenalis cysts that may cause infections in humans and animals if ingested. Consequently, monitoring of both the water column and respective bed sediments for the presence of G.duodenalis is justified to develop strategies for the protection of public health. This study also calls for urgent identification of point sources that are responsible for the contamination of this freshwater source and its sediment. Author summary