Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing.

Several methodological issues currently hamper the study of entire
trematode communities within populations of their intermediate snail
hosts. Here we develop a new workflow using high-throughput amplicon
sequencing to simultaneously genotype snail hosts and their infecting
trematode parasites. We designed primers to amplify 4 snail and 5
trematode markers in a single multiplex PCR. While also applicable to
other genera, we focused on medically and economically important snail
genera within the Superorder Hygrophila and targeted a broad taxonomic
range of parasites within the Class Trematoda. We tested the workflow
using 417 Biomphalaria glabrata specimens experimentally infected with
Schistosoma rodhaini, two strains of Schistosoma mansoni, and combinations
thereof. We evaluated the reliability of infection diagnostics, the
robustness of the workflow, its specificity related to host and parasite
identification, and the sensitivity to detect co-infections, immature
infections, and changes of parasite biomass during the infection process.
Finally, we investigated its applicability in wild-caught snails of other
genera naturally infected with diverse trematode assemblages. After
stringent quality control the workflow allows the identification of snails
to species level, and of trematodes to taxonomic levels ranging from
family to strain. It is sensitive to detect immature infections and
changes in parasite biomass described in previous experimental studies.
Co-infections were successfully identified, opening the possibility to
examine parasite-parasite interactions such as interspecific competition.
Altogether, these results demonstrate that our workflow provides a
powerful tool to analyze the processes shaping trematode communities
within natural snail populations.