In this work we studied the IMS purification comparing acid (n = 12) and heat (n = 12) dissociation procedures and investigated the possible losses of target organism in this step. Reagent water samples were directly inoculated with Giardia spp. cysts and Cryptosporidium spp. oocysts (BTF Easy Seed™). Acid dissociation showed higher mean recovery efficiency and precision than heat dissociation for Giardia spp. cysts and Cryptosporidium spp. oocysts, but there were not significant statistic differences for Cryptosporidium spp. oocysts. Mean recovery efficiency for both protozoa were in accordance with the acceptance criteria of Method 1623 by acid and heat dissociation. The bead–cyst/bead–oocysts dissociation procedure is fundamental for better results whereas a significant loss of organisms occurs in this step.

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