Giardiasis and Intestinal Flagellate Infections

A clinical trial is evaluating a new drug, 'Protozole-X', for giardiasis. In vitro, it inhibits Giardia's pyruvate:ferredoxin oxidoreductase (PFOR) pathway. A patient with metronidazole-resistant giardiasis is enrolled. After treatment, stool antigen tests become negative, but the patient's symptoms of bloating and steatorrhea persist. Duodenal biopsy shows persistent villous atrophy but no trophozoites. What is the MOST likely explanation for this outcome?