Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients

Abstract

Background & Aims Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive ( pks + ) Escherichia coli . Here, we aim to determine whether the pks abundance and persistence of pks + E coli is influenced by pks status of the donor feces. Methods In a cohort of 49 patients with rCDI treated with FMT and matching donor samples—the largest cohort of its kind, to our knowledge—we retrospectively screened fecal metagenomes for pks + E coli and compared the presence of pks in patients before and after treatment and to their respective donors. Results The pks island was more prevalent ( P = .026) and abundant ( P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks ) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks ). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated ( P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks + E coli in pks + patients was correlated to pks in the donor ( P = .004). Conclusions We conclude that FMT contributes to pks + E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks + E coli is unlikely.