Double-edged sword: impact of fecal microbiome transplants on the gut resistome

Abstract

Purpose of reviewFecal microbiome transplants (FMT) show promise in treating various diseases, such as Clostridioides difficile infections. FMT have also demonstrated the capacity to modulate the collection of antibiotic resistance genes (ARGs), termed the resistome, within the gut. The purpose of this review was to critically evaluate the literature regarding the interaction between FMT and the gut resistome and determine whether FMT could be used specifically to reduce ARG carriage in the gut. Recent findingsSeveral studies have demonstrated a decrease in ARG carriage post-FMT administration in various disease states, including recurrent C. difficile infection and after antibiotic usage. However, other studies have reported an expansion of the resistome following FMT. Most studies contained small patient cohorts regardless of the outcome and showed heterogeneity in responses. SummaryResearch on resistome modulation by FMT is preliminary, and human studies currently lack consensus regarding benefits and risks. From a safety perspective, screening donor samples for ARGs in addition to antibiotic-resistant organisms may be advisable. Additional studies on the mechanisms underlying heterogeneity between studies and individuals are required before FMT is considered an efficient approach for resistome amelioration.

A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection

“…We did not perform shotgun metagenomic sequencing on the donor material from the FMT group, so could not ascertain if the ARGs are being introduced by the FMT. However, reports of the effects of FMT on ARG numbers have been heterogeneous ( 23 ). In previous studies, even after extensive screening of donor stool, FMT administration was the source of an antibiotic-resistant E. coli bacteremia ( 24 ), while Leung and colleagues ( 21 ) have reported that FMT may be a source of clinically relevant ARGs.…”

“…FMT may also be a strategy for decolonizing intestinal AROs where eradication rates have ranged from 37.5% to 87.5% in mostly small observational studies lacking a placebo control ( 18 ). However, there is inconclusive evidence that FMT is associated with decreases in antimicrobial resistance genes (ARGs) ( 23 ). Two studies demonstrated a decrease in overall ARGs ( 20 ) and patient-specific ARGs ( 22 ), while another study has shown that FMT is a potential source of ARGs ( 21 ).…”