Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential

Abstract

Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity after exposure to amoxicillin-clavulanic acid (Amox-Clav). Ten healthy participants were enrolled. All received 5 days of Amox-Clav. Half were randomized to autoFMT, derived from stool collected pre-antimicrobial exposure, by enema, and half to saline enema. Participants submitted stool samples pre- and post-Amox-Clav and enema and during a 90-day follow-up period. Shotgun metagenomic sequencing revealed taxonomic composition, resistance gene content, and metabolic capacity. Amox-Clav significantly altered gut taxonomic composition in all participants (n = 10, P < 0.01); however, only three participants exhibited major changes at the phylum level following exposure. In the cohort as a whole, beta-lactamase genes were enriched following Amox-Clav (P < 0.05), and predicted metabolic capacity was significantly altered (P < 0.01). Species composition, metabolic capacity, and beta-lactamase abundance returned to pre-antimicrobial exposure state 7 days after either autoFMT or saline enema (P > 0.05, compared to enrollment). Alterations to microbial metabolic capacity occurred following antimicrobial exposure even in participants without substantial taxonomic disruption, potentially creating open niches for pathogen colonization. Our findings suggest that metabolic potential is an important consideration for complete assessment of antimicrobial impact on the microbiome. AutoFMT was well tolerated and may have contributed to phylogenetic recovery. (This study has been registered at ClinicalTrials.gov under identifier NCT02046525.)IMPORTANCE The spread of multidrug resistance among pathogenic organisms threatens the efficacy of antimicrobial treatment options. The human gut serves as a reservoir for many drug-resistant organisms and their resistance genes, and perturbation of the gut microbiome by antimicrobial exposure can open metabolic niches to resistant pathogens. Once established in the gut, antimicrobial-resistant bacteria can persist even after antimicrobial exposure ceases. Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of amoxicillin-clavulanic acid (Amox-Clav) exposure and autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity. Importantly, we found that metabolic capacity was perturbed even in cases where gross phylogeny remained unchanged and that autoFMT was safe and well tolerated.

Keywords: antimicrobial resistance; fecal microbiota transplantation; metagenomics; microbiome; multidrug resistance.

FIG 1

Taxonomic composition over time was determined by (A) metagenomic sequencing and (B) qualitative culturomics. (C) Shannon index of diversity was calculated using species data from metagenomic sequencing. Species composition was significantly different after Amox-Clav by type II Adonis test of Bray-Curtis distance (P < 0.01). The most obvious change post-Amox-Clav was a Proteobacteria bloom in subject 8. Numbers preceded by “S” at the top of columns indicate participant identification number.

FIG 2

Taxonomic composition and predicted absolute abundance over time by quantitative culturomics. (A) Aerobic and (B) anaerobic cultures were quantified. Note that the aerobic cultures were less dilute, allowing greater sensitivity but a lower upper limit of detection. Also note that the relative abundance in Fig. 1B was calculated using growth observed at the greatest dilution for each species while here species may appear in both anaerobic and aerobic cultures.

FIG 3

Beta-lactamase genes were significantly enriched after Amox-Clav (two-tailed t test, P = 0.0017). Participants randomized to autoFMT (red) and saline (gray) both returned to baseline by day 90. Participant numbers are noted at the beginning and end of each line.

FIG 4

Enrichment of resistance genes by mechanism was determined by comparing normalized counts (RPKM) post-Amox-Clav to enrollment. Beta-lactamases (black) were most enriched and formed a majority of the antibiotic inactivation enzymes enriched. Efflux pumps were also enriched, and functional metagenomic selections suggest cooccurrence of beta-lactamases and efflux pumps on a mobile element.

FIG 5

Principal coordinate analysis (PCA) of metabolic pathway data (IMC) from participants without obvious taxonomic disturbances (all participants excluding 5 and 8). IMC was derived from metagenomic sequencing data. Normally distributed confidence ellipses are shown. Post-Amox-Clav samples have significantly different IMCs than enrollment samples by type II Adonis test of Bray-Curtis distance (P < 0.01). This is true with or without participants 5 and 8. IMC returned to baseline state by 90 days with saline or autoFMT at similar rates.