Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials

Abstract

Antibiotic resistance leads to poor outcomes in cirrhosis. Fecal microbiota transplant (FMT) is associated with reduction in antibiotic resistance gene (ARG) burden in patients without cirrhosis; however, the impact in cirrhosis is unclear. We aimed to study the effect of capsule and enema FMT on ARG abundance in fecal samples, which were collected during two published FMT trials in patients with cirrhosis on rifaximin, lactulose, and proton pump inhibitors. ARGs were identified using metagenomics and mapped against the Comprehensive Antibiotic Resistance Database. Changes in ARG abundance were studied within/between groups. The capsule FMT trial involved a one-time FMT or placebo capsule administration with stool collection at baseline and week 4 postintervention. Antibiotics+enema FMT included preprocedure antibiotics followed by FMT enema versus standard-of-care (SOC). Stool was collected at baseline, postantibiotics, and day 7/15 postintervention. Both trials included 20 patients each. There was no safety/infection signal linked to FMT. In the capsule trial, beta-lactamase (OXY/LEN) expression decreased post-FMT versus baseline. Compared to placebo, patients who were post-FMT had lower abundance of vancomycin (VanH), beta-lactamase (ACT), and rifamycin ARGs; the latter was associated with cognitive improvement. No changes were seen within patients treated with placebo. In the antibiotics+enema trial for postantibiotics at day 7 versus baseline, there was an increase in vancomycin and beta-lactamase ARGs, which decreased at day 15. However, quinolone resistance increased at day 15 versus baseline. Between SOC and FMT, day 7 had largely lower ARG (CfxA beta-lactamase, VanW, and VanX) that continued at day 15 (cepA beta-lactamase, VanW). No changes were seen within the SOC group. Conclusion: Despite differences in routes of administration and preintervention antibiotics, we found that ARG abundance is largely reduced after FMT compared to pre-FMT baseline and non-FMT groups in decompensated cirrhosis.

FIG. 1

Capsular FMT trial. (A) Schema of the trial design with solid arrows where stool samples were analyzed for ARGs. (B) Volcano plot of log2‐fold change and P values between post‐placebo and post‐FMT ARGs using Metastats. Orange shows higher post‐placebo, purple shows higher post‐FMT, green dots are relatively unchanged. (C) Volcano plot of log2‐fold change and P values between pre‐FMT versus post‐FMT ARGs using Metastats. Purple shows higher pre‐FMT compared to post‐FMT, orange shows the reverse, while green dots are unchanged ARGs. Abbreviations: ARG, antibiotic resistance genes; FMT, fecal microbiota transplant.

FIG. 2

Changes in specific AMR gene family relative abundances during the capsular FMT trial. (A) Beta‐lactamases, (B) other ARGs. All relative gene expression abundances are presented as mean ± SEM and compared using within and between groups. *P < 0.05 using Wilcoxon, analysis of variance, or Kruskal‐Wallis test as appropriate. Pre indicates before placebo or FMT; post indicates 4 weeks postintervention. Abbreviation: tRNA, transfer RNA. Abbreviations: ARG, antibiotic resistance genes; FMT, fecal microbiota transplant.

FIG. 3

Antibiotics+enema FMT trial. (A) Schema of the trial design with solid arrows where stool samples were analyzed for ARGs. (B) Volcano plot of log2‐fold change and P values between day 7 post‐SOC and post‐FMT ARGs using Metastats. Orange shows higher day 7 post‐SOC, purple shows higher day 7 post‐FMT, green dots are relatively unchanged. (C) Volcano plot of log2‐fold change and P values between day 14 post‐SOC versus post‐FMT ARGs using Metastats. Orange shows higher post‐SOC versus post‐FMT. (D) Volcano plot of log2‐fold change and P values between baseline versus post‐day 7 FMT ARGs using Metastats. Purple shows higher baseline compared to day 7 post‐FMT, orange shows the reverse, green dots are unchanged ARGs. (E) Volcano plot of log2‐fold change and P values between post‐FMT day 7 versus day 15 ARGs using Metastats. Purple shows higher day 7 compared to day 15 FMT, orange shows the reverse, green dots are unchanged ARGs. (F) Volcano plot of log2‐fold change and P values between baseline versus post‐day 15 ARGs using Metastats. Purple shows higher baseline compared to day 15 FMT, orange shows the reverse, green dots are unchanged ARGs. Abbreviations: ARG, antibiotic resistance genes; FMT, fecal microbiota transplant.

FIG. 4

Changes in specific AMR gene family relative abundances during the antibiotics+enema FMT trial. (A) Beta‐lactamases, (B) vancomycin‐related ARGs, (C) other ARGs. All relative gene expression abundances are presented as mean ± SEM and compared using within and between groups. *P < 0.05, using Wilcoxon, analysis of variance, or Kruskal‐Wallis as appropriate. Abbreviations: ARG, antibiotic resistance genes; FMT, fecal microbiota transplant; FMTBase, baseline; FMTD7, 7 days after FMT; FMTD15, 15 days after FMT; Inact, inactivation; rRNA, ribosomal RNA; SOCBase, standard of care baseline; SOCD7, 7 days after SOC; SOCD15, 15 days after SOC.

FIG. 5

Comparison of donor AROs with post‐FMT AROs in the capsule trial. (A‐D) Common and distinct features of ARG abundance at baseline and post‐FMT in the capsule FMT trial. Donor number was 124_16_1, and V2 is baseline while V4 is post‐FMT. (A) ARGs that are common at baseline; (B) ARGs that are distinct at baseline between the donor and the recipients; (C) ARGs that are common at post‐FMT; (D) ARGs that are distinct post‐FMT between the donor and the recipients. The arrow shows that none of the ARGs that were distinct at baseline were those that ended being common post‐FMT. Abbreviations: ARG, antibiotic resistance genes; FMT, fecal microbiota transplant.

FIG. 6

Comparison of donor AROs with post‐FMT AROs in the enema trial. (A‐D) Common and distinct features of ARG abundance at baseline and post‐FMT in the antibiotics+enema FMT trial. Donor number was 52_0067. (A) ARGs that are common at baseline; (B) ARGs that are distinct at baseline between the donor and the recipients; (C) ARGs that are common at post‐FMT; (D) ARGs that are distinct post‐FMT between the donor and the recipients. The arrow shows that none of the ARGs that were distinct at baseline were those that ended being common post‐FMT. Abbreviations: ARG, antibiotic resistance genes; FMT, fecal microbiota transplant.