Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study

Abstract

Objectives: Fecal microbiota transplantation (FMT) is increasingly being used for treatment of recurrent Clostridium difficile infection (R-CDI) that cannot be cured with antibiotics alone. In addition, FMT is being investigated for a variety of indications where restoration or restructuring of the gut microbial community is hypothesized to be beneficial. We sought to develop a stable, freeze-dried encapsulated preparation of standardized fecal microbiota that can be used for FMT with ease and convenience in clinical practice and research.

Methods: We systematically developed a lyophilization protocol that preserved the viability of bacteria across the taxonomic spectrum found in fecal microbiota and yielded physicochemical properties that enabled consistent encapsulation. We also treated a cohort of R-CDI patients with a range of doses of encapsulated microbiota and analyzed the associated changes in the fecal microbiome of the recipients.

Results: The optimized lyophilized preparation satisfied all our preset goals for physicochemical properties, encapsulation ease, stability at different temperatures, and microbiota viability in vitro and in vivo (germ-free mice). The capsule treatment was administered to 49 patients. Overall, 43/49 (88%) of patients achieved a clinical success, defined as no recurrence of CDI over 2 months. Analysis of the fecal microbiome demonstrated near normalization of the fecal microbial community by 1 month following FMT treatment. The simplest protocol using the lowest dose (2.1-2.5 × 1011 bacteria in 2-3 capsules) without any colon purgative performed equally well in terms of clinical outcomes and microbiota engraftment.

Conclusions: A single administration of encapsulated, freeze-dried fecal microbiota from a healthy donor was highly successful in treating antibiotic-refractory R-CDI syndrome.

Conflict of interest statement

CONFLICT OF INTEREST

Guarantor of the article: Alexander Khoruts, MD.

Specific author contributions: Christopher Staley: analysis and interpretation of data; critical revision of the manuscript for intellectual content; statistical analysis. Matthew J. Hamilton: acquisition of data; analysis and interpretation of data; critical revision of the manuscript for intellectual content. Byron P. Vaughn: acquisition of data; critical revision of the manuscript for intellectual content. Carolyn T. Graiziger: acquisition of data; technical support. Krista M. Newman: acquisition of data. Amanda J. Kabage: administrative and technical support. Michael J. Sadowsky: study concept and design; analysis and interpretation of data; critical revision of the manuscript for intellectual content; obtained funding; study supervision. Alexander Khoruts: study concept and design; acquisition of data; analysis and interpretation of data; drafting the manuscript; obtained funding; study supervision.

Financial support: The study was supported by grants from the NIH 1R21-AI114722-01 (AK, MJS) to analyze the bacterial composition of the fecal samples, CIPAC Limited (AK, MJS) to test various parameters for optimization of microbiota preparation. Additional support for capsule preparation and collection biological specimens was provided by the philanthropic support of Achieving Cures Together, Ms. Emily Haller, and the Hubbard Foundation. None of the sponsors had any roles (other than funding) in the study design, collection, analysis, interpretation of data, or writing of the manuscript.

Potential competing interests: AK and MJS received research grant support from CIPAC Limited. MJH, AJK, and MJS provided consulting services to CIPAC Limited and Crestovo LLC. AK serves on the advisory board for Merck. BPV receives research salary support from Roche and speaking consulting fees from Janssen and Abbvie. The remaining authors declare no conflict of interest.

Figures

Figure 1

Changes in the fecal bacterial composition associated with capsule FMT. (a) Distribution of phyla in fecal samples from successfully treated patients and donors. Samples were collected before fecal microbial transplantation (pre-FMT), within the first 6 days post-FMT (days), between 7 and 21 days post-FMT (weeks), between 30 and 60 days post-FMT (months), or after 2 months post-FMT (>2 months). (b) Phylum-level classification of operational taxonomic units (OTUs) that were associated with donor contribution as estimated by SourceTracker. Error bars reflect s.e.m.