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.

Community dynamics drive punctuated engraftment of the fecal microbiome following transplantation using freeze-dried, encapsulated fecal microbiota

“…More detailed clinical findings regarding the efficacy of capsule FMT are described elsewhere. 15 The frequency of patient sample collection varied for each patient as a result of clinical instruction as the case series evolved. Samples were grouped as: i) pre-FMT, ii) days following FMT, iii) weeks following FMT, iv) months following FMT, and v) longer-term samples (described more thoroughly in methods).…”

“…Administration of capsules, including bacterial concentration, number of capsules, and duration of therapy, varied during the case series as the clinical experience evolved, and is described in detail elsewhere. 15 The total bacterial concentration administered varied from 2.1 £ 10 11 to 2.5 £ 10 12 cells, regardless of the number of capsules administered. DNA sequence analysis was performed on source donor fecal samples as described below, which were maintained at ¡80 C until processed.…”

“…6 The fecal preparation was amended with 5% trehalose, rather than glycerol, freeze-dried, and encapsulated, as described in detail elsewhere. 15 Capsules were maintained at ¡80 C until used. Administration of capsules, including bacterial concentration, number of capsules, and duration of therapy, varied during the case series as the clinical experience evolved, and is described in detail elsewhere.…”

“…Detailed clinical information regarding the patient cohort is described in detail elsewhere, 15 and information related to potential capsule FMT success and microbiota succession is summarized in Supplementary Table S1. Briefly, the cohort consisted of 39 patients who had experienced 2 spontaneous recurrences of C. difficile infection following the initial occurrence, failed to respond to an extended course of antibiotics, and were positive for C. difficile infection by stool testing within 3 months.…”

“…15 Bacterial communities from fecal samples were characterized using Illumina next-generation sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene, and bile acid composition of fecal samples was measured by using liquid chromatography-mass spectrometry (LC-MS). To evaluate the succession of bacterial communities, patient fecal samples were collected before capsule administration and up to 195 d post-FMT.…”