Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium

Abstract

Antibiotic-mediated microbiota destruction and the consequent loss of colonization resistance can result in intestinal domination with vancomycin-resistant Enterococcus (VRE), leading to bloodstream infection in hospitalized patients. Clearance of VRE remains a challenging goal that, if achieved, would reduce systemic VRE infections and patient-to-patient transmission. Although obligate anaerobic commensal bacteria have been associated with colonization resistance to VRE, the specific bacterial species involved remain undefined. Herein, we demonstrate that a precisely defined consortium of commensal bacteria containing the Clostridium cluster XIVa species Blautia producta and Clostridium bolteae restores colonization resistance against VRE and clears VRE from the intestines of mice. While C. bolteae did not directly mediate VRE clearance, it enabled intestinal colonization with B. producta, which directly inhibited VRE growth. These findings suggest that therapeutic or prophylactic administration of defined bacterial consortia to individuals with compromised microbiota composition may reduce inter-patient transmission and intra-patient dissemination of highly antibiotic-resistant pathogens.

Keywords: Blautia product; Enterococcus; Enterococcus faecium; antibiotic resistance; colonization resistance; commensal bacteria; intestinal domination; microbiome; microbiota; vancomycin resistance.

Figure 1. Characterization of ampicillin-resistant and ampicillin-sensitive microbiota

(A) Fecal microbiota composition of the ampicillin-resistant microbiota (ARM) harbored by MyD88^−/− mice and the ampicillin-sensitive microbiota (ASM) of C57BL/6 animals. Each bar corresponds to an individual mouse. Operational taxonomic units (OTUs) at > 0.01% relative abundance are shown. (B) Fecal microbiota diversity (ns = non-significant, Student’s t test; n = 4 mice per group). Data are means ± SEM. (C) Distribution of fecal OTUs (≥ 97% similarity, > 0.01% relative abundance). Data shown is the average of 4 mice per group. (D) Relative abundance of the top 60 OTUs (horizontal bars) in the ileum, cecum and feces of ARM-harboring animals. Each column corresponds to an individual mouse. ARM, antibiotic-resistant microbiota; ASM, antibiotic-sensitive microbiota. Data are means ± SEM. See also Figure S1.

Figure 2. ARM transplantation prevents the loss of intestinal homeostasis caused by antibiotic treatment

(A) Experimental scheme for ARM administration. Three doses of PBS or ARM were administered daily by oral gavage to C57BL/6 ampicillin-treated mice beginning on day 2 of ampicillin treatment. Fecal samples were collected before antibiotics (d0) and on days 1 (prior to transplant), 4, 8 and 15 after antibiotic initiation. (B) Density of 16S rRNA gene copies in fecal samples over time (n = 5 mice per group). Box plots show the median, 25^th percentile and 75^th percentile; whiskers represent minimum and maximum values (*P = 0.0137, ***P = 0.0009, ****P > 0.0001, Student’s t test). (C) Difference in cecum size among the different groups. (D) Visualization of the inner mucus layer and goblet cells (Muc2) as well as all bacteria (16S rRNA gene) in colon cross-sections. Hoechst dye was used to visualize nuclei. Original magnification, 63X. Scale bars, 10μm. (E) Protein extracts from ileal tissues were analyzed by Western blotting with RegIIIγ-specific antiserum and anti-β-tubulin as loading control. (D–F) Representative images and samples from 5 mice per group are shown. See also Figure S2.

Figure 3. ARM transplantation restores resistance against VRE during antibiotic treatment

(A) Prevention and (B) clearance of VRE colonization following PBS or ARM administration to ampicillin-treated mice. Three doses of ARM or PBS were administered daily by oral gavage to C57BL/6 ampicillin-treated mice before VRE challenge (A) or starting on the third day of VRE colonization (B). Fecal pellets were collected at the indicated time points for VRE quantification (n = 6–12 mice per group). Blue bar denotes continuous ampicillin treatment in the drinking water. (C) Clearance of VRE colonization following PBS or ASM administration measured in feces. C57BL/6 mice were challenged with VRE on the seventh day of ampicillin treatment, at which point treatment was stopped. The first of 3 doses of PBS or ASM was administered on day 3 post VRE challenge. L.o.D., limit of detection. CFU, colony-forming units.

Figure 4. Ampicillin-sensitive bacterial strains within ARM confer resistance to VRE

(A–B) Fecal suspensions of ARM were diluted 10⁻⁵-fold and grown on plates containing 0, 10, 50, 100 and 500 μg/ml of ampicillin. (A) Bacterial composition of cultured fecal fractions. Each bar corresponds to pooled cultures from 3 plates per group. (B) Ampicillin-treated mice were administered PBS or cultured fecal fractions from each group by oral gavage on three consecutive days starting on day 2 of ampicillin treatment and challenged with VRE the day following the third gavage. VRE density in fecal samples was determined 3 days after infection (n = 4 mice per group). (C) VRE levels 3 days post challenge of ampicillin-treated mice inoculated with 10⁻⁵ and 10⁻⁶ plate cultures as described in (B) (n = 8–14 mice per group). (D) Spearman correlation of OTUs associated with resistance to VRE colonization. OTUs with P values < 0.05 are plotted. L.o.D., limit of detection. See also Figures S3 and S4 and Table S1.

Figure 5. Adoptive transfer of bacterial consortia containing C. bolteae and B. producta prevents VRE colonization

(A–B) Ampicillin-treated mice were orally gavaged with PBS or a mixture of C. bolteae, B. producta, Blautia_unclassified, E. dolichum, A. muciniphila, P. distasonis and B. sartorii (7-mix) for three consecutive days beginning on day 2 of antibiotic treatment. Mice were challenged with VRE the day following the third gavage and fecal samples were collected at the indicated time points. (A) VRE CFUs in stool samples 1, 3 and 6/8 days post inoculation (p.i.) (****P < 0.0001, Mann-Whitney test; n = 10 mice per group). (B) Fecal microbiota composition of treated mice on day 1 p.i. *, 7-mix input. (C) VRE stool burden 3 days p.i. in mice treated with 7-mix consortia lacking individual bacterial strains as described in (A–B). Bu, Blautia_unclassified; Am, A. muciniphila; Ed, E. dolichum; Cb, C. bolteae; Bp, B. producta (n = 3 mice per group). (D) VRE density 3 days p.i. in mice treated with a consortium of four bacterial strains (CBBP) and combinations thereof. Experimental approach described in (A–B) was followed (n = 3–6 mice per group). (E) Relative abundance levels of B. producta and C. bolteae on day 3 p.i. in feces from mice administered the 7-mix, CBBP or bacterial mixtures lacking C. bolteae, B. producta or P. distasonis (Ps) and B. sartorii (Bs) (n = 3–14 mice per group). Δ indicates the absence of corresponding strain (s).

Figure 6. Administration of a four-bacteria consortium clears VRE from densely colonized mice

(A) VRE clearance with CBBP. Experimental scheme, mice were treated with ampicillin (Amp) for 4 days prior to VRE inoculation Antibiotic-treatment was discontinued at the time of challenge and three days later, the first of three daily doses of PBS, CBBP or CB (C. bolteae and B. producta) was administered orally. Fecal samples were collected on day 3 p.i. prior to PBS, CBBP or CB administration (d0) and on days 3, 6, 9 and 12 after the first gavage. VRE burden in stool samples from the indicated time points (n = 5-10 mice per group) is shown. (B) Fecal microbiota composition of mice treated with CBBP. Each bar represents an individual mouse. Data is representative of two experiments. L.o.D., limit of detection. See also Figure S5.

Figure 7. Blautia producta directly inhibits VRE growth

(A) Ampicillin-treated mice were challenged with VRE on the fourth day of ampicillin treatment (day -3, green arrow) and administered CBBP or PBS for three consecutive days starting on the third day of VRE colonization (day 0). Fecal pellets were collected at the indicated time points to determine VRE CFUs (top graph). For quantification of total fecal VRE excretion (bottom graph), all fecal pellets per cage were collected and weighed at 24-hour intervals and normalized to the initial time point (day -2). An excretion ratio of 1 indicates no change in the excretion rate (*P = 0.0159, **P = 0.0079, ns = non-significant by the Mann-Whitney test; n = 5 mice per group). (B) Ex vivo quantification of VRE cultured in fecal suspensions from antibiotic-naïve mice (NT), antibiotic-treated mice, and antibiotic-treated mice colonized with ARM, 7-mix or CBBP (***P = 0.0007, ****P < 0.0001, Mann-Whitney test; n = 5–10 samples per group). (C) VRE growth in cecal content supplemented with cultures of the indicated CBBP strains prior to seeding with VRE (***P < 0.0001, ns = non-significant, Mann-Whitney test with respect to PBS control; n = 12 samples per group). L.o.D., limit of detection; Amp, ampicillin; Cb, C. bolteae; Bp, B. producta; Pd, P. distasonis; Bs, B. sartorii. See also Figures S6 and S7.