Metagenomic Analysis of the Stool Microbiome in Patients Receiving Allogeneic Stem Cell Transplantation: Loss of Diversity Is Associated with Use of Systemic Antibiotics and More Pronounced in Gastrointestinal Graft-versus-Host Disease

Abstract

Next-generation sequencing of the hypervariable V3 region of the 16s rRNA gene isolated from serial stool specimens collected from 31 patients receiving allogeneic stem cell transplantation (SCT) was performed to elucidate variations in the composition of the intestinal microbiome in the course of allogeneic SCT. Metagenomic analysis was complemented by strain-specific enterococcal PCR and indirect assessment of bacterial load by liquid chromatography-tandem mass spectrometry of urinary indoxyl sulfate. At the time of admission, patients showed a predominance of commensal bacteria. After transplantation, a relative shift toward enterococci was observed, which was more pronounced under antibiotic prophylaxis and treatment of neutropenic infections. The shift was particularly prominent in patients that developed subsequently or suffered from active gastrointestinal (GI) graft-versus-host disease (GVHD). The mean proportion of enterococci in post-transplant stool specimens was 21% in patients who did not develop GI GVHD as compared with 46% in those that subsequently developed GI GVHD and 74% at the time of active GVHD. Enterococcal PCR confirmed predominance of Enterococcus faecium or both E. faecium and Enterococcus faecalis in these specimens. As a consequence of the loss of bacterial diversity, mean urinary indoxyl sulfate levels dropped from 42.5 ± 11 µmol/L to 11.8 ± 2.8 µmol/L in all post-transplant samples and to 3.5 ± 3 µmol/L in samples from patients with active GVHD. Our study reveals major microbiome shifts in the course of allogeneic SCT that occur in the period of antibiotic treatment but are more prominent in association with GI GVHD. Our data indicate early microbiome shifts and a loss of diversity of the intestinal microbiome that may affect intestinal inflammation in the setting of allogeneic SCT.

Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation

“…15 In the case of ASCT, recent data strongly indicate a correlation between the loss of a balanced gut microbiota with a concomitant shift to potentially pathogenic bacteria, such as enterococci and the risk of developing acute GI GvHD and long-term clinical outcome. 4,5,16 A gut flora, in contrast, dominated by mutualistic bacteria from the Clostridium clusters IV and XIVa seems to exert antiinflammatory effects by promoting among others regulatory T-lymphocyte responses. 17 Our growing understanding of microbial influences in the pathogenesis of inflammatory diseases Ciprofloxacin/Metronidazole Rifaximin Figure 1.…”

“…Among cases with favorable outcome, on the other hand, Clostridiales mostly of the genus Blautia dominated, suggesting an imbalance between protective and pathogenic bacteria as a contributing factor to intestinal inflammation. 5,6 We also found urinary 3-indoxyl sulfate (3-IS), a fermental product of commensal colonic bacteria, to be predictive for outcome after ASCT. High levels of 3-IS were correlated with Clostridiales, whereas members of the class of Bacilli were associated with low 3-IS levels.…”

“…Enterococcus (E.) faecium and E. faecalis load was monitored by species-specific quantitative real-time PCR-analysis in collected stool specimens as previously described. 5 Amplified 16S-rDNA PCR products of E. faecium and E. faecalis cloned into a pGEM-T Easy vector (Invitrogen, Carlsbad, CA, USA) served as calibrators. Enterococcal positivity for both germs was used as an indicator of severe microbiome disruption and was defined by either an increase in enterococcal load or by conversion to positivity until day 28.…”

“…This seemed to be influenced by the use of antibiotics as well as acute GvHD itself. 4,5 Consequently, Taur et al demonstrated an association between loss of bacterial diversity at the time of engraftment and transplant-related mortality (TRM) in the first 3 years post transplant. Low-intestinal microbiome diversity correlated with a significantly worse outcome and the emergence of enterococci.…”

How’s your microbiota? Let’s check your urine.

“…GVHD, a common and often severe inflammatory syndrome that occurs in patients undergoing allogeneic hematopoietic transplant, has recently been found by several groups to be closely associated with disruptions in the normal community structure of intestinal commensal bacteria. [2][3][4][5] More recently, studies have found that microbiota injury frequently precedes severe GVHD, raising the possibility that loss of protective commensal bacteria during the course of the transplant may contribute to the development of GVHD pathophysiology. [5][6][7] Clinical strategies to intervene when microbiota injury occurs are being developed.…”