Impact of Gut Mycobiota Composition on Outcomes after Allogeneic Hematopoietic Cell Transplantation

Alterations of gut bacterial microbiota composition have been associated with outcome after allogeneic hematopoietic cell transplantation (alloHCT), including overall survival (OS), graft versus host disease (GVHD) and relapse incidence . Furthermore, the role of eukaryotic gut virome in GVHD was recently shown (Legoff et al., Nature Medicine, 2017). In contrast, the impact of gut fungal microbiota (mycobiota) is still unknown in the alloHCT setting. Earlier studies in patients with inflammatory bowel diseases or primary sclerosing cholangitis, suggested that gut mycobiota composition and diversity contribute to disease severity.

With this background, we examined the role of fecal mycobiota in patients undergoing alloHCT with the aim of identifying fungi factors associated with patients' outcome. Fecal specimens were collected at day 0 of alloHCT (before graft infusion). The fecal mycobioat was characterized by ITS2 sequencing using the MiSeq (illumine) technology. Phylogenetic classification was obtained using the UNITE ITS database (version 12_11). Association of fungal microbiota with clinical predictors and outcomes were assessed using multivariate modeling.

In all, we analyzed 52 patients (28 males and 24 females). Median age was 60 (range, 22-74) years. Disease risk index was low-intermediate in 29 patients, high-very high in 20 patients (not assessed in 3 patients with aplastic anemia). Fourty three patients received a myeloablative reduced toxicity conditioning regimen, while 9 patients received a reduced intensity conditioning regimen. Ten patients received their graft from a matched sibling donor, 11 from a haploidentical donor, and 26 from a matched or mismatched unrelated donor. All patients received anti-thymocyte globulin as part of their conditioning regimen, and patients undergoing alloHCT from a haploidentical donor also received post-transplant cyclophosphamide.

Overall we found a low fungal diversity score of the fungal microbiota at day 0 in all patients from this cohort, with little variations. Therefore, it proved difficult to establish any statistically significant correlations between fungal diversity and patients outcome.

However, in multivariate Cox hazard analysis including the most important parameters associated with patients' outcome, we found that an increased proportion (>median) of Candida albicans and Malassezia genera was associated with a lower OS [Hazard ratio (HR)= 7.12, p=0.02 and HR=14.99, p=0.007, respectively]. We did not find any parameter with a significant impact on progression free survival in multivariate analysis. When investigating acute GVHD, a hight amount of Candida glabrata (>median) was the only parameter associated with grade II-IV acute GVHD in multivariate analysis (HR=4.49, p=0.009). The day 180 cumulative incidence of grade II-IV acute GVHD was 24% in patients with low Candida glabrata colonization (below the median) versus 80% (p=0.0005) in patients with high Candida glabrata colonization (above the median).

In conclusion, we found an important disruption of the fecal mycobiota in patients undergoing alloHCT, as evidenced by the low fungal diversity observed at day 0 . Furthermore, increased amount of Candida albicans and Malassezia genera at the time of alloHCT were independent predictors of mortality. Finally fecal mycobiota might also contribute to acute GVHD as evidenced by the higher incidence of grade II-IV acute GVHD in patients colonized with higher amount of Candida glabrata .

These results indicate that, in addition to bacterial and viral microbiota, the mycobiota might be an important factor influencing outcome after alloHCT.