The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia

Abstract

Background: Despite increasing data on the impact of the microbiome on cancer, the dynamics and role of the microbiome in infection during therapy for acute myelogenous leukemia (AML) are unknown. Therefore, the authors sought to determine correlations between microbiome composition and infectious outcomes in patients with AML who were receiving induction chemotherapy (IC).

Methods: Buccal and fecal specimens (478 samples) were collected twice weekly from 34 patients with AML who were undergoing IC. Oral and stool microbiomes were characterized by 16S ribosomal RNA V4 sequencing using an Illumina MiSeq system. Microbial diversity and genera composition were associated with clinical outcomes.

Results: Baseline stool α-diversity was significantly lower in patients who developed infections during IC compared with those who did not (P = .047). Significant decreases in both oral and stool microbial α-diversity were observed over the course of IC, with a linear correlation between α-diversity change at the 2 sites (P = .02). Loss of both oral and stool α-diversity was associated significantly with the receipt of a carbapenem P < 0.001. Domination events by the majority of genera were transient (median duration, 1 sample), whereas the number of domination events by pathogenic genera increased significantly over the course of IC (P = .002). Moreover, patients who lost microbial diversity over the course of IC were significantly more likely to contract a microbiologically documented infection within the 90 days after IC neutrophil recovery (P = .04).

Conclusions: The current data present the largest longitudinal analyses to date of oral and stool microbiomes in patients with AML and suggest that microbiome measurements could assist with the mitigation of infectious complications of AML therapy. Cancer 2016;122:2186-96. © 2016 American Cancer Society.

Keywords: acute myeloid leukemia; gastrointestinal; induction chemotherapy; infectious complications; microbiome.

Fig. 1. Baseline analyses of stool and oral samples

(A) α-diversity as measured by Shannon diversity index of initial stool (green) and oral (red) of patients from our cohort stratified by site. Also shown are similarly processed data from the Human Microbiome Project dataset 1 using stool (blue) and buccal swab (orange) samples. Bars represent mean ± standard deviation. (B) Correlation of baseline oral and stool Shannon Diversity Index scores from our cohort (n=28). Pearson’s r value and P value for the correlation analysis are shown in the figure panel. Genera composition of baseline stool (C) and oral (D) samples stratified by patient with color coding as indicated in the legend and ordering based on community similarity.

Fig. 2. Baseline α-diversity was associated with development of infectious events during IC as well as neutropenia prior to initiation of IC

For all panels, data plotted are individual samples with bars representing mean ± standard deviation and P values referring to two sample t-test with Welch’s correction. (A) Baseline α-diversity of stool samples as measured by Shannon Diversity Index stratified by development of an infectious event during IC. (B) Data are as for (A) except that FUO patients were moved to the MDI + CDI group. MDI = microbiologically defined infection; CDI = clinically defined infection; FUO = fever of unknown origin; and NIF = non-infectious fever. (C) Baseline α-diversity of oral samples as measured by Shannon Diversity Index stratified by presence of neutropenia prior to initiation of induction chemotherapy. (D) Same as (C) except for baseline α-diversity of stool samples.

Fig. 3. Change in oral and stool microbiome α-diversity over the course of IC

(A) Linear Mixed- effects model of Shannon Diversity Index measurements for samples by day of chemotherapy administration stratified for each patient (gray lines). Dark black line represents the overall regression line. When applying a linear mixed-effects model with patient-level random effects on both slope and intercept, the bootstrapped slope values are −0.012 and −0.018 with 95% confidence intervals of (−0.023, −0.001) and (−0.036, −0.002) for saliva and stool respectively. P-values are computed by using the Satterthwaite’s approximation for the degrees of freedom. (B) Change in Shannon Diversity Index measurements of final and initial samples stratified by source. Individual values are plotted whereas bars show mean ± standard deviation. P value refers to Student’s t-test comparing stool and oral samples. (C) Correlation of changes in Shannon diversity index between oral and stool samples. Pearson’s r value and derived P value are shown in figure. (D) Changes in relative concentration of indicated genera between final and initial stool sample. (E) Changes in relative concentration of indicated genera between final and initial oral sample. For (D, E) data plotted are mean ± standard error of the mean (SEM). The Wilcoxon rank test was used to test for differences among non-normally distributed data and the Benjamini-Hochberg false discovery rate was applied to account for multiple comparisons.

Fig. 4. Domination of GI microbiome over the course of IC

(A) Domination events stratified by genus and by site of domination (stool vs. oral) as defined in the legend. The top 19 genera in terms of number of domination events are graphed. (B) Data graphed are percent of domination events that were due to a pathogen vs. a commensal (complete list of this classification is shown in Supporting Information) stratified by week of chemotherapy. Line shows linear regression of the percent over time with P value for the null hypothesis that the slope of the line is equal to 0.