What question did this study set out to answer?

The study aims to characterize the enteric microbiome in fluoroquinolone-resistant Enterobacterales-colonized hematopoietic cell transplant recipients and its association with bloodstream infections.

May 9, 2026Open Access

339 Enteric colonization with fluoroquinolone-resistant Enterobacterales is associated with increased Enterobacterales and Bacteroidales in hematopoietic cell transplant recipients prior to transplantation

Key Points

The study aims to characterize the enteric microbiome in fluoroquinolone-resistant Enterobacterales-colonized hematopoietic cell transplant recipients and its association with bloodstream infections.
Prospective cohort study of HCT recipients at Weill Cornell Medicine from November 2016 to August 2019.
Stool samples collected before and after levofloxacin prophylaxis; quantitative culture and 16S rRNA sequencing were performed.
Analysis conducted using phyloseq in R.
FQRE-colonized HCT recipients showed higher relative abundances of Bacteroidales and Enterobacterales pre-transplant.
Post-transplant, non-FQRE-colonized recipients had decreased Enterobacterales relative abundance, which was not seen in FQRE-colonized recipients.
FQRE BSI cases had a lower relative abundance of Bacteroidales compared to those without BSI, with no significant difference in FQRE colonization density.

Abstract

Objectives/Goals: Our objectives were to determine enteric microbiome characteristics in fluoroquinolone-resistant Enterobacterales (FQRE)-colonized and non-FQRE-colonized hematopoietic cell transplant (HCT recipients, and to understand the enteric microbiome-specific factors associated with the development of FQRE BSI in FQRE-colonized HCT recipients. Methods/Study Population: This was a prospective cohort study of patients undergoing HCT at Weill Cornell Medicine from November 2016 to August 2019. All participants received levofloxacin prophylaxis during post-HCT neutropenia. Stool samples were collected prior to levofloxacin prophylaxis initiation and during the week after HCT. Our overall study population consisted of 26 FQRE-colonized HCT recipients and 69 non-FQRE-colonized HCT recipients. Samples underwent selective quantitative culture for FQRE, as well as 16S rRNA sequencing. Raw sequence data were processed and aligned to a custom SILVA database. Analysis of 16S rRNA sequencing was conducted in R using phyloseq. Results/Anticipated Results: We saw significant differences in microbiome composition in comparing pre-HCT samples from FQRE-colonized HCT recipients to non-FQRE-colonized HCT recipients, including significantly higher relative abundances of Bacteroidales and Enterobacterales in colonized recipients. MaAslin2 demonstrated significantly differential abundance of Bacteroides and Escherichia-Shigella ASVs. We observed a significant decrease in Enterobacterales relative abundance in non-FQRE-colonized recipients after HCT, but no such change in FQRE-colonized recipients. FQRE-colonized recipients who developed FQRE BSI had a lower relative abundance of Bacteroidales as compared to those who did not. No significant difference in FQRE colonization density as measured by quantitative FQRE stool culture was observed. Discussion/Significance of Impact: FQRE-colonized HCT recipients represent a unique subgroup of HCT recipients. Colonized HCT recipients with FQRE BSI had lower relative abundance of Bacteroidales compared to those without BSI. Further work is needed to determine the mechanism behind this association and to further characterize the microbiome in this subgroup of HCT recipients.

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