Gut microbiome signatures of nursing home residents carrying Enterobacteria Producing Extended-spectrum β-lactamases [journal]
Journal
Antimicrobial Resistance & Infection Control - July 14, 2020
Authors
Quentin Le Bastard, Guillaume Chapelet, Gabriel Birgand, Benjamin M Hillmann (Ph.D. student), François Javaudin, Niki Hayatgheib, Céline Bourigault, Pascale Bemer, Laure De Decker, Eric Batard, Didier Lepelletier, Emmanuel Montassier
Abstract
Background
The prevalence of extended beta-lactamase producing Enterobacteriaceae (ESBL-E) has been constantly increasing over the last few decades. These microorganisms that have acquired broad antibiotic resistance are now common human pathogens. Changes in the gut microbiome, induced by antibiotics or other drugs, enable expansion of these microorganisms, but the mechanisms are not yet fully understood.
Objectives
The main objective was to identify specific bacteria and functional pathways and genes characterizing the gut microbiome of nursing home residents carrying ESBL-E, using metagenomics.
Subjects and methods
We included 144 residents living in two different nursing homes. All fecal samples were screened for ESBL-E and gut microbiome was characterized using shallow shotgun metagenomic DNA sequencing.
Results
Ten nursing home residents were colonized by ESBL-E, namely Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae species, and were compared to non-carriers. We found that ESBL-E carriers had an alteration in within-sample diversity. Using a bootstrap algorithm, we found that the gut microbiome of ESBL-E carriers was depleted in butyrate-producing species, enriched in succinate-producing species and enriched in pathways involved in intracellular pH homeostasis compared to non-carriers individuals. Several energy metabolism pathways were overrepresented in ESBL-E carriers suggesting a greater ability to metabolize multiple microbiota and mucus layer-derived nutrients.
Conclusions
The gut microbiome of ESBL-E carriers in nursing homes harbors specific taxonomic and functional characteristics, conferring an environment that enables Enterobacteriaceae expansion. Here we describe new functional features associated with ESBL-E carriage that could help us to elucidate the complex interactions leading to colonization persistence in the human gut microbiota.
Link to full paper
Keywords
bioinformatics, computational biology