Dataset Information

Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases.

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.

SUBMITTER: Le Bastard Q

PROVIDER: S-EPMC7359458 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Publications

Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases.

Le Bastard Quentin Q Chapelet Guillaume G Birgand Gabriel G Hillmann Benjamin M BM Javaudin François F Hayatgheib Niki N Bourigault Céline C Bemer Pascale P De Decker Laure L Batard Eric E Lepelletier Didier D Montassier Emmanuel E

Antimicrobial resistance and infection control 20200714 1

<h4>Background</h4>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.<h4>Objectives</h4>The main objective was to identify specific bacteria and functio ...[more]

PMID: 32665016

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Project description:BackgroundUnderstanding changes in nursing home (NH) resident pain over time would provide a more informed perspective, allowing opportunities to alter the course of illness, plan care, and set priorities. Therefore, the purpose of this analysis was to identify and characterize clinically meaningful, dynamic pain trajectories in NH residents.MethodsRetrospective longitudinal analysis of NH resident pain scores with a length of stay >100 days (N = 4864). Group-based trajectory modeling was applied to Minimum Data Set 3.0 assessments to identify pain trajectories. Trajectories were then characterized using unadjusted and adjusted cross-sectional associations between residents' demographic and clinical characteristics and their pain trajectory.ResultsWe identified four distinct trajectories: (1) consistent pain absence (48.9%), (2) decreasing-increasing pain presence (21.8%), (3) increasing-decreasing pain presence (15.3%), and (4) persistent pain presence (14.0%). Demographics of younger age and living in a rural area were associated with the persistent pain presence trajectory. Clinical variables of obesity and intact cognition were associated with being in the persistent pain presence trajectory. A smaller proportion of residents with moderately or severely impaired cognition were in any of the trajectory groups with pain.ConclusionsWe identified and characterized four pain trajectories among NH residents, including persistent pain presence which was associated with demographic characteristics (younger, female, rural) and clinical factors (obese, fracture, contracture). Moreover, residents with a diagnosis of Alzheimer's disease or dementia were less likely to be in any of the three trajectories with pain, likely representing the difficulty in evaluating pain in these residents. It is important that NH staff understand, recognize, and respond to the factors associated with the identified pain trajectories to improve mitigation of potentially persistent pain (e.g., hip fracture, contracture) or improve proxy pain assessment skills for residents at risk for under reporting of pain (e.g., Alzheimer's Disease).

Project description:Background In 2016, a study in a Dutch nursing home showed prolonged colonization duration of extended-spectrum β-lactamase-producing (ESBL)-ST131 compared to ESBL-non-ST131. In this study, we assessed the duration of rectal ESBL-producing E. coli (ESBL-EC) colonization in residents in the same nursing home for an extended period of six years. We aimed to estimate the influence of a possible bias when follow up is started during an outbreak. Methods Between 2013 and 2019, repetitive point prevalence surveys were performed by culturing rectal or faecal swabs from all residents. Kaplan–Meier survival analysis was performed to calculate the median time to clearance of ESBL-EC with a log-rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131. Results The study showed a median time to clearance of 13.0 months (95% CI 0.0–27.9) for ESBL-ST131 compared to 11.2 months (95% CI 4.8–17.6) for ESBL-non-ST131 (p = 0.044). In the subgroup analysis of residents who were ESBL-EC positive in their first survey, the median time to clearance for ST131 was 59.7 months (95% CI 23.7–95.6) compared to 16.2 months (95% CI 2.1–30.4) for ESBL-non-ST131 (p = 0.036). In the subgroup analysis of residents who acquired ESBL-EC, the median time to clearance for ST131 was 7.2 months (95% CI 2.1–12.2) compared to 7.9 months (95% CI 0.0–18.3) for ESBL-non-ST131 (p = 0.718). The median time to clearance in the ESBL-ST131 group was significantly longer in residents who were ESBL-ST131 colonised upon entering the study than in residents who acquired ESBL-ST131 during the study (p = 0.001). Conclusion A prolonged colonization with ESBL-ST131 was only found in the subgroup who was ESBL-EC positive upon entering the study. The prolonged duration with ESBL-ST131 in the previous study was probably biased by factors that occured during (the start of) the outbreak. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01132-9.

Dataset Information

Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases.

Background

Objectives

Subjects and methods

Results

Conclusions

Publications

Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases.

Similar Datasets

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