2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21073025
SRA accession
spire_mag_02481576
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
2019
collection date
63.93
%
completeness score
checkm2 0.1.3
completeness software
0.95
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR7528807 of study ERP133335.
description
rectal swab
environmental medium
Denmark
geographic location (country and/or sea)
missing: third party data
DD
geographic location (latitude)
missing: third party data
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Bacteroides uniformis
organism
Background: Hospitalization and treatment with antibiotics increase the risk of acquiring multidrug-resistant bacteria due to antibiotic-mediated changes in patient microbiota. This study aimed to investigate how broad and narrow antibiotics affect the gut microbiome and the resistome in antibiotic naïve patients during neurointensive care.Materials/methods: Patients admitted to neurointensive care unit were treated with broad-spectrum (meropenem or piperacillin/tazobactam) or narrow-spectrum antibiotic treatment (including ciprofloxacin, cefuroxime, vancomycin and dicloxacillin) according to clinical indications. A rectal swab was collected from each patient before and after 5-7 days of antibiotic therapy (N=34). Shotgun metagenomic sequencing was performed and composition of metagenomic species (MGS) was determined. The resistome (as collection of antibiotic resistance genes) was characterized with CARD RGI software and CARD database. As a measure for selection pressure in the patient, we used sum of number of days with each antibiotic (antibiotic days).Results: We observed a significant increase in richness and a tendency for an increase in Shannon index after narrow-spectrum treatment. For broad-spectrum treatment the effect was more diverse with some patients increasing and some decreasing in richness and Shannon index. This was studied further by comparison of patients who had gained or lost >10 MGS, respectively. Selection pressure was significantly higher in patients with decreased richness (p = 0.0054) and decreased Shannon index (p = 0.012) these patients tended to have received a higher number of antibiotics (for richness: P= 0.063 for Shannon index: P = 0.086). A decrease in MGS richness was significantly correlated to number of drugs administered and selection pressure of the patient. Bray-Curtis dissimilarities were significant between the pre- and post-treatment of samples in the narrow group, indicating that the longer the narrow-spectrum treatment, the higher the differences between the pre- and the post-treatment microbial composition. Changes in resistome followed MGS composition and was independent of administered antibiotics. We did not find significant differences between pre- and at post-treatment for both antibiotic spectrum treatments, however we observed that most of the antibiotic class resistance genes were higher in abundance in post-treatment after broad-spectrum treatment Conclusions:The MGS composition of the microbiome changed independently of the applied antibiotic treatment. Patients who received narrow-spectrum treatment exhibited an increase in alpha diversity, whereas patients who received broad-spectrum treatment exhibited opposite effects depending on the duration of the treatment with selection pressure and duration of treatment being higher in patients with a decreased MGS diversity. The selection pressure in the patient may be a better predictor of the effect on the microbiome than the spectrum of the antibiotics.
project name
SAMEA10833588
sample derived from
Bacteroides uniformis
scientific_name
Illumina NovaSeq 6000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02481576
title