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ERX12831220: Illumina MiSeq paired end sequencing
1 ILLUMINA (Illumina MiSeq) run: 403,499 spots, 170.8M bases, 90.4Mb downloads

Submitted by: elisabeth-tweesteden hospital
Study: One decade of point-prevalence surveys for carriage of extended-spectrum beta-lactamase-producing Enterobacterales: whole genome sequencing based prevalence and genetic characterization in a large Dutch teaching hospital from 2013-2022
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Objectives: To determine the prevalence, trends, and potential nosocomial transmission events of the hidden reservoir of rectal carriage of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). Methods: From 2013 to 2022, yearly point prevalence surveys were conducted in a large Dutch teaching hospital. On the day of the survey, all admitted patients were screened for ESBL-E rectal carriage using peri-anal swabs and a consistent and sensitive selective culturing method. All Enterobacterales phenotypically suspected of ESBL production were analysed using whole genome sequencing for ESBL gene detection and clonal relatedness analysis. Results: On average, the ESBL-E prevalence was 4.6% (188/4,119 patients), ranging from 2.1% to 6.6% per year. The ESBL-prevalence decreased on average 5.5% per year. After time trend correction, the prevalence in 2016 and 2020 was lower compared to the other year. Among the ESBL-E, Escherichia coli (80%) and CTX-M genes (85%) predominated. Potential nosocomial transmission events could be found in 5.9% (11/188) of the ESBL-E carriers. Conclusions: The ESBL-E rectal carriage prevalence among hospitalized patients was 4.6% with a downward trend from 2013 to 2022. The decrease in ESBL-E prevalence in 2020 could have been due to the COVID-19 pandemic and subsequent countrywide measures as no nosocomial transmission events were detected in 2020. However, the persistently low ESBL-E prevalences in 2021 and 2022 suggest that the decline in ESBL-E prevalence goes beyond the COVID-19 pandemic, indicating that overall ESBL-E carriage rates are declining over time. Continuous monitoring of ESBL-E prevalence and transmission rates can aid infection control policy to keep antibiotic resistance rates in hospitals low.
Sample: PPS047
SAMEA115892019 • ERS20826454 • All experiments • All runs
Library:
Name: Nextera
Instrument: Illumina MiSeq
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED
Runs: 1 run, 403,499 spots, 170.8M bases, 90.4Mb
Run# of Spots# of BasesSizePublished
ERR13461248403,499170.8M90.4Mb2024-08-05

ID:
34608298

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