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SRX10142667: Metatranscriptomic sequencing of UPMC Hospital Surfaces
1 ILLUMINA (NextSeq 550) run: 6.9M spots, 1G bases, 367.2Mb downloads

Design: Libraries were prepared from concentrated RNA from each sample spiked 5 pg of a synthetic RNA construct to serve as an internal control and used the input to the NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs, Ipswich MA) following manufacturer protocol. Once complete, each sample was quantified with a Quant-iT 1X dsDNA High Sensitivity Assay (Thermo Fisher Scientific, Waltham MA). A sequencing library was set up by combining an equivalent mass from each sample library. Each sequencing library was finally purified with Ampure XP beads (0.9X ratio) and quantified with a Qubit 1X dsDNA HS assay. Quantified sequencing libraries were diluted, denatured, and sequenced on an Illumina NextSeq 550 using a 150 cycle High Output v2.5 kit following Illumina standard protocols.
Submitted by: Contamination Source Identification
Study: Metatranscriptome sequencing of hospital surfaces before and after AIONX cleanSURFACE intervention
show Abstracthide Abstract
Hospital acquired infections (HAIs) pose a serious threat to patients. Accordingly, hospitals spend a large amount of time and money trying to prevent them. Many HAIs are due to contamination from workers hands and contact with high-touch surfaces. Therefore, we set out to test the efficacy of a new preventative technology, AIONX Antimicrobial Technologies, Incs cleanSURFACES, which is designed to continuously prevent re-colonization of cleaned surfaces. To that end, we swabbed surfaces before (Pre-Baseline) and after (Post) application of the cleanSURFACES at various timepoints (Day 1, Day 7, and Day 28). Previous studies have examined the hospital microbiome using the 16S rRNA gene. However, here, the swabs were processed for metatranscriptomic analysis to allow for greater taxonomic resolution and the detection of fungi and viruses. Overall, there was a global reduction in microbial diversity in Post samples. Additionally, Post samples clustered together much more closely than baseline samples, suggesting a defined shift after application in most cases. This shift was characterized by a general depletion of most microbes, as the entire domain Bacteria was significantly reduced in Post samples, with multiple phyla also being reduced over the duration of the study. Notably, specific pathogens of interest, including Staphylococcus aureus and Streptococcus, were depleted too. Taken together, these findings strongly indicate that cleanSURFACES effectively inhibit colonization by a wide variety of microbes, including many important pathogens.
Sample: DOD00111
SAMN18016237 • SRS8295853 • All experiments • All runs
Library:
Name: DOD00111
Instrument: NextSeq 550
Strategy: RNA-Seq
Source: METATRANSCRIPTOMIC
Selection: RANDOM
Layout: SINGLE
Runs: 1 run, 6.9M spots, 1G bases, 367.2Mb
Run# of Spots# of BasesSizePublished
SRR137560186,914,8001G367.2Mb2021-02-21

ID:
13270243

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