The operating room microbes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB11484 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1084850.fastq.gz | Fastqsanger.gz | |||
| ERR1084860.fastq.gz | Fastqsanger.gz | |||
| ERR1084870.fastq.gz | Fastqsanger.gz | |||
| ERR1084880.fastq.gz | Fastqsanger.gz | |||
| ERR1084890.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The first microbial environment of infants born by C-section: The operating room microbes
| PRJNA299062 | ENA
Project description:Microbiome of a C section Operating Room Raw sequence reads
| PRJNA553099 | ENA
Project description:BACKGROUND:Newborns delivered by C-section acquire human skin microbes just after birth, but the sources remain unknown. We hypothesized that the operating room (OR) environment contains human skin bacteria that could be seeding C-section born infants. RESULTS:To test this hypothesis, we sampled 11 sites in four operating rooms from three hospitals in two cities. Following a C-section procedure, we swabbed OR floors, walls, ventilation grids, armrests, and lamps. We sequenced the V4 region of the 16S rRNA gene of 44 samples using Illumina MiSeq platform. Sequences were analyzed using the QIIME pipeline. Only 68 % of the samples (30/44, >1000 sequences per site) yielded sufficient DNA reads to be analyzed. The bacterial content of OR dust corresponded to human skin bacteria, with dominance of Staphylococcus and Corynebacterium. Diversity of bacteria was the highest in the ventilation grids and walls but was also present on top of the surgery lamps. Beta diversity analyses showed OR dust bacterial content clustering first by city and then by hospital (t test using unweighted UniFrac distances, p?<?0.05). CONCLUSIONS:We conclude that the dust from ORs, collected right after a C-section procedure, contains deposits of human skin bacteria. The OR microbiota is the first environment for C-section newborns, and OR microbes might be seeding the microbiome in these babies. Further studies are required to identify how this OR microbiome exposure contributes to the seeding of the neonatal microbiome. The results might be relevant to infant health, if the current increase in risk of immune and metabolic diseases in industrialized societies is related to lack of natural exposure to the vaginal microbiome during labor and birth.
| S-EPMC4665759 | biostudies-literature
Project description:mRNA expression was assayed from bronchial epithelial cell samples from smokers with and without lung cancer. A subset of the samples (2 of the lung cancer samples and 3 of the no cancer samples) were pooled and underwent whole transcriptome sequencing. The goals were to compare whole transcriptome sequencing gene expression levels to gene expression levels derived from these samples run on the Affymetrix HGU133A 2.0 platform. Current and former smokers with cancer (n=8) and without cancer (n=5) undergoing flexible bronchoscopy in the operating room for resection of a suspicious lung nodule at Boston University Medical Center were recruited. Patients were classified as having no lung cancer based on the pathological results from the lung biopsy. Patients with no cancer were diagnosed with alternative benign diseases of the chest including organizing pneumonitis, sarcoidosis and chronic inflammation due to foreign body material.
2011-06-01 | E-GEOD-28835 | biostudies-arrayexpress
Project description:An Easy Operating Pathogen Microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed and further implemented in a user-friendly interface. A microarray was designed with probes for vertebrate-infecting virus sequences in EMBL, 18S rRNA fungi and parasite sequences from EMBL, and 16S rRNA sequences of bacteria from RDP, synthesized on the Agilent platform. The array was tested using 2 color dyes on cultured microbes and on clinical samples from sick and healthy people, looking for differences in clinically ill people compared to a number of healthy "controls".
2013-07-01 | E-GEOD-45860 | biostudies-arrayexpress
Project description:It is unclear why preterm birth increases risk of cardiovascular disease later in life. Studies in mice indicate excess oxygen typically used to treat preterm infants causes pulmonary hypertension, cardiac failure, and shortens lifespan. We previously reported neonatal hyperoxia causes pulmonary hypertension in aged mice as defined pathologically by pulmonary capillary rarefaction, dilation of pulmonary arterioles and veins, right ventricular hypertrophy, and reduced lifespan. These changes were preceded by a pronounced growth inhibition of cardiomyocytes lining the pulmonary vein and extending into the left atria, resulting in diastolic heart failure as the mice aged. To identify transcriptional changes by which hyperoxia suppresses proliferation of these cardiomyocytes, newborn mice were exposed to room air or 100% oxygen between birth and postnatal day 4. RNA was then isolated from atria of 3 room air and 4 hyperoxia-exposed mice and used to probe Affymetrix mouse array 430 versus 2.0
2021-02-23 | E-MTAB-9008 | biostudies-arrayexpress
Project description:IntroductionOperating room (OR) fire can be a devastating and costly event to patients and health care providers. Prevention and effective management of such fires may present difficulties even for experienced OR staff.MethodsThis simulation involved a 52-year-old man presenting for excisional biopsy of a cervical lymph node to be performed under sedation. Participants were expected to identify and manage both contained and uncontained fires resulting from ignition by electrosurgical cautery. We conducted weekly multidisciplinary simulations in the mock OR at Massachusetts General Hospital. Participants included surgery and anesthesiology residents, certified registered nurse anesthetists, registered nurses, and surgical technicians. Participants were unaware of the scenario content. Each 90-minute session was divided into three parts: an orientation (10 minutes), the case with rapid cycle debriefing (65 minutes), and a final debriefing with course evaluations (15 minutes). Equipment consisted of a simulation OR with general surgery supplies, general anesthesia equipment, a high-fidelity Laerdal SimMan 3G simulator, a code cart, a defibrillator, dry ice for smoke effects, and a projector with a fire image.ResultsFrom April to June 2015, 86 participants completed this simulation. Participants reported that the simulation scenario was realistic (80%), was relevant to their clinical practice (93%), changed their practice (82%), and promoted teamwork (80%).DiscussionPrevention and management of OR fire require collaboration and prompt coordination between anesthesiologists, surgeons, and nurses. This simulation case scenario was implemented to train multidisciplinary learners in the identification and crisis management of such an event.
| S-EPMC7012309 | biostudies-literature
Project description:Experiment1: 2 day old baby mice were exposed to hyperoxia (75% O2) continuously for 7 days. Control baby mice were housed in room air (normoxia). Plasma and bronchoalveolar lavage fluid (BALF) were harvested after 7 days of exposure (on Day of life 9). Experiment2: 2 day old baby mice were exposed to room air or hyperoxia for 14 days and subsequently treated with RV1 or sham.Plasma was collected 5 days after treatment. Human tracheal aspirates were collected from prematurely born infants undergoing mechanical ventilation for respiratory distress syndrome in the first week of life.Tracheal aspirate supernatants are submitted for the assay. We would like to measure adenosine, AMP, ADP and ATP levels.
2015-03-26 | ST000304 | MetabolomicsWorkbench
Project description:It is unclear why preterm birth increases risk of cardiovascular disease later in life. Studies in mice indicate excess oxygen used to treat preterm infants causes pulmonary hypertension, cardiac failure, and shortens lifespan. We previously reported neonatal hyperoxia causes pulmonary hypertension in aged mice as defined pathologically by pulmonary capillary rarefaction, dilation of pulmonary arterioles and veins, right ventricular hypertrophy, and reduced lifespan. Here, affymetrix gene arrays were used to identify early transcriptional changes in lungs of young adult mice exposed to room air or 100% oxygen between postnatal days 0-4.
2018-01-01 | E-MTAB-6074 | biostudies-arrayexpress
Project description:The rate of cesarean delivery (CD) in China has risen sharply and the high rate was reported to be associated with increased risk of disease in the offspring. However, there is little research on the molecular mechanism of critical pathways and gene signatures involved in the neonatal immunity of cesarean-born infants. This study was undertaken to identify unique gene signatures which was involved in the neonatal immunity of cesarean-born infants through large-scale RNA-sequencing. Genes differentially expressed in cesarean-born infants were identified and further validated through quantitative real-time PCR (RT-qPCR). Moreover, we employed weighted gene co-expression network analysis (WGCNA) to identify highly connected genes that were correlated with neonatal inflammation. In total, 73 differentially expressed genes (DEGs) were identified between cesarean-born infants and normal vagina childbirth. The results obtained by secondary validation indicated that GATM, MIF, IFI27, IL1B, CA1, and EPHB1 were significantly upregulated in phenotype CD, while CYP2A6 and DLK1 were significantly down regulated. Further, functional and pathway enrichment analysis reveals perturbation of several DEGs involved in signaling pathways pertaining to immunoregulation, inflammation, apoptosis, and nervous development. Additionally, HLA-DOB popped out as a core gene in the process of inflammation, which might indicate the risk of cesarean-born infants for inflammatory disease. Notably, our study for the first time has documented gene signatures PIK3CA, PTPRC, SOS1, IL6ST, and MALT1, which were found to be involved in neonatal inflammation. Taken together, the full expression repertoire including the differentially expressed gene sets and core differentially co-expressed genes should provide an excellent resource for identifying potential biomarkers of cesarean-born infants with inflammation, and formulating new hypotheses for physiological functions and the discovery of novel therapeutic targets for inflammatory disease.
2019-01-23 | GSE125421 | GEO