Genomic epidemiology of a nosocomial outbreak in a tertiary hospital from Valencia, Spain
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB70513 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12321100.fastq.gz | Fastqsanger.gz | |||
| ERR12321101.fastq.gz | Fastqsanger.gz | |||
| ERR12321102.fastq.gz | Fastqsanger.gz | |||
| ERR12321103.fastq.gz | Fastqsanger.gz | |||
| ERR12321104.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 38 |
Similar Datasets
Project description:This study aims to determine the epidemiology of Enterobacteriaceae resistant to antibiotics of last resort in pregnant women in labour at a tertiary hospital, Pretoria, South Africa. Rectal swabs shall be used to screen for colonisation with CRE and colistin-resistant Enterobacteriales in pregnant women during labour. Carbapenem and colistin-resistant Enterobacterales can cause the following infections: bacteraemia; nosocomial pneumonia; urinary tract infections, and intra-abdominal infections. Due to limited treatment options, infections caused by these multidrug-resistant organisms are associated with a mortality rate of 40-50%. Screening for colonisation of carbapenem-resistant Enterobacteriaceae (CRE) and colistin-resistant Enterobacteriaceae will help implement infection and prevention measures to limit the spread of these multidrug-resistant organisms.
2022-07-20 | GSE208573 | GEO
Project description:Candida auris has been globally recognized as a multidrug-resistant human fungal pathogen that contributes for the worldwide occurrence of nosocomial outbreaks. It has been reported that C. auris was able to avoid neutrophil attack, suggestive of an impaired innate immune response. Whether C. auris evades the innate immune recognition of BMDM (bone marrow derived macrophage) remains poorly understood, and as for well-known Candida species -C. albicans, it can trigger immune response. To determine whether occurs difference between immune response stimulated by C. auris or C. albicans, we performed mRNA-seq of BMDM stimulated by C. auris or C. albicans.
2022-05-21 | GSE203508 | GEO
Project description:Background and aimThe present study was aimed at assessing the characteristics of children with nosocomial multidrug-resistant Acinetobacter baumannii complex (MDR ABC) in a tertiary hospital of eastern China. MDR ABC poses a serious threat to public health. However, information on nosocomial MDR ABC in children is lacking.MethodThis study retrospectively reviewed the cases in a tertiary hospital of eastern China between January 1, 2011, and December 31, 2014 (excluding outpatients).ResultsA total of 377 non-duplicated nosocomial ABC isolates were collected from various samples including 200 (53.1%) MDR ABC isolates. Moreover, 158 of the 200 MDR ABC isolates were collected from intensive care units (ICUs; MDR constituent ratios, 62.5%), while 98 of the 200 MDR ABC isolates were collected from children older than 1 year (MDR constituent ratios, 62.8%). Multivariate logistic analysis revealed that being in the surgical intensive care unit (SICU), prolonged hospital stay, surgical intervention, and mechanical ventilation were independent risk factors for MDR acquisition among children with nosocomial ABC. The interleukin (IL)-6 level of children with nosocomial MDR ABC was significantly lower than that of the children with nosocomial non-MDR ABC.ConclusionNosocomial MDR ABC infection is a serious concern in pediatric patients. Being in the SICU, prolonged hospital stay, surgical intervention, and mechanical ventilation increased the risk of nosocomial MDR ABC. IL-6 might be involved in developing nosocomial MDR ABC among children.
| S-EPMC5007015 | biostudies-literature
Project description:Real-time molecular survey of Mycobacterium tuberculosis isolates from 2008 to 2018 reveals tuberculosis transmission in a tertiary-care university hospital
| PRJEB33569 | ENA
Project description:The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.
2024-10-14 | GSE271825 | GEO
Project description:Citrus sinensis cultivar:Valencia sweet orange Raw sequence reads
| PRJNA1076522 | ENA
Project description:Studies have shown high intussusception rates in Spain. We performed a hospital-based retrospective observational study of the intussusception risk following rotavirus vaccinations among infants in Valencia, a region of Spain with an annual birth cohort of approximately 48,000 children, during 2007-2011, using a self-controlled case series design. We performed medical record review of all cases using Brighton Collaboration's case definition and assessed the positive predictive value (PPV) of the intussusception diagnosis code. Among 151 hospitalized cases discharged as intussusception, we confirmed 136 as Brighton Collaboration's Levels 1 or 2, resulting in a PPV of 93% (95% CI: 87%-96%). Three confirmed cases occurred within days 1-7 following the first rotavirus vaccination. The incidence rate ratio was 9.0 (95% CI: 0.9-86.5) (crude) and 4.7 (95% CI:0.3-74.1)(age adjusted). In this first study in Europe, the intussusception risk point estimate was comparable to other studies, although results were not statistically significant, maybe due to limited power. The high PPV found will facilitate implementation of a larger study without requiring medical record review. Our finding of very few vaccinated cases despite a thorough 5-year investigation in a country that, according to previous studies, may have a large background rate of intussusception is reassuring and should contribute to deliberations about the need to include rotavirus vaccines in the official Spanish calendars.
| S-EPMC4517458 | biostudies-literature
Project description:Hepatitis delta virus (HDV) is the most aggressive form of chronic viral hepatitis, yet substantial knowledge gaps exist regarding its epidemiology and optimal diagnostic workflows. From February 2019 to March 2022, an HBV screening project was conducted across various healthcare settings in Valencia, Spain. This included twenty-six primary care centers, six sexual and reproductive health centers, three mental health centers, three addiction treatment centers, selected hospital departments, outpatient clinics, and a penitentiary center. A retrospective analysis of HDV diagnostic and prevalence (2007-2020) was followed by prospective HDV screening using reflex testing from April to October 2022. Of 31,995 patients screened, 141 were HBsAg-positive (0.44% seroprevalence). Previously unknown HBV infection prevalence was 0.36%. Among HBsAg-positive patients, 5.15% had HDV IgG/IgM antibodies, and 2% had HDV RNA. Reflex single-step HDV testing increased HDV diagnosis coverage from 24 to 99.4%. This study highlights the effectiveness of reflex HDV testing, which significantly increased diagnostic coverage and simplified the screening process. Reflex testing provides a cost-effective and efficient approach, particularly benefiting high-risk populations such as migrants, who accounted for 77.8% of HBsAg-positive cases. Its implementation is crucial for improving patient outcomes and addressing gaps in HDV diagnosis and management.
| S-EPMC11880328 | biostudies-literature
Project description:Single-molecule correlated chemical probing (smCCP) is an experimentally concise strategy for characterizing higher-order structural interactions in RNA. smCCP data yield rich, but complex, structural information on base pairing, conformational ensembles, and tertiary interactions. To date, through-space communication specifically measuring RNA tertiary structure has been difficult to isolate from structural communication reflective of other interactions. Here we introduce mutual information as a filtering metric to isolate tertiary structure communication contained within smCCP data and use this strategy to characterize the structural ensemble of the SAM-III riboswitch. We identified a smCCP fingerprint that is selective for states containing tertiary structure that forms concurrently with cognate ligand binding. We then successfully applied mutual information filters to independent RNAs and isolated through-space tertiary interactions in riboswitches and large RNAs with complex structures. smCCP, coupled with mutual information criteria, can now be used as a tertiary structure discovery tool, including to identify specific states in an ensemble that have higher-order structure. These studies pave the way for use of the straightforward smCCP experiment for discovery and characterization of tertiary structure motifs in complex RNAs.
2024-10-23 | GSE278422 | GEO
Project description:Acinetobacter baumannii is an opportunistic infectious agent that affects primarily immunocompromised individuals. A. baumannii is highly prevalent in hospital settings being commonly associated with nosocomial transmission and drug resistance. Here, we report the identification and genetic characterization of A. baumannii strains among patients in a tertiary level hospital in Mexico. Whole genome sequencing analysis was performed to establish their genetic relationship and drug resistance mutations profile. Ten genetically different, extensively drug resistant strains were identified circulating among seven wards. The genetic profiles showed resistance primarily against aminoglycosides and beta-lactam antibiotics. Importantly, no mutants conferring resistance to colistin were observed. The results highlight the importance of implementing robust classification schemes for advanced genetic characterization of A. baumannii clinical isolates and simultaneous detection of drug resistance markers for adequate patient's management in clinical settings.
| S-EPMC7164640 | biostudies-literature