Characterization of extensively-drug-resistant Acinetobacter baumannii international clone II and I lineages isolated from intensive care units
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ABSTRACT:
PROVIDER: PRJEB30466 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3079300_1.fastq.gz | Fastqsanger.gz | |||
| ERR3079300_2.fastq.gz | Fastqsanger.gz | |||
| ERR3079298_1.fastq.gz | Fastqsanger.gz | |||
| ERR3079298_2.fastq.gz | Fastqsanger.gz | |||
| ERR3079299_1.fastq.gz | Fastqsanger.gz |
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Project description:<p>Monogenic diseases are frequent causes of neonatal morbidity and mortality, and disease presentations are often undifferentiated at birth. More than 3,500 monogenic diseases have been characterized, but clinical testing is available for only some of them and many feature clinical and genetic heterogeneity. As such, an immense unmet need exists for improved molecular diagnosis in infants. Because disease progression is extremely rapid, albeit heterogeneous, in newborns, molecular diagnoses must occur quickly to be relevant for clinical decision-making. We describe 50-hour differential diagnosis of genetic disorders by whole-genome sequencing (WGS) that features automated bioinformatic analysis and is intended to be a prototype for use in neonatal intensive care units. Retrospective 50-hour WGS identified known molecular diagnoses in two children. Prospective WGS disclosed potential molecular diagnosis of a severe <i>GJB2</i>-related skin disease in one neonate; <i>BRAT1</i>-related lethal neonatal rigidity and multifocal seizure syndrome in another infant, identified <i>BCL9L</i> as a novel, recessive visceral heterotaxy gene (<i>HTX6</i>) in a pedigree, and ruled out known candidate genes in one infants. Sequencing of parents or affected siblings expedited the identification of disease gene in prospective cases. Thus, rapid WGS can potentially broaden and foreshorten differential diagnosis, resulting in fewer empirical treatments and faster progression to genetic and prognostic counseling.</p> <p>Reprinted from Saunders et. al, Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units. Sci. Transl. Med. 4, 154ra135 (2012; <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Rapid%20Whole-Genome%20Sequencing%20for%20Genetic%20Disease%20Diagnosis%20in%20Neonatal%20Intensive%20Care%20Units">PMID: 23035047 </a>) with permission from AAAS.</p>
| phs000564.v1.p1 | EGA
Project description:intensive care unit shotgun raw sequences Metagenome
| PRJNA562118 | ENA
Project description:BACKGROUND: On average 7% of patients admitted to intensive-care units (ICUs) suffer from a potentially preventable ventilator-associated pneumonia (VAP). Our objective was to survey attitudes and practices of ICUs doctors in the field of VAP prevention. METHODS: A questionnaire was made available online in 6 languages from April, 1st to September 1st, 2012 and disseminated through international and national ICU societies. We investigated reported practices as regards (1) established clinical guidelines for VAP prevention, and (2) measurement of process and outcomes, under the assumption "if you cannot measure it, you cannot improve it"; as well as attitudes towards the implementation of a measurement system. Weighted estimations for Europe were computed based on countries for which at least 10 completed replies were available, using total country population as a weight. Data from other countries were pooled together. Detailed country-specific results are presented in an online additional file. RESULTS: A total of 1730 replies were received from 77 countries; 1281 from 16 countries were used to compute weighted European estimates, as follows: care for intubated patients, combined with a measure of compliance to this guideline at least once a year, was reported by 57% of the respondents (95% CI: 54-60) for hand hygiene, 28% (95% CI: 24-33) for systematic daily interruption of sedation and weaning protocol, and 27% (95%: 23-30) for oral care with chlorhexidine. Only 20% (95% CI: 17-22) were able to provide an estimation of outcome data (VAP rate) in their ICU, still 93% (95% CI: 91-94) agreed that "Monitoring of VAP-related measures stimulates quality improvement". Results for 449 respondents from 61 countries not included in the European estimates are broadly comparable. CONCLUSIONS: This study shows a low compliance with VAP prevention practices, as reported by ICU doctors in Europe and elsewhere, and identifies priorities for improvement.
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Project description:BackgroundIn recent years, numerous dosing studies have been conducted to optimize therapeutic antibiotic exposures in patients with serious infections. These studies have led to the inclusion of dose optimization recommendations in international clinical practice guidelines. The last international survey describing dosing, administration and monitoring of commonly prescribed antibiotics for critically ill patients was published in 2015 (ADMIN-ICU 2015). This study aimed to describe the evolution of practice since this time.MethodsA cross-sectional international survey distributed through professional societies and networks was used to obtain information on practices used in the dosing, administration and monitoring of vancomycin, piperacillin/tazobactam, meropenem and aminoglycosides.ResultsA total of 538 respondents (71% physicians and 29% pharmacists) from 409 hospitals in 45 countries completed the survey. Vancomycin was mostly administered as an intermittent infusion, and loading doses were used by 74% of respondents with 25 mg/kg and 20 mg/kg the most favoured doses for intermittent and continuous infusions, respectively. Piperacillin/tazobactam and meropenem were most frequently administered as an extended infusion (42% and 51%, respectively). Therapeutic drug monitoring was undertaken by 90%, 82%, 43%, and 39% of respondents for vancomycin, aminoglycosides, piperacillin/tazobactam, and meropenem, respectively, and was more frequently performed in high-income countries. Respondents rarely used dosing software to guide therapy in clinical practice and was most frequently used with vancomycin (11%).ConclusionsWe observed numerous changes in practice since the ADMIN-ICU 2015 survey was conducted. Beta-lactams are more commonly administered as extended infusions, and therapeutic drug monitoring use has increased, which align with emerging evidence.
| S-EPMC10278304 | biostudies-literature
Project description:Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Comprehensively capturing the host physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index and APACHE II score were poor predictors of survival. Instead, using plasma proteomes quantifying 302 plasma protein groups at 387 timepoints in 57 critically ill patients on invasive mechanical ventilation, we found 14 proteins that showed trajectories different between survivors and non-survivors. A proteomic predictor trained on single samples obtained at the first time point at maximum treatment level (i.e. WHO grade 7) and weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81, n=49). We tested the established predictor on an independent validation cohort (AUROC of 1.0, n=24). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that predictors derived from plasma protein levels have the potential to substantially outperform current prognostic markers in intensive care.
2022-03-03 | PXD029009 | Pride
Project description:intensive care unit shotgun raw sequences GML Raw sequence reads
| PRJNA562155 | ENA
Project description:BackgroundThe intensive care unit is increasingly recognized as a stressful environment for healthcare professionals. This context has an impact on the health of these professionals but also on the quality of their personal and professional life. However, there is currently no validated scale to measure specific stressors perceived by healthcare professionals in intensive care. The aim of this study was to construct and validate in three languages a perceived stressors scale more specific to intensive care units (ICU).ResultsWe conducted a three-phase study between 2016 and 2019: (1) identification of stressors based on the verbatim of 165 nurses and physicians from 4 countries (Canada, France, Italy, and Spain). We identified 99 stressors, including those common to most healthcare professions (called generic), as well as stressors more specific to ICU professionals (called specific); (2) item elaboration and selection by a panel of interdisciplinary experts to build a provisional 99-item version of the scale. This version was pre-tested with 70 professionals in the 4 countries and enabled us to select 50 relevant items; (3) test of the validity of the scale in 497 ICU healthcare professionals. Factor analyses identified six dimensions: lack of fit with families and organizational functioning; patient- and family-related emotional load; complex/at risk situations and skill-related issues; workload and human resource management issues; difficulties related to team working; and suboptimal care situations. Correlations of the PS-ICU scale with a generic stressors measure (i.e., the Job Content Questionnaire) tested its convergent validity, while its correlations with the Maslach Burnout Inventory-HSS examined its concurrent validity. We also assessed the test-retest reliability of PS-ICU with intraclass correlation coefficients.ConclusionsThe perceived stressors in intensive care units (PS-ICU) scale have good psychometric properties in all countries. It includes six broad dimensions covering generic or specific stressors to ICU, and thus, enables the identification of work situations that are likely to generate high levels of stress at the individual and unit levels. For future studies, this tool will enable the implementation of targeted corrective actions on which intervention research can be based. It also enables national and international comparisons of stressors' impact.
| S-EPMC8036172 | biostudies-literature
Project description:BackgroundInitiating parenteral nutrition (PN) within 24 h in critically ill children is inferior to withholding PN during the first week, as was found in the PEPaNIC study. The aims of this study were to investigate de-implementation of early initiation of PN at PICUs worldwide, and to identify factors influencing de-implementation.MethodsA cross-sectional online survey was conducted (May - October 2017), consisting of 41 questions addressing current PN practices, the degree of de-implementation, and factors affecting de-implementation.ResultsWe analysed 81 responses from 39 countries. Of these 81 respondents, 53 (65%) were aware of the findings of the PEPaNIC study, and 43 (53%) have read the article. In these 43 PICUs, PN was completely withheld during the first week in 10 PICUs, of which 5 already withheld PN (12%), and 5 de-implemented early initiation of PN (12%). Partial de-implementation was reported by 17 (40%) and no de-implementation by 16 (37%). Higher de-implementation rates were observed when the interpreted level of evidence and grade of recommendation of PEPaNIC was high. Predominant reasons for retaining early initiation of PN were concerns on withholding amino acids, the safety in undernourished children and neonates, and the long-term consequences. Furthermore, the respondents were waiting for updated guidelines.ConclusionsOne year after the publication of the PEPaNIC trial, only two-thirds of the respondents was aware of the study results. Within this group, early initiation of PN was de-implemented completely in 12% of the PICUs, while 40% asserted partial de-implementation. Increasing the awareness, addressing the intervention-specific questions and more frequently revising international guidelines might help to accelerate de-implementation of ineffective, unproven or harmful healthcare.
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Project description:ObjectivesTo describe the variation across neonatal intensive care units (NICUs) in missed nursing care in disproportionately black and non-black-serving hospitals. To analyze the nursing factors associated with missing nursing care.Data sources/study settingSurvey of random samples of licensed nurses in four large U.S. states.Study designThis was a retrospective, secondary analysis of 1,037 staff nurses in 134 NICUs classified into three groups based on their percent of infants of black race. Measures included the average patient load, individual nurses' patient loads, professional nursing characteristics, nurse work environment, and nursing care missed on the last shift.Data collectionSurvey data from a Multi-State Nursing Care and Patient Safety Study were analyzed (39 percent response rate).Principal findingsThe patient-to-nurse ratio was significantly higher in high-black hospitals. Nurses in high-black NICUs missed nearly 50 percent more nursing care than in low-black NICUs. Lower nurse staffing (an additional patient per nurse) significantly increased the odds of missed care, while better practice environments decreased the odds.ConclusionsNurses in high-black NICUs face inadequate staffing. They are more likely to miss required nursing care. Improving staffing and workloads may improve the quality of care for the infants born in high-black hospitals.
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