Draft Genome Sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., Strains OUH 308042T (= ATCC BAA-2681T) and OUH 334697 (= ATCC BAA-2682), Isolated from Blood Cultures from Two Different Patients

We announce here the draft genome sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., strains OUH 308042(T) (= DSM 28342(T) = ATCC BAA-2681(T)) and OUH 334697 (= DSM 28341 = ATCC BAA-2682), isolated from blood cultures from two different patients and composed of 51 and 39 contigs for totals of 3,385,516 and 3,410,672 bp, respectively

Cerebrospinal fluid pleocytosis level as a diagnostic predictor?:A cross-sectional study

Abstract Background Lumbar puncture with quantification of leukocytes and differential count of cellular subsets in the cerebrospinal fluid is a standard procedure in cases of suspected neuroinfectious conditions. However, a number of non-infectious causes may result in a low leukocyte number (0–1000 cells/ml). We wanted to assess the diagnostic diversity of unselected adult patients with pleocytosis in the cerebrospinal fluid. Methods The study is based on data from cerebrospinal fluid (CSF) analyses of all adult patients (15 years or older) admitted to a large university hospital in Denmark during a two-year period (2008–2009). Data from the local patient administrative system supplied with data from patient charts were combined with laboratory data. Results A total of 5390 cerebrospinal fluid samples from 3290 patients were included. Pleocytosis >5 leucocytes/μl was found in samples from 262 patients of which 106 (40.5%) were caused by infection of the central nervous system (CNS), 20 (7.6%) by infection outside CNS, 79 (30.2%) due to non-infectious neurological diseases, 23 (8.8%) by malignancy, and 34 (13.0%) caused by other conditions. Significantly higher mean CSF leukocytes was found in patients suffering from CNS infection (mean 1135 cells/μl, p-value <0.0001). Conclusions CNS infection, non-infectious neurological disease, malignancy, and infection outside CNS can cause pleocytosis of the cerebrospinal fluid. Leukocyte counts above 100/μl is mainly caused by CNS infection, whereas the number of differential diagnoses is higher if the CSF leukocyte counts is below 50/μl. These conditions are most commonly caused by non-infectious neurological diseases including seizures

<雜録>沈默ト承認

Bacteroides fragilis constitutes the most frequent anaerobic bacterium causing bacteremia in humans. The genetic background for antimicrobial resistance in B. fragilis is diverse with some genes requiring insertion sequence (IS) elements inserted upstream for increased expression. To evaluate whole genome shotgun sequencing as a method for predicting antimicrobial resistance properties, one meropenem resistant and five multidrug-resistant blood culture isolates were sequenced and antimicrobial resistance genes and IS elements identified using ResFinder 2.1 (http://cge.cbs.dtu.dk/services/ResFinder/) and a custom BLAST database. Combinations of cfxA, cepA, cfiA, nimA, nimD, nimE, nimJ, tetQ, ermB, ermF, bexB, linAn2 and mefEn2 genes were identified in the six isolates. blaOXA-347, an open reading frame predicted to be a beta-lactamase (Cheng et al., 2012), was identified in one strain. Full length IS elements were identified directly upstream of four genes, but in most cases contigs terminated 100-150 bases upstream of the gene in question. Even though partial IS elements were identified in these short sequences, certain identification could not be ascertained. Full antiobiograms for B. fragilis from genetic data will most likely require complete or nearly complete genomes. Current approaches to this are laborious and/or costly. Emerging technologies such as nanopore based single DNA strand sensing could perhaps provide a solution in the future

Contaminated dicloxacillin capsules as the source of an NDM-5/OXA-48-producing Enterobacter hormaechei ST79 outbreak, Denmark and Iceland, 2022 and 2023

Publisher Copyright: © 2023 European Centre for Disease Prevention and Control (ECDC). All rights reserved.From October 2022 through January 2023, nine patients with NDM-5/OXA-48-carbapenemase-producing Enterobacter hormaechei ST79 were detected in Denmark and subsequently one patient in Iceland. There were no nosocomial links between patients, but they had all been treated with dicloxacillin capsules. An NDM-5/OXA-48-carbapenemase-producing E. hormaechei ST79, identical to patient isolates, was cultured from the surface of dicloxacillin capsules in Denmark, strongly implicating them as the source of the outbreak. Special attention is required to detect the outbreak strain in the microbiology laboratory.Peer reviewe

Work pressure and job dissatisfaction: Challenges in Danish general practice

A main objective of the Nordic healthcare systems is to deliver timely and equal access to high-quality healthcare to the entire population. Health care providers, such as general practitioners (GPs), may therefore experience pressure to deliver care from both the health authorities and patients. However, if GPs’ gains do not outweigh their costs of providing the demanded care, it may lead to job dissatisfaction and thereby potentially to poorer quality of care. This study contributes to the literature by estimating the association between different sources of experienced work pressure and job dissatisfaction among GPs. We use data from a nation-wide survey of Danish GPs distributed in 2019. The study includes six items covering GPs’ experienced work pressure, which we categorise based on the degree to which they are related to demands from either patients or health authorities. Using a series of ordered logit models with a rich set of explanatory variables, we estimate the association between the pressure measures and GP job dissatisfaction. We find that GPs reporting high or considerable work pressure have an increased likelihood of also reporting job dissatisfaction. However, we find considerable heterogeneity in this relationship across different sources of work pressure as well as across GP, practice, and area characteristics. For example, the relationship between pressure from patients’ demands for consultations and job dissatisfaction is stronger among GPs practicing in areas with an undersupply of GPs. Solo practitioners, who cannot share their administrative burdens with colleagues, experience a stronger association between pressure from the health authorities and job dissatisfaction. Policymakers should consider this heterogeneity when implementing new schemes and organisational structures affecting GPs’ work pressure. Published: Online January 2022

Example input and output for RSYD-BASIC pipeline

Input data: 20230914-data-overview.xlsx: mapping of placeholder sample numbers to original SRA accession numbers 1199234567-*.fastq.gz: renamed Illumina MiSeq reads; reads for 1199234567-5 have been obtained by downsampling SRR10955980 madsdata: LIS report and bacteria list used for LIS-specific results Expected results: Results of the RSYD-BASIC pipeline, version 1.8.0, with the test datase

Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022

Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2