Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data

Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases

<i>Staphylococcus aureus</i> Bacteremia from Diffuse Muscular Infection Following Acupuncture Visualized by F-FDG PET/CT and MRI

We describe the clinical course of a 60-year old male admitted with Staphylococcus aureus bacteremia and back-pain. The patient was suspected of having spondylitis and treated as such with antibiotics; however, both fluorine-18 fluoro-2-deoxy-d-glucose (18F-FDG) positron-emission tomography and magnetic resonance imaging (MRI) with iv contrast showed significant inflammation of muscles and subcutaneous soft tissue in relation to the patients back and left shoulder, but no signs of the working diagnosis of spondylitis. The unusual location of the infection was not explained until a few days prior to being discharged when the patient reported visits to a local physiotherapist where he would have acupuncture performed for non-specific back pain. His last acupunctural procedure had been performed 6 days prior to admission. This case is, to our knowledge, the first to show muscular inflammation on both 18-F-FDG PET/CT and MRI following acupuncture due to S. aureus. This case highlights the need for clinicians to search for alternative explanations when imaging does not support the diagnosis

Prognostic accuracy of qSOFA in predicting 28-day mortality among infected patients in an emergency department:a prospective validation study

BACKGROUND: Few prospective studies have evaluated the quick Sequential (Sepsis-Related) Organ Failure Assessment (qSOFA) criteria in emergency department (ED)settings. The aim of this study was to determine the prognostic accuracy of qSOFA compared with systemic inflammatory response syndrome (SIRS) in predicting the 28-day mortality of infected patients admitted to an ED.METHODS: A prospective observational cohort study of all adult (≥18 years) infected patients admitted to the ED of Slagelse Hospital, Denmark, was conducted from 1 October 2017 to 31 March 2018. Patients were enrolled consecutively and data related to SIRS and qSOFA criteria were obtained from electronic triage record. Information regarding mortality was obtained from the Danish Civil Registration System. The original cut-off values of ≥2 was used to determine the prognostic accuracy of SIRS and qSOFA criteria for predicting 28-day mortality and was assessed by analyses of sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratios and area under the receiver operating characteristic curve (AUROC) with 95% confidence intervals (CI).RESULTS: A total of 2112 patients were included in this study. A total of 175 (8.3%) patients met at least two qSOFA criteria, while 1012 (47.9%) met at least two SIRS criteria on admission. A qSOFA criteria of at least two for predicting 28-day mortality had a sensitivity of 19.5% (95% CI 13.6% to 26.5%) and a specificity of 92.6% (95% CI 91.4% to 93.7%). A SIRS criteria of at least two for predicting 28-day mortality had a sensitivity of 52.8% (95% CI 44.8% to 60.8%) and a specificity of 52.5% (95% CI 50.2% to 54.7%). The AUROC values for qSOFA and SIRS were 0.63 (95% CI 0.59 to 0.67) and 0.52 (95% CI 0.48 to 0.57), respectively.CONCLUSION: Both SIRS and qSOFA had poor sensitivity for 28-day mortality. qSOFA improved the specificity at the expense of the sensitivity resulting in slightly higher prognostic accuracy overall.</p

Existing Data Sources for Clinical Epidemiology:The Danish Study Group of Infections of the Brain Database (DASGIB)

Central nervous system (CNS) infections are rare diseases that are associated with considerable morbidity and mortality. Increased knowledge based on contemporary data is a prerequisite for improved management and prevention of these serious conditions. Yet, population-based databases of patients hospitalized with CNS infections remain scarce. The Danish Study Group of Infections of the Brain (DASGIB) has prospectively registered information on all adults ≥18 years of age admitted with CNS infections at departments of infectious diseases in Denmark since 2015. The main variables collected are baseline demographics, blood and cerebrospinal fluid tests, imaging results, and outcome using the Glasgow Outcome Scale score. To investigate important aspects for each type of CNS infections, additional variables are included specifically for bacterial meningitis, viral meningitis, encephalitis, brain abscess, neurosyphilis, and Lyme neuroborreliosis. From 2015 to 2020, a total of 3579 cases of CNS infections have been recorded in the DASGIB database. Using the unique civil registration number assigned to all Danish residents, the database can be unambiguously linked with nationwide healthcare registries at the individual level. This enables researchers to conduct detailed population-based and longitudinal observational studies of risk and prognosis of CNS infections and to compare them with matched population cohorts. The database is well-suited for epidemiological research and the DASGIB network forms a solid infrastructure for future national and international collaborations.</p

Risk factors and prognosis of seizures in adults with community-acquired bacterial meningitis in Denmark:observational cohort studies

Objective To examine predefined risk factors and outcome of seizures in community-acquired bacterial meningitis (CABM).Design Observational cohort studiesSetting DenmarkParticipants In the derivation cohort, we retrospectively included all adults (&gt;15 years of age) with CABM in North Denmark Region from 1998 to 2014 and at Hvidovre and Hillerød hospitals from 2003 to 2014. In the validation cohort, we prospectively included all adults (&gt;18 years of age) with CABM treated at all departments of infectious diseases in Denmark from 2015 to 2017.Primary and secondary outcome measures In the derivation cohort, we used modified Poisson regression to compute adjusted relative risks (RRs) with 95% confidence intervals for predefined risk factors for seizures during CABM as well as for risks of death and unfavourable outcome assessed by the Glasgow Outcome Scale score (1-4). Next, results were validated in the validation cohort.Results In the derivation cohort (n=358), risk factors for seizures at any time were pneumococcal aetiology (RR 1.69, 1.01–2.83) and abnormal cranial imaging (RR 2.27, 1.46–3.53), while the impact of age &gt;65 years and immunocompromise was more uncertain. Examining seizures occurring after admission, risk factors were abnormal cranial imaging (RR 2.23, 1.40–3.54) and immunocompromise (RR 1.59, 1.01–2.50). Seizures at any time were associated with increased risks of in-hospital mortality (RR 1.45, 1.01–2.09) and unfavourable outcome at discharge (RR 1.27, 1.02–1.60). In the validation cohort (n=379), pneumococcal aetiology (RR 1.69, 1.10–2.59) and abnormal cranial imaging (RR 1.68, 1.09–2.59) were confirmed as risk factors for seizures at any time. For seizures occurring after admission, only pneumococcal meningitis (RR 1.92, 1.12–3.29) remained significant. Seizures at any time were also associated with in-hospital mortality (RR 3.26, 1.83–5.80) and unfavourable outcome (RR 1.23, 1.00–1.52) in this cohort.Conclusions Pneumococcal aetiology, immunocompromise and abnormal cranial imaging were risk factors for seizures in CABM. Seizures were strongly associated with mortality and unfavourable outcome

Dexamethasone in adults with viral meningitis: an observational cohort study

ObjectivesTo investigate whether there is a dose-dependent association between empiric dexamethasone and outcome in viral meningitis.MethodsObservational cohort study of adults hospitalized for viral meningitis, both with and without a microbiologically confirmed diagnosis, in Denmark between 2015 and 2020. Dose-dependent associations between dexamethasone (one dose = 10 mg) and an unfavourable outcome (Glasgow Outcome Scale score 1–4) at 30 days after discharge were assessed using weighted logistic regression. Entropy balancing was used to compute weights.ResultsOf 1025 included patients, 658 (64%) did not receive dexamethasone, 115 (11%) received 1–2 doses, 131 (13%) received 3–4 doses, and 121 (12%) received ≥5 doses. Among patients treated with dexamethasone, the median number of doses was higher for those without an identified pathogen than for those with a microbiologically confirmed viral aetiology (5 [interquartile range (IQR) 3–8] vs. 3 [IQR 2–5]; p &lt; 0.001). Using no doses of dexamethasone as a reference, the weighted OR for an unfavourable outcome were 0.55 (95% CI, 0.29–1.07) for 1–2 doses, 1.13 (95% CI, 0.67–1.89) for 3–4 doses, and 1.43 (95% CI, 0.77–2.64) for ≥5 doses. In the subgroup of enteroviral meningitis, the weighted OR was 3.08 (95% CI, 1.36–6.94) for ≥5 doses, but decreased to 2.35 (95% CI, 0.65–8.40) when the reference group was restricted to patients treated with antibiotics for suspected bacterial meningitis.DiscussionThis study showed no dose-dependent association between dexamethasone and an unfavourable outcome in patients with viral meningitis. In enteroviral meningitis, ≥5 doses were associated with an increased risk of an unfavourable outcome. However, sensitivity analysis indicated that the association was affected by unmeasured or residual confounding by severity

Neurosyphilis among people with and without HIV infection:A Danish nationwide prospective, population-based cohort study 2015-2021

Background: Comparative data on clinical presentation, laboratory characteristics, treatment, and outcome of neurosyphilis (NS) in people living with HIV (PLWH) and NS patients without HIV are scarce. Methods: Nationwide, population-based, prospective cohort study on all adults with NS diagnosed between 2015 and 2021 at departments of infectious diseases in Denmark. Results: We identified 108 patients with NS, which equals a yearly incidence of 0.3/100,000 adults. The median age was 49 years, 85 (79%) were male, 43 (40%) were men having sex with men and 20 (22%) were PLWH. Ninety-five (88%) had early NS, 37 (34%) had ocular or ocular and otogenic NS, and 27 (25%) had symptomatic meningitis. Most common symptoms were visual disturbance (44%), skin rash (40%), fatigue (26%) and chancre (17%). Median CSF leukocyte count was 27 × 106 cells/L. PLWH less often had neurological deficits (p = 0.02). Unfavorable outcome was observed in 23 (21%) at discharge of whom 0 were PLWH (p = 0.01). Among the 88 NS patients without HIV a CSF leukocyte count of ≥ 30 × 106 cells/L was associated with unfavorable outcome (OR = 3.3 (95% confidence interval: 1.1–10.4)). Conclusions: PLWH with NS have better outcomes than NS patients without HIV infection.</p

Varicella Zoster Virus encephalitis in Denmark from 2015 to 2019:A nationwide prospective cohort study

BACKGROUND: Knowledge of the epidemiology and clinical characteristics of varicella zoster virus (VZV) encephalitis remains limited. METHODS: Nationwide prospective cohort study of adults treated for microbiologically confirmed VZV encephalitis at Danish departments of infectious diseases from 2015 to 2019. Modified Poisson regression analysis was used to compute adjusted relative risks (RRs) of unfavorable outcome. RESULTS: We identified 92 adults (49% female) with VZV encephalitis, yielding an incidence of 5.3/1 000 000 per year (95% CI, 4.2-6.6). Median age was 75 years (IQR, 67-83) and immunocompromising conditions were frequent (39%). Predominant symptoms were confusion (76%), headache (56%), nausea (45%), gait disturbance (42%), and personality changes (41%). Cranial imaging showed cerebral vasculitis (including infarction and hemorrhage) in 14 (16%) patients and encephalitic abnormalities in 11 (13%) with predilection for the brainstem and deep brain structures. Intravenous acyclovir treatment was initiated a median (IQR) of 13.4 hours (5.2-46.3) since admission, while cranial imaging and lumbar puncture were performed after 6.3 hours (2.5-31.0) and 18.5 hours (4.9-42.0). In-hospital, 1-month, and 3-month mortalities were 4%, 9%, and 11%, respectively. Unfavorable outcome (Glasgow Outcome Score of 1-4) was found in 69% at discharge, with age (adjusted RR [aRR], 1.02; 95% CI, 1.01-1.03), vasculitis (aRR, 1.38; 95% CI, 1.02-1.86), and Glasgow Coma Scale (GCS) &lt;15 (aRR, 1.32; 95% CI, 1.01-1.73) identified as independent risk factors. CONCLUSIONS: VZV encephalitis occurs primarily in elderly or immunocompromised patients with a higher incidence than previously estimated. The diagnosis is often delayed; risk factors for unfavorable outcome are age, cerebral vasculitis, and GCS &lt;15.</p