Disability in Chronic Fatigue Syndrome and Idiopathic Chronic Fatigue

The current investigation classified 31 people with chronic fatigue syndrome (CFS) and 44 people with idiopathic chronic fatigue (ICF) into mild, moderate, and severe/very severe categories of self reported functional impairment. Differences in sociodemographic characteristics, symptom frequency, symptom severity, and functional impairment were examined between individuals with CFS and ICF, and were examined among the three categories of functional impairment. Results indicated that there were no differences between the CFS and ICF groups in their functional impairment classification. People who were classified into the more disabled categories reported more severe symptoms, and were more likely to have scores indicating higher disability on other measures of functional status. Implications of these findings are discussed

Louisville Coronavirus Surveillance Program

An important feature of COVID-19, the disease produced by the new coronavirus SARS-CoV-2, is the high number of health care workers (HCWs) that acquire the disease. In an initial report of 138 patients hospitalized with COVID-19 pneumonia in China, 40 patients (29%) were HCWs. One reason why HCWs are at higher risk of acquiring COVID-19 is because some patients with COVID-19 are admitted to the hospital without the classical presentation, and are therefore not tested for the disease early during hospitalization. Presently in the US, it is recommended to test for COVID-19 when physicians suspect the disease. This subjective approach may allow hospital transmission of COVID-19 from patients without the classical clinical presentation. The primary objective of this study is to establish a surveillance system for early identification of patients hospitalized with COVID-19 to allow for early implementation of infection control interventions in an attempt to prevent transmission of COVID-19 to HCWs and other hospitalized patients. We are proposing to test all patients who present to the emergency departments and/or are hospitalized with signs and symptoms of respiratory infection or gastrointestinal infection for SARS-CoV-2, regardless of clinical suspicion of COVID-19. Biological samples obtained from all patients having symptoms of respiratory or gastrointestinal infection will be tested using real-time polymerase chain reaction (RT-PCR) for detection of SARS-CoV-2. Using a robotic instrument, the CMP laboratory will be able to test more than 500 samples a day. Data will be reported in real-time to participating hospitals for rapid implementation of infection control measures

The Population Affected by the Syndemic of COVID-19 and Poverty is More Likely to be Hospitalized with SARS-CoV-2 Pneumonia

Background Lockdown measures to control COVID-19 have exacerbated the poverty epidemic. We hypothesized that the synergistic interaction of COVID-19 and poverty epidemics favors the development of more severe forms of COVID-19 in the population living in poverty. To test this hypothesis, we assessed whether an ecological association exists between the geographic distribution of hospitalized patients with SARS-CoV-2 pneumonia and markers of poverty in the city of Louisville, KY. Methods Using the geomasked home addresses of hospitalized patients with SARS-CoV-2 pneumonia in the city of Louisville, a kernel density heatmap was created. Kuldorff’s spatial scan statistic was used to calculate areas of increased risk for SARS-CoV-2 pneumonia hospitalization. Heat maps were created for census tract–level demographics according to income, age, race, and ethnicity to assess whether an ecological association exists with the spatial distribution of SARS-CoV-2 pneumonia hospitalization. Results Four areas of increased risk of hospitalization due to SARS-CoV-2 pneumonia were identified in the western and central sections of the city, with relative risks (RRs) ranging from 2.3 to 3.2 (p Conclusions Residents from low-income areas are almost three times more likely to develop SARS-CoV-2 pneumonia requiring hospitalization. Current efforts to decrease the number of COVID-19 hospitalizations through vaccination of populations at risk should be concentrated in city areas with a low-income level population

Bioinformatics in bacterial molecular epidemiology and public health:databases, tools and the next-generation sequencing revolution

Advances in typing methodologies have been the driving force in the field of molecular epidemiology of pathogens. The development of molecular methodologies, and more recently of DNA sequencing methods to complement and improve phenotypic identification methods, was accompanied by the generation of large amounts of data and the need to develop ways of storing and analysing them. Simultaneously, advances in computing allowed the development of specialised algorithms for image analysis, data sharing and integration, and for mining the ever larger amounts of accumulated data. In this review, we will discuss how bioinformatics accompanied the changes in bacterial molecular epidemiology. We will discuss the benefits for public health of specialised online typing databases and algorithms allowing for real-time data analysis and visualisation. The impact of the new and disruptive next-generation sequencing methodologies will be evaluated, and we will look ahead into these novel challenges

Antimicrobial Stewardship in Hospitalized Patients with Respiratory Infections: Ten-Year Experience from the Robley Rex Louisville VA Medical Center

Rationale: Antibiotic stewardship has been defined as coordinated interventions designed to improve and measure the appropriate use of antibiotic agents. Respiratory infections are the most common infectious reason for hospitalization in the United States. Therefore, one could extrapolate that respiratory infections are then also the most common reason for hospital antibiotic use and possess the highest potential for hospital antibiotic misuse. The primary objective of this article was to evaluate the role of antimicrobial stewardship on improving antibiotic use for respiratory infections in hospitalized patients on intravenous (IV) antibiotics at the Robley Rex Louisville VAMC over a 10-year period. Methods: This was a retrospective review of the Robley Rex Louisville VAMC ASP Switch Therapy and Antimicrobial Review database. The study included all Robley Rex Louisville VAMC patients admitted to the hospital and placed on IV antibiotics between January 1st 2007 and December 31st 2016. Results: Recommendations from an antimicrobial stewardship team (AST) improve hospital IV antibiotic use in respiratory infections to a level above 90%. Conclusion: AST recommendations regarding antibiotic use for respiratory infections improve compliance with hospital guidelines. There is an ongoing role for antimicrobial stewardship programs overtime

DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing

© 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License.Dengue virus (DENV) represents a public health threat and economic burden in affected countries. The availability of genomic data is key to understanding viral evolution and dynamics, supporting improved control strategies. Currently, the use of high-throughput sequencing (HTS) technologies, which can be applied both directly to patient samples (shotgun metagenomics) and to PCR-amplified viral sequences (amplicon sequencing), is potentially the most informative approach to monitor viral dissemination and genetic diversity by providing, in a single methodological step, identification and characterization of the whole viral genome at the nucleotide level. Despite many advantages, these technologies require bioinformatics expertise and appropriate infrastructure for the analysis and interpretation of the resulting data. In addition, the many software solutions available can hamper the reproducibility and comparison of results. Here we present DEN-IM, a one-stop, user-friendly, containerized and reproducible workflow for the analysis of DENV short-read sequencing data from both amplicon and shotgun metagenomics approaches. It is able to infer the DENV coding sequence (CDS), identify the serotype and genotype, and generate a phylogenetic tree. It can easily be run on any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement for extensive bioinformatics expertise. Using DEN-IM, we successfully analysed two types of DENV datasets. The first comprised 25 shotgun metagenomic sequencing samples from patients with variable serotypes and genotypes, including an in vitro spiked sample containing the four known serotypes. The second consisted of 106 paired-end and 76 single-end amplicon sequences of DENV 3 genotype III and DENV 1 genotype I, respectively, where DEN-IM allowed detection of the intra-genotype diversity. The DEN-IM workflow, parameters and execution configuration files, and documentation are freely available at https://github.com/B-UMMI/DEN-IM).C. I. M. was supported by the Fundação para a Ciência e Tecnologia (grant SFRH/BD/129483/2017). E. L. received a Abel Tasman Talent Program grant from the UMCG, University of Groningen, Groningen, The Netherlands. This work was partly supported by the ONEIDA project (LISBOA-01–0145-FEDER-016417) co-funded by FEEI–Fundos Europeus Estruturais e de Investimento from Programa Operacional Regional Lisboa 2020 and by national funds from FCT–Fundação para a Ciência e a Tecnologia and by UID/BIM/50005/2019, project funded by Fundação para a Ciência e a Tecnologia (FCT)/ Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) through Fundos do Orçamento de Estado.info:eu-repo/semantics/publishedVersio

Research Support Infrastructure: Implementing a Clinical Research Coordinating Center

Insufficient infrastructure is one of the challenges facing investigators in the field of clinical research. At the University of Louisville (UofL) Division of Infectious Diseases, we developed a multidisciplinary coordinating center with the aim to support investigators in all aspects of the clinical research process. The objective of this article is to describe the composition and the role of the different units of the UofL Clinical Research Coordinating Center. The different components of the Center can serve as a template for institutions interested in developing a clinical research support infrastructure

Measured and modeled humidification factors of fresh smoke particles from biomass burning: role of inorganic constituents

During the 2006 FLAME study (<b>F</b>ire <b>L</b>aboratory <b>a</b>t <b>M</b>issoula <b>E</b>xperiment), laboratory burns of biomass fuels were performed to investigate the physico-chemical, optical, and hygroscopic properties of fresh biomass smoke. As part of the experiment, two nephelometers simultaneously measured dry and humidified light scattering coefficients (<i>b</i><sub>sp(dry) </sub> and <i>b</i><sub>sp(RH)</sub>, respectively) in order to explore the role of relative humidity (RH) on the optical properties of biomass smoke aerosols. Results from burns of several biomass fuels from the west and southeast United States showed large variability in the humidification factor (<i>f</i>(RH)=<i>b</i><sub>sp(RH)</sub>/<i>b</i><sub>sp(dry)</sub>). Values of <i>f</i>(RH) at RH=80–85% ranged from 0.99 to 1.81 depending on fuel type. We incorporated measured chemical composition and size distribution data to model the smoke hygroscopic growth to investigate the role of inorganic compounds on water uptake for these aerosols. By assuming only inorganic constituents were hygroscopic, we were able to model the water uptake within experimental uncertainty, suggesting that inorganic species were responsible for most of the hygroscopic growth. In addition, humidification factors at 80–85% RH increased for smoke with increasing inorganic salt to carbon ratios. Particle morphology as observed from scanning electron microscopy revealed that samples of hygroscopic particles contained soot chains either internally or externally mixed with inorganic potassium salts, while samples of weak to non-hygroscopic particles were dominated by soot and organic constituents. This study provides further understanding of the compounds responsible for water uptake by young biomass smoke, and is important for accurately assessing the role of smoke in climate change studies and visibility regulatory efforts

Estimating HIV transmissions in a large U.S. clinic-based sample: effects of time and syndemic conditions

Introduction: Little is known about onward HIV transmissions from people living with HIV (PLWH) in care. Antiretroviral therapy (ART) has increased in potency, and treatment as prevention (TasP) is an important component of ending the epidemic. Syndemic theory has informed modelling of HIV risk but has yet to inform modelling of HIV transmissions. Methods: Data were from 61,198 primary HIV care visits for 14,261 PLWH receiving care through the Centers for AIDS Research (CFAR) Network of Integrated Clinical Systems (CNICS) at seven United States (U.S.) sites from 2007 to 2017. Patient-reported outcomes and measures (PROs) of syndemic conditions – depressive symptoms, anxiety symptoms, drug use (opiates, amphetamines, crack/cocaine) and alcohol use – were collected approximately four to six months apart along with sexual behaviours (mean = 4.3 observations). Counts of syndemic conditions, HIV sexual risk group and time in care were modelled to predict estimated HIV transmissions resulting from sexual behaviour and viral suppression status (HIV RNA \u3c 400/mL) using hierarchical linear modelling. Results: Patients averaged 0.38 estimated HIV transmissions/100 patients/year for all visits with syndemic conditions measured (down from 0.83, first visit). The final multivariate model showed that per 100 patients, each care visit predicted 0.05 fewer estimated transmissions annually (95% confidence interval (CI): 0.03 to 0.06; p \u3c 0.0005). Cisgender women, cisgender heterosexual men and cisgender men of undisclosed sexual orientation had, respectively, 0.47 (95% CI: 0.35 to 0.59; p \u3c 0.0005), 0.34 (95% CI: 0.20 to 0.49; p \u3c 0.0005) and 0.22 (95% CI: 0.09 to 0.35; p \u3c 0.005) fewer estimated HIV transmissions/100 patients/year than cisgender men who have sex with men (MSM). Each within-patient syndemic condition predicted 0.18 estimated transmissions/100 patients/year (95% CI: 0.12 to 0.24; p \u3c 0.0005). Each between-syndemic condition predicted 0.23 estimated HIV transmissions/100 patients/year (95% CI: 0.17 to 0.28; p \u3c 0.0005). Conclusions: Estimated HIV transmissions among PLWH receiving care in well-resourced U.S. clinical settings varied by HIV sexual risk group and decreased with time in care, highlighting the importance of TasP efforts. Syndemic conditions remained a significant predictor of estimated HIV transmissions notwithstanding the effects of HIV sexual risk group and time in care