Translational Medical Research Commons^™

H1n1 Influenza Virus (Swine Flu): A Comprehensive Insight Into Escalating Catch-22 Scenarios, Muhammad Shahzaib, Ehsan Ul Haq

The University of Louisville Journal of Respiratory Infections

Introduction: Viruses have always been a major cause of various disastrous pandemics in mankind’s history. H1N1 became a threat when its original strain was first discovered back in the swine flu pandemic of 2009. It became highly catastrophic on a large scale because none of the therapeutic interventions and methodologies that were already present at the time were effective against the virus.

Methods: A vast amount of literature and research is available regarding H1N1 influenza from different reputable sources online. The data were gathered with the contrasting and relative situations of 1918 and 2009 pandemics in mind. The overall extracted …

Assessment Of Pneumonia Severity Indices As Mortality Predictors, Connor L. English, Thomas Chandler, Brian E. Guinn, Stephen P. Furmanek, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

BACKGROUND

The leading cause of infectious disease death in the United States is community-acquired pneumonia (CAP). Several pneumonia severity indices exist and are widely used as tools to assist physicians regarding site of care based on risk of death. However, limited data exists that discerns which of the most commonly used severity scores is the best predictor of mortality across multiple time points. The objective of this study is to determine the best mortality predictor at different time points between four of the most commonly used pneumonia severity scores.

METHODS

This was a secondary analysis of a prospective, multicenter, population-based, …

Towards Multi-Lingual Pneumonia Research Data Collection Using The Community-Acquired Pneumonia International Cohort Study Database, William A. Mattingly, Kimberley A. Buckner, Senen Pena

The University of Louisville Journal of Respiratory Infections

Background: Although multilingual interfaces are preferred by most users when they have a choice, organizations are often unable to support and troubleshoot problems involving multiple user languages. Software that has been structured with multiple languages and data interlinking considerations early in its development is more likely to be easily maintained. We describe the process of adding multilingual support to the CAPO international Cohort study database using REDCap.

Methods: Using Google Translate API we extend the supported Spanish language version of REDCap to the most recent version used by CAPO, 8.1.4. We then translate the English data dictionary for CAPO to …

Clinical Research In Pneumonia: Role Of Artificial Intelligence, Timothy L. Wiemken, Robert R. Kelley, William A. Mattingly, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Beta-Lactam Plus Macrolide Vs Fluoroquinolone For Empiric Therapy Of Hospitalized Patients With Cap: Results From The University Of Louisville Pneumonia Study, Vidyulata Salunkhe, Stephen P. Furmanek, Forest W. Arnold

The University of Louisville Journal of Respiratory Infections

Background

Current guidelines recommend a β-lactam plus a macrolide or fluoroquinolone monotherapy as initial empiric antibiotic therapy for treatment of patients hospitalized with community-acquired pneumonia (CAP). Multiple studies have shown different results comparing the two regimens for the treatment of CAP. Our objective, in a city-wide prospective study, was to compare outcomes among hospitalized patients with CAP who received empiric treatment either with a β-lactam plus a macrolide or fluoroquinolone monotherapy.

Methods

This was a propensity score matched case-control study of the University of Louisville Pneumonia Study. It was a prospective population-based cohort study of all hospitalized adults with CAP. …

Pulmonary Aspergillosis: A Review On Diagnosis And Management, Bilal A. Jalil, Juan M. Galvis, Karim A. El Kersh, Mohamed Saad, Mostafa M. Fraig, Juan J. Guardiola Ii

The University of Louisville Journal of Respiratory Infections

Aspergillosis is acquired by inhalation of spores of Aspergillus, a ubiquitous species in the environment. In normal hosts, spore inhalation rarely causes lung disease.

Pulmonary aspergillosis covers a wide spectrum of clinical syndromes depending on the interaction between Aspergillus and the host (immune-status, prior bronchopulmonary disease). It runs the gamut from invasive aspergillosis to Aspergillus bronchitis and colonization.

Invasive aspergillosis occurs in severely immunocompromised patients, typically with neutropenia. Chronic pulmonary aspergillosis affects patients with chronic structural lung disease such as chronic obstructive pulmonary disease, mycobacterial lung disease, but without significant immunocompromise. Aspergillus bronchitis affects patients with bronchial disease such …

A Continuum Of Disease From Community-Acquired Pneumonia To Multiple Organ Dysfunction Syndrome, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Characteristics And Clinical Outcomes Of Hospitalized Patients With Community-Acquired Pneumonia Who Are Active Intravenous Drug Users, Vidyulata Salunkhe, Paula Peyrani, Leslie A. Beavin, Stephen P. Furmanek, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Background: Intravenous drug users (IVDU) have a 10-fold increased risk of community-acquired pneumonia (CAP) compared to the general population. There is scarce data available evaluating the clinical outcomes of IVDU hospitalized patients with CAP and that data mostly focuses on mortality. The objective of this study was to evaluate the clinical characteristics, incidence and outcomes of hospitalized patients with CAP in active intravenous drug users in Louisville, Kentucky.

Methods: This was a secondary data analysis of the University of Louisville Pneumonia study. IVDU patients were propensity score matched to a non-IVDU group. Study outcomes were time to clinical stability (TCS), …

Pulmonary Histoplasmosis In A Patient With Cough, Dyspnea, Pulmonary Nodule And Rheumatologic Manifestations: Case Report And Review, Johnson Britto

The University of Louisville Journal of Respiratory Infections

In this case report we describe a case of pulmonary histoplasmosis in a healthy adult female living in Kentucky. The patient presented with two months history of poly-arthralgia and myalgia, intermittent dry cough, chest tightness, exertional dyspnea, malaise, fatigue and one week history of skin rash. She did not respond to broad-spectrum antibiotic therapy and she also had extensive endocrine and rheumatologic work up that was negative. A diagnosis of histoplasmosis was established based on radiological findings as well as endobronchial ultrasound-guided transbronchial needle aspiration cytology (EBUS-TBNA) of mediastinal lymph nodes demonstrating necrotizing granuloma with fungal stains positive for Histoplasma. …

A Software Tool For Automated Upload Of Large Clinical Datasets Using Redcap And The Capo Database, William A. Mattingly, Christopher Sinclair, Danna Williams, Matthew Grassman, Stephen Furmanek, Kimberley Buckner, Mohammad Tahboub

The University of Louisville Journal of Respiratory Infections

Introduction: Obtaining clinical data from healthcare sources is necessary for conducting clinical research. New technologies now allow for connecting a research database to Electronic Medical Records remotely, allowing the automatic import of clinical research data. In this paper we design and evaluate a REDCap extension to import clinical records from an external health database.

Methods: Many hospital EHRs are designed to use secure file transfer protocol (SFTP) repositories for data communication. We develop a REDCap plugin to connect to an external SFTP file repository for the import of clinical record data. We use the CAPO instance of REDCap and a …

Duration Of Antibiotic Therapy For Patients With Bacteremic Staphylococcus Aureus Community-Acquired Pneumonia, Julio A. Ramirez, Thomas File, Daniel Musher

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Non-Resolving Community Acquired Pneumonia (Cap) Due To Blastomyces Dermatitidis (Pulmonary Blastomycosis): Case Report And Review Of Literature, Johnson Britto

The University of Louisville Journal of Respiratory Infections

In this case report, we describe a case of progressive acute pulmonary blastomycosis in a healthy adult living in Kentucky, initially presenting with flu like illness with a left sided consolidation, who did not respond to antibiotic therapy. Patient’s clinical condition deteriorated with development of necrotizing bronchopneumonia, mediastinal lymphadenopathy, tree-in-bud reticulonodularity and pleural effusion. A diagnosis of progressive pulmonary blastomycosis was established by radiological findings as well as transbronchial needle aspiration cytology and bronchoalveolar lavage culture demonstrating Blastomyces dermatitidis. Patient showed significant clinical improvement with resolution of pulmonary lesions on antifungal treatment. Since symptoms of blastomycosis are often similar to …

An Hiv-Positive Patient With Copd Admitted To The Icu With Respiratory Failure, Bhavani Puskur, Veronica Corcino, Srikant Ramachandruni, Viswanathan Nagarajan, Forest W. Arnold

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Communication Between Clinicians And The Hospital-Based Microbiology Laboratory: Strategies For 2018 And Beyond, Hans H. Liu

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Real-Time Pcr Detection Of Mycoplasma Pneumoniae, Chlamydia Pneumoniae And Legionella Pneumophila In Respiratory Specimens Using The Aries® System, Subathra Marimuthu, Leslie A. Wolf, James T. Summersgill

The University of Louisville Journal of Respiratory Infections

Background: Mycoplasma pneumoniae (Mpn), Chlamydia pneumoniae (Cpn), and Legionella pneumophila (Lpn) can cause both epidemic and endemic occurrences of acute respiratory disease and are responsible for up to 22% of cases of community acquired pneumonia. Due to the limited availability of FDA-approved molecular diagnostic assays, we developed and evaluated a multiplexed Real-time PCR assay for the detection of these agents in two respiratory specimen types on the Luminex ARIES® instrument. The instrument provides for nucleic acid extraction plus PCR amplification and target detection in the same cassette. The ARIES® instrument generates a cycle threshold value and a confirmatory melt curve …

Adult Patients Living With Human Immunodeficiency Virus Hospitalized For Community-Acquired Pneumonia In The United States: Incidence And Outcomes, Leslie A. Beavin, Stephen P. Furmanek, Paula Peyrani, Anupama Raghuram, Forest W. Arnold, Mark Burns, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Background: Community-acquired pneumonia (CAP) is a common infectious reason for hospitalization of adults in the United States (US), including those with Human Immunodeficiency Virus (HIV). While there are studies detailing the incidence and outcomes for all adults with CAP we are not aware of a recent study detailing incidence and outcomes in adult HIV patients hospitalized with CAP. The objectives of this study were (1) to define the current incidence and outcomes of adult HIV patients hospitalized with CAP in Louisville, Kentucky, and (2) to estimate the burden of CAP in the US HIV adult population.

Methods: This was a …

Mycobacterium Kansasii As The Primary Etiology Of Pulmonary Infections Due To Non-Tuberculous Mycobacterium (Ntm) In Patients Without Human Immunodeficiency Virus (Hiv): Experience From A Center In Buenos Aires, Argentina, Gabriel Yusti, Marcela Heres, Alejandra González, Mariano Fielli, Adrian Ceccato, Alejandra Zapata

The University of Louisville Journal of Respiratory Infections

Introduction: Pulmonary diseases due to non-tuberculous mycobacterium (NTM) lung infection in HIV-negative patients are rarely described in the literature. Currently, NTM consist of more than 150 species, and they are globally ubiquitous in both natural and man-made environments.The objective of this study was to define the most frequent species of NTM causing pulmonary disease in HIV-negative patients in the city of Buenos Aires, Argentina. The prevalence of pulmonary diseases caused by NTM is difficult to determine since the isolation of NTM does not necessarily indicate disease.

Methods: A retrospective review of all the respiratory cultures positive for NTM in the …

Effectiveness Of The Influenza Vaccine In Preventing Hospitalizations Of Patients With Influenza Community-Acquired Pneumonia, Thomas Chandler, Stephen P. Furmanek, Connor L. English, Connor Glick, Wesley Trail, Lara Daniels, Ugochukwu Owolabi, Ruth Carrico, Julio A. Ramirez, Timothy L. Wiemken

The University of Louisville Journal of Respiratory Infections

Introduction: Influenza vaccination is the primary strategy for prevention of influenza infection. Influenza infection can vary from mild or even asymptomatic illness to severe community-acquired pneumonia (CAP). Although many national and international investigators and organizations report annual estimates of influenza vaccine effectiveness for prevention of influenza infection in the community, few studies report estimates for the prevention of hospitalizations due to influenza CAP, the most severe form of the infection. The objective of this study is to determine the effectiveness of the influenza vaccine for prevention of hospitalization in patients with influenza-associated CAP.

Methods: This was a test-negative study using …

Research Support Infrastructure: Implementing A Clinical Research Coordinating Center, Julio A. Ramirez, Paula Peyrani, William A. Mattingly, Forest W. Arnold, Timothy L. Wiemken, Robert R. Kelley, Leslie A. Wolf, Ruth M. Carrico, The Clinical Research Coordinating Center Team

The University of Louisville Journal of Respiratory Infections

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.

Bacteremic Pneumococcal Pneumonia: A Longitudinal Study In 279 Adult Patients From A Single Center, Jorge H. Gentile, Claudia Hernandez, Monica D. Sparo, Edgardo M. Rodriguez, Carolina Ceriani, Florencia Bruggesser

The University of Louisville Journal of Respiratory Infections

Background: Bacteremic pneumococcal pneumonia (BPP) is the most common clinical presentation of invasive pneumococcal disease (IPD). Although it has been extensively studied, there is little knowledge in our region in relation to burden of disease, demographic and outcome features.

Methods: We conducted a prospective, longitudinal, observational study from 1989 to 2015 in adult patients with BPP, in order to deepen our knowledge of the characteristics of this disease in our community hospital in Tandil, Argentina.

Results: 279 patients were included. The mean incidence was 2.8/1000 admissions with a sharp decrease in the last two years, reaching 0.8/1000 admissions. Mean patient …

Clinical Research: From Idea To Publication, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Julio A. Ramirez, M.D., FACP, Professor of Medicine/Associate Professor of Microbiology and Immunology; Chief, Division of Infectious Diseases; Director, Infectious Diseases Fellowship Training Program and Founding Director, Global Health Initiative at The University of Louisville, presented "Clinical Research: From Idea to Publication" at University of Louisville Department of Medicine Grand Rounds on February 15, 2018. The talk focused on performing an overview of clinical study designs, describing the planning and performing of a clinical study, reviewing the process for statistical and clinical analysis, and presenting the structure of a Clinical Research Coordinating Center.

Research Support Infrastructure: Implementing A Clinical Research Coordinating Center, Julio A. Ramirez, Paula Peyrani, William A. Mattingly, Forest W. Arnold, Timothy L. Wiemken, Robert R. Kelley, Leslie A. Wolf, Ruth M. Carrico, Andrea Reyes-Vega

Faculty Scholarship

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.

Distributing Data And Analysis Software Containers For Better Data Sharing In Clinical Research, William A. Mattingly Phd, Stephen Furmanek, Christopher M. Sinclair, Timothy L. Wiemken Phd

The University of Louisville Journal of Respiratory Infections

Introduction: Data sharing in clinical research is critical for increasing knowledge discovery. Data and software tools should be FAIR: Findable, Accessible, Inter-operable and Re-usable. Many bottlenecks exist in the process of a clinical investigator using shared data including data acquisition and statistical analysis. The objective of this project is to develop a structure for sharing data and providing rapid automated statistical analysis through creation of a pre-packaged, open-source software container.

Methods: We use the open source software container technologies VirtualBox and Vagrant to create a template for sharing clinical data and analysis scripts as a single container. We use …

Streptococcus Pneumoniae Antigen, Missing Opportunities Of A Promising Point Of Care Diagnostic Test, Magdelina Słomka, Ruby Gupta, Baltej Singh, Venkatesh Gondhi, Siddartha Bhandary, Ekezie Francis, Jose Bordon

The University of Louisville Journal of Respiratory Infections

Background: The etiologic diagnosis of community acquired pneumonia (CAP) and community-acquired meningitis (CAM) are still far from optimal accuracy and turnaround time. The most common bacterial pathogen identified in both CAP and CAM is Streptococcus pneumoniae.

Methods: We reviewed the literature on S. pneumoniae antigen to highlight opportunities to optimize its use as a point of care diagnostic test to maximize quality of patient care, antimicrobial stewardship outcomes and cost saving. A PubMed search was performed using key words “S. pneumoniae antigen; rapid diagnostic tests for S. pneumoniae”. We selected articles in English and sorted into randomized …

Most Common Statistical Methodologies In Recent Clinical Studies Of Community-Acquired Pneumonia, Stephen Furmanek, Connor L. English, Thomas Chandler, Timothy L. Wiemken Phd

The University of Louisville Journal of Respiratory Infections

Background: Training new individuals in pneumonia research is imperative to produce a new generation of clinical investigators with the expertise necessary to fill gaps in knowledge. Clinical investigators are often intimidated by their unfamiliarity with statistics. The objective of this study is to define the most common statistical methodologies in recent clinical studies of CAP to inform teaching approaches in the field.

Methods: Articles met inclusion criteria if they were clinical research with an emphasis on incidence, epidemiology, or patient outcomes, searchable via PubMed or Google Scholar, published within the timeframe of January 1st 2012 to August 1st 2017, …

Rationale And Methods Of The Study Protocol: Streptococcus Pneumoniae Serotypes In Adults 18 Years And Older With Radiographically-Confirmed Community-Acquired Pneumonia (Cap), Ronika Alexander, Paula Peyrani, Julio A. Ramirez, Wesley H. Self Md, Mph, Carlos Grijalva, Francis Counselman, Gregory A. Volturo, Heidi Kabler, Luis Ostrosky-Zeichner, Richard Wunderink, Robert L. Sherwin, Senen Pena, Thomas File, Timothy L. Wiemken, Sharon Gray, Michael Pride, Kimbal D. Ford, Qin Jiang, Raul Isturiz

The University of Louisville Journal of Respiratory Infections

This study was an active, prospective surveillance study of adults 18 years and older hospitalized with community-acquired pneumonia (CAP) due to Streptococcus pneumoniae conducted at 21 hospitals in ten cities across the United States. This report describes the surveillance methodology applied between October 7, 2013 and September 30, 2016, including the identification and description of surveillance areas and populations at-risk for CAP hospitalization for estimation of incidence rates for selected study sites.

Pneumonia Pathogenesis And The Lung Microbiome: Back To The Drawing Board, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Level Of Recall Bias Regarding Pneumococcal Vaccination History Among Adults Hospitalized With Community-Acquired Pneumonia: Results From The University Of Louisville Pneumonia Study, Sarah Van Heiden, Ruth Carrico, Timothy L. Wiemken, Ronika Alexander, John M. Mclaughlin, Qin Jiang, Paula Peyrani, William A. Mattingly, Stephen P. Furmanek, Connor L. English, Senen Pena, Raul Isturiz, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Background: Recall bias is likely to occur in vaccine effectiveness studies using self-reported vaccination history. The validity of patient-reported vaccination status for adults is not well defined. The objective of this study was to evaluate the validity of self-reported pneumococcal vaccination history among patients hospitalized with community-acquired pneumonia (CAP).

Methods: Prospective ancillary study of a population-based observational study of hospitalized patients with CAP in the city of Louisville. To be included in the analysis, patients had to (i) be reached by phone 30-days after discharge from the hospital and (ii) report that they remembered whether or not they received a …

Preliminary Evaluation Of An Lyta Pcr Assay For Detection Of Streptococcus Pneumoniae In Urine Specimens From Hospitalized Patients With Community-Acquired Pneumonia, Subathra Marimuthu, James T. Summersgill, Kuldeep Ghosh, Leslie A Wolf

The University of Louisville Journal of Respiratory Infections

Community acquired pneumonia (CAP) due to Streptococcus pneumoniae still occurs in at risk populations, despite the availability of effective vaccines. Laboratory confirmation of S. pneumoniae remains challenging in cases of CAP despite advances in blood culture techniques and the availability of nucleic acid amplification tests such as PCR-based methods. Urine specimens are an attractive sample type because they are non-invasive compared to bronchial washes or whole blood specimens for patients with CAP. While urine specimens have been used successfully in antigen detection assays, they have not been extensively evaluated for PCR-based assays. In this preliminary study, we evaluated the potential …

Antimicrobial Stewardship In Hospitalized Patients With Respiratory Infections: Ten-Year Experience From The Robley Rex Louisville Va Medical Center, Leslie A. Beavin, Forest W. Arnold, Paula Peyrani, Anupama Raghuram, David Newman, Ronald Smith, Carmen Sciortino, Stephen P. Furmanek, Ruth M. Carrico, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

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: …