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Ephraim Tsalik

Adjunct Associate Professor in the Department of Medicine
Medicine, Infectious Diseases
Box 102359 DUMC, Durham, NC 27710
Room 157 Hanes House Trent DRI, Box 102359, Durham, NC 27710

Selected Publications


Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Patients With Pneumonia: A Prospective Observational Study.

Journal Article Clin Infect Dis · March 20, 2024 BACKGROUND: Pneumonia is a common cause of morbidity and mortality, yet a causative pathogen is identified in a minority of cases. Plasma microbial cell-free DNA sequencing may improve diagnostic yield in immunocompromised patients with pneumonia. METHODS: ... Full text Link to item Cite

Implementation of a Prospective Index-Cluster Sampling Strategy for the Detection of Presymptomatic Viral Respiratory Infection in Undergraduate Students.

Journal Article Open Forum Infect Dis · March 2024 BACKGROUND: Index-cluster studies may help characterize the spread of communicable infections in the presymptomatic state. We describe a prospective index-cluster sampling strategy (ICSS) to detect presymptomatic respiratory viral illness and its implement ... Full text Link to item Cite

Moving Beyond Mortality: Development and Application of a Desirability of Outcome Ranking (DOOR) Endpoint for Hospital-Acquired Bacterial Pneumonia and Ventilator-Associated Bacterial Pneumonia.

Journal Article Clin Infect Dis · February 17, 2024 BACKGROUND: Hospital-acquired and ventilator-associated bacterial pneumonia (HABP/VABP) are frequently caused by multidrug-resistant organisms. Patient-centered endpoints in clinical trials are needed to develop new antibiotics for HABP/VABP. Desirability ... Full text Link to item Cite

Epigenetic and transcriptional responses in circulating leukocytes are associated with future decompensation during SARS-CoV-2 infection.

Journal Article iScience · January 19, 2024 To elucidate host response elements that define impending decompensation during SARS-CoV-2 infection, we enrolled subjects hospitalized with COVID-19 who were matched for disease severity and comorbidities at the time of admission. We performed combined si ... Full text Open Access Link to item Cite

Host-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance.

Journal Article Sci Rep · December 18, 2023 Diagnostic limitations challenge management of clinically indistinguishable acute infectious illness globally. Gene expression classification models show great promise distinguishing causes of fever. We generated transcriptional data for a 294-participant ... Full text Link to item Cite

Peripheral Transcriptomics in Acute and Long-Term Kidney Dysfunction in SARS-CoV2 Infection.

Journal Article medRxiv · October 27, 2023 BACKGROUND: Acute kidney injury (AKI) is common in hospitalized patients with SARS-CoV2 infection despite vaccination and leads to long-term kidney dysfunction. However, peripheral blood molecular signatures in AKI from COVID-19 and their association with ... Full text Link to item Cite

RADx-UP Testing Core: Access to COVID-19 Diagnostics in Community-Engaged Research with Underserved Populations.

Journal Article J Clin Microbiol · August 23, 2023 Research on the COVID-19 pandemic revealed a disproportionate burden of COVID-19 infection and death among underserved populations and exposed low rates of SARS-CoV-2 testing in these communities. A landmark National Institutes of Health (NIH) funding init ... Full text Open Access Link to item Cite

Viewing both sides of the coin for infectious disease diagnosis.

Journal Article J Clin Invest · April 17, 2023 Optimal management of lower respiratory tract infection relies on distinguishing infectious from noninfectious etiologies and identifying the microbiologic cause if applicable. This process is complicated by overlapping clinical symptoms and the colonizing ... Full text Link to item Cite

Efficacy and safety of azithromycin versus placebo to treat lower respiratory tract infections associated with low procalcitonin: a randomised, placebo-controlled, double-blind, non-inferiority trial.

Journal Article Lancet Infect Dis · April 2023 BACKGROUND: Lower respiratory tract infections are frequently treated with antibiotics, despite a viral cause in many cases. It remains unknown whether low procalcitonin concentrations can identify patients with lower respiratory tract infection who are un ... Full text Open Access Link to item Cite

Clinically Adjudicated Reference Standards for Evaluation of Infectious Diseases Diagnostics.

Journal Article Clin Infect Dis · March 4, 2023 Lack of a gold standard can present a challenge for evaluation of diagnostic test accuracy of some infectious diseases tests, particularly when the test's accuracy potentially exceeds that of its predecessors. This approach may measure agreement with an im ... Full text Open Access Link to item Cite

Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease.

Journal Article Cell Rep Methods · February 27, 2023 Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stabi ... Full text Open Access Link to item Cite

Screening tools for predicting mortality of adults with suspected sepsis: an international sepsis cohort validation study.

Journal Article BMJ Open · February 20, 2023 OBJECTIVES: We evaluated the performance of commonly used sepsis screening tools across prospective sepsis cohorts in the USA, Cambodia and Ghana. DESIGN: Prospective cohort studies. SETTING AND PARTICIPANTS: From 2014 to 2021, participants with two or mor ... Full text Open Access Link to item Cite

Murine Host Response to Typical and Atypical Pneumonia

Conference AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE · 2023 Cite

Access to COVID-19 testing by individuals with housing insecurity during the early days of the COVID-19 pandemic in the United States: a scoping review.

Journal Article Front Public Health · 2023 INTRODUCTION: The COVID-19 pandemic focused attention on healthcare disparities and inequities faced by individuals within marginalized and structurally disadvantaged groups in the United States. These individuals bore the heaviest burden across this pande ... Full text Open Access Link to item Cite

Omic approaches to infectious disease testing

Chapter · January 1, 2023 A pathogen-based approach to infectious disease diagnosis has long been the gold standard, despite poor sensitivity, specificity, or long time to result with this method. The host response offers a robust and complementary approach to infectious disease di ... Full text Cite

Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature.

Journal Article Cell Syst · December 21, 2022 The identification of a COVID-19 host response signature in blood can increase the understanding of SARS-CoV-2 pathogenesis and improve diagnostic tools. Applying a multi-objective optimization framework to both massive public and new multi-omics data, we ... Full text Link to item Cite

Host Gene Expression to Predict Sepsis Progression.

Journal Article Crit Care Med · December 1, 2022 OBJECTIVES: Sepsis causes significant mortality. However, most patients who die of sepsis do not present with severe infection, hampering efforts to deliver early, aggressive therapy. It is also known that the host gene expression response to infection pre ... Full text Link to item Cite