The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches.

Abstract

Background

Candidemia is one of the most common nosocomial bloodstream infections in the United States, causing significant morbidity and mortality in hospitalized patients, but the breadth of the host response to Candida infections in human patients remains poorly defined.

Methods

In order to better define the host response to Candida infection at the transcriptional level, we performed RNA sequencing on serial peripheral blood samples from 48 hospitalized patients with blood cultures positive for Candida species and compared them to patients with other acute viral, bacterial, and non-infectious illnesses. Regularized multinomial regression was utilized to develop pathogen class-specific gene expression classifiers.

Results

Candidemia triggers a unique, robust, and conserved transcriptomic response in human hosts with 1641 genes differentially upregulated compared to healthy controls. Many of these genes corresponded to components of the immune response to fungal infection, heavily weighted toward neutrophil activation, heme biosynthesis, and T cell signaling. We developed pathogen class-specific classifiers from these unique signals capable of identifying and differentiating candidemia, viral, or bacterial infection across a variety of hosts with a high degree of accuracy (auROC 0.98 for candidemia, 0.99 for viral and bacterial infection). This classifier was validated on two separate human cohorts (auROC 0.88 for viral infection and 0.87 for bacterial infection in one cohort; auROC 0.97 in another cohort) and an in vitro model (auROC 0.94 for fungal infection, 0.96 for bacterial, and 0.90 for viral infection).

Conclusions

Transcriptional analysis of circulating leukocytes in patients with acute Candida infections defines novel aspects of the breadth of the human immune response during candidemia and suggests promising diagnostic approaches for simultaneously differentiating multiple types of clinical illnesses in at-risk, acutely ill patients.

Department

Description

Provenance

Citation

Published Version (Please cite this version)

10.1186/s13073-021-00924-9

Publication Info

Steinbrink, Julie M, Rachel A Myers, Kaiyuan Hua, Melissa D Johnson, Jessica L Seidelman, Ephraim L Tsalik, Ricardo Henao, Geoffrey S Ginsburg, et al. (2021). The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches. Genome medicine, 13(1). p. 108. 10.1186/s13073-021-00924-9 Retrieved from https://hdl.handle.net/10161/26027.

This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.

Scholars@Duke

Steinbrink

Julie Steinbrink

Assistant Professor of Medicine

I am a transplant infectious diseases physician. My clinical care focuses on the management of infections in immunocompromised patients, including solid organ and bone marrow transplant recipients, as well as cancer patients. My research focuses on developing noninvasive biomarker diagnostics and severity prognostic tools for infectious diseases in immunocompromised patients.

Johnson

Melissa DePaoli Johnson

Professor in Medicine

Prognostic indicators for patients with Candida spp. bloodstream infections
Antifungal pharmacokinetics/pharmacodynamics
Immunogenetics among patients with candidiasis
Management of the HIV infected patient and antiretroviral pharmacotherapy
Antibacterial drug utilization, resistance, and appropriate prescribing
Antimicrobial Stewardship

Tsalik

Ephraim Tsalik

Adjunct Associate Professor in the Department of Medicine

My research at Duke has focused on understanding the dynamic between host and pathogen so as to discover and develop host-response markers that can diagnose and predict health and disease.  This new and evolving approach to diagnosing illness has the potential to significantly impact individual as well as public health considering the rise of antibiotic resistance.

With any potential infectious disease diagnosis, it is difficult, if not impossible, to determine at the time of presentation what the underlying cause of illness is.  For example, acute respiratory illness is among the most frequent reasons for patients to seek care. These symptoms, such as cough, sore throat, and fever may be due to a bacterial infection, viral infection, both, or a non-infectious condition such as asthma or allergies.  Given the difficulties in making the diagnosis, most patients are inappropriately given antibacterials.  However, each of these etiologies (bacteria, virus, or something else entirely) leaves a fingerprint embedded in the host’s response. We are very interested in finding those fingerprints and exploiting them to generate new approaches to understand, diagnose, and manage disease.

These principles also apply to sepsis, defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Just as with acute respiratory illness, it is often difficult to identify whether infection is responsible for a patient’s critical illness.  We have embarked on a number of research programs that aim to better identify sepsis; define sepsis subtypes that can be used to guide future clinical research; and to better predict sepsis outcomes.  These efforts have focused on many systems biology modalities including transcriptomics, miRNA, metabolomics, and proteomics.  Consequently, our Data Science team has utilized these highly complex data to develop new statistical methods, furthering both the clinical and statistical research communities.

These examples are just a small sampling of the breadth of research Dr. Tsalik and his colleagues have conducted.  

In April 2022, Dr. Tsalik has joined Danaher Diagnostics as the VP and Chief Scientific Officer for Infectious Disease, where he is applying this experience in biomarkers and diagnostics to shape the future of diagnostics in ID. 

Henao

Ricardo Henao

Associate Professor in Biostatistics & Bioinformatics
Ginsburg

Geoffrey Steven Ginsburg

Adjunct Professor in the Department of Medicine

Dr. Geoffrey S. Ginsburg's research interests are in the development of novel paradigms for developing and translating genomic information into medical practice and the integration of personalized medicine into health care.

Alexander

Barbara Dudley Alexander

Professor of Medicine

Clinical research related to infectious complications of solid organ and bone marrow transplantation, with a particular interest in the treatment and rapid diagnosis of fungal disease. Training the next generation of Transplant Infectious Disease Physicians is a special focus of mine as the Principal Investigator of our Interdisciplinary T32 Training Program funded the NIH. 

McClain

Micah Thomas McClain

Associate Professor of Medicine

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