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Pneumonia in the ImmunoCompromised - Use of the Karius Test for the Detection of Undiagnosed Pathogens (PICKUP)

The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Know the risks and potential benefits of clinical studies and talk to your health care provider before participating. Read our disclaimer for details. Identifier: NCT04047719
Recruitment Status : Recruiting
First Posted : August 7, 2019
Last Update Posted : February 19, 2020
Duke Clinical Research Institute
Information provided by (Responsible Party):
Karius, Inc.

Brief Summary:
Given the need for a more sensitive pathogen detection test in patients with immunocompromised pneumonia, this study will evaluate the performance of the Karius Test, a novel NGS blood test for the diagnosis of infectious diseases. We will compare the performance of the Karius Test to the results of microbiologic tests obtained as part of usual care for immunocompromised patients undergoing evaluation for suspected pneumonia.

Condition or disease Intervention/treatment
Pneumonia, Bacterial Pneumonia, Viral Pneumonia Fungal Pneumonia Cavitary Immunocompromised Host Diagnostic Test: Karius Test

Detailed Description:

Pneumonia is a major cause of morbidity and mortality in highly immunocompromised individuals such as patients with hematologic malignancies or undergoing hematopoietic stem-cell transplantation. These patients can be infected by a broad range of potential pathogens, including viral, bacterial, and fungal etiologies and sometimes with multiple pathogens simultaneously. Diagnostic testing often fails to identify a microbial etiology for lower respiratory illness even with bronchoalveolar lavage (BAL). In fact, culture methods, PCR, and antigen testing on BAL samples yields a positive result only 30-67% of the time. Additionally, Idiopathic Pulmonary Syndrome (IPS), a non-infectious pulmonary complication of transplant, can have many overlapping symptoms with infectious pneumonia. Treatment for IPS is administration of steroids which can exacerbate infections. Given these reasons, there is a need for better diagnostics to aid in the management of immunocompromised patients with pneumonia.

Karius has developed a microbial cell-free plasma next-generation sequencing test for pathogen detection capable of detecting >1,000 organisms including DNA viruses, bacteria, yeasts, molds, and other eukaryotic pathogens. The test is performed in a CLIA-certified/CAP-accredited laboratory with results typically provided within one day from sample receipt. Given the need for a more sensitive diagnostic test for pneumonia in this population, we are evaluating the performance of the Karius Test for pathogen detection.

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Study Type : Observational
Estimated Enrollment : 195 participants
Observational Model: Cohort
Time Perspective: Prospective
Official Title: Pneumonia in the ImmunoCompromised - Use of the Karius Test for the Detection of Undiagnosed Pathogens
Actual Study Start Date : November 5, 2019
Estimated Primary Completion Date : November 30, 2020
Estimated Study Completion Date : December 31, 2020

Resource links provided by the National Library of Medicine

MedlinePlus related topics: Pneumonia

Group/Cohort Intervention/treatment
Intent-to-Diagnose Population
All subjects enrolled in the study that have at least one Karius Test with a valid result
Diagnostic Test: Karius Test
Karius Test for detection of microbial cell free DNA (mcfDNA) in plasma

Primary Outcome Measures :
  1. Additive clinical diagnostic value [ Time Frame: 7 days ]
    Percent of patients with ≥1 pathogen identified by the Karius Test at enrollment adjudicated as a definite or probable cause of the subject's index pneumonia event with no pathogen identified as a definite or probable cause of the subject's index pneumonia event from an adjudicated composite of all microbiologic test results performed per standard of care iwth results available within 7 days of study enrollment

Biospecimen Retention:   Samples With DNA

Information from the National Library of Medicine

Choosing to participate in a study is an important personal decision. Talk with your doctor and family members or friends about deciding to join a study. To learn more about this study, you or your doctor may contact the study research staff using the contacts provided below. For general information, Learn About Clinical Studies.

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Ages Eligible for Study:   18 Years to 80 Years   (Adult, Older Adult)
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Sampling Method:   Probability Sample
Study Population
Immunocompromised patients with hematologic malignancies ≥ 18 years of age who are being evaluated for infectious pneumonia

Inclusion Criteria:

Patients are eligible for the study if they meet all of the following criteria:

  1. ≥ 18 years of age
  2. Have one of the following hematologic malignancies: Acute Lymphoblastic Leukemia (ALL), Acute Myelogenous Leukemia (AML), Myelodysplastic Syndrome (MDS), Lymphoma (all types), or Multiple Myeloma (MM)
  3. Are immunocompromised defined as having at least one of the following:

    1. Received chemotherapy within the past 30 days
    2. Undergone hematopoietic stem cell transplantation (HSCT) within the past 1 year
    3. Active graft vs host disease (GVHD) requiring immunosuppressive pharmacologic treatment
  4. Are admitted to the hospital with suspected infectious pneumonia warranting diagnostic evaluation and treatment
  5. Have a planned diagnostic bronchoscopy or have undergone a diagnostic bronchoscopy for the evaluation of the microbiologic etiology of pneumonia within the 24 hours prior to enrollment

Exclusion Criteria:

Patients are not eligible for the study if they meet any of the following criteria:

  1. Patient or patient's legally authorized representative does not provide consent for the study
  2. Patient is moribund and, in the opinion of the treating physician, is not expected to survive >24 hours beyond the time of potential study enrollment visit
  3. Microbiologic etiology of index pneumonia event has already been identified per usual care testing
  4. Patient was previously enrolled in this study
  5. Patient has any condition that, in the opinion of the treating physician, will prevent the patient from completing the study

Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its identifier (NCT number): NCT04047719

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Contact: Sudeb Dalai, MD, PhD 650-409-5007 ext 167
Contact: Stacy Meluskey, BS 510-258-9079

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United States, North Carolina
Duke University Recruiting
Durham, North Carolina, United States, 27710
Contact: Stephen Bergin    919-613-6394   
Contact: Matthew Kummerer    919-668-3135   
Principal Investigator: Stephen Bergin, MD         
United States, Pennsylvania
University of Pittsburgh Recruiting
Pittsburgh, Pennsylvania, United States, 15025
Contact: Ghady Haidar, MD    412-648-6212   
Contact: Joshua Kohl    412-648-6556   
Principal Investigator: Haidar Ghady, MD         
United States, Washington
Fred Hutchinson Cancer Center Recruiting
Seattle, Washington, United States, 98109
Contact: Joshua Hill, MD    206-667-6504   
Contact: Jacob Keane-Candib    206-667-6504   
Principal Investigator: Joshua Hill, MD         
Sponsors and Collaborators
Karius, Inc.
Duke Clinical Research Institute
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Principal Investigator: Stephen Bergin, MD Duke University

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Responsible Party: Karius, Inc. Identifier: NCT04047719    
Other Study ID Numbers: KDC-010
First Posted: August 7, 2019    Key Record Dates
Last Update Posted: February 19, 2020
Last Verified: August 2019
Individual Participant Data (IPD) Sharing Statement:
Plan to Share IPD: Undecided

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Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No
Keywords provided by Karius, Inc.:
cell free DNA
microbial cell free DNA
Additional relevant MeSH terms:
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Pneumonia, Bacterial
Pneumonia, Viral
Lung Diseases
Respiratory Tract Diseases
Respiratory Tract Infections
Virus Diseases
Bacterial Infections