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

February 7, 2023 updated by: Karius, Inc.
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.

Study Overview

Status

Completed

Conditions

Intervention / Treatment

Detailed Description

Pneumonia is a major cause of morbidity and mortality in highly immunocompromised individuals such as patients with hematologic malignancies and/or hematopoietic stem cell transplant. 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.

Study Type

Observational

Enrollment (Actual)

257

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Contact Backup

Study Locations

  • United States
    • California
      • Duarte, California, United States, 91010
        • City of Hope Comprehensive Cancer Center
      • San Francisco, California, United States, 94143
        • UCSF Department of Medicine
    • Colorado
      • Aurora, Colorado, United States, 80045
        • University of Colorado Denver
    • Louisiana
      • New Orleans, Louisiana, United States, 70112
        • Tulane Section of Infectious Disease
    • New York
      • New York, New York, United States, 10065
        • Memorial Sloan Kettering Cancer Center
      • New York, New York, United States, 10021
        • Weill Cornell Medicine
    • North Carolina
      • Durham, North Carolina, United States, 27710
        • Duke University
    • Pennsylvania
      • Pittsburgh, Pennsylvania, United States, 15025
        • University of Pittsburgh
    • Texas
      • Houston, Texas, United States, 77030
        • MD Anderson Cancer Center
    • Washington
      • Seattle, Washington, United States, 98109
        • Fred Hutchinson Cancer Center

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

18 years to 80 years (ADULT, OLDER_ADULT)

Accepts Healthy Volunteers

No

Genders Eligible for Study

All

Sampling Method

Probability Sample

Study Population

Immunocompromised adult patients being evaluated for pneumonia who have undergone hematopoietic stem cell transplantation for any clinical indication or are receiving active chemotherapy for treatment of a hematologic malignancy.

Description

Inclusion Criteria:

Subjects must meet all of the criteria in Section A and all of the criteria in either Section B, Section C or Section D.

Section A:

  1. Patient is ≥ 18 years of age.
  2. Is currently admitted to the hospital.
  3. Has a suspected infectious pneumonia warranting diagnostic evaluation and treatment.
  4. Has undergone a diagnostic bronchoscopy for the evaluation of microbiologic etiology of pneumonia within 1 day prior to or has a scheduled bronchoscopy within 5 days following enrollment.
  5. Patient or patient's Legally Authorized Representative (LAR) has provided consent for the study.

Section B:

  1. Has one of the following hematologic malignancies: Acute Lymphoblastic Leukemia (ALL), Acute Myelogenous Leukemia (AML), Myelodysplastic Syndrome (MDS), Lymphoma (any type), Multiple Myeloma (MM) or malignant transformation of Chronic Lymphocytic Leukemia (CLL/SLL).

  2. Are immunocompromised defined as having at least one of the following:

    1. Received chemotherapy within the last 45 days.
    2. A relapse of hematologic malignancy for which chemotherapy treatment is anticipated within the next 45 days.
    3. ANC<500 for a minimum of 14 days and within 8 weeks prior to enrollment.

Section C:

  1. Has undergone autologous hematopoietic stem cell transplantation (e.g. bone marrow transplantation) for one of the following hematologic malignancies: Acute Lymphoblastic Leukemia (ALL), Acute Myelogenous Leukemia (AML), Myelodysplastic Syndrome (MDS), Lymphoma (any type), or Multiple Myeloma (MM);), or malignant transformation of Chronic Lymphocytic Leukemia (CLL/SLL).

  2. Are immunocompromised defined as having at least one of the following:

    1. Undergone autologous hematopoietic stem cell transplantation (HSCT) within the past 6 months.
    2. Received chemotherapy within the last 45 days.
    3. A relapse of hematologic malignancy for which chemotherapy treatment is anticipated within the next 45 days.

Section D:

  1. Has undergone allogeneic hematopoietic stem cell transplantation (e.g., bone marrow transplantation) for any clinical indication.

  2. Are immunocompromised defined as having at least one of the following:

    1. Has undergone hematopoietic stem cell transplantation (HCST) within the past 1 year.
    2. Has active graft versus host disease (GVHD) requiring immunosuppressive pharmacologic treatment.

Exclusion Criteria:

  1. 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.
  2. Microbiologic etiology of index pneumonia event has already been identified per local Standard of Care testing.
  3. Patient was previously enrolled in this study.
  4. Patient has any condition that, in the opinion of the treating physician, will prevent the patient from completing the study. (Note: a qualified patient may still enroll in the study if they decline to have exploratory research sample collected.)
  5. Patient is positive for SARS-COV-2 by any molecular testing within the 14 days prior to enrollment.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Observational Models: Cohort
  • Time Perspectives: Prospective

Cohorts and Interventions

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

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Additive clinical diagnostic value
Time Frame: 7 days
Percent of patients with ≥1 pathogen identified by the Karius Test collected at enrollment that is adjudicated as a probable cause of the subject's index pneumonia event with no pathogen identified as a probable cause of the subject's index pneumonia event from an adjudicated composite of all microbiologic test results performed per Standard of Care with results available within 7 days of study enrollment.
7 days

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Karius, Inc.

Collaborators

Duke Clinical Research Institute

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (ACTUAL)

November 5, 2019

Primary Completion (ACTUAL)

June 6, 2022

Study Completion (ACTUAL)

June 6, 2022

Study Registration Dates

First Submitted

August 5, 2019

First Submitted That Met QC Criteria

August 5, 2019

First Posted (ACTUAL)

August 7, 2019

Study Record Updates

Last Update Posted (ESTIMATE)

February 9, 2023

Last Update Submitted That Met QC Criteria

February 7, 2023

Last Verified

February 1, 2023

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • KDC-010

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

UNDECIDED

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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