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Pneumonia, BacterialPICKUPNCT04047719

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

An observational study of Pneumonia, Bacterial and Pneumonia, Viral, run by Karius, Inc. at 10 sites in United States.

Completed

Finished. The study has ended and is not enrolling. Results may be posted on the official record.

Official record
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Trial 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. Read more about this study

Who is it for?
Ages 18 to 80 years
What is being tested?
Karius Test
How many people
257 participants
Where
10 sitesUnited States
Study dates
5 Nov 2019to 6 Jun 2022
Phase
Observational
Are there results?
None posted in the registry

Key requirements

Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.

  • Ages 18 to 80 years
  • All sexes
  • No healthy volunteers
  • Adult, Older adult

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.

Who may be able to join

  • 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:
  • Patient is ≥ 18 years of age.
  • Is currently admitted to the hospital.
  • Has a suspected infectious pneumonia warranting diagnostic evaluation and treatment.
  • 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.
Show all 24Show fewer
  • Patient or patient's Legally Authorized Representative (LAR) has provided consent for the study.
  • Section B:
  • 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).
  • Are immunocompromised defined as having at least one of the following:
  • Received chemotherapy within the last 45 days.
  • A relapse of hematologic malignancy for which chemotherapy treatment is anticipated within the next 45 days.
  • ANC<500 for a minimum of 14 days and within 8 weeks prior to enrollment.
  • Section C:
  • 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).
  • Are immunocompromised defined as having at least one of the following:
  • Undergone autologous hematopoietic stem cell transplantation (HSCT) within the past 6 months.
  • Received chemotherapy within the last 45 days.
  • A relapse of hematologic malignancy for which chemotherapy treatment is anticipated within the next 45 days.
  • Section D:
  • Has undergone allogeneic hematopoietic stem cell transplantation (e.g., bone marrow transplantation) for any clinical indication.
  • Are immunocompromised defined as having at least one of the following:
  • Has undergone hematopoietic stem cell transplantation (HCST) within the past 1 year.
  • Has active graft versus host disease (GVHD) requiring immunosuppressive pharmacologic treatment.

Who cannot join

  • 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.
  • Microbiologic etiology of index pneumonia event has already been identified per local Standard of Care testing.
  • Patient was previously enrolled in this study.
  • 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.)
  • Patient is positive for SARS-COV-2 by any molecular testing within the 14 days prior to enrollment.

Trial locations and contacts

10 sites in 1 country.

10 sites in 1 country

United States10 sites
  • University of Colorado Denver

    Aurora, Colorado, 80045

  • City of Hope Comprehensive Cancer Center

    Duarte, California, 91010

  • Duke University

    Durham, North Carolina, 27710

  • MD Anderson Cancer Center

    Houston, Texas, 77030

  • Tulane Section of Infectious Disease

    New Orleans, Louisiana, 70112

  • Weill Cornell Medicine

    New York, New York, 10021

  • Memorial Sloan Kettering Cancer Center

    New York, New York, 10065

  • University of Pittsburgh

    Pittsburgh, Pennsylvania, 15025

  • UCSF Department of Medicine

    San Francisco, California, 94143

  • Fred Hutchinson Cancer Center

    Seattle, Washington, 98109

Other trials in United States

About this study

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.

Read the 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.

Being tested
Karius Test
Keywords
Pneumonia, NGS, cell free DNA, microbial cell free DNA, immunocompromised
Medical subject headings
Pneumonia, Bacterial, Pneumonia, Viral, Pneumonia

What participants receive

What participants receive. In a randomised study each person is assigned to one group by chance.

  • Karius TestDiagnostic test

    Karius Test for detection of microbial cell free DNA (mcfDNA) in plasma

Study groups in NCT04047719
Study groupRoleWhat they receive
Intent-to-Diagnose PopulationAll subjects enrolled in the study that have at least one Karius Test with a valid result
Receives: Diagnostic Test: Karius Test

What is being measured

The primary outcome is the main question the study is designed to answer.

  1. Additive clinical diagnostic value

    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.

    Measured: 7 days

Timeline

From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.

  1. First posted7 Aug 2019
  2. Study start5 Nov 2019
  3. Primary completion6 Jun 2022
  4. Study completion6 Jun 2022

Resources

More details

For doctors and researchers: how the study is designed, who runs it, and its registry IDs.

Study design
Study type
Observational
Observational model
Cohort
Time perspective
Prospective
Enrolment
257 participants (actual)
IDs, dates and publications
ClinicalTrials.gov ID
NCT04047719
Sponsor's protocol ID
KDC-010
Acronym
PICKUP
Status last verified
Feb 2023
First submitted
5 Aug 2019
Last updated
9 Feb 2023
Results posted
No
Data monitoring committee
Yes
FDA-regulated drug
No
FDA-regulated device
No
Individual data sharing
Undecided

Publications

  • Norton ME, Baer RJ, Wapner RJ, Kuppermann M, Jelliffe-Pawlowski LL, Currier RJ. Cell-free DNA vs sequential screening for the detection of fetal chromosomal abnormalities. Am J Obstet Gynecol. 2016 Jun;214(6):727.e1-6. doi: 10.1016/j.ajog.2015.12.018. Epub 2015 Dec 18.

    PubMed 26709085
  • Alix-Panabieres C, Pantel K. Clinical Applications of Circulating Tumor Cells and Circulating Tumor DNA as Liquid Biopsy. Cancer Discov. 2016 May;6(5):479-91. doi: 10.1158/2159-8290.CD-15-1483. Epub 2016 Mar 11.

    PubMed 26969689
  • Evans SE, Ost DE. Pneumonia in the neutropenic cancer patient. Curr Opin Pulm Med. 2015 May;21(3):260-71. doi: 10.1097/MCP.0000000000000156.

    PubMed 25784246
  • Schuster MG, Cleveland AA, Dubberke ER, Kauffman CA, Avery RK, Husain S, Paterson DL, Silveira FP, Chiller TM, Benedict K, Murphy K, Pappas PG. Infections in Hematopoietic Cell Transplant Recipients: Results From the Organ Transplant Infection Project, a Multicenter, Prospective, Cohort Study. Open Forum Infect Dis. 2017 Mar 22;4(2):ofx050. doi: 10.1093/ofid/ofx050. eCollection 2017 Spring.

    PubMed 28491889
  • Chen CS, Boeckh M, Seidel K, Clark JG, Kansu E, Madtes DK, Wagner JL, Witherspoon RP, Anasetti C, Appelbaum FR, Bensinger WI, Deeg HJ, Martin PJ, Sanders JE, Storb R, Storek J, Wade J, Siadak M, Flowers ME, Sullivan KM. Incidence, risk factors, and mortality from pneumonia developing late after hematopoietic stem cell transplantation. Bone Marrow Transplant. 2003 Sep;32(5):515-22. doi: 10.1038/sj.bmt.1704162.

    PubMed 12942099
  • Harris B, Geyer AI. Diagnostic Evaluation of Pulmonary Abnormalities in Patients with Hematologic Malignancies and Hematopoietic Cell Transplantation. Clin Chest Med. 2017 Jun;38(2):317-331. doi: 10.1016/j.ccm.2016.12.008.

    PubMed 28477642
  • Hohenthal U, Itala M, Salonen J, Sipila J, Rantakokko-Jalava K, Meurman O, Nikoskelainen J, Vainionpaa R, Kotilainen P. Bronchoalveolar lavage in immunocompromised patients with haematological malignancy--value of new microbiological methods. Eur J Haematol. 2005 Mar;74(3):203-11. doi: 10.1111/j.1600-0609.2004.00373.x.

    PubMed 15693789
  • Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vilfan ID, Kawli T, Christians FC, Venkatasubrahmanyam S, Wall GD, Cheung A, Rogers ZN, Meshulam-Simon G, Huijse L, Balakrishnan S, Quinn JV, Hollemon D, Hong DK, Vaughn ML, Kertesz M, Bercovici S, Wilber JC, Yang S. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 2019 Apr;4(4):663-674. doi: 10.1038/s41564-018-0349-6. Epub 2019 Feb 11.

    PubMed 30742071
  • Bergin SP, Chemaly RF, Dadwal SS, Hill JA, Lee YJ, Haidar G, Luk A, Drelick A, Chin-Hong PV, Benamu E, Khawaja F, Nanayakkara D, Papanicolaou GA, Small CB, Fung M, Barron MA, Davis T, McClain MT, Maziarz EK, Madut DB, Bedoya AD, Gilstrap DL, Todd JL, Barkauskas CE, Bigelow R, Leimberger JD, Tsalik EL, Wolf O, Mughar M, Hollemon D, Duttagupta R, Lupu DS, Bercovici S, Perkins BA, Blauwkamp TA, Fowler VG Jr, Holland TL. Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Patients With Pneumonia: A Prospective Observational Study. Clin Infect Dis. 2024 Mar 20;78(3):775-784. doi: 10.1093/cid/ciad599.

    PubMed 37815489

Questions about this trial

What is this clinical trial studying?

An observational study of Pneumonia, Bacterial and Pneumonia, Viral, run by Karius, Inc. at 10 sites in United States.

The full registered description is in the About this study section and the official record.

Who may be eligible to take part?

The sponsor lists 24 inclusion and 5 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.

Is this clinical trial currently recruiting?

The record says: finished, as of the sponsor's last update on 9 Feb 2023. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 10 sites in United States. Whether a site is taking part right now should be confirmed with that site. See every site.

What are the possible benefits and risks?

They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.

Are results available for this study?

The study is completed, but results are not available in the source record. That does not mean the treatment did or did not work.

How can a doctor refer a patient or contact the research team?

The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.

What does the primary outcome measure?

Additive clinical diagnostic value (time frame: 7 days). It is what the study was designed to measure, not a finding.

Where can I read the original study information?

On the ClinicalTrials.gov record for NCT04047719, which also lists 9 linked publications.

Does a listing mean the treatment is approved or proven to work?

No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.

How often is this information updated?

AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 9 Feb 2023; AzTrials last refreshed its copy on 7 Nov 2026.

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