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Next-Generation Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections (KDG-002)

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ClinicalTrials.gov Identifier: NCT03846804
Recruitment Status : Not yet recruiting
First Posted : February 20, 2019
Last Update Posted : July 5, 2019
Sponsor:
Collaborator:
Karius, Inc.
Information provided by (Responsible Party):
James Wood, Indiana University

Study Description
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Brief Summary:
The purpose of this study is to evaluate the use of a blood test: Karius® plasma-based next-generation sequencing test (Karius Test), to see if we can detect and measure the infection causing agent in children with musculoskeletal infections (MSKI).

Condition or disease Intervention/treatment
Musculoskeletal Infection Acute Hematogenous Osteomyelitis Septic Arthritis Osteomyelitis Pyomyositis Diagnostic Test: Karius Test

Detailed Description:
children admitted to Riley Hospital for Children (RHC) with musculoskeletal infections (osteomyelitis, septic arthritis, or pyomyositis) over a 12-month period will be prospectively enrolled. Eligible subjects will be identified by referral from the infectious diseases and orthopedic services at RHC. Blood samples will be obtained on the day of admission (within 48hrs), and 24 hours after the admission sample for real-time NGS testing at Karius Laboratory (Redwood City, CA). If a pathogen is identified by NGS, in either of the first two samples, subsequent samples will be sent every 48-72 hours while inpatient, and then collected every 1-2 weeks after hospital discharge, while being treated for MSKI (maximum 3 follow-up samples). If both of the initial inpatient NGS samples are negative, no further samples will be sent for NGS. Pathogen identification by NGS will be compared to standard cultures methods, and quantitative cfDNA will be evaluated over time.
Study Design
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Study Type : Observational
Estimated Enrollment : 38 participants
Observational Model: Cohort
Time Perspective: Prospective
Official Title: Plasma-Based Next-Generation Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections
Estimated Study Start Date : September 1, 2019
Estimated Primary Completion Date : March 15, 2020
Estimated Study Completion Date : September 30, 2020

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Groups and Cohorts
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Intervention Details:
  • Diagnostic Test: Karius Test
    Next-generation sequencing of blood and synovial fluid samples for pathogen identification in children with musculoskeletal infections

Outcome Measures
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Primary Outcome Measures :
  1. To evaluate and compare pathogen identification of children with musculoskeletalTo compare pathogen identification using the Karius Test and standard culture methods [ Time Frame: IP1- Within 48 hours of admission ]
    Pathogen identification (genus and species) by Karius Test vs. standard culture methods

  2. To evaluate and compare pathogen identification of children with musculoskeletalTo compare pathogen identification using the Karius Test and standard culture methods [ Time Frame: IP2- Within 48 hours of the admission sample ]
    Pathogen identification (genus and species) by Karius Test vs. standard culture methods

  3. Compare the quantity of cfDNA to clinical symptoms and inflammatory markers at admission [ Time Frame: IP1- Within 48 hours of admission ]
    Quantification of cfDNA in molecules per microliter (MPM)

  4. Compare the quantity of cfDNA to clinical symptoms and inflammatory markers at admission [ Time Frame: IP2- Within 48 hours of the admission sample ]
    Quantification of cfDNA in molecules per microliter (MPM)

  5. Compare the quantity of cfDNA to clinical symptoms and inflammatory markers [ Time Frame: IP3- Within 48 hours of the second inpatient sample ]
    Quantification of cfDNA in molecules per microliter (MPM)

  6. Compare the quantity of cfDNA to clinical symptoms and inflammatory markers [ Time Frame: IP4- Within 48 hours of the third inpatient sample ]
    Quantification of cfDNA in molecules per microliter (MPM)

  7. Compare the quantity of cfDNA to clinical symptoms and inflammatory markers [ Time Frame: OP1- 1-2 weeks after hospital discharge ]
    Quantification of cfDNA in molecules per microliter (MPM)

  8. Compare the quantity of cfDNA to clinical symptoms and inflammatory markers [ Time Frame: OP2- 3-6 weeks after hospital discharge ]
    Quantification of cfDNA in molecules per microliter (MPM)

  9. Compare the quantity of cfDNA to clinical symptoms and inflammatory markers [ Time Frame: OP3- 6-8 weeks after hospital discharge ]
    Quantification of cfDNA in molecules per microliter (MPM)

  10. Evaluate whether admission sample quantitative cfDNA predicts severe disease in children with MSKI [ Time Frame: From hospital admission to hospital discharge, up to 3 months ]
    Determine the correlation of cfDNA level in MPM to severity of infection


Biospecimen Retention:   Samples With DNA
5ml of whole blood will be collected in a plasma preparation tube (PPT) for NGS testing and centrifuged at 1,100 RCF for 10 minutes at room temperature, within 6 hours of blood draw. Alternatively, for patients in whom 5 ml of blood cannot be drawn, 2ml of blood will drawn in EDTA tubes, centrifuged, and the plasma transferred into sterile polypropylene tubes.

Eligibility Criteria
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Ages Eligible for Study:   6 Months to 18 Years   (Child, Adult)
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Sampling Method:   Non-Probability Sample
Study Population
Children admitted to Riley Hospital for Children (RHC), Indianapolis, Indiana, with clinical presentation consistent with a musculoskeletal infection (osteomyelitis, septic arthritis, or pyomyositis; MSKI).
Criteria

Inclusion Criteria:

  1. 6 months (to ensure adequate blood volume drawn) to 18 years of age.
  2. Strong clinical suspicion of MSKI as evidenced by fever, osteoarticular pain (e.g. tenderness to palpation of a joint, bone pain, or refusal to bear weight); and elevated ESR or CRP.

Exclusion Criteria:

  • Subjects will be excluded if they have clinical evidence suggesting an alternative diagnosis; inability or unwillingness to consent for the study
Contacts and Locations
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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 ClinicalTrials.gov identifier (NCT number): NCT03846804


Contacts
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Contact: James B Wood, MD, MSCI 317-278-9612 woodjb@iu.edu
Contact: Carrie Nijak, RN 317-274-8804 canijak@iu.edu

Sponsors and Collaborators
Indiana University
Karius, Inc.
Investigators
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Principal Investigator: James Wood, MD, MSCI Indiana University School of Medicine - Pediatrics
More Information
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Responsible Party: James Wood, Assistant Professor of Pediatrics, Indiana University
ClinicalTrials.gov Identifier: NCT03846804    
Other Study ID Numbers: 1901296571
First Posted: February 20, 2019    Key Record Dates
Last Update Posted: July 5, 2019
Last Verified: July 2019
Individual Participant Data (IPD) Sharing Statement:
Plan to Share IPD: No

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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 James Wood, Indiana University:
infection
plasma based next generation sequencing
blood culture
 tissue culture
joint fluid culture
pathogen identification
Additional relevant MeSH terms:
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Infection
Communicable Diseases
Osteomyelitis
Arthritis, Infectious
Pyomyositis
Arthritis
Joint Diseases
Musculoskeletal Diseases
 Bone Diseases, Infectious
Bone Diseases
Suppuration
Myositis
Muscular Diseases
Neuromuscular Diseases
Nervous System Diseases