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

Plasma-Based Next-Generation Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections

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).

Study Overview

• Status: Completed
• Conditions: Osteomyelitis; Septic Arthritis; Musculoskeletal Infection; Acute Hematogenous Osteomyelitis; Pyomyositis
• Intervention / Treatment: 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 (next-generation sequencing) 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 (cell-free DNA) will be evaluated over time.

• Study Type: Interventional
• Enrollment (Actual): 38
• Phase: Not Applicable

Contacts and Locations

Study Locations

• United States
  • Indiana
    • Indianapolis, Indiana, United States, 46202
      • Riley Hospital for Children

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 6 months to 18 years (Child, Adult)
• Accepts Healthy Volunteers: No

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).

Description

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 (erythrocyte sedimentation rate) or CRP (C-reactive protein).

Exclusion Criteria:

• Subjects will be excluded if they have clinical evidence suggesting an alternative diagnosis; inability or unwillingness to consent for the study

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Diagnostic
• Allocation: N/A
• Interventional Model: Single Group Assignment
• Masking: None (Open Label)

Number of Arms

1

Arms and Interventions

Participant Group / Arm	Intervention / Treatment
Experimental: Karius Test; Participants will have additional blood drawn for the purposes of analysis with the Karius test.	Diagnostic test: Karius Test; Next-generation sequencing of blood and synovial fluid samples for pathogen identification in children with musculoskeletal infections

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Number of Participants With a Pathogen Identified by the Initial Karius Test (IP1) and Standard Culture Methods	We evaluated the total number of participants that had a pathogen identified by the initial (IP1) Karius Test ("positive Karius Test"). We compared the results of the Karius Test to cultures (gold standard) for each participant. Karius Test results that matched cultures results (same genus and species) were considered "positive agreement". We also evaluated at the number of participants who had negative cultures, but had a positive Karius Test.	Inpatient Sample 1 (IP1) - Within 48 hours of admission
Number of Participants With a Pathogen Identified by the Karius Test (at Time Point IP2) and Standard Culture Methods	We evaluated the total number of participants that had a pathogen identified by the Karius Test ("positive Karius Test") at time point IP2 (within 48 hours of the initial sample). We compared the results of the Karius Test to those with a positive culture (gold standard) for each participant. Karius Test results that matched cultures results (same genus and species) were considered "positive agreement". Karius Test results that identified an organism different from the organism identified in culture were considered "discordant results" Karius Tests results that did not identify any organism were consider "negative"	Inpatient Sample 2 (IP2) - Within 48 hours of the initial sample

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Microbial Cell Free DNA Level (cfDNA) in Molecules Per Microliter (MPM)	We compared the microbial cfDNA level (on initial samples, IP1) between patients with non-severe MSKI to those with severe MSKI (defined as need for intensive care unit (ICU) care; infection in two or more non-contiguous anatomic sites (disseminated disease); need for more than 1 debridement procedure; deep vein thrombosis or thromboembolic disease; or pathologic fracture). Only those with a positive agreement between initial Karius Test (IP1) and culture were analyzed (n=15). Mann-Whitney U was used to compare median microbial cfDNA between those with non-severe vs. severe MSKI.	From hospital admission to hospital discharge, up to 3 months
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1	We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and white blood cell count (WBC), common inflammatory markers followed in children with MSKI. Spearman's correlation was used to compare the MPM value to the CRP, ESR and WBC	Inpatient Sample 1 (IP1) - Within 48 hours of admission
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP2	We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI). Spearman's correlation was used to compare the MPM value to the CRP	Inpatient Sample 2 (IP2) - Within 48 hours of the admission sample
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Timepoint IP3	We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI) at time point IP3 in participants with positive agreement between the Karius Test and culture. Spearman's correlation was used to compare the MPM value to the CRP	Inpatient Sample 3 (IP3) - Within 48 hours of the second inpatient sample
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP4	We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI).	Inpatient Sample 4 (IP4) - Within 48 hours of the third inpatient sample
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP1	We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI).	Outpatient Sample 1 (OP1) - 1-2 weeks after hospital discharge
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP2	We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI).	Outpatient Sample 2 (OP2) - 3-6 weeks after hospital discharge
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP3	We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI).	Outpatient Sample 3 (OP3) - 6-8 weeks after hospital discharge

Collaborators and Investigators

• Sponsor: Indiana University
• Collaborators: Karius, Inc.
• Investigators: Principal Investigator: Jack G Schneider, MD, Indiana University School of Medicine - Pediatrics

Study record dates

Study Major Dates

• Study Start (Actual): September 1, 2019
• Primary Completion (Actual): June 2, 2022
• Study Completion (Actual): June 2, 2022

Study Registration Dates

• First Submitted: February 13, 2019
• First Submitted That Met QC Criteria: February 15, 2019
• First Posted (Actual): February 20, 2019

Study Record Updates

• Last Update Posted (Estimated): December 1, 2023
• Last Update Submitted That Met QC Criteria: November 11, 2023
• Last Verified: November 1, 2023

More Information

Terms related to this study

• Keywords: infection; plasma based next generation sequencing; blood culture; tissue culture; joint fluid culture; pathogen identification
• Additional Relevant MeSH Terms: Pathologic Processes; Nervous System Diseases; Disease Attributes; Joint Diseases; Musculoskeletal Diseases; Arthritis; Muscular Diseases; Neuromuscular Diseases; Bone Diseases; Suppuration; Myositis; Bone Diseases, Infectious; Infections; Communicable Diseases; Arthritis, Infectious; Osteomyelitis; Pyomyositis
• Other Study ID Numbers: 1901296571

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: Yes
• product manufactured in and exported from the U.S.: No