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

Study Overview
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Brief Summary
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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).

Detailed Description
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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.

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

Conditions
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Musculoskeletal Infection, Acute Hematogenous Osteomyelitis, Septic Arthritis, Osteomyelitis, Pyomyositis

Intervention / Treatment
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* Diagnostic Test: Karius Test


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: 6 months (to ensure adequate blood volume drawn) to 18 years of age. 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

Ages Eligible for Study
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Minimum Age: 6 Months
Maximum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Design Details

Primary Purpose: Diagnostic
Intervention Model: Single Group Assignment
Masking: None (Open Label)


Arms and Interventions

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

What is the study measuring?
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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 | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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blood culture, infection, plasma based next generation sequencing, tissue culture, joint fluid culture, pathogen identification