Acute Hematogenous Osteomyelitis, Musculoskeletal Infection, Osteomyelitis, Pyomyositis, Septic Arthritis
Conditions
Keywords
infection, plasma based next generation sequencing, blood culture, tissue culture, joint fluid culture, pathogen identification
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).
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.
Interventions
DIAGNOSTIC_TESTKarius Test
Next-generation sequencing of blood and synovial fluid samples for pathogen identification in children with musculoskeletal infections
Sponsors
Karius, Inc.
Indiana University
Study design
Allocation
NA
Intervention model
SINGLE_GROUP
Primary purpose
DIAGNOSTIC
Masking
NONE
Eligibility
Sex/Gender
ALL
Age
6 Months to 18 Years
Healthy volunteers
No
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
Design outcomes
Primary
| Measure | Time frame | Description |
|---|---|---|
| Number of Participants With a Pathogen Identified by the Initial Karius Test (IP1) and Standard Culture Methods | Inpatient Sample 1 (IP1) - Within 48 hours of admission | 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. |
| Number of Participants With a Pathogen Identified by the Karius Test (at Time Point IP2) and Standard Culture Methods | Inpatient Sample 2 (IP2) - Within 48 hours of the initial sample | 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 |
Secondary
| Measure | Time frame | Description |
|---|---|---|
| Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP2 | Inpatient Sample 2 (IP2) - Within 48 hours of the admission sample | 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 |
| Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Timepoint IP3 | Inpatient Sample 3 (IP3) - Within 48 hours of the second inpatient sample | 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 |
| Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP4 | Inpatient Sample 4 (IP4) - Within 48 hours of the third inpatient sample | We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI). |
| Microbial Cell Free DNA Level (cfDNA) in Molecules Per Microliter (MPM) | From hospital admission to hospital discharge, up to 3 months | 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. |
| Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP2 | Outpatient Sample 2 (OP2) - 3-6 weeks after hospital discharge | We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI). |
| Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP3 | Outpatient Sample 3 (OP3) - 6-8 weeks after hospital discharge | We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI). |
| Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP1 | Outpatient Sample 1 (OP1) - 1-2 weeks after hospital discharge | We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI). |
| Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1 | Inpatient Sample 1 (IP1) - Within 48 hours of admission | 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 |
Countries
United States
Participant flow
Participants by arm
| Arm | Count |
|---|---|
| Pediatric Musculoskeletal Infections Children 6 months to 18 years of age admitted to Riley Hospital for Children (Indianapolis, IN), from July 2019 to May 2022. Potential study participants were identified by daily screening of the pediatric infectious diseases and hospitalist patient censuses, and approached for enrollment if there was a strong clinical suspicion of MSKI as evidenced by fever, musculoskeletal pain (e.g. tenderness to palpation of a joint/bone, or refusal to bear weight); and elevated C-reactive protein (CRP) or erythrocyte sedimentation rate (ESR) | 36 |
| Total | 36 |
Withdrawals & dropouts
| Period | Reason | FG000 |
|---|---|---|
| Overall Study | Protocol Violation | 1 |
| Overall Study | Refused blood draw | 1 |
Baseline characteristics
| Characteristic | Pediatric Musculoskeletal Infections |
|---|---|
| Age, Continuous | 7 years |
| Ethnicity (NIH/OMB) Hispanic or Latino | 1 Participants |
| Ethnicity (NIH/OMB) Not Hispanic or Latino | 31 Participants |
| Ethnicity (NIH/OMB) Unknown or Not Reported | 4 Participants |
| Race (NIH/OMB) American Indian or Alaska Native | 0 Participants |
| Race (NIH/OMB) Asian | 1 Participants |
| Race (NIH/OMB) Black or African American | 3 Participants |
| Race (NIH/OMB) More than one race | 0 Participants |
| Race (NIH/OMB) Native Hawaiian or Other Pacific Islander | 0 Participants |
| Race (NIH/OMB) Unknown or Not Reported | 4 Participants |
| Race (NIH/OMB) White | 28 Participants |
| Sex: Female, Male Female | 11 Participants |
| Sex: Female, Male Male | 25 Participants |
Adverse events
| Event type | EG000 affected / at risk |
|---|---|
| deaths Total, all-cause mortality | 0 / 36 |
| other Total, other adverse events | 0 / 36 |
| serious Total, serious adverse events | 0 / 36 |
Outcome results
Primary
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.
Time frame: Inpatient Sample 1 (IP1) - Within 48 hours of admission
Population: 36 children had a culture obtained (either blood or surgical or both) 33 children had a Karius Test available for analysis (1 sample failed quality control and 2 participants did not have an initial inpatient Karius Test sample drawn) 23 children had a positive culture, however, 1 participant with a positive culture had a Karius sample that failed quality control, leaving 22 available for positive agreement analysis
| Arm | Measure | Group | Value (COUNT_OF_PARTICIPANTS) |
|---|---|---|---|
| Pediatric Musculoskeletal Infections | Number of Participants With a Pathogen Identified by the Initial Karius Test (IP1) and Standard Culture Methods | Children with Positive Culture (blood or surgical) | 23 Participants |
| Pediatric Musculoskeletal Infections | Number of Participants With a Pathogen Identified by the Initial Karius Test (IP1) and Standard Culture Methods | Children with a positive Karius Test (IP1) | 26 Participants |
| Pediatric Musculoskeletal Infections | Number of Participants With a Pathogen Identified by the Initial Karius Test (IP1) and Standard Culture Methods | Positive agreement between culture and Karius Test (both tests identified the same organism) | 15 Participants |
Primary
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
Time frame: Inpatient Sample 2 (IP2) - Within 48 hours of the initial sample
Population: 23 children had a positive culture, however, 5 participant with a positive culture did not have an IP2 Karius sample drawn, leaving 18 available for positive agreement analysis
| Arm | Measure | Category | Value (COUNT_OF_PARTICIPANTS) |
|---|---|---|---|
| Pediatric Musculoskeletal Infections | Number of Participants With a Pathogen Identified by the Karius Test (at Time Point IP2) and Standard Culture Methods | Karius Test positive agreement with culture (blood or surgical) | 10 Participants |
| Pediatric Musculoskeletal Infections | Number of Participants With a Pathogen Identified by the Karius Test (at Time Point IP2) and Standard Culture Methods | Karius test discordant with culture (any) | 3 Participants |
| Pediatric Musculoskeletal Infections | Number of Participants With a Pathogen Identified by the Karius Test (at Time Point IP2) and Standard Culture Methods | Karius test negative | 5 Participants |
Secondary
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
Time frame: Inpatient Sample 1 (IP1) - Within 48 hours of admission
Population: Patients with a positive agreement between Karius Test and culture who had a Karius Test, CRP, ESR and WBC obtained at time point IP1
| Arm | Measure | Group | Value (NUMBER) |
|---|---|---|---|
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1 | MPM vs. CRP | 0.43 Spearman's correlation coefficient |
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1 | MPM vs. ESR | 0.36 Spearman's correlation coefficient |
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1 | MPM vs. WBC | 0.33 Spearman's correlation coefficient |
Secondary
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
Time frame: Inpatient Sample 2 (IP2) - Within 48 hours of the admission sample
Population: Patients with a positive agreement between Karius Test and culture who had both a Karius Test and CRP obtained at time point IP2
| Arm | Measure | Value (NUMBER) |
|---|---|---|
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP2 | 0.79 Spearman's correlation coefficient |
Secondary
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
Time frame: Inpatient Sample 3 (IP3) - Within 48 hours of the second inpatient sample
Population: Patients with a positive agreement between Karius Test and culture who had both a Karius Test and CRP obtained at timepoint IP3
| Arm | Measure | Value (NUMBER) |
|---|---|---|
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Timepoint IP3 | 1.0 Spearman's correlation coefficient |
Secondary
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).
Time frame: Inpatient Sample 4 (IP4) - Within 48 hours of the third inpatient sample
Population: Patients with a positive agreement between Karius Test and culture who had both a Karius Test and CRP obtained at timepoint IP4
| Arm | Measure | Value (NUMBER) |
|---|---|---|
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP4 | NA Spearman's correlation coefficient |
Secondary
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).
Time frame: Outpatient Sample 1 (OP1) - 1-2 weeks after hospital discharge
Population: Participants with a Karius Test and CRP drawn at time point OP1
| Arm | Measure | Value (NUMBER) |
|---|---|---|
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP1 | NA Spearman's correlation coefficient |
Secondary
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).
Time frame: Outpatient Sample 2 (OP2) - 3-6 weeks after hospital discharge
Population: Participants with a Karius Test and CRP drawn at time point OP2
| Arm | Measure | Value (NUMBER) |
|---|---|---|
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP2 | NA Spearman's correlation coefficient |
Secondary
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).
Time frame: Outpatient Sample 3 (OP3) - 6-8 weeks after hospital discharge
Population: Participants with a Karius Test and CRP drawn at time point OP3
Secondary
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.
Time frame: From hospital admission to hospital discharge, up to 3 months
Population: Patients with a positive agreement between the Karius Test and cultures
| Arm | Measure | Group | Value (MEDIAN) |
|---|---|---|---|
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA Level (cfDNA) in Molecules Per Microliter (MPM) | Severe Infection | 408 MPM |
| Pediatric Musculoskeletal Infections | Microbial Cell Free DNA Level (cfDNA) in Molecules Per Microliter (MPM) | Non-Severe Infection | 322 MPM |
p-value: 0.36Wilcoxon (Mann-Whitney)