Trial Outcomes & Findings for Next-Generation Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections (NCT NCT03846804)

Results Overview

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.

Recruitment status

COMPLETED

Study phase

NA

Target enrollment

38 participants

Primary outcome timeframe

Inpatient Sample 1 (IP1) - Within 48 hours of admission

Results posted on

2023-12-01

Participant Flow

Participant milestones

Participant milestones
Measure	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)
Overall Study STARTED	38
Overall Study COMPLETED	36
Overall Study NOT COMPLETED	2

Reasons for withdrawal

Reasons for withdrawal
Measure	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)
Overall Study Refused blood draw	1
Overall Study Protocol Violation	1

Baseline Characteristics

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

Baseline characteristics by cohort

Baseline characteristics by cohort
Measure	Pediatric Musculoskeletal Infections n=36 Participants 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)
Age, Continuous	7 years n=5 Participants
Sex: Female, Male Female	11 Participants n=5 Participants
Sex: Female, Male Male	25 Participants n=5 Participants
Ethnicity (NIH/OMB) Hispanic or Latino	1 Participants n=5 Participants
Ethnicity (NIH/OMB) Not Hispanic or Latino	31 Participants n=5 Participants
Ethnicity (NIH/OMB) Unknown or Not Reported	4 Participants n=5 Participants
Race (NIH/OMB) American Indian or Alaska Native	0 Participants n=5 Participants
Race (NIH/OMB) Asian	1 Participants n=5 Participants
Race (NIH/OMB) Native Hawaiian or Other Pacific Islander	0 Participants n=5 Participants
Race (NIH/OMB) Black or African American	3 Participants n=5 Participants
Race (NIH/OMB) White	28 Participants n=5 Participants
Race (NIH/OMB) More than one race	0 Participants n=5 Participants
Race (NIH/OMB) Unknown or Not Reported	4 Participants n=5 Participants

PRIMARY outcome

Timeframe: 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

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.

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=36 Participants 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)
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
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
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 outcome

Timeframe: 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

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"

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=18 Participants 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)
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
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
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 outcome

Timeframe: From hospital admission to hospital discharge, up to 3 months

Population: Patients with a positive agreement between the Karius Test and cultures

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.

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=15 Participants 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)
Microbial Cell Free DNA Level (cfDNA) in Molecules Per Microliter (MPM) Severe Infection	408 MPM Interval 358.0 to 49185.0
Microbial Cell Free DNA Level (cfDNA) in Molecules Per Microliter (MPM) Non-Severe Infection	322 MPM Interval 92.0 to 1357.0

SECONDARY outcome

Timeframe: 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

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

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=15 Participants 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)
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1 MPM vs. CRP	0.43 Spearman's correlation coefficient
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1 MPM vs. ESR	0.36 Spearman's correlation coefficient
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP1 MPM vs. WBC	0.33 Spearman's correlation coefficient

SECONDARY outcome

Timeframe: 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

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

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=7 Participants 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)
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP2	0.79 Spearman's correlation coefficient

SECONDARY outcome

Timeframe: 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

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

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=3 Participants 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)
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Timepoint IP3	1.0 Spearman's correlation coefficient

SECONDARY outcome

Timeframe: 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

We evaluated whether cfDNA level (in MPM) correlated with C-reactive protein (a common inflammatory marker used to track inflammation in children with MSKI).

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=2 Participants 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)
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point IP4	NA Spearman's correlation coefficient Only 2 participants with positive agreement between the Karius Test and culture had a sample drawn at time point IP4. Analysis requires at least 3 participants.

SECONDARY outcome

Timeframe: Outpatient Sample 1 (OP1) - 1-2 weeks after hospital discharge

Population: Participants with a Karius Test and CRP drawn 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).

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=1 Participants 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)
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP1	NA Spearman's correlation coefficient Only 1 participant with a positive agreement between the Karius Test and culture had an OP1 drawn. Analysis could not be done with only 1 participant

SECONDARY outcome

Timeframe: Outpatient Sample 2 (OP2) - 3-6 weeks after hospital discharge

Population: Participants with a Karius Test and CRP drawn 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).

Outcome measures

Outcome measures
Measure	Pediatric Musculoskeletal Infections n=1 Participants 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)
Microbial Cell Free DNA (cfDNA) in Molecules Per Microliter (MPM) at Time Point OP2	NA Spearman's correlation coefficient Only 1 participant with a positive Karius Test drawn at OP2. Analysis could not be done with only 1 participant

SECONDARY outcome

Timeframe: Outpatient Sample 3 (OP3) - 6-8 weeks after hospital discharge

Population: Participants with a Karius Test and CRP drawn 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).

Outcome measures

Outcome data not reported

Adverse Events

Karius Test

Serious events: 0 serious events

Other events: 0 other events

Deaths: 0 deaths

Serious adverse events

Adverse event data not reported

Other adverse events

Adverse event data not reported

Additional Information

James Wood, MD

Indiana University School of Medicine

Phone: 317-944-7260

Email: [email protected]

Results disclosure agreements

Principal investigator is a sponsor employee
Publication restrictions are in place