Evaluation of Plasma Microbial Cell-Free DNA Sequencing to Predict Bloodstream Infection in Pediatric Patients With Relapsed or Refractory Cancer

Abstract

Importance: Bloodstream infection (BSI) is a common, life-threatening complication of treatment for cancer. Predicting BSI before onset of clinical symptoms would enable preemptive therapy, but there is no reliable screening test.

Objective: To estimate sensitivity and specificity of plasma microbial cell-free DNA sequencing (mcfDNA-seq) for predicting BSI in patients at high risk of life-threatening infection.

Design, setting, and participants: A prospective pilot cohort study of mcfDNA-seq for predicting BSI in pediatric patients (<25 years of age) with relapsed or refractory cancers at St Jude Children's Research Hospital, a specialist quaternary pediatric hematology-oncology referral center. Remnant clinical blood samples were collected during chemotherapy and hematopoietic cell transplantation. Samples collected during the 7 days before and at onset of BSI episodes, along with negative control samples from study participants, underwent blinded testing using a mcfDNA-seq test in a Clinical Laboratory Improvement Amendments/College of American Pathologists-approved laboratory.

Main outcomes and measures: The primary outcomes were sensitivity of mcfDNA-seq for detecting a BSI pathogen during the 3 days before BSI onset and specificity of mcfDNA-seq in the absence of fever or infection in the preceding or subsequent 7 days.

Results: Between August 9, 2017, and June 4, 2018, 47 participants (27 [57%] male; median age [IQR], 10 [5-14] years) were enrolled; 19 BSI episodes occurred in 12 participants, and predictive samples were available for 16 episodes, including 15 bacterial BSI episodes. In the 3 days before the onset of infection, predictive sensitivity of mcfDNA-seq was 75% for all BSIs (12 of 16; 95% CI, 51%-90%) and 80% (12 of 15; 95% CI, 55%-93%) for bacterial BSIs. The specificity of mcfDNA-seq, evaluated on 33 negative control samples from enrolled participants, was 82% (27 of 33; 95% CI, 66%-91%) for any bacterial or fungal organism and 91% (30 of 33; 95% CI, 76%-97%) for any common BSI pathogen, and the concentration of pathogen DNA was lower in control than predictive samples.

Conclusions and relevance: A clinically relevant pathogen can be identified by mcfDNA-seq days before the onset of BSI in a majority of episodes, potentially enabling preemptive treatment. Clinical application appears feasible pending further study.

Trial registration: ClinicalTrials.gov identifier: NCT03226158.

Conflict of interest statement

Conflict of Interest Disclosures: Dr Ahmed reports being an employee of Karius Inc. Dr Brenner reports receiving nonfinancial support from Karius Inc and grants from the National Cancer Institute. Dr Gawad reports receiving nonfinancial support from Karius Inc; support from a Career Award for Medical Scientists from the Burroughs Wellcome Fund, a Scholar Award from the Hyundai Foundation for Pediatric Cancer Research, and a Special Fellow award from the Leukemia & Lymphoma Society; and developmental funds from the St Jude Children’s Research Hospital Cancer Center. Ms Hollemon reports being an employee of Karius Inc. Dr Hong reports receiving personal fees as an employee of Karius Inc. Dr Inaba reports receiving nonfinancial support from Karius Inc. Dr Wolf reports receiving nonfinancial support from Karius Inc and research support from Merck, Astellas, Cempra, and CareFusion. No other disclosures were reported.

Figures

Figure 1.. Sensitivity of mcfDNA-seq for the Prediction or Diagnosis of BSI by Day Before the Onset of Infection

Logical derivation was used to impute values for missing data. BSI indicates bloodstream infection; mcfDNA-seq, plasma microbial cell-free DNA sequencing. Error bars show 95% CIs. Overall specificity of mcfDNA-seq was 82% (95% CI, 66%-91%), and specificity for common BSI pathogens was 91% (95% CI, 76%-97%).

Figure 2.. Population Kinetics of Pathogen DNA by Day Before the Onset of BSI

Circles represent individual values, lines represent penalized B-spline smoothing curves for bloodstream infection (BSI) episodes, and bands represent 95% CIs. Orange dots indicate a gram-negative pathogen; dark blue dots, a gram-positive pathogen; brown dots, overlapping samples.