Plasma Microbial Cell-free DNA Next-generation Sequencing in the Diagnosis and Management of Febrile Neutropenia

Abstract

Background: Standard testing fails to identify a pathogen in most patients with febrile neutropenia (FN). We evaluated the ability of the Karius microbial cell-free DNA sequencing test (KT) to identify infectious etiologies of FN and its impact on antimicrobial management.

Methods: This prospective study (ClinicalTrials.gov; NCT02912117) enrolled and analyzed 55 patients with FN. Up to 5 blood samples were collected per subject within 24 hours of fever onset (T1) and every 2 to 3 days. KT results were compared with blood culture (BC) and standard microbiological testing (SMT) results.

Results: Positive agreement was defined as KT identification of ≥1 isolate also detected by BC. At T1, positive and negative agreement were 90% (9/10) and 31% (14/45), respectively; 61% of KT detections were polymicrobial. Clinical adjudication by 3 independent infectious diseases specialists categorized Karius results as: unlikely to cause FN (N = 0); definite (N = 12): KT identified ≥1 organism also found by SMT within 7 days; probable (N = 19): KT result was compatible with a clinical diagnosis; possible (N = 10): KT result was consistent with infection but not considered a common cause of FN. Definite, probable, and possible cases were deemed true positives. Following adjudication, KT sensitivity and specificity were 85% (41/48) and 100% (14/14), respectively. Calculated time to diagnosis was generally shorter with KT (87%). Adjudicators determined real-time KT results could have allowed early optimization of antimicrobials in 47% of patients, by addition of antibacterials (20%) (mostly against anaerobes [12.7%]), antivirals (14.5%), and/or antifungals (3.6%); and antimicrobial narrowing in 27.3% of cases.

Clinical trials registration: NCT02912117.

Conclusion: KT shows promise in the diagnosis and treatment optimization of FN.

Keywords: Febrile neutropenia; infection; next-generation sequencing.

Figure 1.

Patient enrollment and overall results at T1. Exclusion reasons: enrollment blood sample for Karius test did not pass quality acceptance criteria (n = 1), blood culture at enrollment was contaminated (n = 1). *1 case with positive tooth abscess culture (Prevotella spp.); 1 case with positive bronchoalveolar lavage culture (A niger). Abbreviations: BC, blood culture; CA, clinical adjudication; KT, Karius test; mITD, modified intent to diagnose; MT, standard microbiological test.

Figure 2.

Positive results with standard microbiological tests and Karius test in subjects with clinical diagnosis of infection. Abbreviation: Micro tests, microbiological tests.

Figure 3.

Time to diagnosis.