304 - Rapid, Non-invasive Plasma-Based Microbial Cell-free DNA Next Generation Sequencing (The Karius Test) Outperforms the Standard of Care for the Detection of Kingella kingae Pediatric Spinal Infections

Poster Number: 304
Publication Number: 304.114

Asim A. Ahmed, Karius, Redwood City, CA, United States; Aparna Arun, Karius, Redwood City, CA, United States; Martin S. Lindner, Karius, Weinheim, Baden-Wurttemberg, Germany; Adriana Sarmiento Clemente, Baylor College of Medicine, Houston, TX, United States; Ana Del Valle Penella, Baylor College of Medicine, Houston, TX, United States; Marcelo Laufer, Nicklaus Children’s Hospital, Miami, FL, United States; Carolina Sanchez-Vegas, Nicklaus Children’s Hospital, Miami, FL, United States; Manuel R. Cotilla, Nicklaus Children’s Hospital, Miami, FL, United States; Marian Melish, Kapi'olani Medical Center for Women and Children, Honolulu, HI, United States; Connie Trieu, University of Florida College of Medicine, Gainesville, FL, United States; Nazia Kabani, University of Alabama at Birmingham, Birmingham, AL, United States; Joshua Cooper, University of Alabama School of Medicine, Birmingham, AL, United States; Audrey R. Lloyd, Children's of Alabama, Birmingham, AL, United States; John Arnold, UCSD, San Diego, CA, United States; Alejandro Jordan-Villegas, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, United States; Lori E. Patterson, East Tennessee Children's Hospital, Knoxville, TN, United States; David Kimberlin, University of Alabama at Birmingham, Birmingham, AL, United States; Catherine Foster, Baylor College of Medicine, Houston, TX, United States; Pablo Yagupsky, Soroka University Medical Center, Ben Gurion University of the Negev, Beer-Sheva, HaDarom, Israel

Background: Diagnosis of pediatric Kingella kingae skeletal spinal infections is largely dependent on blood culture given the reluctance to biopsy spinal locations and is challenging due to the fastidious nature of the organism, even when infected tissue is obtained. A sensitive, rapid, non-invasive test may overcome these limitations and would enable targeted therapy. Detection of circulating microbial cell-free DNA (mcfDNA) in the plasma by next-generation sequencing (NGS) has shown utility as a non-invasive test and may offer promise in spinal infections.

Objective: The objective of this study is to compare the diagnostic performance of plasma mcfDNA to real-world conventional standard of care (SOC) testing for the diagnosis of K. kingae spinal infections in children.

Design/Methods: The Karius TestTM (KT) developed and validated in Karius’s CLIA certified/CAP accredited lab (Redwood City, CA) detects circulating mcfDNA in plasma by NGS. KT results were reviewed for detections of K. kingae in pediatric vertebral or intervertebral disc infections from June 2018 to December 2020. Chart review was performed by the treating pediatric infectious diseases physicians at each participating institution after IRB exception or approval. McNemar’s test was used for statistical comparison of the performance of KT and SOC diagnostic procedures.

Results: Ten cases of K. kingae pediatric spinal infections were identified across seven institutions (Table). The median age was 16.5 months. All 10 patients had osteomyelitis and 9 had discitis; the lumbar spine was involved in 9 patients. In all cases blood cultures were negative empiric MRSA therapy was initiated. McfDNA was the only means of specific K. kingae microbiological diagnosis in 9 patients and was the earliest means of diagnosis in all cases, with a time to diagnosis of one day from sample receipt. Conventional SOC testing yielded a K. kingae etiology in one patient (by K. kingae bone PCR). KT was significantly more sensitive than conventional SOC testing (McNemar’s test 6.25, 2-tailed p=0.0133). K. kingae mcfDNA was detected in all 5 patients with antibiotic pretreatment. The detection of K. kingae mcfDNA resulted in narrowed antimicrobial coverage in 9 patients and enabled diagnosis without biopsy in 8 patients.Conclusion(s): Plasma NGS of circulating mcfDNA offers a rapid, non-invasive means of detecting pediatric K. kingae spinal infections. In this series KT was more sensitive than SOC diagnostic testing. This culture-independent approach may enable microbiological diagnosis despite antibiotic pretreatment and obviate the need for a biopsy.
Table: Pediatric Cases of Kingella kingae Spinal Infection Detected by Plasma-based Microbial Cell-free DNA Next-Generation SequencingSummary of clinical and laboratory parameters of ten cases of K. kingae pediatric spinal infections detected by plasma mcfDNA NGS across seven institutions.
Cases #1 & #3 are from the same institution; cases #4, #7 and #10 are from the same institution; all other cases represent unique cases at the participating institutions. Among the ten children with K. kingae mcfDNA detected in plasma, conventional standard of care testing yielded a K. kingae etiology in one patient (by K. kingae bone PCR in patient #10). Abbreviations as follows:
HD = hospital day;
wks = weeks;
mo = months;
PTA = prior to admission;
URI = upper respiratory tract infection;
RRP = Rapid Respiratory Panel;
%Nf % neutrophils;
CSF = Cerebrospinal Fluid;
Cx = Culture;
G/S = Gram stain;
NOS = no organisms seen;
ND = not done;
N/A = not applicable;
TAT = turnaround time;
MPM = molecules per microliter of microbial cell-free DNA;
RI = reference interval of a particular pathogen's abundance in MPM which is defined as the 97.5%ile MPM of that particular pathogen's mcfDNA by the Karius Test across a cohort of 684 asymptomatic healthy subjects (which included 0 detections of K. kingae, 42 detections of H. influenzae, 1 detection of S. pneumoniae, 1 detection of M. catarrhalis).
*Indicates detection of a pathogen under the Karius Test commercial threshold (this detection was not included in the performance comparison to SOC testing for the most conservative evaluation of KT performance).
^Same day care exposure was linked to two other cases of invasive K. kingae infection during a twelve-month period.