Abstract
BACKGROUND: Identification of Coxiella burnetii, the etiologic agent of Q Fever, in culture-negative endocarditis (CNE) remains challenging, and strain-level information is typically unavailable through conventional testing. We used a novel next-generation sequencing (NGS) assay on plasma cell-free DNA to facilitate rapid diagnosis and genotyping in a patient with C. burnetii CNE. METHODS: NGS was performed on plasma by Karius, Inc. (Redwood City, California). Human reads were removed and remaining sequences were aligned to a curated database of over 1,000 pathogens. Organisms present above a predefined significance threshold were reported. For C. burnetti strain-typing, alignments to different Coxiella strains in the pathogen database were compared by BLAST bit-score to determine the most closely related strain to the infecting organism. C. burnetii genotype group was also determined by in silico analysis of polymorphic ORF deletion markers known to distinguish groups I–VI. RESULTS: Twenty-nine-year-old male with history of Tetralogy of Fallot, multiple pulmonary valve replacement (PVR), and 18 months of intermittent fever and night sweats were admitted. Relevant history included travel in South and South East Asia, the use of a LivaNova 3T Heater-Cooler device during surgery (i.e., at risk for Mycobacterium chimaera), and drinking unpasteurized milk. Cardiac CT showed 2 pulmonary opacities concerning for septic emboli and echocardiography showed echodensity on pulmonic valve. Blood cultures were negative. NGS detected C. burnetii within 48 hours of sample receipt. On the basis of these results, hydroxychloroquine and doxycycline were initiated with symptomatic improvement. Strain-typing demonstrated highest relatedness to the CbuK_Q154 (group IV) strain typically seen in North America. Genotype group was independently confirmed by inference of a pattern of ORF deletion most similar to group IV (and highly related group VII). Serologic testing for C. burnetii confirmed the diagnosis. After 4 weeks of antibiotics, the patient underwent successful PVR with graft exchange. CONCLUSION: NGS testing aided in diagnosis of C. burnetii CNE, enabling early targeted antimicrobial therapy. It also allowed inference of strain-level information, supporting further investigations regarding epidemiologic origins of this pathogen. DISCLOSURES: S. Dalai, Karius, Inc.: Consultant, Consulting fee. S. Venkatasubrahmanyam, Karius, Inc.: Employee, Salary.