Methods: NGS was performed on plasma by Karius, Inc. (Redwood City, CA). Human reads were removed and remaining sequences were aligned to a curated database of over 1000 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: 29 yo male with history of Tetralogy of Fallot, multiple pulmonary valve replacement (PVR), and 18 months of intermittent fever and night sweats was admitted. Relevant history included travel in South and South East Asia, use of a LivaNova 3T Heater-Cooler device during surgery (i.e. at risk for Mycobacterium chimaera), and drinking unpasteurized milk. Cardiac CT showed two 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. Based on 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.
L. Westblade, None
S. Venkatasubrahmanyam, Karius, Inc.: Employee , Salary .
N. Eisenberg, None
K. M. Marks, None