395 - Rapid, Non-invasive Detection of Infection Using Plasma-based Next-Generation Sequencing for Microbial Cell-free DNA in Individuals Testing Negative for SARS-CoV-2 in a Pandemic Setting

Background: The clinical presentation of patients with severe COVID-19 infection can be protracted and deteriorate to ARDS and multi-organ dysfunction with prolonged fever. As such, there is clinical overlap with many infectious diseases especially those that cause pneumonia. Due to of the prevalence of COVID-19 illness amidst the pandemic, concerns about testing sensitivity and the attendant risk to health care personnel (HCP) delivering care, patients are frequently tested multiple times to ascertain that they are SARS-CoV-2 free. Often, alternative diagnoses are not considered because some diagnostic modalities—such as bronchoalveolar lavage (BAL)—pose an unacceptable risk to the patient and/or HCP.

Methods: We interrogated plasma for microbial cell-free DNA from 58 patients who were known to be SARS-CoV-2 negative. Clinical information is taken from information submitted with the test requisition or obtained at the time of result reporting from clinical consultations with the ordering provider. In each case, a plasma sample was analyzed with the Karius Test (KT) which is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test designed to detect and quantify circulating microbial cell-free DNA (mcfDNA), which can assist with the diagnosis of deep-seated infections. After mcfDNA is extracted and NGS performed, human reads are removed and remaining sequences are aligned to a curated database of >1400 organisms. Organisms present above a statistical threshold are reported. The time to result is on average 24 hours from sample receipt.

Results: In a subset of 20 samples, we found a broad range of pathogens. Pneumocystis jirovecii was the most common. These detections were unexpected in the majority of these patients. (see Table)Broad range of Karius detected pathogens (including fastidious bacteria, mycobacteria, fungi and viruses)


Conclusion: Open-ended, plasma-based NGS for mcfDNA with the KT provides a rapid, non-invasive method to diagnose deep-seated infection like pneumonia. This broad-based test detected a wide range of pathogens – many unsuspected – in patients with severe pneumonia and other invasive infections during the COVID-19 pandemic. These detections highlight the utility of the tool; which allowed better management including de-escalation of SARS-CoV-2 testing and selection of appropriate antibiotic therapy for the unexpected diagnoses.