Session: 069. What's New in Clinical Practice?, Thursday, 12:15-1:30 p.m.
Background : Infection disease (ID) groups covering inpatient and office, antimicrobial stewardship, and infection prevention duties may welcome an opportunity to streamline diagnostics via metagenomic next-generation sequencing (NGS). But the appropriate patient profile for NGS has yet to be defined. In 2019, we began using the Karius Test (KT), an NGS test that identifies and quantifies microbial cell-free DNA in plasma.
Methods : On 1/10/19 our ID group (7 MDs and an APN covering 14 Illinois hospitals) began using the KT (Redwood City, CA). 5 ml of whole blood is collected, spun to plasma, & shipped to Karius for analysis. Following NGS, human sequences are removed and remaining sequences are aligned to a curated pathogen database of > 1000 organisms. Organisms present above a statistical threshold are quantified in DNA molecules per microliter (MPM) & reported.
Results : Over 90 days 45 KTs were ordered on 42 patients (mean age = 46); including 3 repeat tests. 36 were inpatients (8 in the ICU) with a mean 4.7 days to ID consult and length-of-stay of 16 days. 31% (13/42) were immunocompromised: i.e., transplant, oncology, or HIV/AIDS. Fine needle or open biopsies were performed on 13 patients and 13 patients had bronchoscopy; 30.8% (8/26) were diagnostic of infection. A valid KT result was returned in 44/45 tests (mean 3.5 days from ID consult). 56.8% (25/44) of tests were positive for one or more organisms (a single pathogen was detected on 11 KTs). Among positive tests, 56% (14/25 - 10 bacterial & 4 fungal infections) were confirmed by culture, antigen, or PCR. Mean time to diagnosis for culture, PCR, antigen, and KT was 16.4, 3, 5.5, and.3.5 days, respectively. In 3 cases, the KT was the only positive test but correlated with the clinical scenario resulting in antimicrobial changes (Pneumocystis jirovecii pneumonia in AIDS, pulmonary aspergillosis in AIDS, and Fusobacterium nucleatum septic thrombophlebitis).
We identified 4 clinical scenarios where the KT provided value: patients with suspected invasive fungal infections, culture-negative endovascular infections/endocarditis, possible discitis or paravertebral infection, and pulmonary disease in AIDS. Future efforts will include outreach for prevention of invasive diagnostic procedures when a KT is pending or positive.
John Farrell– Professor, University of Illinois College of Medicine, Peoria, IL
Trisha Stetzler– Nurse Practitioner, University of Illinois College of Medicine, Peoria, IL
Sharjeel Ahmad– Director - Positive Health Solutions, University of Illinois College of Medicine, Peoria, IL
Mohammad Almoujahed– Assistant Professor, University of Illinois College of Medicine, Peoria, IL
David Hong– Vice President, Medical Affairs and Clinical Development, Karius, Inc., Redwood City, CA
Douglas Kasper– Chairman - Division of Infectious Diseases, University of Illinois College of Medicine, Peoria, IL
Joseph Kim– Assistant Professor, University of Illinois College of Medicine, Los Angeles, CA
Rone Lin– Assistant Professor of Clinical Medicine, Univ of Illinois College of Medicine at Peoria, Peoria, IL
Marlynn Patel– Assistant Professor, University of Illinois College of Medicine, Peoria, IL