Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA

Grace Lisius; Radha Duttagupta; Asim A Ahmed; Matthew Hensley; Nameer Al-Yousif; Michael Lu; William Bain; Faraaz Shah; Timothy A Blauwkamp; Sivan Bercovici; Caitlin Schaefer; Shulin Qin; Xiaohong Wang; Yingze Zhang; Kevin J Mitchell; Ellen K Hughes; Jana L Jacobs; Asma Naqvi; Ghady Haidar; John W Mellors; Barbara Methé; Bryan J McVerry; Alison Morris; Georgios D Kitsios

doi:10.1016/j.isci.2023.108093

Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA

iScience. 2023 Oct 11;26(11):108093. doi: 10.1016/j.isci.2023.108093. eCollection 2023 Nov 17.

Authors

Grace Lisius¹, Radha Duttagupta², Asim A Ahmed², Matthew Hensley¹, Nameer Al-Yousif³, Michael Lu¹, William Bain^{1

4}, Faraaz Shah^{1

4}, Timothy A Blauwkamp², Sivan Bercovici², Caitlin Schaefer¹, Shulin Qin^{1

5}, Xiaohong Wang^{1

5}, Yingze Zhang¹, Kevin J Mitchell⁶, Ellen K Hughes⁶, Jana L Jacobs⁷, Asma Naqvi⁷, Ghady Haidar⁷, John W Mellors⁷, Barbara Methé^{1

5}, Bryan J McVerry^{1

5}, Alison Morris^{1

5}, Georgios D Kitsios^{1

5}

Affiliations

¹ Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
² Karius Inc, Redwood City, CA 94065, USA.
³ Division of Pulmonary, Critical Care, and Sleep Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA.
⁴ Veterans Affairs Pittsburgh Health System, Pittsburgh, PA 15240, USA.
⁵ Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA.
⁶ Computer Vision Group, VeyTel LLC, Pittsburgh, PA 15217, USA.
⁷ University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, PA 15213, USA.

Abstract

Secondary infection (SI) diagnosis in severe COVID-19 remains challenging. We correlated metagenomic sequencing of plasma microbial cell-free DNA (mcfDNA-Seq) with clinical SI assessment, immune response, and outcomes. We classified 42 COVID-19 inpatients as microbiologically confirmed-SI (Micro-SI, n = 8), clinically diagnosed-SI (Clinical-SI, n = 13, i.e., empiric antimicrobials), or no-clinical-suspicion-for-SI (No-Suspected-SI, n = 21). McfDNA-Seq was successful in 73% of samples. McfDNA detection was higher in Micro-SI (94%) compared to Clinical-SI (57%, p = 0.03), and unexpectedly high in No-Suspected-SI (83%), similar to Micro-SI. We detected culture-concordant mcfDNA species in 81% of Micro-SI samples. McfDNA correlated with LRT 16S rRNA bacterial burden (r = 0.74, p = 0.02), and biomarkers (white blood cell count, IL-6, IL-8, SPD, all p < 0.05). McfDNA levels were predictive of worse 90-day survival (hazard ratio 1.30 [1.02-1.64] for each log₁₀ mcfDNA, p = 0.03). High mcfDNA levels in COVID-19 patients without clinical SI suspicion may suggest SI under-diagnosis. McfDNA-Seq offers a non-invasive diagnostic tool for pathogen identification, with prognostic value on clinical outcomes.

Keywords: Classification description immunology; Sequence analysis; Virology.

Abstract

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