Utility of Whole-Genome Next-Generation Sequencing of Plasma in Identifying Opportunistic Infections in HIV/AIDS

Yang Zhou1, Vagish Hemmige2, Sudeb C. Dalai3, 6, David K. Hong3, Kenneth Muldrew4, Mayar Al Mohajer5, *
1 Department of Internal Medicine, Baylor College of Medicine, Houston, TX, USA
2 Department of Infectious Disease, Montefiore Medical Center, Bronx, NY, USA
3 Department of Medical Affairs, Karius, Inc., Redwood City, CA, USA
4 Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
5 Infection Prevention and Antimicrobial Stewardship, Baylor St. Luke's Medical Center, Houston, TX, USA
6 Division of Infectious Diseases, Stanford University Medical Center, Stanford, CA, USA

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© 2019 Zhou et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Baylor College of Medicine, Infection Prevention and Antimicrobial Stewardship, Baylor St. Luke's Medical Center, Houston, TX, United States; Tel: (832) 355-7848; E-mail:



AIDS-associated Opportunistic Infections (OIs) have significant morbidity and mortality and can be diagnostically challenging, requiring invasive procedures as well as a combination of culture and targeted molecular approaches.


We aimed to demonstrate the clinical utility of Next-generation Sequencing (NGS) in pathogen identification; NGS is a maturing technology enabling the detection of miniscule amounts of cell-free microbial DNA from the bloodstream.


We utilized a novel Next-generation Sequencing (NGS) test on plasma samples to diagnose a series of HIV-associated OIs that were diagnostically confirmed through conventional microbial testing.


In all cases, NGS test results were available sooner than conventional testing. This is the first case series demonstrating the utility of whole-genome NGS testing to identify OIs from plasma in HIV/AIDS patients.


NGS approaches present a clinically-actionable, comprehensive means of diagnosing OIs and other systemic infections while avoiding the labor, expense, and delays of multiple tests and invasive procedures.

Keywords: Human immunodeficiency virus, Acquired Immune Deficiency Syndrome, Opportunistic infections, Next-generation sequencing, Cell-free DNA, Toxoplasma gondii, Toxoplasmosis, Mycobacterium avium complex, Mycobacterium tuberculosis, Cryptosporidium.