Application of Pathogen Discovery/Metagenomic Sequencing in CNS HIV

• Published in: Current HIV/AIDS reports 2020-10, Vol.17 (5), p.507-513
• Main Author: Thakur, Kiran T.
• Format: Article
• Language: English
• Subjects: Acquired immune deficiency syndrome; Acquired Immunodeficiency Syndrome - diagnosis; AIDS; Bioinformatics; Central nervous system; Central Nervous System - pathology; Central Nervous System - virology; Central Nervous System and Cognition (SS Spudich; Cerebrospinal fluid; Chronic illnesses; Cognition; Diagnosis; Genetic analysis; High-Throughput Nucleotide Sequencing - methods; HIV; HIV Infections - diagnosis; HIV-1 - genetics; HIV-1 - isolation & purification; Human immunodeficiency virus; Humans; Infections; Invasiveness; Medicine; Medicine & Public Health; Metagenomics; Metagenomics - methods; Morbidity; Next-generation sequencing; Pathogens; Section Editor; Topical Collection on Central Nervous System and Cognition
• ISSN: 1548-3568; 1548-3576; 1548-3576
• DOI: 10.1007/s11904-020-00514-1

Purpose of Review Neurological conditions associated with HIV/AIDS including central nervous system (CNS), opportunistic infections (OI), chronic conditions including HIV-associated neurocognitive disorder, and cerebrospinal fluid (CSF) viral escape remain major contributors to morbidity and mortality worldwide. CNS infections in HIV-infected patients are often challenging to diagnose by traditional microbiological testing, impacting treatment and outcome. Recent Findings Recent advances in diagnostic techniques, including metagenomic next-generation sequencing (mNGS), are changing the landscape of microbiological testing, mainly in resource-rich settings. Pathogen discovery techniques offer a hypothesis-free approach to diagnostic testing, yielding comprehensive analysis of microbial genetic material. Given the extent of genetic material produced, deep sequencing tools not only hold promise in the diagnosis of CNS infections but also in defining key pathogenic steps which have previously been unanswered. Summary Significant challenges remain to implementing pathogen discovery techniques in routine clinical practice including cost, expertise and infrastructure needed including laboratory and bioinformatics support, and sample contamination risk. The use in resource-limited regions where the burden of CNS complications due to HIV/AIDS is highest remains poorly defined. Though, major opportunities utilizing pathogen discovery techniques exist to enhance surveillance and diagnosis and improve our understanding of mechanisms of neuroinvasion in CNS conditions associated with HIV.