Advances in molecular diagnostic testing for central nervous system infections

Abstract

Purpose of review Central nervous system (CNS) infections present an ongoing diagnostic challenge for clinicians, with an aetiological agent remaining unidentified in the majority of cases even in high income settings. This review summarises developments in a range of diagnostic methods published in the past 18 months. Recent findings Several commercial assays exist for the detection of viral, bacterial and fungal pathogens using single multiplex PCR. Multicentre validation of the Biofire FilmArray panel illustrated high sensitivity for bacterial and fungal pathogens, but poor results for Cryptococcus species detection. The development of microarray cards for bacterial CNS pathogens shows promise but requires further validation. Few developments have been made in proteomics and transcriptomics, contrasted with significant increase in the use of metagenomic (or unbiased) sequencing. Novel viruses causing CNS infection have been described using this technique but contamination, cost, expertise and turnaround time requirements remain restrictive. Finally, the development of Gene Xpert and Ultra have revolutionised TB meningitis diagnostics with newly released recommendations for their use from the World Health Organisation.

A comparison of the accuracy of the CapitalBio Mycobacterium real-time polymerase chain reaction and the Xpert MTB/RIF assay for the diagnosis of tuberculous meningitis

“…The prognosis of TBM in patients diagnosed with acquired immunodeficiency syndrome (AIDS) represents an even greater problem (Cox et al, 2015). The early diagnosis of TBM is very difficult at present (Houlihan et al, 2019). Although AFB smears are the most convenient and least expensive, this sensitivity of this method is very low and cannot provide a reliable early diagnosis of TBM (Wang and Xie, 2018).…”

Cerebrospinal fluid analysis: current diagnostic methods in central nervous system infectious diseases

“…Like culture, PCR, and antigen-based testing, metagenomic NGS is fundamentally a direct-detection method and relies on the presence of nucleic acid from the causative pathogen in the CSF sample. While this approach is promising, constraints around cost, bioinformatics expertise and clinically relevant turnaround times have limited clinical use of NGS to date, as discussed later 12,13 . As subacute and chronic meningitis are diagnostically challenging given the wide range of potential infectious, autoimmune, neoplastic, paraneoplastic, parameningeal, and toxic causes CSF metagenomics NGS can be more useful in establishing the etiologic diagnosis.…”

“…Like culture, PCR, and antigen-based testing, metagenomic NGS is fundamentally a direct-detection method and relies on the presence of nucleic acid from the causative pathogen in the CSF sample. While this approach is promising, constraints around cost, bioinformatics expertise and clinically relevant turnaround times have limited clinical use of NGS to date, as discussed later 12 , 13 .…”

Biofire FilmArray Meningitis/Encephalitis panel for the aetiological diagnosis of central nervous system infections: A systematic review and diagnostic test accuracy meta-analysis

“…6 Consequently, different molecular biology techniques have recently been developed. 7 The use of molecular panels for the simultaneous diagnosis of several microorganisms employing multiplex PCR has opened up new possibilities and new challenges. 8 The FilmArray Meningitis/Encephalitis panel (Bio-Fire Diagnostics Ò ) (FA/ME), approved by the Food and Drug Administration in 2015, is a panel that simultaneously detects 14 pathogens in cerebrospinal fluid (CSF).…”

“… 6 Consequently, different molecular biology techniques have recently been developed. 7 The use of molecular panels for the simultaneous diagnosis of several microorganisms employing multiplex PCR has opened up new possibilities and new challenges. 8 …”