Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

Abstract

BACKGROUND Metagenomic next-generation sequencing (NGS) of cerebrospinal fluid (CSF) has the potential to identify a broad range of pathogens in a single test. METHODS In a 1-year, multicenter, prospective study, we investigated the usefulness of metagenomic NGS of CSF for the diagnosis of infectious meningitis and encephalitis in hospitalized patients. All positive tests for pathogens on metagenomic NGS were confirmed by orthogonal laboratory testing. Physician feedback was elicited by teleconferences with a clinical microbial sequencing board and by surveys. Clinical effect was evaluated by retrospective chart review. RESULTS We enrolled 204 pediatric and adult patients at eight hospitals. Patients were severely ill: 48.5% had been admitted to the intensive care unit, and the 30-day mortality among all study patients was 11.3%. A total of 58 infections of the nervous system were diagnosed in 57 patients (27.9%). Among these 58 infections, metagenomic NGS identified 13 (22%) that were not identified by clinical testing at the source hospital. Among the remaining 45 infections (78%), metagenomic NGS made concurrent diagnoses in 19. Of the 26 infections not identified by metagenomic NGS, 11 were diagnosed by serologic testing only, 7 were diagnosed from tissue samples other than CSF, and 8 were negative on metagenomic NGS owing to low titers of pathogens in CSF. A total of 8 of 13 diagnoses made solely by metagenomic NGS had a likely clinical effect, with 7 of 13 guiding treatment. CONCLUSIONS Routine microbiologic testing is often insufficient to detect all neuroinvasive pathogens. In this study, metagenomic NGS of CSF obtained from patients with meningitis or encephalitis improved diagnosis of neurologic infections and provided actionable information in some cases. (Funded by the National Institutes of Health and others; PDAID ClinicalTrials.gov number, .)

Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System?

“…A fast and accurate diagnosis would certainly improve prognosis for patients with a suspected CNS infection. Identification of a specific virus provides relevant information on how to treat a patient; therefore, the development of modern technologies, such as high throughput sequencing (Next Generation Sequencing) are warranted as it represents a potentially unbiased marvelous tool for rapid and robust diagnosis of unexplained encephalitis or other types of encephalopathies or neuronal manifestations, especially in the context where more traditional techniques have failed to identify the etiological agent [21,108,111,244,321,322]. Therefore, although our attention is mainly on a few different viruses such as HSV, arboviruses and enteroviruses, it may now be the time to look at CNS viral infection from another perspective.…”

Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China

“…At the meantime, 300μl of UTM were sent for a fast, simultaneous, multiplexed real-time reverse transcription nucleic acid amplification assay for qualitative detection and identification of multiple respiratory viral and bacterial nucleic acids in nasopharyngeal swabs using Qiagen ResPlex II V2.0 kit, which including more than 22 Total RNA was extracted using the QIAamp Viral RNA Mini Kit (QIAGEN, Germany), and sent for the metagenomic sequencing. During metagenomic sequencing, RNA was reversetranscribed into cDNA, with which sequencing library was prepared.…”

High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection

“…Traditional testing methods such as PCR, serological typing, bacterial culture and antibody detection, are regarded as the "gold standard" and widely used in ARI diagnosis 6,7 . However, despite an ongoing effort to include multiple pathogens in a single assay 8,9 , it remains difficult to simultaneously identify all potential ARI pathogens and capture new or uncommon respiratory pathogens 10 .Metagenomic next-generation sequencing (mNGS) is an unbiased way of discovering a broad range of infectious agents [11][12][13] , and has been recently introduced into clinical research to investigate the microbial cause of unusual disease cases 14 , perform broad-scale surveys for pathogens in undiagnosed diseases 15,16 , and understand the role of opportunistic infections 17,18 . For example, a study of severe pneumonia revealed that mNGS is both efficient and reliable 19,20 .…”