Identify elusive pathogenic microorganisms

Central nervous system (CNS) infections, among them meningitis, encephalitis, and brain abscesses, can be devastating to affected patients and are associated with substantial mortality and long-term effects.1 Treatment for certain infections is available. Identifying the type of infection through accurate laboratory diagnosis can lead to ideal outcomes.

The broad range of pathogenic causes for CNS infections, which include bacteria, fungi, viruses, and parasites, can present a diagnostic challenge.

Metagenomics Test menu


When first-line testing approaches, including culture and antigen staining, and other advanced testing methods, such as a multiplex polymerase chain reaction (PCR) panel, fail to yield a diagnosis, our metagenomic assay can offer precision answers to guide care.  

Shotgun metagenomic sequencing holistically sequences all the DNA and RNA present in cerebrospinal fluid. Bioinformatic analysis of those sequences identifies the presence of all pathogens, including viruses, bacteria, parasites, and fungi. Our world-renowned clinical microbiology physicians interpret results and provide clinical consultation, as needed. A broad menu of microbiology tests is immediately available to confirm or follow up on unusual or confusing findings.

More information

Certain clinical diagnostic methods, such as culture and specific PCR assays, are limited in the ability to detect nonviable organisms or nucleic acids not targeted by specific assays, respectively. Unbiased metagenomic sequencing overcomes diagnostic test limitations by interrogating microbiota without bias toward viable or specific microorganism(s).

Key testing


  1. Giovane RA, Lavender PD. Central nervous system infections. Prim Care. 2018 Sep;45(3):505-518. doi:10.1016/j.pop.2018.05.007. Epub 2018 Jul 9. PMID: 30115337.
  2. Citation Rodino KG, Toledano M, Norgan AP, et al. 2020. Retrospective review of clinical utility of shotgun metagenomic sequencing testing of cerebrospinal fluid from a U.S. tertiary care medical center. J Clin Microbiol. 58:e01729-20.

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