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16S Bacterial Meningitis PCR with Reflex to NGS

Test Code: 3530802
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Clinical Utility

The 16S Bacterial Meningitis PCR with Reflex to Next Generation Sequencing (NGS) assay is designed to detect and taxonomically characterize etiological agents of bacterial meningitis. Culture-based methods are considered the gold standard for confirming and characterizing central nervous system infections, yet suffer from poor turnaround times and suboptimal sensitivity.  Current molecular methods address these concerns but are limited by the scope of pathogens detected.  The 16S Bacterial Meningitis PCR with Reflex to NGS test can help providers identify both common and cryptic meningitis pathogens which can aid in reducing time to application of targeted treatment(s).

About 16S Bacterial Meningitis PCR with Reflex to NGS

Although bacterial meningitis is rare in the United States, there is substantial mortality and long-term sequelae associated with the disease. Knowing the specific pathogen involved in central nervous system (CNS) infection is crucial for selection of the appropriate therapeutic to achieve rapid convalescence and minimize the risk of permanent CNS damage.

Hallmark symptoms like fever, headache and stiff neck are most commonly associated with meningitis, but other symptoms include nausea and vomiting, light sensitivity and an altered mental state. Symptoms can develop over a week’s time, or quickly over a few days. Bacterial meningitis can be spread through person to person contact, during labor and birth, or through aerosols or contaminated bodily fluids. Risk factors for meningitis include age, certain medical conditions or procedures, working with causative pathogens and travel to regions where infections are endemic. The best method of prevention for high-risk groups is to receive both the pneumococcal (Prevnar® or Synflorix®) and meningococcal vaccines (Menactra® or Menveo®).

Current methods of diagnosing bacterial meningitis include neurological exams, brain imaging and blood tests. Sampling CSF via lumbar puncture for analysis is standard practice where meningitis is suspected. Typically, culture and microscopy (Gram stain) are performed alongside additional diagnostics such as white blood cell count, and quantification of glucose and/or protein levels. Depending on the healthcare providers’ initial management approach, a CSF culture may be ordered. CSF cultures can be monitored for up to 10 days to account for slow growing and/or fastidious bacteria. If possible, CSF submitted for culture should be obtained before administration of antibiotics, as this can impact results by increasing the risk of a false-negative. One advantage of molecular methods over culture is that nucleic acid amplification techniques are generally not affected by the use of preemptive antimicrobial therapy. While pathogen-specific or multiplexed PCR allows for the detection and/or identification of the targeted organism(s), broad-range 16S PCR followed by NGS allows for universal template amplification across a diverse group of organisms followed by simultaneous sequencing of heterogeneous mixtures of templates without the loss of resolution characteristic of poly-microbial samples when sequenced with Sanger sequencing. These performance differentiators should allow 16S NGS to be successfully leveraged alongside culture methods to increase the likelihood of an accurate and timely diagnosis.


PCR is used to amplify the bacterial 16S gene from patient cerebrospinal fluid (CSF) using highly conserved primer sequences. The amplified 16S gene is then sequenced using next-generation sequencing (NGS) and the results are processed through a custom bioinformatics pipeline to generate bacterial identities. The assay was validated to detect and identify the most common bacterial pathogens associated with meningitis including: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Listeria monocytogenes, Streptococcus agalactiae (Group B Strep) and Escherichia coli as well as other less common pathogens that are clinically important in immunocompromised patient populations (HIV-positive, solid organ transplant or hematopoietic cell transplant patients). The 16S sequence database includes a large number of sequences encompassing both common and rare meningitis pathogens that have been identified in immunocompromised patients. In addition to the organisms listed above, the 16S NGS assay was validated against a collection of atypical meningitis pathogens from the following genera: Mycobacterium, Staphylococcus, Klebsiella, Salmonella, Pseudomonas, Serratia and Enterobacter. The 16S sequence database contains records for over 10,000 bacterial species including the aforementioned pathogens.


The 16S Bacterial Meningitis PCR with Reflex to NGS assay is designed to detect and taxonomically characterize etiological agents of bacterial meningitis

3 business days from receipt of specimen.

Specimen Type Order Code CPT Code NY Approved Volume Assay Range Special Instructions
CSF 3530802 87800 (PCR) / 81479 (NGS) Yes

1 mL (500 µL min.)


  • Collect CSF from lumbar puncture in a sterile screw top tube
  • Send the third tube collected
  • Ensure the tube is not placed on lab automation equipment
  • Ship frozen on dry ice

Ship Monday through Friday. Friday shipments must be labeled for Saturday delivery. All specimens must be labeled with patient's name and collection date. A Viracor Eurofins test requisition form must accompany each specimen. Multiple tests can be run on one specimen. Ship specimens FedEx Priority Overnight® to: Viracor Eurofins, 1001 NW Technology Dr, Lee's Summit, MO 64086.

Causes for Rejection

Specimens received ambient.

Specimens are approved for testing in New York only when indicated in the Specimen Information field above.

The CPT codes provided are based on Viracor Eurofins' interpretation of the American Medical Association's Current Procedural Terminology (CPT) codes and are provided for general informational purposes only. CPT coding is the sole responsibility of the billing party. Questions regarding coding should be addressed to your local Medicare carrier. Viracor Eurofins assumes no responsibility for billing errors due to reliance on the CPT codes illustrated in this material.


Bacterial Meningitis. (2017, January 25). Retrieved from

Lora AJM & Young J. Central Nervous System Infections: Diagnosis and Treatment – Hospital Physician Board Review Manual. Infectious Diseases (2015), Vol 16:1.

He T, Kaplan S, Kamboj M, and Tang YW. Laboratory Diagnosis of Central Nervous System Infection. Current Infectious Disease Reports (2016), 18:35.

Laban JT & O’Neill K. CNS Infection. Neurosurgery (2009), 27:3.

Meningitis and Encephalitis Fact Sheet. (2018, July 6). Retrieved from

Tunkel AR, Hasbun R, Bhimraj A, et. al. 2017 Infectious Diseases Society of America’s Clinical Practice Guidelines for Healthcare-Associated Ventriculitis and Meningitis. (2017, October 1). Retrieved from



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