Syndromic Testing for Infectious Diseases, Part 3: Central Nervous System Infections

Expires December 2020

  • Presenter

    Elitza Theel, Ph.D., is a Consultant for the Department of Laboratory Medicine and Pathology in Clinical Microbiology at Mayo Clinic in Rochester, Minnesota. She holds the academic rank of Associate Professor of Laboratory Medicine and Pathology.


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    Transcript and References


    Hi, I’m Matt Binnicker, the Director of Clinical Virology and Vice Chair of Practice in the Department of Laboratory Medicine and Pathology at Mayo Clinic. Did you know that following the introduction of the Haemophilus influenza type B vaccination in 1990 and the pneumococcal conjugate vaccines in 2000 that the incidence of cases of bacterial meningitis decline significantly? However, bacterial infections of the central nervous system continue to be a problem in children less than two months of age and in the elderly. In addition, viral and fungal causes of meningitis and encephalitis continue to be a cause of morbidity and mortality worldwide. In this month’s “Hot Topic,” my colleague Dr. Elli Theel will give Part 3 of a four-part series on the use of syndromic molecular panels in the diagnosis of infectious diseases. Specifically, she’ll discuss how the use of these panels may improve the coverage for detecting infectious agents and reduce the turnaround time for reporting results. I hope you enjoy this month’s “Hot Topic,” and I want to personally thank you for allowing Mayo Clinic the opportunity to partner in your patients’ health care.


    Thank you for joining us today to discuss syndromic testing for infections in the central nervous system. Before we begin, I just want to note, I have no relevant financial disclosures to share.

    Utilization Message

    As you view the following presentation, consider the following important points regarding testing. How is this testing going to be used in your practice? When should the tests be used, and how will results impact patient management?

    Central Nervous System Infections

    While we will be discussing central nervous system (CNS) infections in general during this presentation, it is important to recognize that these infections are differentiated based on what region of the CNS is affected and how the patient presents. Additionally, certain infectious agents have a tropism or a predilection for infecting certain areas of the CNS, further helping to guide a differential diagnosis. The general definitions of meningitis, encephalitis, meningoencephalitis, myelitis, and encephalomyelitis are presented here for your reference

    Meningitis vs. Encephalitis

    Meningitis, or inflammation of the meninges, and encephalitis, which is defined as inflammation of the brain matter or parenchyma, are among the most commonly encountered types of CNS infection. As this table shows, while certain symptoms or manifestations appear specific to meningitis, such as photophobia and neck stiffness, or encephalitis, including altered mental status, many symptoms overlap between these two clinical entities.

    Additionally, CNS infections may be caused by any number of microbiologic agents, including bacterial, viral, fungal, or parasitic organisms. Important to remember however, is that CNS disease may also be caused by non-infectious processes.

    Ultimately, therefore, diagnostic testing is necessary to determine the precise cause of CNS disease and to help guide subsequent management.

    Common Causes of CNS Infection

    When considering infectious causes of CNS infection, there are many possible agents. However, some of the more common bacterial agents to consider include Streptococcus pneumoniae, Streptococcus agalactiae, Neisseria meningitidis, Haemophilus influenzae, and Listeria monocytogenes.

    Common viral agents include CMV, HSV, enterovirus, and West Nile Virus, and finally, Cryptococcus species are among the most common causes of fungal CNS infection.

    Diagnosis of CNS Infections

    When considering infectious causes of CNS disease, a differential diagnosis can be established by considering patient presentation, including their symptoms, exposure history, and season of onset, their vaccination history, and importantly, their immune status.

    Cerebrospinal fluid is typically collected from patients with suspected CNS disease, and this table summarizes the appearance and other general findings in CSF collected from healthy individuals and in those with CNS disease due to either viral, bacterial, or fungal agents. Key things to note include the appearance of the CSF, which is often turbid in patients with bacterial CNS infections, who also have markedly elevated protein levels alongside markedly decreased CSF glucose levels.

    Despite these general trends, many of these finding can overlap between infectious causes of CNS infections, thus requiring dedicated microbiologic testing to be performed to help establish a definitive diagnosis.

    Diagnosis of CNS Infections: Traditional Laboratory Methods

    Traditional laboratory methods for detection of CNS infection include performing Gram and fungal stains, bacterial and fungal cultures, and depending on the patient risk factors, antigen detection for Cryptococcus species and Streptococcus pneumoniae. Some of the limitations of these methods include the limited sensitivity of Gram stains, which can range from approximately 90% for patients with Strep pneumoniae to 35% in patients with Listeria monocytogenes. Also, for culture-based testing, sensitivity is often significantly decreased if antibiotics were initiated prior to specimen collection.

    In cases of suspected CNS infection due to a viral etiology, CSF may likewise be cultured, though more and more commonly, singleplex molecular testing for common viral agents such as HSV, is performed directly off of the CSF sample, and a number of these commercially available assays have already received FDA-clearance.

    Additionally, for most neurotropic arboviruses such as West Nile Virus or St. Louis encephalitis virus, serologic testing of CSF is the method of choice due to generally low sensitivity of molecular testing for these viruses.

    Meningitis and Encephalitis Panel (MEP)

    In 2015, the FDA approved the first multiplex molecular panel for detection of 14 different infectious agents, offered from BioFire. This meningitis/encephalitis panel is performed on the FilmArray® platform and can detect nucleic acid in CSF from 6 bacterial, 7 viral, and 1 fungal agent as listed on this slide.

    This multiplex assay is advantageous for a number of reasons, including its broad coverage of infectious agents, providing direct sample-to-answer information, and it’s fairly rapid, with a run time of approximately 60 minutes from sample addition to result.

    So, now that this meningitis/encephalitis multiplex panel is available, how and when should it be used?

    The Meningitis/Encephalitis Panel: To Use or Not to Use?

    And, to get at this important test-utilization question, we will go through two scenarios highlighting the advantages and limitations of multiplex, syndromic panel testing for CNS infections.

    Case #1

    For the first case, we have a 20-year-old male who presented to the emergency department with sudden onset fever, headache, neck stiffness, and photophobia. He indicates that he recently returned from a mission trip to Mali and that he is otherwise healthy, though he hasn’t had any vaccines since the age of 8.

    Due to his presentation, a CSF sample was collected, which was noted to be cloudy and subsequently reported to have elevated protein and 150 white blood cells, predominantly neutrophils. His glucose was also noted to be low, at 20% of his blood glucose.

    So, the question to consider here is whether the meningitis/encephalitis multiplex panel should be performed.

    Case #1 Resolution

    The findings for this patient are clearly suggestive of a bacterial meningitis. Additionally, you note that he has recently traveled to a region in Africa that is endemic for Neisseria meningitidis and is in fact referred to as the “meningitis belt” in Africa. Additionally, you note that he is not up to date on his Neisseria meningitidis or Streptococcus pneumoniae vaccines.

    So, the meningitis/encephalitis panel would be an appropriate first-line test for this patient as the differential for bacterial meningitis is broad, and if the causative agent is on the panel, a result would be achieved quickly compared to culture.

    However, Gram and fungal stains, alongside cultures should still be performed in the case that the causative bacterial agent is not covered by the multiplex panel. Additionally, isolates may still be needed for susceptibility testing and also, public health laboratories may require isolates for typing purposes.

    Case #2

    For our second case, we have an HIV-positive patient with a CD4 cell count of 105 who presents with photophobia, headache, fever, and progressive, unintentional weight loss. The patient indicates that he recently helped his local church clean the bell tower, which was covered with bird droppings.

    Again, the question here is, “Should the meningitis/encephalitis syndromic panel be ordered on CSF for this patient”?

    Case #2 Resolution

    It is important to consider the patient’s presentation, which is suggestive of meningitis, his risk factors, which include HIV-associated immunosuppression, and his exposure to bird droppings, all of which collectively point to Cryptococcus being a very likely cause of his meningitis.

    So, instead of jumping immediately to the meningitis/encephalitis syndromic panel, providers should consider performing the rapid, sensitive, and inexpensive Cryptococcus antigen test on both CSF and serum first, alongside traditional Gram and fungal stains and cultures.

    Should the Cryptococcus antigen testing be negative, the meningitis/encephalitis panel should be considered.

    Advantages of Syndromic Panel Testing for Meningitis and Encephalitis

    So, in summary, there are a number of advantages for the syndromic panel for meningitis and encephalitis, including the fact that it is a broad panel for bacterial, viral, and fungal infectious agents, and it includes testing for human parechovirus, a viral agent that is not routinely tested for in clinical laboratories.

    The assay itself is fairly rapid, with a test-to-result turnaround time of approximately 60 minutes compared to traditional methods such as culture, which may take days. Also, this panel is potentially more sensitive in patients who have received antibiotics prior to collection of CSF, which may decrease the chance of the organism growing in culture. And finally, from a laboratory perspective, this rapid assay has minimal technologist hands-on time.

    Limitations of Syndromic Panel Testing for Meningitis and Encephalitis

    There are, however, a number of limitations that should be considered when it comes to such syndromic panel testing. This includes the cost of these assays, which can be quite high. For this reason, targeted testing may be more appropriate in patients with a sufficiently high probability of infection with a specific agent for which alternative testing is available, such as in our second case of cryptococcal meningitis.

    Also, while broad, these panels are not in fact all-inclusive and do not target all possible causes of meningitis and encephalitis.

    Another challenge associated with this syndromic panel includes the interpretation of certain positive results. For example, a positive result for HHV6 in CSF may indicate that it is the true cause of CNS disease, however, this may alternatively indicate germline integration of HHV6.

    Additionally, prior studies have shown that false-positive results may occur, and this has specifically been documented for the Streptococcus pneumoniae target. Studies have also shown that multiple targets may be detected in CSF specimens, leading to further interpretive challenges.

    Finally, as presented in the both cases, CSF Gram and fungal stains, alongside culture should still be performed even with the meningitis/encephalitis panel is ordered. The reason for this is to ensure that isolates are available for any necessary susceptibility testing and for public health lab requirements.


    • Leber AL, Everhart K, Balada-Llasat JM, et al. Multicenter evaluation of BioFire FilmArray® meningitis/encephalitis panel for detection of bacteria, viruses, and yeast in cerebrospinal fluid specimens. J Clin Microbiol. 2016;54:2251-2261.
    • Rhein J, Bahr NC, Hemmert AC, et al. Diagnostic performance of a multiplex PCR assay for meningitis in an HIV-infected population in Uganda. Diagn Microbiol Infect Dis. 2016; 84:268-273.
    • Graf EH, Farquharson MV, Cardenas AM. Comparative evaluation of the FilmArray meningitis/encephalitis molecular panel in a pediatric population. Diagn Microbiol Infect Dis. 2017;87:92-94.
    Elitza Theel (@elitzatheel)

    Elitza Theel

    Elitza Theel, Ph.D., is a Consultant for the Department of Laboratory Medicine and Pathology in Clinical Microbiology at Mayo Clinic in Rochester, Minnesota. She holds the academic rank of Associate Professor of Laboratory Medicine and Pathology.