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Central nervous system (CNS) infections are often life-threatening and can have severe sequelae. These infections cause inflammation and edema within the unyielding cranium, resulting in damage to brain tissue and loss of function. The most common causes of CNS infections are bacteria and viruses, but fungi, protozoa, and helminths also cause these infections.

In addition to the history and physical examination, clinical diagnosis of CNS infections requires a spinal fluid analysis combined with neuroimaging using either magnetic resonance imaging (MRI) or computed tomography (CT) scan. Microbiologic diagnosis of bacterial infections frequently is made using Gram stain and culture of spinal fluid and blood. Polymerase chain reaction (PCR) assays and serologic tests are also useful. Antimicrobial therapy requires that the antibiotics be bactericidal and that they penetrate the blood–brain barrier. Some CNS infections, such as a brain abscess, often require surgical drainage.


Examination of cerebrospinal fluid (CSF) is critical in making the diagnosis of CNS infections. CSF is obtained by performing a lumbar puncture at the L3–L4 interspace. During the process, the CSF pressure is measured and fluid obtained for analysis of cells (both number and cell type, i.e., neutrophils or lymphocytes), protein, and glucose. The results of CSF analysis in acute bacterial meningitis, acute viral meningitis, and subacute meningitis are described in Table 72–1.

TABLE 72–1Spinal Fluid Findings in Acute and Subacute Meningitis

Although CSF analysis is a very important step in the diagnosis of many CNS infections, a lumbar puncture should not be performed if there are signs of increased intracranial pressure, such as papilledema or focal neurologic signs, because herniation of the brainstem and death may occur. A CT scan should be performed prior to the lumbar puncture to determine whether a mass lesion, such as a brain abscess or cancer, is present. If a mass lesion is seen, a lumbar puncture should not be performed.


A causative organism is not identified in more than 50% of cases of meningitis and encephalitis. To address this problem, metagenomic next-generation sequencing (mNGS) techniques are being applied.

In the mNGS process, all of the DNA and RNA in the patient’s specimen is sequenced and known cellular sequences are disregarded. The sequences that remain are then compared to those in a database that contains the sequences ...

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