Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing.

Importance: Identifying infectious causes of subacute or chronic meningitis can be challenging. Enhanced, unbiased diagnostic approaches are needed. Objective: To present a case series of patients with diagnostically challenging subacute or chronic meningitis using metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) supported by a statistical framework generated from mNGS of control samples from the environment and from patients who were noninfectious. Design, Setting, and Participants: In this case series, mNGS data obtained from the CSF of 94 patients with noninfectious neuroinflammatory disorders and from 24 water and reagent control samples were used to develop and implement a weighted scoring metric based on z scores at the species and genus levels for both nucleotide and protein alignments to prioritize and rank the mNGS results. Total RNA was extracted for mNGS from the CSF of 7 participants with subacute or chronic meningitis who were recruited between September 2013 and March 2017 as part of a multicenter study of mNGS pathogen discovery among patients with suspected neuroinflammatory conditions. The neurologic infections identified by mNGS in these 7 participants represented a diverse array of pathogens. The patients were referred from the University of California, San Francisco Medical Center (n = 2), Zuckerberg San Francisco General Hospital and Trauma Center (n = 2), Cleveland Clinic (n = 1), University of Washington (n = 1), and Kaiser Permanente (n = 1). A weighted z score was used to filter out environmental contaminants and facilitate efficient data triage and analysis. Main Outcomes and Measures: Pathogens identified by mNGS and the ability of a statistical model to prioritize, rank, and simplify mNGS results. Results: The 7 participants ranged in age from 10 to 55 years, and 3 (43%) were female. A parasitic worm (Taenia solium, in 2 participants), a virus (HIV-1), and 4 fungi (Cryptococcus neoformans, Aspergillus oryzae, Histoplasma capsulatum, and Candida dubliniensis) were identified among the 7 participants by using mNGS. Evaluating mNGS data with a weighted z score-based scoring algorithm reduced the reported microbial taxa by a mean of 87% (range, 41%-99%) when taxa with a combined score of 0 or less were removed, effectively separating bona fide pathogen sequences from spurious environmental sequences so that, in each case, the causative pathogen was found within the top 2 scoring microbes identified using the algorithm. Conclusions and Relevance: Diverse microbial pathogens were identified by mNGS in the CSF of patients with diagnostically challenging subacute or chronic meningitis, including a case of subarachnoid neurocysticercosis that defied diagnosis for 1 year, the first reported case of CNS vasculitis caused by Aspergillus oryzae, and the fourth reported case of C dubliniensis meningitis. Prioritizing metagenomic data with a scoring algorithm greatly clarified data interpretation and highlighted the problem of attributing biological significance to organisms present in control samples used for metagenomic sequencing studies.

Neurologic infections in diabetes mellitus.

Even at a time when HIV/AIDS and immunosuppressive therapy have increased the number of individuals living with significant immunocompromise, diabetes mellitus (DM) remains a major comorbid disorder for several rare but potentially lethal infections, including rhino-orbital-cerebral mucormycosis and malignant external otitis. DM is also a commonly associated condition in patients with nontropical pyomyositis, pyogenic spinal infections, Listeria meningitis, and blastomycosis. As West Nile virus spread to and across North America over a decade ago, DM appeared in many series as a risk factor for death or neuroinvasive disease. More recently, in several large international population-based studies, DM was identified as a risk factor for herpes zoster. The relationships among infection, DM, and the nervous system are multidirectional. Viral infections have been implicated in the pathogenesis of type 1 and type 2 DM, while parasitic infections have been hypothesized to protect against autoimmune disorders, including type 1 DM. DM-related neurologic disease can predispose to systemic infection - polyneuropathy is the predominant risk factor for diabetic foot infection. Because prognosis for many neurologic infections depends on timely institution of antimicrobial and sometimes surgical therapy, neurologists caring for diabetic patients should be familiar with the clinical features of the neuroinfectious syndromes associated with DM.

Altered mental status in HIV-infected patients.

HIV-infected patients are vulnerable to developing altered mental status (AMS) for myriad reasons, including the effects of HIV itself, the accompanying immune dysfunction, associated systemic illness, comorbid psychiatric disorders, and complicated medication regimens. Combination antiretroviral therapy (ART) has decreased the incidence of central nervous system (CNS) opportunistic infections (OIs) and HIV-associated dementia, but the benefits are not absolute. In addition to CNS OIs and complications of complex multisystem disease, immune reconstitution events developing in the early weeks and months after initiating ART may affect the brain and cause AMS. This article examines the epidemiology, diagnosis, and currently available treatment for patients with HIV-related AMS.

CNS viruses--diagnostic approach.

Diagnosis of CNS viral infections is challenging; yet, significant progress in laboratory diagnosis of CNS infections has come through applications of serology and polymerase chain reaction (PCR) to CSF and tissues. Advances in molecular and laboratory techniques, together with neuroimaging, epidemiologic, and surveillance efforts, are yielding greater success in CNS viral diagnosis and treatment.

Treatment of neurosyphilis.

In 2001, the incidence of primary and secondary syphilis increased in the United States for the first time in a decade. Increasing rates of early syphilis among men who have sex with men have been reported in many American cities, with similar outbreaks noted in Canada and Europe. In San Francisco, the increase has been particularly sharp and accompanied by an increase in the incidence of neurosyphilis. Early neurosyphilis develops within weeks to years of primary infection and primarily involves the meninges. Syndromes include syphilitic meningitis (often accompanied by cranial neuropathies), meningovascular syphilis (with associated ischemic stroke), or asymptomatic neurosyphilis. Late neurosyphilis occurs years to decades after exposure as cerebral or spinal gummatous disease or the classic parenchymal forms affecting the brain (general paresis or syphilitic encephalitis) or spinal cord and nerve roots (tabes dorsalis). Treponema pallidum, the causative agent, cannot be cultured in vitro, and microscopic techniques are laborious. Thus, diagnosis depends on serologic tests and cerebrospinal fluid (CSF) examination. The suboptimal sensitivity and specificity of these tests complicate diagnosis, particularly among patients coinfected with HIV. CSF examination should be performed to evaluate for neurosyphilis in all patients with positive serum syphilis serology and neurologic, ophthalmic, or tertiary disease, or in those who have failed therapy, and in HIV-infected patients with late latent syphilis or syphilis of unknown duration. Intravenous penicillin G is the recommended treatment for all forms of neurosyphilis and for syphilitic eye disease. An outpatient alternative, if adherence can be assured, is intramuscular benzathine penicillin with oral probenecid. Newer drugs that penetrate CSF, such as ceftriaxone or azithromycin, have not yet been adequately tested for neurosyphilis. Syphilis facilitates transmission of HIV (and vice versa), and thus all patients diagnosed with syphilis should be offered HIV testing.