Molecular methods for diagnosis of viral encephalitis

Bovine astrovirus and its role in lymphocytic encephalitis in cattle in Ontario, Canada, 1988-2019

Astroviruses have been found in cattle and other species with encephalitis. Our objective was to determine the frequency of neurotropic bovine astrovirus (BoAstV) in cases of encephalitis in cattle ≥ 4-mo-old. Of 56 cases of idiopathic lymphocytic encephalitis examined retrospectively (1988-2019), fixed brain from 11 cases (19%) tested positive by semi-quantitative RT-PCR for BoAstV CH13/NeuroS1. None of the control cases tested positive, including 32 with other forms of encephalitis and 40 with no neurologic disease. Most astrovirus-positive cases were 1-2-y-old, with a range of 7 mo to 7 y, and affected both beef and dairy breeds with wide geographic distribution. BoAstV-positive cases had acute onset of neurologic signs of 12 h to 7 d before death or euthanasia. Affected cattle had lymphocytic inflammation throughout the brain including cerebrum, thalamus, midbrain, cerebellum, medulla oblongata, and spinal cord, and affecting gray and white matter. Further PCR testing identified a possible cause in 9 of the 45 (20%) remaining idiopathic cases of lymphocytic encephalitis, including eastern equine encephalitis virus, Listeria monocytogenes, bovine viral diarrhea virus, bovine alphaherpesvirus 1, and ovine gammaherpesvirus 2 (malignant catarrhal fever); we found no cases of infection by West Nile virus, rabies virus, or Chlamydia spp. No cause was identified in 36 of 56 (64%) cases of lymphocytic encephalitis. We frequently identified neurotropic BoAstV in cases of lymphocytic encephalitis that had no previously identified cause. Neurotropic BoAstV infections had gone undetected for decades, but the frequency of BoAstV infections has not increased among contemporary cases.

The diagnosis of central nervous system infections in resource-limited settings and the use of novel and molecular diagnostic platforms to improve diagnosis

INTRODUCTION

Central nervous system infections (CNSI) disproportionately affect individuals in low-resource settings where diagnosis is challenging; large proportions of patients never receive a confirmed microbiological diagnosis resulting in inadequate management and high mortality. The epidemiology of CNSI varies globally and conventional diagnostics deployed in resource-limited settings have significant limitations, with an urgent need for improved diagnostic strategies.

AREAS COVERED

This review describes molecular platforms and other novel diagnostics used in the diagnosis of CNSI that are applicable to resource-limited settings. An extensive literature search of Medline and PubMed was performed. The emphasis is on investigations targeting infections of relevance to resource-limited settings either due to variation in regional CNSI epidemiology or due to increased prevalence in patients with immunosuppression. This includes commercially available multiplex PCR platforms, mycobacterial PCR platforms, and rapid diagnostics tests. To offer a framework for the optimal implementation in clinical settings, existing evidence highlighting the advantages and limitations of available platforms is reviewed.

EXPERT OPINION

The implementation of molecular platforms and other novel diagnostics has the potential to transform CNSI diagnosis in resource-limited settings, with several examples of successful rollout of novel diagnostics such as Xpert MTB/RIF Ultra and cryptococcal antigen testing.

Laboratory diagnosis of CNS infections in children due to emerging and re-emerging neurotropic viruses

Recent decades have witnessed the emergence and re-emergence of numerous medically important viruses that cause central nervous system (CNS) infections in children, e.g., Zika, West Nile, and enterovirus/parechovirus. Children with immature immune defenses and blood-brain barrier are more vulnerable to viral CNS infections and meningitis than adults. Viral invasion into the CNS causes meningitis, encephalitis, brain imaging abnormalities, and long-term neurodevelopmental sequelae. Rapid and accurate detection of neurotropic viral infections is essential for diagnosing CNS diseases and setting up an appropriate patient management plan. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis/encephalitis. However, the expansion of test menu has led to new challenges in selecting appropriate tests and making accurate interpretation of test results. There are unmet gaps in development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses. Herein we will discuss the advances and challenges in the laboratory diagnosis of viral CNS infections in children. This review not only sheds light on selection and interpretation of a suitable diagnostic test for emerging/re-emerging neurotropic viruses, but also calls for more research on development and clinical utility study of novel molecular assays. IMPACT: Children with immature immune defenses and blood-brain barrier, especially neonates and infants, are more vulnerable to viral central nervous system infections and meningitis than adults. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis and encephalitis. There are unmet gaps in the development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses.

miRNAs: Targets to Investigate Herpesvirus Infection Associated with Neurological Disorders

Herpesvirus is associated with various neurological disorders and a specific diagnosis is associated with a better prognosis. MicroRNAs (miRNAs) are potential diagnostic and prognostic biomarkers of neurological diseases triggered by herpetic infection. In this review, we discuss miRNAs that have been associated with neurological disorders related to the action of herpesviruses. Human miRNAs and herpesvirus-encoded miRNAs were listed and discussed. This review article will be valuable in stimulating the search for new diagnostic and prognosis alternatives and understanding the role of these miRNAs in neurological diseases triggered by herpesviruses.

Updates in Molecular Diagnostics in Solid Organ Transplantation Recipients

Advances in molecular diagnostics have the potential to improve patient care among solid organ transplant recipients by reducing time to pathogen identification and informing directed therapy. Although cultures remain the cornerstone of traditional microbiology, advanced molecular diagnostics, such as metagenomic next-generation sequencing (mNGS), may increase detection of pathogens. This is particularly true in the settings of prior antibiotic exposure, and when causative organisms are fastidious. mNGS also offers a hypothesis-free diagnostic method of testing. This is useful in situations whereby the differential is broad or when the infectious agent is unlikely to be detected by routine methods.

Molecular diagnostics of infectious disease: Detection and characterization of microbial agents in cytology samples

BACKGROUND

Cytology samples are widely used to diagnose various infectious diseases by detection and identification of causative infectious agents, including bacteria, fungi, and viruses. The role of cytopathology in infectious disease has expanded tremendously in the past decades with the advances in molecular techniques. Molecular diagnostic methods, compared to conventional methods, have shown improved patient outcome, reduction in cost, and shortened hospital stay times. The aim of this article is to review molecular testing in cytology samples for diagnosis of infectious diseases.

METHODS

The literature search for molecular testing in common cytology samples for diagnosis of infectious diseases was performed. The findings of the studies were summarized. The common cytology samples included in this article were gynecologic specimens, cerebrospinal fluid, bronchoalveolar lavage, and urine samples.

CONCLUSIONS

There are a number of molecular diagnostic tests that are available to be used in common cytology samples to detect infectious agents. Each test has its own advantages and limitations. It is our hope that upon reading this review article, the readers will have better understanding of molecular diagnostic testing of infectious diseases utilizing commonly sampled cytology specimens in daily practice.

Multiplex detection of meningitis and encephalitis pathogens: A study from laboratory to clinic

Introduction

Infectious meningitis and encephalitis (ME) are life-threatening conditions are caused by various pathogens. Conventional laboratory tests with low sensitivity and specificity cannot help with early diagnosis.

Methods

A prospective study using the novel multiplex PCR detection for 18 pathogens of ME (MME-18) was conducted to investigate the clinical utilization and the epidemiology characteristics of ME in southwestern China. Patients with suspected intracranial infection were recruited between May and October 2019 at West China Hospital of Sichuan University. The MME-18 was used to detect cerebrospinal fluid, and conventional experiments including cryptococcal capsular antigen detection, GeneXpert, real-time PCR, and clinical feedback were used to verify the result of MME-18.

Results

Among 581 tested patients, 139 eligible individuals were enrolled in the study. Among them, Mycobacterium tuberculosis was the most common pathogen in mono-infection. Viruses and Cryptococcus neoformans were also frequently detected. Of 139 infected patients, 12 cases were diagnosed by MME-18 only, 57 patients by conventional testing only, and 70 cases by both comparator tests and MME-18. There were 96.3% (79/82) diagnoses made by MME-18 had a favorable outcome, and two of twelve diagnoses, made solely by MME-18, had a likely unclear clinical significance.

Discussion

The MME-18 showed satisfactory consistency with expert clinical consensus for patients presenting with ME. Combined with conventional testing and clinical suspicion, MME-18 may help clinicians with the early identification of pathogens.

Progressive multifocal leukoencephalopathy 10 years following transplant: 5HT receptor antagonism as an adjunct to immune reconstitution

We report a case of a patient presenting with subacute neurological symptoms 10 years postkidney transplant. Cognitive deficits included acalculia and left upper limb dysesthesia, progressing to hemiplegic upper motor neuron weakness. Investigations included an MRI with multiple FLAIR hyperintensities, while a lumbar puncture was sterile with negative flow cytometry. Ultimately, PCR testing for John Cunningham virus was positive on cerebrospinal fluid. The diagnosis of progressive multifocal leukoencephalopathy (PML) was confirmed on the basis of the above.Initially, the patient was managed with withdrawal of immunosuppressants and close observation. Mirtazapine was commenced based on case reports of successful use in non-transplant patients; the patient's recovery was temporally related to withdrawal of immunosuppression and increasing mirtazapine dosage. The patient is currently maintained on prednisolone and mirtazapine with stable graft function and improved mobility and cognitive function.

The experience of using FilmArray Meningitis/Encephalitis Panel for the diagnosis of meningitis and encephalitis in pediatric patients

BACKGROUND/PURPOSE

Central nervous system infections can cause severe complications and even death in children. Early diagnosis of the causative pathogen can guide appropriate treatment and improve outcomes. The BioFire® FilmArray® Meningitis/Encephalitis Panel (FA-ME) is a multiplex polymerase chain reaction (PCR) assay targeting 14 pathogens. We aimed to examine FA-ME performance compared with conventional assays and its effect on antimicrobial usage.

METHODS

We prospectively enrolled 55 pediatric patients with suspected meningitis or encephalitis and simultaneously performed FA-ME and conventional assays. Sixty-three hospitalized patients with CNS infection before implementing FA-ME were considered controls. We compared the FA-ME results with conventional assays and the empiric antimicrobial usage and hospital stay between the two study groups.

RESULTS

Nine patients (16.4%) tested positive by FA-ME, four were bacterial, and five were viral. Three additional pathogens were detected by conventional assays: Enterococcus faecalis, Leptospira, and herpes simplex virus type 2. In the control group, two bacterial pathogens were detected by CSF culture and four viral pathogens by single PCRs. Compared with the control group, the FA-ME group had a shorter time for pathogen detection, but there were no significant differences in pathogen detection rate, duration of empiric antimicrobial therapy, and length of hospital stay.

CONCLUSION

Although no significant difference was found in empiric antimicrobial duration and length of stay between patients tested with FA-ME and conventional assays, FA-ME had the advantage of a shorter detection time and early exclusion of potential causative pathogens. The FA-ME results should be interpreted carefully based on the clinical presentation.

Viral meningitis in Sudanese children: Differentiation, etiology and review of literature

Diagnosis of viral meningitis (VM) is uncommon practice in Sudan and there is no local viral etiological map. We therefore intended to differentiate VM using standardized clinical codes and determine the involvement of herpes simplex virus types-1 and 2 (HSV-1/2), varicella zoster virus, non-polio human enteroviruses (HEVs), and human parechoviruses in meningeal infections in children in Sudan. This is a cross-sectional hospital-based study. Viral meningitis was differentiated in 503 suspected febrile attendee of Omdurman Hospital for Children following the criteria listed in the Clinical Case Definition for Aseptic/Viral Meningitis. Patients were children age 0 to 15 years. Viral nucleic acids (DNA/RNA) were extracted from cerebrospinal fluid (CSF) specimens using QIAamp® UltraSens Virus Technology. Complementary DNA was prepared from viral RNA using GoScriptTM Reverse Transcription System. Viral nucleic acids were amplified and detected using quantitative TaqMan® Real-Time and conventional polymerase chain reactions (PCRs). Hospital diagnosis of VM was assigned to 0%, when clinical codes were applied; we considered 3.2% as having VM among the total study population and as 40% among those with proven infectious meningitis. Two (0.4%) out of total 503 CSF specimens were positive for HSV-1; Ct values were 37.05 and 39.10 and virus copies were 652/PCR run (261 × 103/mL CSF) and 123/PCR run (49.3 × 103/mL CSF), respectively. Other 2 (0.4%) CSF specimens were positive for non-polio HEVs; Ct values were 37.70 and 38.30, and the approximate virus copies were 5E2/PCR run (~2E5/mL CSF) and 2E2/PCR run (~8E4/mL CSF), respectively. No genetic materials were detected for HSV-2, varicella zoster virus, and human parechoviruses. The diagnosis of VM was never assigned by the hospital despite fulfilling the clinical case definition. Virus detection rate was 10% among cases with proven infectious meningitis. Detected viruses were HSV-1 and non-polio HEVs. Positive virus PCRs in CSFs with normal cellular counts were seen.

Determining an infectious or autoimmune etiology in encephalitis

Objectives

Early presentation and workup for acute infectious (IE) and autoimmune encephalitis (AE) are similar. This study aims to identify routine laboratory markers at presentation that are associated with IE or AE.

Methods

This was a multi‐center retrospective study at three tertiary care hospitals in New York City analyzing demographic and clinical data from patients diagnosed with definitive encephalitis based on a confirmed pathogen and/or autoantibody and established criteria for clinical syndromes.

Results

Three hundred and thirty‐three individuals with confirmed acute meningoencephalitis were included. An infectious‐nonbacterial (NB) pathogen was identified in 151/333 (45.40%), bacterial pathogen in 95/333 (28.50%), and autoantibody in 87/333 (26.10%). NB encephalitis was differentiated from AE by the presence of fever (NB 62.25%, AE 24.10%; p < 0.001), higher CSF white blood cell (WBC) (median 78 cells/μL, 8.00 cells/μL; p < 0.001), higher CSF protein (76.50 mg/dL, 40.90 mg/dL; p < 0.001), lower CSF glucose (58.00 mg/dL, 69.00 mg/dL; p < 0.001), lower serum WBC (7.80 cells/μL, 9.72 cells/μL; p < 0.050), higher erythrocyte sedimentation rate (19.50 mm/HR, 13.00 mm/HR; p < 0.05), higher C‐reactive protein (6.40 mg/L, 1.25 mg/L; p = 0.005), and lack of antinuclear antibody titers (>1:40; NB 11.54%, AE 32.73%; p < 0.001). CSF‐to‐serum WBC ratio was significantly higher in NB compared to AE (NB 11.3, AE 0.99; p < 0.001). From these findings, the association of presenting with fever, CSF WBC ≥50 cells/μL, and CSF protein ≥75 mg/dL was explored in ruling‐out AE. When all three criteria are present, an AE was found to be highly unlikely (sensitivity 92%, specificity 75%, negative predictive value 95%, and positive predictive value 64%).

Interpretations

Specific paraclinical data at initial presentation may risk stratify which patients have an IE versus AE.

Surveillance of Viral Encephalitis in the Context of COVID-19: A One-Year Observational Study among Hospitalized Patients in Dakar, Senegal

The burden of encephalitis and its associated viral etiology is poorly described in Africa. Moreover, neurological manifestations of COVID-19 are increasingly reported in many countries, but less so in Africa. Our prospective study aimed to characterize the main viral etiologies of patients hospitalized for encephalitis in two hospitals in Dakar. From January to December 2021, all adult patients that met the inclusion criteria for clinical infectious encephalitis were enrolled. Cerebrospinal fluids, blood, and nasopharyngeal swabs were taken and tested for 27 viruses. During the study period, 122 patients were enrolled. Viral etiology was confirmed or probable in 27 patients (22.1%), with SARS-CoV-2 (n = 8), HSV-1 (n = 7), HHV-7 (n = 5), and EBV (n = 4) being the most detected viruses. Age groups 40–49 was more likely to be positive for at least one virus with an odds ratio of 7.7. The mortality was high among infected patients, with 11 (41%) deaths notified during hospitalization. Interestingly, SARS-CoV-2 was the most prevalent virus in hospitalized patients presenting with encephalitis. Our results reveal the crucial need to establish a country-wide surveillance of encephalitis in Senegal to estimate the burden of this disease in our population and implement strategies to improve care and reduce mortality.

Screening for Viral Nucleic Acids in the Cerebrospinal Fluid of Dogs With Central Nervous System Inflammation

Central nervous system (CNS) inflammation is a common cause of neurological dysfunction in dogs. Most dogs with CNS inflammation are diagnosed with presumptive autoimmune disease. A smaller number are diagnosed with an infectious etiology. Additionally, at necropsy, a subset of dogs with CNS inflammation do not fit previously described patterns of autoimmune disease and an infectious cause is not readily identifiable. Because viral infection is a common cause of meningoencephalitis in people, we hypothesize that a subset of dogs presented with CNS inflammation have an occult viral infection either as a direct cause of CNS inflammation or a trigger for autoimmunity. The goal of this research was to screen cerebrospinal fluid from a large number dogs with CNS inflammation for occult viral infection. One hundred seventy-two dogs with neurological dysfunction and cerebrospinal fluid (CSF) pleocytosis were identified. Of these, 42 had meningoencephalitis of unknown origin, six had steroid-responsive meningitis-arteritis, one had eosinophilic meningoencephalitis, five had documented infection, 21 had and undetermined diagnosis, and 97 had a diagnosis not consistent with primary inflammatory disease of the CNS (e.g., neoplasia). CSF samples were subsequently screened with broadly reactive PCR for eight viral groups: adenovirus, bunyavirus, coronavirus, enterovirus, flavivirus, herpesvirus, paramyxovirus, and parechovirus. No viral nucleic acids were detected from 168 cases screened for eight viral groups, which does not support occult viral infection as a cause of CNS inflammation in dogs. La Crosse virus (LACV) nucleic acids were detected from four cases in Georgia. Subclinical infection was supported in two of these cases but LACV could not be ruled-out as a cause of infection in the other two cases, suggesting further research is warranted to determine if LACV is an occult cause of CNS inflammation in dogs.

Uveo-meningeal syndrome secondary to Herpes Simplex Virus related acute retinal necrosis

Purpose

To present a rare case of uveo-meningeal syndrome secondary to herpes simplex virus (HSV-1) in a patient with acute retinal necrosis.

Observations

A 49-year-old female with a past medical history of herpes simplex encephalitis 18 years prior presented with a 3-day history of right sided headache and decreased vision of the right eye. Her visual acuity was 20/30 in the right eye and 20/20 in the left eye. Clinical examination revealed right relative afferent pupillary defect, panuveitis, and retinal necrosis. Examination of the left eye was unremarkable. Cerebral spinal fluid (CSF) analysis by polymerase chain reaction (PCR) was negative for herpes simplex virus 1 (HSV-1) but did reveal pleocytosis consistent with meningitis. The patient was admitted and empirically treated with intravenous acyclovir (10 mg/kg every 8 hours) and systemic steroids. Topical steroids and cycloplegia were also started. Magnetic resonance imaging revealed no leptomeningeal, pachymeningeal, or parenchymal enhancement. Systemic autoimmune and infectious workup were unremarkable. Based on clinical exam findings and negative PCR results, an anterior chamber tap was performed with aqueous fluid PCR testing which revealed 71,000 copies of HSV-1. A repeat lumbar puncture was performed on day three of admission and revealed a decrease in pleocytosis after initiation of acyclovir therapy and remained negative for HSV on PCR testing. She was discharged home on intravenous acyclovir, topical steroids, and topical cycloplegics. Her retinal necrotic lesions continued to regress and her headaches continued to improve.

Conclusions and importance

Uveo-meningeal syndromes are a rare clinical entity that involve the uvea, retina, and meninges. This case highlights the importance of aqueous fluid PCR testing despite negative CSF PCR, as it may hasten treatment with antiviral therapies to preserve vision and limit neurologic sequelae.

The Causes and Long-Term Consequences of Viral Encephalitis

Reports regarding brain inflammation, known as encephalitis, have shown an increasing frequency during the past years. Encephalitis is a relevant concern to public health due to its high morbidity and mortality. Infectious or autoimmune diseases are the most common cause of encephalitis. The clinical symptoms of this pathology can vary depending on the brain zone affected, with mild ones such as fever, headache, confusion, and stiff neck, or severe ones, such as seizures, weakness, hallucinations, and coma, among others. Encephalitis can affect individuals of all ages, but it is frequently observed in pediatric and elderly populations, and the most common causes are viral infections. Several viral agents have been described to induce encephalitis, such as arboviruses, rhabdoviruses, enteroviruses, herpesviruses, retroviruses, orthomyxoviruses, orthopneumovirus, and coronaviruses, among others. Once a neurotropic virus reaches the brain parenchyma, the resident cells such as neurons, astrocytes, and microglia, can be infected, promoting the secretion of pro-inflammatory molecules and the subsequent immune cell infiltration that leads to brain damage. After resolving the viral infection, the local immune response can remain active, contributing to long-term neuropsychiatric disorders, neurocognitive impairment, and degenerative diseases. In this article, we will discuss how viruses can reach the brain, the impact of viral encephalitis on brain function, and we will focus especially on the neurocognitive sequelae reported even after viral clearance.

Detection of Major Human Herpesviruses in Iranian Patients with Suspected Encephalitis Using Multiplex Polymerase Chain Reaction

BACKGROUND

The Herpesviridae family plays a significant etiological role in central nervous system viral infections during primary infection or reactivation from a latent form. Early detection is crucial because prescribing some antivirals can prevent severe side effects or life-threatening conditions.

METHODS

In this study, 251 CSF specimens were collected from patients with clinical suspicion of viral encephalitis in Pars Hospital, Tehran, Iran. DNA was extracted, and a multiplex PCR was designed to investigate the presence of herpes simplex virus-1, herpes simplex virus-2, varicella zoster virus, Epstein-Barr virus, and cytomegalovirus.

RESULTS

Overall, 59 cases of the 251 CSF samples were positive for multiplex PCR (23.5%). The most frequent positive findings were EBV and HSV, with a prevalence of 10.3% and 8.7% (5.5% HSV-1 and 3.1% HSV-2), respectively. Four co-infections were also seen in this study.

CONCLUSIONS

This multiplex PCR assay detects simultaneously different herpesviruses in CSF samples of patients with suspected encephalitis in 2 rounds of PCR amplification; therefore, it is a reliable and cost-saving diagnostic method for evaluating patients infected with herpesvirus with neurological disorders.

Cerebrospinal fluid in COVID-19 neurological complications: Neuroaxonal damage, anti-SARS-Cov2 antibodies but no evidence of cytokine storm

OBJECTIVE

To study in cerebrospinal fluid (CSF) of COVID-19 subjects if a "cytokine storm" or neuroinflammation are implicated in pathogenesis of neurological complications.

METHODS

Cross-sectional study of CSF neuroinflammatory profiles from 18 COVID-19 subjects with neurological complications categorized by diagnosis (stroke, encephalopathy, headache) and illness severity. COVID-19 CSF was compared with CSF from healthy, infectious and neuroinflammatory disorders and stroke controls (n = 82). Cytokines (IL-6, TNFα, IFNγ, IL-10, IL-12p70, IL-17A), inflammation and coagulation markers (high-sensitivity-C Reactive Protein [hsCRP], ferritin, fibrinogen, D-dimer, Factor VIII) and neurofilament light chain (NF-L), were quantified. SARS-CoV2 RNA and SARS-CoV2 IgG and IgA antibodies in CSF were tested with RT-PCR and ELISA.

RESULTS

CSF from COVID-19 subjects showed absence of pleocytosis or specific increases in pro-inflammatory markers (IL-6, ferritin, or D-dimer). Although pro-inflammatory cytokines (IL-6, TNFα, IL-12p70) and IL-10 were increased in CSF of stroke COVID-19 subjects, a similar increase was observed in non-COVID-19 stroke subjects. Anti-SARS-CoV2 antibodies in CSF of COVID-19 subjects (77%) were observed despite no evidence of SARS-CoV2 viral RNA. CSF-NF-L was elevated in subjects with stroke and critical COVID-19 as compared to controls and other COVID-19 severity categories. CSF-hsCRP was present in all subjects with critical stages of COVID-19 (7/18) but only in 1/82 controls.

CONCLUSION

The paucity of neuroinflammatory changes in CSF of COVID-19 subjects and lack of SARS-CoV2 RNA do not support the presumed neurovirulence of SARS-CoV2 or neuroinflammation in pathogenesis of neurological complications in COVID-19. The role of CSF SARS-CoV2 IgG antibodies and mechanisms of neuronal damage are still undetermined.

Neurologic Infections in Patients on Immunomodulatory and Immunosuppressive Therapies

PURPOSE OF REVIEW

Both broadly immunosuppressive medications and selective immunomodulatory agents that act on particular components of the immune system are increasingly used in the treatment of neurologic and non-neurologic diseases. These therapies predispose patients to particular infections, some of which may affect the nervous system. Therefore, familiarity with the clinical and radiologic features of neurologic infections associated with specific immunomodulatory therapies is of importance for the practicing neurologist. This article reviews these neuroinfectious conditions, as well as other neurologic complications unique to transplant recipients and other patients who are immunocompromised.

RECENT FINDINGS

Diagnosis of infectious pathogens in patients who are immunocompromised may be particularly challenging because a decreased immune response can lead to atypical imaging or laboratory findings. Next-generation sequencing and other novel diagnostic modalities may improve the rate of early identification of neurologic infections in patients who are immunocompromised and ultimately ameliorate outcomes in this vulnerable population.

SUMMARY

A broad range of bacterial, viral, fungal, and parasitic infections of the nervous system can complicate solid organ and hematopoietic cell transplantation as well as other forms of immunocompromise. In addition to neurologic infections, such patients are at risk of neurotoxic and neuroinflammatory complications related to immunomodulatory and immunosuppressive therapies. Early recognition of infectious and noninfectious complications of immunocompromise is essential to guide appropriate treatment, which can include antimicrobial therapy and, in some cases, withdrawal of the predisposing medication with a transition to an alternative regimen.

Assessment of the FilmArray ME panel in 4199 consecutively tested cerebrospinal fluid samples

OBJECTIVES

In central nervous system infections, early and correct management is of utmost importance. Rapid syndromic panel testing can potentially provide valuable guidance. The FilmArray meningitis/encephalitis (ME) panel detects 14 pathogens through multiplex PCR. Our study objectives were to assess its performance compared with established diagnostic procedures, especially real-time quantitative PCR for detection of viruses, and to determine the diagnostic and clinical significance of discrepant results.

METHODS

All cerebrospinal fluid samples sent for viral diagnostics to our microbiological laboratory over 34 months were analysed with the ME panel and in-house real-time PCR for herpes simplex virus type 1 (HSV-1), HSV-2, varicella zoster virus and enteroviruses. Other pathogens detected by the panel were confirmed by routine diagnostic procedures. Discrepant results were analysed through interpretation of biological and clinical data, and performance data were calculated for individual pathogens.

RESULTS

Altogether, 315 pathogens were detected by the ME panel in 4199 cerebrospinal fluid samples (7.5%) and an additional 21 viral targets were identified using real-time PCR. Thirty-four ME panel detections were not confirmed, totalling 55 discrepant results. After discrepancy analysis, 20 false-positive and 21 false-negative ME panel results remained. Performance varied between pathogens. Sensitivity for HSV-1 was calculated at 82.4% (59.0%-93.8%) with three false-negative results. Also noteworthy were 13 false-negative enterovirus and eight false-positive Streptococcus pneumoniae results.

CONCLUSIONS

Our analysis shows good performance for the ME panel in diagnosing central nervous system infection. The risk of false-negative HSV-1 results, however, warrants additional testing when encephalitis is suspected. Uncertainties in interpretation of enterovirus and S. pneumoniae results represent other limitations.

Herpesvirus encephalitis diagnosed by polymerase chain reaction at the National Institute of Neurology of Mexico

The frequency of central nervous system infections due to herpesvirus have been studied in various populations; however, studies in Mexican mestizo patients are scant. This paper documents the frequency of herpesvirus encephalitis in Mexican mestizo patients from the National Institute of Neurology and Neurosurgery (NINN) of Mexico. To study the frequency of herpetic viral encephalitis at the NINN in the period from 2004 to 2009. We reviewed clinical records from patients with clinically suspected encephalitis; polymerase chain reaction assays were done for detection of herpesviruses in cerebrospinal fluid (CSF) samples. The total number of patients studied was 502; in 59 (12%), the diagnosis of herpetic encephalitis was confirmed by PCR-based testing of CSF. Of them, 21 (36%) were positive for herpes simplex virus type 1, 15 (25%) for Epstein-Barr virus, 10 (17%) for varicella zoster virus, 8 (14%) for cytomegalovirus, 3 (5%) for human herpesvirus 6, and 2 (3%) for herpes simplex virus 2. Our results show a varied frequency of viral encephalitis in mestizo patients due to herpesviruses in a tertiary neurological center and point out the importance of modern molecular technology to reach the etiological diagnosis in cases of encephalitis.

The role of antibody indexes in clinical virology

BACKGROUND

Serological techniques are an essential part of the diagnostic tools used in clinical virology. Among these techniques, antibody indexes are not novel, but do require specific expertise. Their niche has expanded substantially in recent years due to increasing evidence of their performance to diagnose viral infections.

OBJECTIVES

This narrative review describes the background and clinical applications of antibody indexes. The first objective is to provide an overview of the theoretical background, insights for implementation, limitations and pitfalls. The second objective is to review the available evidence for the diagnostic performance, with a specific focus on viral encephalitis and uveitis.

SOURCES

A comprehensive literature search was performed in PubMed, including original studies and reviews, with no time limit on the studies included. The following search terms were used: antibody index, Goldmann-Witmer coefficient, Reibergram, viral encephalitis, viral uveitis, herpes simplex virus, varicella zoster virus, cytomegalovirus, Epstein-Barr virus, rubella virus, measles virus, enterovirus, influenza virus, flaviviruses.

CONTENT

Antibody indexes can support the diagnosis of a spectrum of viral infections in immune privileged sites such as the central nervous system and the eye, through the demonstration of virus-specific intrathecal or intraocular antibody production. This is especially useful in situations where PCR has a lower positivity rate: infections with rapid viral clearance due to natural immunity or treatment and chronic stages of viral infections.

IMPLICATIONS

Antibody indexes expand the clinical microbiologist's diagnostic toolbox. Careful interpretation of the results of these assays is crucial and further standardization of methods is required to improve interchangeability of results between laboratories.

Clinical utility of cerebrospinal fluid vitamin D-binding protein as a novel biomarker for the diagnosis of viral and bacterial CNS infections

Background

Rapid and accurate diagnosis of central nervous system (CNS) infections is important, and laboratory tests help diagnose CNS infections. Even when the patient has symptoms, laboratory tests often do not reveal any specific findings. The potential of vitamin D-binding protein (VDBP) to be used as a biomarker for viral and bacterial CNS infections was studied.

Methods

A total of 302 subjects with suspected CNS infection who underwent lumbar puncture were included. Clinical and laboratory data were collected retrospectively. VDBP levels were measured in the cerebrospinal fluid (CSF) samples. Genotyping for the GC gene encoding VDBP was also performed. VDBP levels were analyzed and compared by CNS infection, pathogen, CSF opening pressure, and GC genotype.

Results

A CNS infection group (n = 90) and a non-CNS infection group (n = 212) were studied. In terms of its receiver operating characteristic, CSF VDBP showed an area under the curve of 0.726 for the diagnosis of CNS infection. CSF VDBP levels were significantly different between the CNS infection and non-infection groups. The CNS infection group with enterovirus showed a statistically lower distribution of CSF VDBP levels than the other virus groups. The group with CSF opening pressure > 25 cmH₂O showed higher CSF VDBP levels than the other groups. There was no significant difference in GC gene allele distribution between the CNS infection and non-infection groups.

Conclusions

CSF VDBP levels were increased in patients with CNS infection. The CSF VDBP showed potential as a new biomarker for viral and bacterial CNS infections.

Cerebrospinal fluid in COVID-19 neurological complications: no cytokine storm or neuroinflammation

BACKGROUND

Neurological complications occur in COVID-19. We aimed to examine cerebrospinal fluid (CSF) of COVID-19 subjects with neurological complications and determine presence of neuroinflammatory changes implicated in pathogenesis.

METHODS

Cross-sectional study of CSF neuroinflammatory profiles from 18 COVID-19 subjects with neurological complications categorized by diagnosis (stroke, encephalopathy, headache) and illness severity (critical, severe, moderate, mild). COVID-19 CSF was compared with CSF from healthy, infectious and neuroinflammatory disorders and stroke controls (n=82). Cytokines (IL-6, TNFα, IFNγ, IL-10, IL-12p70, IL-17A), inflammation and coagulation markers (high-sensitivity-C Reactive Protein [hsCRP], ferritin, fibrinogen, D-dimer, Factor VIII) and neurofilament light chain (NF-L), were quantified. SARS-CoV2 RNA and SARS-CoV2 IgG and IgA antibodies in CSF were tested with RT-PCR and ELISA.

RESULTS

CSF from COVID-19 subjects showed a paucity of neuroinflammatory changes, absence of pleocytosis or specific increases in pro-inflammatory markers or cytokines (IL-6, ferritin, or D-dimer). Anti-SARS-CoV2 antibodies in CSF of COVID-19 subjects (77%) were observed despite no evidence of SARS-CoV2 viral RNA. A similar increase of pro-inflammatory cytokines (IL-6, TNFα, IL-12p70) and IL-10 in CSF of COVID-19 and non-COVID-19 stroke subjects was observed compared to controls. CSF-NF-L was elevated in subjects with stroke and critical COVID-19. CSF-hsCRP was present almost exclusively in COVID-19 cases.

CONCLUSION

The paucity of neuroinflammatory changes in CSF of COVID-19 subjects and lack of SARS-CoV2 RNA do not support the presumed neurovirulence of SARS-CoV2 or neuroinflammation in pathogenesis of neurological complications in COVID-19. Elevated CSF-NF-L indicates neuroaxonal injury in COVID-19 cases. The role of CSF SARS-CoV2 IgG antibodies is still undetermined.

FUNDING

This work was supported by NIH R01-NS110122 and The Bart McLean Fund for Neuroimmunology Research.

Positive Impact of Routine Testing for Enterovirus and Parechovirus on Length of Hospitalization and Antimicrobial Use among Inpatients ≤6 Months of Age

Enterovirus (EV) and parechovirus (PeV) are leading viral causes of central nervous system (CNS) infection among hospitalized neonates and young infants, yet testing for PeV is not routinely performed. The goal of our study was to determine how EV and PeV CSF RT-PCR testing impacted the duration of antibiotic use and the length of hospitalization (LOS) in children ≤6 months old with suspected CNS infection. This retrospective cohort study at Children's Mercy Kansas City evaluated data from patients ≤6 months old for whom routine CSF EV and PeV reverse transcription-PCR (RT-PCR) testing was performed during January 2011 to December 2018. Electronic data were abstracted from the electronic medical record, including demographics, systemic antimicrobial use, imaging data, herpes simplex virus (HSV) testing, and overall hospital charges. Among 1,926 patients, 345 (17.9%) were RT-PCR positive for EV and 172 (8.9%) were positive for PeV. A significantly shorter LOS was observed for patients with EV (51.6 h; P < 0.001) and PeV (66.3 h; P = 0.048) compared to patients that tested negative for both viruses (74.1 h). Discontinuation of empirical antibiotic therapy following test result availability occurred more frequently for PeV patients (57.8%; P = 0.03) and EV patients (65.4%; P < 0.001) than RT-PCR-negative patients (48.5%). Routine EV/PeV RT-PCR testing of cerebrospinal fluid (CSF) samples in children impacted care of hospitalized neonates and young infants. Rapid and prompt diagnosis has the potential to reduce antibiotic usage, length of stay, and patient charges.

The Prevalence of Viruses in the Cerebrospinal Fluid of Children with Aseptic Meningitis in Shiraz, Iran

Objectives: The current study aimed to evaluate the causative agents of viral meningitis through real-time PCR among children with aseptic meningitis. Methods: Children aged 1 month to 16 years with suspected viral meningitis were enrolled in this study (March 2014-February 2015). Cerebrospinal fluid samples were analyzed by real-time PCR for detection of enterovirus, mumps, measles, adenovirus, EBV, CMV, VZV, hhv 6, and rubella viruses. Demographic information, laboratory data, and clinical presentations of patients were also collected. Results: Of 56 patients suspected to viral meningitis, 21 (38.9 %) had a positive PCR result. Enterovirus (42.85%) and mumps (38.1%) were the most prevalent viruses, and VZV and measles were not detected. Three children were coinfected with enterovirus/hhv6, enterovirus/EBV, and mump/adenovirus. Fever, headache, and nausea/vomiting were the most common symptoms in children. The rates of symptoms were not statistically significant among children with positive and negative PCR tests. Conclusions: In the present study Enterovirus and mumps viruses were the most common causes of viral meningitis in children. PCR, as a rapid test for the diagnosis of viral meningitis, can be used to decrease hospitalization length.

Varicella-Zoster Virus Meningitis and Encephalitis: An Understated Cause of Central Nervous System Infections

Background Varicella-zoster virus (VZV) and herpes zoster cause infections of the central nervous system (CNS) manifesting as meningitis or encephalitis. As compared to enterovirus (EV) and herpes simplex virus 1 (HSV-1) and 2 (HSV-2), it is not often tested in CNS infections due to VZV and herpes zoster. There is a certain tendency to think that the findings in the cerebrospinal fluid in infections of the CNS by viruses are comparable among themselves. The exact proportion of patients with VZV primary and reactivation infection who present with lesions prior to or concomitant to its involvement in the CNS is unknown. It is also not known about the risk factors that lead to the reactivation of VZV and CNS involvement. Objective To describe the clinical characteristics and laboratory results of patients with a positive VZV polymerase chain reaction (PCR) and neurological signs and symptoms. Methods A retrospective and descriptive study was performed at the Hospital Universitario de la Pontificia Universidad Católica de Chile (Hospital Clínico UC CHRISTUS) from September 2012 to July 2014. The following parameters were recorded: neurological signs and symptoms, PCR for VZV in cerebrospinal fluid (CSF), comorbidities, personal medical history, cutaneous lesions, CSF characteristics, CNS imaging, electroencephalography (EEG), treatment, mortality, and neurological sequelae. Adult patients with meningitis, encephalitis, or meningoencephalitis due to VZV diagnosed with PCR were included. Results Out of 70 CSF samples analyzed in the previously mentioned period, 21 cases were VZV positive, 16 cases that had clinical information available were included. The mean age with VZV CNS reactivation was 47 years (range 19-80 years). Five patients (31.25%) were immunocompromised: three had human immunodeficiency virus (HIV), one had kidney transplantation, and one had primary immunodeficiency. Clinical presentation was meningitis in 11 patients (68.75%) and encephalitis in five patients (31.25%). Pleocytosis in CSF was observed in all the samples. The five immunocompromised patients had cutaneous lesions. All patients received antiviral treatment. Therapy duration was from 10 up to 21 days. The clinical course was positive in most patients and the mean hospitalization time was 15 days (range 5-60 days). No mortality was observed. Conclusions VZV is a worldwide virus and a common cause of CNS infection. The rising incidence is probably due to a better diagnostic method and a frequent clinical suspicion even in the absence of cutaneous lesions, except in immunocompromised cases, as it was observed in the present study. CNS infection presented as a wide spectrum of clinical manifestations with possible neurological sequelae. There was a reduction in neurological morbidity with antiviral therapy. Nonetheless, both the incidence and the morbidity of CNS VZV infection are expected to be diminished by varicella and herpes zoster vaccination. Additionally, there was no increase in mortality in these patients.

State-of-the-art polymeric nanoparticles as promising therapeutic tools against human bacterial infections

Infectious diseases kill over 17 million people a year, among which bacterial infections stand out. From all the bacterial infections, tuberculosis, diarrhoea, meningitis, pneumonia, sexual transmission diseases and nosocomial infections are the most severe bacterial infections, which affect millions of people worldwide. Moreover, the indiscriminate use of antibiotic drugs in the last decades has triggered an increasing multiple resistance towards these drugs, which represent a serious global socioeconomic and public health risk. It is estimated that 33,000 and 35,000 people die yearly in Europe and the United States, respectively, as a direct result of antimicrobial resistance. For all these reasons, there is an emerging need to find novel alternatives to overcome these issues and reduced the morbidity and mortality associated to bacterial infectious diseases. In that sense, nanotechnological approaches, especially smart polymeric nanoparticles, has wrought a revolution in this field, providing an innovative therapeutic alternative able to improve the limitations encountered in available treatments and capable to be effective by theirselves. In this review, we examine the current status of most dangerous human infections, together with an in-depth discussion of the role of nanomedicine to overcome the current disadvantages, and specifically the most recent and innovative studies involving polymeric nanoparticles against most common bacterial infections of the human body.

Central Nervous System Manifestations Associated with COVID-19

Purpose of Review

Coronavirus disease 2019 (COVID-19) has become a global health crisis of our time. The disease arises from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that binds to angiotensin-converting enzyme 2 (ACE2) receptors on host cells for its internalization. COVID-19 has a wide range of respiratory symptoms from mild to severe and affects several other organs, increasing the complexity of the treatment. There is accumulating evidence to suggest that SARS-CoV-2 can target the nervous system. In this review, we provide an account of the COVID-19 central nervous system (CNS) manifestations.

Recent Findings

A broad spectrum of the CNS manifestations including headache, impaired consciousness, delirium, loss of smell and taste, encephalitis, seizures, strokes, myelitis, acute disseminated encephalomyelitis, neurogenic respiratory failure, encephalopathy, silent hypoxemia, generalized myoclonus, neuroleptic malignant syndrome and Kawasaki syndrome has been reported in patients with COVID-19.

Summary

CNS manifestations associated with COVID-19 should be considered in clinical practice. There is a need for modification of current protocols and standing orders to provide better care for COVID-19 patients presenting with neurological symptoms.

Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations

Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of encephalitis remains unclear. The aim of the present study was to determine the sensitivity of shotgun metagenomic sequencing protocols, which include preamplification, and testing it against cerebrospinal fluid (CSF) samples from encephalitis patients. For sensitivity testing HIV and HBV positive sera were serially diluted in CSF from an uninfected patient. NGS repeatedly detected HIV and HBV sequences present at concentrations from 10⁵ to 10² and from 10⁵ to 10 viral copies/reaction, respectively. However, when the same protocols were applied to RT-PCR/PCR positive CSF samples from 6 patients with enteroviral encephalitis (median viral load 47 copies/ml) and 15 patients with HSV, CMV or VZV encephalitis (median viral load 148 copies/ml), only 7 (28.6%) were identified as positive. In conclusions, while NGS has the advantage of being able to identify a wide range of potential pathogens it seems to be less sensitive compared to the standard amplification-based assays in the diagnosis of encephalitis, where low viral loads are common.

Effective Antiviral Medicinal Plants and Biological Compounds Against Central Nervous System Infections: A Mechanistic Review

BACKGROUND AND OBJECTIVE

Infectious diseases are amongst the leading causes of death in the world and central nervous system infections produced by viruses may either be fatal or generate a wide range of symptoms that affect global human health. Most antiviral plants contain active phytoconstituents such as alkaloids, flavonoids, and polyphenols, some of which play an important antiviral role. Herein, we present a background to viral central nervous system (CNS) infections, followed by a review of medicinal plants and bioactive compounds that are effective against viral pathogens in CNS infections.

METHODS

A comprehensive literature search was conducted on scientific databases including: PubMed, Scopus, Google Scholar, and Web of Science. The relevant keywords used as search terms were: "myelitis", "encephalitis", "meningitis", "meningoencephalitis", "encephalomyelitis", "central nervous system", "brain", "spinal cord", "infection", "virus", "medicinal plants", and "biological compounds".

RESULTS

The most significant viruses involved in central nervous system infections are: Herpes Simplex Virus (HSV), Varicella Zoster Virus (VZV), West Nile Virus (WNV), Enterovirus 71 (EV71), Japanese Encephalitis Virus (JEV), and Dengue Virus (DENV). The inhibitory activity of medicinal plants against CNS viruses is mostly active through prevention of viral binding to cell membranes, blocking viral genome replication, prevention of viral protein expression, scavenging reactive Oxygen Species (ROS), and reduction of plaque formation.

CONCLUSION

Due to the increased resistance of microorganisms (bacteria, viruses, and parasites) to antimicrobial therapies, alternative treatments, especially using plant sources and their bioactive constituents, appear to be more fruitful.

Emergent Viral Infections of the CNS

Biological evolution of the microbiome continually drives the emergence of human viral pathogens, a subset of which attack the nervous system. The sheer number of pathogens that have appeared, along with their abundance in the environment, demand our attention. For the most part, our innate and adaptive immune systems have successfully protected us from infection; however, in the past 5 decades, through pathogen mutation and ecosystem disruption, a dozen viruses emerged to cause significant neurologic disease. Most of these pathogens have come from sylvatic reservoirs having made the energetically difficult, and fortuitously rare, jump into humans. But the human microbiome is also replete with agents already adapted to the host that need only minor mutations to create neurotropic/toxic agents. While each host/virus symbiosis is unique, this review examines virologic and immunologic principles that govern the pathogenesis of different viral CNS infections that were described in the past 50 years (Influenza, West Nile Virus, Zika, Rift Valley Fever Virus, Hendra/Nipah, Enterovirus-A71/-D68, Human parechovirus, HIV, and SARS-CoV). Knowledge of these pathogens provides us the opportunity to respond and mitigate infection while at the same time prepare for inevitable arrival of unknown agents.

Imaging Features of Acute Encephalopathy in Patients with COVID-19: A Case Series

Coronavirus disease 2019 was declared a global pandemic by the World Health Organization on March 11, 2020. There is a scarcity of data on coronavirus disease 2019-related brain imaging features. We present 5 cases that illustrate varying imaging presentations of acute encephalopathy in patients with coronavirus disease 2019. MR features include leukoencephalopathy, diffusion restriction that involves the GM and WM, microhemorrhages, and leptomeningitis. We believe it is important for radiologists to be familiar with the neuroradiologic imaging spectrum of acute encephalopathy in the coronavirus disease 2019 population.

Metagenomics for neurological infections - expanding our imagination

Over the past two decades, the diagnosis rate for patients with encephalitis has remained poor despite advances in pathogen-specific testing such as PCR and antigen assays. Metagenomic next-generation sequencing (mNGS) of RNA and DNA extracted from cerebrospinal fluid and brain tissue now offers another strategy for diagnosing neurological infections. Given that mNGS simultaneously assays for a wide range of infectious agents in an unbiased manner, it can identify pathogens that were not part of a neurologist’s initial differential diagnosis either because of the rarity of the infection, because the microorganism has not been previously associated with a clinical phenotype or because it is a newly discovered organism. This Review discusses the technical advantages and pitfalls of cerebrospinal fluid mNGS in the context of patients with neuroinflammatory syndromes, including encephalitis, meningitis and myelitis. We also speculate on how mNGS testing potentially fits into current diagnostic testing algorithms given data on mNGS test performance, cost and turnaround time. Finally, the Review highlights future directions for mNGS technology and other hypothesis-free testing methodologies that are in development.

This Review discusses the advantages and pitfalls of metagenomic next-generation sequencing (mNGS) in patients with encephalitis, meningitis and myelitis. The authors outline data on mNGS test performance, cost and turnaround time and highlight future directions for mNGS technology.

Meningoencephalitis remains a challenging diagnosis owing to the multitude of possible infectious and autoimmune causes.

Meningoencephalitis is associated with a high rate of morbidity and mortality and requires prompt diagnosis and treatment.

Metagenomic next-generation sequencing (mNGS) is now a clinically validated test for neuroinfectious diseases that can aid clinicians with a timely diagnosis.

mNGS can improve the detection of pathogens that were missed by clinicians or on standard direct testing.

mNGS does not perform well when indirect tests are required to make the diagnosis (for example, serology), when infections are compartmentalized and for certain low abundance pathogens.

The clinical context of the case is required when interpreting the results of mNGS.

Diagnostic Testing of Neurologic Infections

Neuroinfectious diseases continue to cause morbidity and mortality worldwide, with many emerging or reemerging infections resulting in neurologic sequelae. Careful clinical evaluation coupled with appropriate laboratory investigations still forms the bedrock for making the correct etiologic diagnosis and implementing appropriate management. The treating physician needs to understand the individual test characteristics of each of the many conventional candidate-based diagnostics: culture, pathogen-specific polymerase chain reaction, antigen, antibody tests, used to diagnose the whole array of neuroinvasive infections. In addition, there is a growing need for more comprehensive, agnostic testing modalities that can identify a diversity of infections with a single assay.

Diagnostic Testing in Central Nervous System Infection

Patients with central nervous system (CNS) infection experience very high levels of morbidity and mortality, in part because of the many challenges inherent to the diagnosis of CNS infection and identification of a causative pathogen. The clinical presentation of CNS infection is nonspecific, so clinicians must often order and interpret many diagnostic tests in parallel. This can be a daunting task given the large number of potential pathogens and the availability of different testing modalities. Here, we review traditional diagnostic techniques including Gram stain and culture, serology, and polymerase chain reaction (PCR). We highlight which of these are recommended for the pathogens most commonly tested among U.S. patients with suspected CNS infection. Finally, we describe the newer broad-range diagnostic approaches, multiplex PCR and metagenomic sequencing, which are increasingly used in clinical practice.

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

BACKGROUND

Metagenomic next-generation sequencing (NGS) of cerebrospinal fluid (CSF) has the potential to identify a broad range of pathogens in a single test.

METHODS

In a 1-year, multicenter, prospective study, we investigated the usefulness of metagenomic NGS of CSF for the diagnosis of infectious meningitis and encephalitis in hospitalized patients. All positive tests for pathogens on metagenomic NGS were confirmed by orthogonal laboratory testing. Physician feedback was elicited by teleconferences with a clinical microbial sequencing board and by surveys. Clinical effect was evaluated by retrospective chart review.

RESULTS

We enrolled 204 pediatric and adult patients at eight hospitals. Patients were severely ill: 48.5% had been admitted to the intensive care unit, and the 30-day mortality among all study patients was 11.3%. A total of 58 infections of the nervous system were diagnosed in 57 patients (27.9%). Among these 58 infections, metagenomic NGS identified 13 (22%) that were not identified by clinical testing at the source hospital. Among the remaining 45 infections (78%), metagenomic NGS made concurrent diagnoses in 19. Of the 26 infections not identified by metagenomic NGS, 11 were diagnosed by serologic testing only, 7 were diagnosed from tissue samples other than CSF, and 8 were negative on metagenomic NGS owing to low titers of pathogens in CSF. A total of 8 of 13 diagnoses made solely by metagenomic NGS had a likely clinical effect, with 7 of 13 guiding treatment.

CONCLUSIONS

Routine microbiologic testing is often insufficient to detect all neuroinvasive pathogens. In this study, metagenomic NGS of CSF obtained from patients with meningitis or encephalitis improved diagnosis of neurologic infections and provided actionable information in some cases. (Funded by the National Institutes of Health and others; PDAID ClinicalTrials.gov number, NCT02910037.).

Clinical metagenomics

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.

Varicella Zoster Meningitis with Hypoglycorrhachia on Cerebrospinal Fluid (CSF) Analysis in a Young Immunocompetent Host without a Rash

BACKGROUND Varicella zoster virus (VZV) is a common viral infection, with primary infection presenting as fevers and pruritic vesicular rash. After staying dormant in the dorsal root ganglia, reactivation can lead to secondary infection. Meningitis is a rare a complication of VZV infection. CASE REPORT We report a case of a 44-year-old woman with no past medical history, presenting with severe frontal headache without meningeal signs or fevers, found to have VZV meningitis. CSF analysis revealed hypoglycorrhachia and she was treated successfully with combination of intravenous acyclovir and oral valacyclovir. CONCLUSIONS VZV meningitis can present with subtle clinical signs and symptoms and should be considered as a possible etiology for headaches without identifiable cause.

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.

Usefulness of the FilmArray meningitis/encephalitis (M/E) panel for the diagnosis of infectious meningitis and encephalitis in Taiwan

BACKGROUND/PURPOSE

Early recognition of causative pathogens is critical for the appropriate management of central nervous system infection and improved outcomes. The BioFire^® FilmArray^® Meningitis/Encephalitis Panel (BioFire^® ME Panel, BioFire Diagnostics) is the first U.S. Food and Drug Administration (FDA)-approved multiplex PCR assay that allows the rapid detection of 14 pathogens, including bacteria (n = 6), viruses (n = 7), and fungi (n = 1), from cerebrospinal fluid (CSF). The performance of the panel is expected to be dependent on the epidemiology of M/E in different geographical regions.

METHODS

In this preliminary study, we used the BioFire^® ME Panel in 42 subjects who presented to the emergency department with symptoms of M/E in our hospital. The results were compared to conventional culture, antigen detection, PCR, and various laboratory findings.

RESULTS

The panel detected six positive samples, of which five were viral and one bacterial. We observed an overall agreement rate of 88% between the BioFire^® ME Panel results and the conventional methods. There were no false-positive findings, but five discordant results were observed for enterovirus, herpes simplex virus type 1, Escherichia coli, and Cryptococcus species.

CONCLUSIONS

The BioFire^® ME Panel performed equivalently to the traditional PCR methods for virus detection, and better than bacterial cultures. This revolutionary system represents a paradigm shift in the diagnosis of M/E and may aid in the rapid identification of community-acquired M/E. However, the usefulness of this tool is limited in regions with a high prevalence of infectious M/E caused by microorganisms not included in the panel.

Adenovirus cerebellitis in an immunocompetent 2-year-old girl

Acute cerebellitis (AC) is a principal cause of acute cerebellar dysfunction in previously well children. Although the condition is usually benign, fatal complications include obstructive hydrocephalus and brainstem compression; therefore, prompt accurate diagnosis is vital. ¹ There are various pathogens reported in the literature as aetiological agents of AC; however, adenovirus is very rarely mentioned, with only one previous case report in the literature to the best of our knowledge. ² This case demonstrates the importance of recognising adenovirus as a cause of AC, particularly when preceded by a respiratory tract infection in the paediatric age group. Furthermore, we highlight the role of early neuroimaging in differentiating AC from other causes of acute cerebellar dysfunction, which require different management. Our patient made a full recovery with no long-term deficits demonstrating that comprehensive investigation and consideration of atypical pathogens in the context of AC is vital in securing a favourable outcome.

Development and validation of an advanced fragment analysis-based assay for the detection of 22 pathogens in the cerebrospinal fluid of patients with meningitis and encephalitis

Background

Meningitis and encephalitis (ME) are central nervous system (CNS) infections mainly caused by bacteria, mycobacteria, fungi, viruses, and parasites that result in high morbidity and mortality. The early, accurate diagnosis of pathogens in the cerebrospinal fluid (CSF) and timely medication are associated with better prognosis. Conventional methods, such as culture, microscopic examination, serological detection, CSF routine analysis, and radiological findings, either are time‐consuming or lack sensitivity and specificity.

Methods

To address these clinical needs, we developed an advanced fragment analysis (AFA)‐based assay for the multiplex detection of 22 common ME pathogens, including eight viruses, 11 bacteria, and three fungi. The detection sensitivity of each target was evaluated with a recombinant plasmid. The limits of detection of the 22 pathogens ranged from 15 to 120 copies/reaction. We performed a retrospective study to analyze the pathogens from the CSF specimens of 170 clinically diagnosed ME patients using an AFA‐based assay and compared the results with culture (bacteria and fungi), microscopic examination (fungi), polymerase chain reaction (PCR) (Mycobacterium tuberculosis), and Sanger sequencing (virus) results.

Results

The sensitivity of the AFA assay was 100% for 10 analytes. For Cryptococcus neoformans, the sensitivity was 63.6%. The overall specificity was 98.2%. The turnaround time was reduced to 4‐6 hours from the 3‐7 days required using conventional methods.

Conclusions

In conclusion, the AFA‐based assay provides a rapid, sensitive, and accurate method for pathogen detection from CSF samples.

Identification of Cerebrospinal Fluid Metabolites as Biomarkers for Enterovirus Meningitis

Enteroviruses are among the most common causes of viral meningitis. Enteroviral meningitis continues to represent diagnostic challenges, as cerebrospinal fluid (CSF) cell numbers (a well validated diagnostic screening tool) may be normal in up to 15% of patients. We aimed to identify potential CSF biomarkers for enteroviral meningitis, particularly for cases with normal CSF cell count. Using targeted liquid chromatography-mass spectrometry, we determined metabolite profiles from patients with enteroviral meningitis (n = 10) and subdivided them into those with elevated (n = 5) and normal (n = 5) CSF leukocyte counts. Non-inflamed CSF samples from patients with Bell’s palsy and normal pressure hydrocephalus (n = 19) were used as controls. Analysis of 91 metabolites revealed considerable metabolic reprogramming in the meningitis samples. It identified phosphatidylcholine PC.ae.C36.3, asparagine, and glycine as an accurate (AUC, 0.92) combined classifier for enterovirus meningitis overall, and kynurenine as a perfect biomarker for enteroviral meningitis with an increased CSF cell count (AUC, 1.0). Remarkably, PC.ae.C36.3 alone emerged as a single accurate (AUC, 0.87) biomarker for enteroviral meningitis with normal cell count, and a combined classifier comprising PC.ae.C36.3, PC.ae.C36.5, and PC.ae.C38.5 achieved nearly perfect classification (AUC, 0.99). Taken together, this analysis reveals the potential of CSF metabolites as additional diagnostic tools for enteroviral meningitis, and likely other central nervous system (CNS) infections.

Varicella zoster virus encephalitis in solid organ transplant recipients: Case series and review of literature

Herpes zoster encephalitis (HZE) is a rare complication of varicella zoster virus (VZV) infection. We report two cases of HZE in solid organ transplant (SOT) recipients and review 10 other cases in the literature. In this review, rash was present in 67% of cases. Despite the absence of a rash, high clinical suspicion for HZE is necessary and empiric antiviral therapy should be considered. While with variable outcome, it was associated with high mortality rate of 42%. Prompt initiation of antiviral therapy remains crucial in decreasing morbidity and mortality from this fatal disease.

Interplay between Rapid Diagnostic Tests and Antimicrobial Stewardship Programs among Patients with Bloodstream and Other Severe Infections

BACKGROUND

Antimicrobial stewardship programs (ASPs) aim to provide optimal antimicrobial therapy to patients quickly to improve the likelihood of overcoming infection while reducing the risk of adverse effects. Rapid diagnostic tests (RDTs) for infectious diseases have become an integral tool for ASPs to achieve these aims.

CONTENT

This review explored the demonstrated clinical value of longer-standing technologies and implications of newer RDTs from an antimicrobial stewardship perspective. Based on available literature, the focus was on the use of RDTs in bloodstream infections (BSIs), particularly those that perform organism identification and genotypic resistance detection, phenotypic susceptibility testing, and direct specimen testing. Clinical implications of rapid testing among respiratory, central nervous system, and gastrointestinal infections are also reviewed.

SUMMARY

Coupling RDTs with ASPs facilitates the appropriate and timely use of test results, translating into improved patient outcomes through optimization of antimicrobial use. These benefits are best demonstrated in the use of RDT in BSIs. Rapid phenotypic susceptibility testing offers the potential for early pharmacokinetic/pharmacodynamic optimization, and direct specimen testing on blood may allow ASPs to initiate appropriate therapy and/or tailor empiric therapy even sooner than other RDTs. RDTs for respiratory, central nervous system, and gastrointestinal illnesses have also shown significant promise, although more outcome studies are needed to evaluate their full impact.

Detection of central nervous system viral infections in adults in Manado, North Sulawesi, Indonesia

Central nervous system (CNS) viral infections are important causes of morbidity and mortality worldwide but the systematic survey of patients admitted to hospitals with CNS infections in many countries, including Indonesia, is limited. To obtain more information regarding the causes of CNS infections in Indonesia, this study was performed to detect and identify viral agents associated with CNS infections amongst in-patients at a referral hospital in Manado, North Sulawesi, Indonesia. Adult patients admitted to R.D. Kandou General Hospital with presumed CNS infection were enrolled. Cerebrospinal fluid, serum, and throat swab samples were collected and tested using molecular, serological, and virus isolation assays. A confirmed viral etiology was established in three and a probable/possible in 11 out of 74 patients. The most common was herpes simplex virus 1 (7/74, 9.5%), followed by Epstein-Barr virus (2/74, 2.7%), cytomegalovirus (1/74, 1.4%), enterovirus D68 (1/74, 1.4%), rhinovirus A (1/74, 1.4%), dengue virus (1/64, 1.6%), and Japanese encephalitis virus (1/64, 1.6%). There were 20 fatal cases (27.0%) during hospitalization in which eight were associated with viral causes. We identified herpes simplex virus 1 as the most common cause of CNS infection among adults in North Sulawesi with most of the cases remaining undiagnosed. Our study highlights the challenges in establishing the etiology of viral CNS infections and the importance of using a wide range of molecular and serological detection methods to identify CNS viruses.

FilmArray® meningitis/encephalitis (ME) panel, a rapid molecular platform for diagnosis of CNS infections in a tertiary care hospital in North India: one-and-half-year review

BACKGROUND

Acute meningitis and encephalitis (AME) is a syndrome of central nervous system (CNS) infections, which could lead to neurological damage and fatality. This study evaluates the multiplex FilmArray® ME Panel which is aimed to diagnose agents causing suspect CNS infections in north India.

METHODS

A total number of 969 cerebrospinal fluid (CSF) samples collected between August 2016 and January 2018 from patients who showed clinical symptoms of CNS infections were analyzed using the FilmArray® ME Panel. Also a comparison of molecular diagnosis and various laboratory and radiological findings for Streptococcus pneumoniae, Enterovirus and Cryptococcus neoformans positive cases was done.

RESULT

Out of the 969 CSF samples, 101 cases were found to be positive for viral (n = 55), bacterial (n = 38), fungal (n = 7), and poly-microbial (n = 1) agents. Out of the 55 viral positive cases, the most detected pathogen was Enterovirus (n = 23) with predominance in the age group of 2-17 years, followed by Varicella Zoster virus (n = 14) and HSV1(n = 9) cases. Streptococcus pneumoniae (n = 26) was found to be the predominant bacterial pathogen, of which 17 were detected in the age group above 35 years. Cryptococcus neoformans was found in 7 cases.

CONCLUSION

The FilmArray® ME Panel aids in rapid detection of 14 pathogens directly from CSF. When compared to gram stain, culture, antigen detection, and CSF biochemical analysis, the FilmArray® ME Panel has detected more cases, some of which are difficult to diagnose by conventional methods. This rapid technology will help the clinicians in case of early patient management, outcomes and provide aid in antimicrobial stewardship.