Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances

Autoimmune and infectious encephalitis: development of a discriminative tool for early diagnosis and initiation of therapy

BACKGROUND

Encephalitis originates from diverse autoimmune and infectious etiologies. Diagnostic challenges arise due to the spectrum of presentation and the frequent absence of specific biomarkers. This study aimed to comprehensively characterize and differentiate autoimmune encephalitis (AE) from infectious encephalitis (IE) in adults, and disentangle clinical, paraclinical, and therapeutic differences.

METHODS

A cohort study spanning 10 years was conducted across three Austrian tertiary care hospitals. Inclusion criteria comprised adults with probable or definite encephalitis. Demographics, clinical features, technical findings, treatment modalities, and outcomes were collected from the electronic patient files. A follow-up was performed via telephone interviews and clinical visits.

RESULTS

Of 149 patients, 17% had AE, 73% IE, and 10% encephalitis of unknown etiology. Significant differences between AE and IE included the prevalence of acute symptomatic seizures (AE: 85% vs. IE: 20%, p < 0.001), fever (8% vs. 72%, p < 0.001), headache (15% vs. 61%, p < 0.001), and focal neurological deficits (56% vs. 23%, p = 0.004), respectively. Paraclinical differences comprised lower CSF pleocytosis in AE compared to IE (median 6 cells/µl vs. 125 cells/µl, p < 0.001). Epileptic discharges on EEG and MRI lesions were more prevalent in AE than IE (50% vs. 14%, p < 0.001; 50% vs. 28%, p = 0.037). The modified Rankin Scale scores at discharge and last follow-up (median duration 2304 days, IQR 1433-3274) indicated favorable outcomes in both groups.

CONCLUSION

This comprehensive analysis provides insights into the epidemiology, clinical, paraclinical, and therapeutic aspects and the outcomes of AE and IE in adults. We developed a diagnostic tool that facilitates early differentiation between AE and IE, aiding in timely therapeutic decision-making.

Study on the gut microbiota, HPA, and cytokine levels in infantile spasms

Objective

The mechanisms driving the progression of infantile spasms are not well understood. We aimed to investigate the changes and correlations of the gut microbiota, the hypothalamus-pituitary-adrenal (HPA) axis hormones, and the inflammatory cytokines in children with infantile spasms before and after treatment in order to provide a reference for future pathogenesis research.

Methods

Children with infantile spasms who were admitted to our hospital were recruited into the case group. The case group was divided into the pre-treatment group (group A, n = 14), the 2 weeks after treatment group (group B), and the 1 month after treatment group (group C). On the other hand, healthy children with the same sex ratio as the case group were recruited into the control group (group D, n = 14). Three stool and blood samples were collected before treatment, 2 weeks after treatment, and 1 month after treatment. The serum samples were analyzed using cytometric bead array (CBA), enzyme-linked immunosorbent assay (ELISA), and chemiluminescent immunoassay (CLIA) to measure the levels of HPA axis hormones and inflammatory cytokines. The collected stool samples were sequenced using 16S rDNA.

Results

The pre-treatment group demonstrated elevated levels of corticotropin-releasing hormone (CRH), interleukin 2 (IL-2), IL-4, IL-6, and IL-17α, which decreased with treatment. The level of CRH was lower in the effective group than that in the ineffective group. Sutterellaceae was lower in the pre-treatment group than that in the control group. Lachnospiracea_incertae_sedis was positively associated with CRH concentration (p < 0.05). After treatment, Sutterellaceae was negatively associated with IL-2 and TNF-α (p < 0.05).

Conclusion

This study found that imbalance of the gut microbiota may be involved in the pathogenesis of infantile spasms and is related to the response to adrenocorticotropic hormone (ACTH). Lachnospiraceae and Lachnospiracea_incertae_sedis might be involved in the disease onset. Sutterellaceae might have a link to children's improved health.

The incidence and risk factors of secondary epilepsy after viral encephalitis in children: A 10-year single-center retrospective analysis

Secondary epilepsy is a common concomitant disease of viral encephalitis (VE) in children. However, the risk factors for secondary epilepsy after VE remain debated. The aim of this study was to perform a 10-year single-center retrospective analysis to investigate the incidence and risk factors of secondary epilepsy after VE in children. A total of 8691 patients suffered from VE in our hospital between December 2011 and February 2022 were included. The patients were divided into control group (Group C) and epilepsy group (Group E) according to whether they followed secondary epilepsy. Information about treatment process was collected from medical records to determine the incidence. Univariate analysis and multivariate logistic regression analysis were performed to identify the independent risk factors. In the current study, the occurrence of secondary epilepsy after VE in pediatric patients was 10.99% (385 of 3503). The results of univariate and multivariate analysis showed that unconsciousness, convulsions, times of epilepsy >2, epileptiform discharge of Electroencephalogram (EEG), and cortical and subcortical damage of magnetic resonance imaging/computer tomography were the significant risk factors for secondary epilepsy after VE. Nearly one tenth of pediatric patients suffered from secondary epilepsy after VE. Interventions for identified risk factors should be used to prevent the occurrence of secondary epilepsy.

CXCL13 in Cerebrospinal Fluid: Clinical Value in a Large Cross-Sectional Study

C-X-C-motif chemokine ligand 13 (CXCL13) in cerebrospinal fluid (CSF) is increasingly used in clinical routines, although its diagnostic specificity and divergent cut-off values have been defined so far mainly for neuroborreliosis. Our aim was to evaluate the value of CSF-CXCL13 as a diagnostic and treatment response marker and its role as an activity marker in a larger disease spectrum, including neuroborreliosis and other neuroinflammatory and malignant CNS-disorders. Patients who received a diagnostic lumbar puncture (LP) (n = 1234) between July 2009 and January 2023 were included in our retrospective cross-sectional study. The diagnostic performance of CSF-CXCL13 for acute neuroborreliosis was highest at a cut-off of 428.92 pg/mL (sensitivity: 92.1%; specificity: 96.5%). In addition, CXCL13 levels in CSF were significantly elevated in multiple sclerosis with clinical (p = 0.001) and radiographic disease activity (p < 0.001). The clinical utility of CSF-CXCL13 appears to be multifaceted. CSF-CXCL13 is significantly elevated in patients with neuroborreliosis and shows a rapid and sharp decline with antibiotic therapy, but it is not specific for this disease and is also highly elevated in less common subacute neuroinfectious diseases, such as neurosyphilis and cryptococcal meningitis or in primary/secondary B-cell lymphoma.

Tick-Borne Encephalitis (TBE): From Tick to Pathology

Tick-borne encephalitis (TBE) is a viral arthropod infection, endemic to large parts of Europe and Asia, and is characterised by neurological involvement, which can range from mild to severe, and in 33-60% of cases, it leads to a post-encephalitis syndrome and long-term morbidity. While TBE virus, now identified as Orthoflavivirus encephalitidis, was originally isolated in 1937, the pathogenesis of TBE is not fully appreciated with the mode of transmission (blood, tick, alimentary), viral strain, host immune response, and age, likely helping to shape the disease phenotype that we explore in this review. Importantly, the incidence of TBE is increasing, and due to global warming, its epidemiology is evolving, with new foci of transmission reported across Europe and in the UK. As such, a better understanding of the symptomatology, diagnostics, treatment, and prevention of TBE is required to inform healthcare professionals going forward, which this review addresses in detail. To this end, the need for robust national surveillance data and randomised control trial data regarding the use of various antivirals (e.g., Galidesivir and 7-deaza-2'-CMA), monoclonal antibodies, and glucocorticoids is required to improve the management and outcomes of TBE.

Evolving etiologies, comorbidities, survival, and costs of care in adult encephalitis

Encephalitis is a central nervous system disorder, often caused by infectious agents or aberrant immune responses. We investigated causes, comorbidities, costs, and outcomes of encephalitis in a population-based cohort. ICD-10 codes corresponding to encephalitis were used to identify health services records for all adults from 2004 to 2019. Data were cross-validated for identified diagnoses based on laboratory confirmation using univariate and multivariate statistical analyses. We identified persons with a diagnosis of encephalitis and abnormal cerebrospinal fluid (CSF) results (n = 581) in whom viral genome was detected (n = 315) in a population of 3.2 million adults from 2004 to 2019. Viral genome-positive CSF samples included HSV-1 (n = 133), VZV (n = 116), HSV-2 (n = 34), enterovirus (n = 4), EBV (n = 5), and CMV (n = 3) with the remaining viruses included JCV (n = 12) and HHV-6 (n = 1). The mean Charlson Comorbidity Index (2.0) and mortality rate (37.6%) were significantly higher in the CSF viral genome-negative encephalitis group although the mean costs of care were significantly higher for the CSF viral genome-positive group. Cumulative incidence rates showed increased CSF VZV detection in persons with encephalitis, which predominated in persons over 65 years with a higher mean Charlson index. We detected HSV-2 and VZV more frequently in CSF from encephalitis cases with greater material-social deprivation. The mean costs of care were significantly greater for HSV-1 encephalitis group. Encephalitis remains an important cause of neurological disability and death with a viral etiology in 54.2% of affected adults accompanied by substantial costs of care and mortality. Virus-associated encephalitis is evolving with increased VZV detection, especially in older persons.

UltraSEQ, a Universal Bioinformatic Platform for Information-Based Clinical Metagenomics and Beyond

Applied metagenomics is a powerful emerging capability enabling the untargeted detection of pathogens, and its application in clinical diagnostics promises to alleviate the limitations of current targeted assays. While metagenomics offers a hypothesis-free approach to identify any pathogen, including unculturable and potentially novel pathogens, its application in clinical diagnostics has so far been limited by workflow-specific requirements, computational constraints, and lengthy expert review requirements. To address these challenges, we developed UltraSEQ, a first-of-its-kind accurate and scalable metagenomic bioinformatic tool for potential clinical diagnostics and biosurveillance utility. Here, we present the results of the evaluation of our novel UltraSEQ pipeline using an in silico-synthesized metagenome, mock microbial community data sets, and publicly available clinical data sets from samples of different infection types, including both short-read and long-read sequencing data. Our results show that UltraSEQ successfully detected all expected species across the tree of life in the in silico sample and detected all 10 bacterial and fungal species in the mock microbial community data set. For clinical data sets, even without requiring data set-specific configuration setting changes, background sample subtraction, or prior sample information, UltraSEQ achieved an overall accuracy of 91%. Furthermore, as an initial demonstration with a limited patient sample set, we show UltraSEQ's ability to provide antibiotic resistance and virulence factor genotypes that are consistent with phenotypic results. Taken together, the above-described results demonstrate that the UltraSEQ platform offers a transformative approach for microbial and metagenomic sample characterization, employing a biologically informed detection logic, deep metadata, and a flexible system architecture for the classification and characterization of taxonomic origin, gene function, and user-defined functions, including disease-causing infections. IMPORTANCE Traditional clinical microbiology-based diagnostic tests rely on targeted methods that can detect only one to a few preselected organisms or slow, culture-based methods. Although widely used today, these methods have several limitations, resulting in rates of cases of an unknown etiology of infection of >50% for several disease types. Massive developments in sequencing technologies have made it possible to apply metagenomic methods to clinical diagnostics, but current offerings are limited to a specific disease type or sequencer workflow and/or require laboratory-specific controls. The limitations associated with current clinical metagenomic offerings result from the fact that the backend bioinformatic pipelines are optimized for the specific parameters described above, resulting in an excess of unmaintained, redundant, and niche tools that lack standardization and explainable outputs. In this paper, we demonstrate that UltraSEQ uses a novel, information-based approach that enables accurate, evidence-based predictions for diagnosis as well as the functional characterization of a sample.

Co-Circulation of West Nile, Usutu, and Tick-Borne Encephalitis Viruses in the Same Area: A Great Challenge for Diagnostic and Blood and Organ Safety

Viral infections caused by viruses from the family Flaviviridae such as Zika (ZIKV), Dengue (DENV), yellow fever (YFV), tick-borne encephalitis (TBEV), West Nile (WNV), and Usutu (USUV) are some of the most challenging diseases for recognition in clinical diagnostics and epidemiological tracking thanks to their short viremia, non-specific symptoms, and high cross-reactivity observed in laboratory techniques. In Central Europe, the most relevant endemic flaviviruses are mosquito-borne WNV and USUV, and tick-borne TBEV. All three viruses have been recognised to be responsible for human neuroinvasive diseases. Moreover, they are interrupting the blood and transplantation safety processes, when the great efforts made to save a patient's life could be defeated by acquired infection from donors. Due to the trend of changing distribution and abundance of flaviviruses and their vectors influenced by global change, the co-circulation of WNV, USUV, and TBEV can be observed in the same area. In this perspective, we discuss the problems of flavivirus diagnostics and epidemiology monitoring in Slovakia as a model area of Central Europe, where co-circulation of WNV, USUV, and TBEV in the same zone has been recently detected. This new situation presents multiple challenges not only for diagnostics or surveillance but particularly also for blood and organ safety. We conclude that the current routinely used laboratory diagnostics and donor screening applied by the European Union (EU) regulations are out of date and the novel methods which have become available in recent years, e.g., next-gene sequencing or urine screening should be implemented immediately.

Detection and Diagnostic Value of Cytokines in Serum of Children with Acute Viral Encephalitis

Acute viral encephalitis is one of the serious infectious diseases. In order to analyze the diagnostic efficacy of serum procalcitonin (PCT), C-reactive protein (CRP), and S100B protein in acute viral encephalitis, a total of 100 children with acute viral encephalitis from July 2019 to December 2021 are selected and included in the viral encephalitis group. The results show that S100B protein model has high specificity and sensitivity and is simple to operate. It provides new ideas and directions for differential diagnosis, improvement, and optimization of relevant clinical diagnosis and treatment schemes and has high clinical value.

Patients with Infections of The Central Nervous System Have Lowered Gut Microbiota Alpha Diversity

There are multiple lines of evidence for the existence of communication between the central nervous system (CNS), gut, and intestinal microbiome. Despite extensive analysis conducted on various neurological disorders, the gut microbiome was not yet analyzed in neuroinfections. In the current study, we analyzed the gut microbiome in 47 consecutive patients hospitalized with neuroinfection (26 patients had viral encephalitis/meningitis; 8 patients had bacterial meningitis) and in 20 matched for age and gender health controls. Using the QIIME pipeline, 16S rRNA sequencing and classification into operational taxonomic units (OTUs) were performed on the earliest stool sample available. Bacterial taxa such as Clostridium, Anaerostipes, Lachnobacterium, Lachnospira, and Roseburia were decreased in patients with neuroinfection when compared to controls. Alpha diversity metrics showed lower within-sample diversity in patients with neuroinfections, though there were no differences in beta diversity. Furthermore, there was no significant change by short-term (1-3 days) antibiotic treatment on the gut microbiota, although alpha diversity metrics, such as Chao1 and Shannon's index, were close to being statistically significant. The cause of differences between patients with neuroinfections and controls is unclear and could be due to inflammation accompanying the disease; however, the effect of diet modification and/or hospitalization cannot be excluded.

Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metatranscriptomic sequencing

Encephalitis is most often caused by a variety of infectious agents identified through diagnostic tests utilizing cerebrospinal fluid. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic sequencing of residual clinical samples from multiple tissue types and independent clinical review. Forty-three specimens were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing ('metatranscriptomics') to determine the presence and abundance of potential pathogens, and to describe the possible aetiologies of unexplained encephalitis. Using this protocol, we identified five RNA and two DNA viruses associated with human infection from both non-sterile and sterile sites, which were confirmed by PCR. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases. Immune-mediated encephalitis was considered likely in six cases and metatranscriptomics did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasizes the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that non-central-nervous-system sampling in encephalitis clinical guidelines and protocols could improve the diagnostic yield.

Alterations of oral microbiota in Chinese children with viral encephalitis and/or viral meningitis

The role of oral microbiota in viral encephalitis and/or viral meningitis (VEVM) remains unclear. In this hospital-based, frequency-matched study, children with clinically diagnosed VEVM (n = 68) and those with other diseases (controls, n = 68) were recruited. Their oral swab samples were collected and the oral microbiota was profiled using 16S rRNA gene sequencing. The oral microbiota of children with VEVM exhibited different beta diversity metrics (unweighted UniFrac distance: P < 0.001, R² = 0.025, Bray-curtis dissimilarity: P = 0.045, R² = 0.011, and Jaccard dissimilarity: P < 0.001, R² = 0.017) and higher relative abundances of taxa identified by Linear discriminant analysis (LDA) with effect size (Enterococcus, Pedobacter, Massilia, Prevotella_9, Psychrobacter, Butyricimonas, Bradyrhizobium, etc., LDA scores > 2.0) when compared with the control group. The higher pathway abundance of steroid hormone biosynthesis predicted by oral microbiota was suggested to be linked to VEVM (q = 0.020). Further, a model based on oral microbial traits showed good predictive performance for VEVM with an area under the receiver operating characteristic curve of 0.920 (95% confidence interval: 0.834–1.000). Similar results were also obtained between children with etiologically diagnosed VEVM (n = 43) and controls (n = 68). Our preliminary study identified VEVM-specific oral microbial traits among children, which can be effective in the diagnosis of VEVM.

Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis

OBJECTIVES

Many patients with meningitis have no aetiology identified leading to unnecessary antimicrobials and prolonged hospitalisation. We used viral capture sequencing to identify possible pathogenic viruses in adults with community-acquired meningitis.

METHODS

Cerebrospinal fluid (CSF) from 73 patients was tested by VirCapSeq-VERT, a probe set designed to capture viral targets using high throughput sequencing. Patients were categorised as suspected viral meningitis - CSF pleocytosis, no pathogen identified (n = 38), proven viral meningitis - CSF pleocytosis with a pathogen identified (n = 15) or not meningitis - no CSF pleocytosis (n = 20).

RESULTS

VirCapSeq-VERT detected virus in the CSF of 16/38 (42%) of those with suspected viral meningitis, including twelve individual viruses. A potentially clinically relevant virus was detected in 9/16 (56%). Unexpectedly Toscana virus, rotavirus and Saffold virus were detected and assessed to be potential causative agents.

CONCLUSION

VirCapSeq-VERT increases the probability of detecting a virus. Using this agnostic approach we identified Toscana virus and, for the first time in adults, rotavirus and Saffold virus, as potential causative agents in adult meningitis. Further work is needed to determine the prevalence of atypical viral candidates as well as the clinical impact of using sequencing methods in real time. This knowledge can help to reduce antimicrobial use and hospitalisations leading to both patient and health system benefits.

Micro and Nanoscale Technologies for Diagnosis of Viral Infections

Viral infection is one of the leading causes of mortality worldwide. The growth of globalization significantly increases the risk of virus spreading, making it a global threat to future public health. In particular, the ongoing coronavirus disease 2019 (COVID-19) pandemic outbreak emphasizes the importance of devices and methods for rapid, sensitive, and cost-effective diagnosis of viral infections in the early stages by which their quick and global spread can be controlled. Micro and nanoscale technologies have attracted tremendous attention in recent years for a variety of medical and biological applications, especially in developing diagnostic platforms for rapid and accurate detection of viral diseases. This review addresses advances of microneedles, microchip-based integrated platforms, and nano- and microparticles for sampling, sample processing, enrichment, amplification, and detection of viral particles and antigens related to the diagnosis of viral diseases. Additionally, methods for the fabrication of microchip-based devices and commercially used devices are described. Finally, challenges and prospects on the development of micro and nanotechnologies for the early diagnosis of viral diseases are highlighted.

Toll-like Receptors in Viral Encephalitis

Viral encephalitis is a rare but serious syndrome. In addition to DNA-encoded herpes viruses, such as herpes simplex virus and varicella zoster virus, RNA-encoded viruses from the families of Flaviviridae, Rhabdoviridae and Paramyxoviridae are important neurotropic viruses. Whereas in the periphery, the role of Toll-like receptors (TLR) during immune stimulation is well understood, TLR functions within the CNS are less clear. On one hand, TLRs can affect the physiology of neurons during neuronal progenitor cell differentiation and neurite outgrowth, whereas under conditions of infection, the complex interplay between TLR stimulated neurons, astrocytes and microglia is just on the verge of being understood. In this review, we summarize the current knowledge about which TLRs are expressed by cell subsets of the CNS. Furthermore, we specifically highlight functional implications of TLR stimulation in neurons, astrocytes and microglia. After briefly illuminating some examples of viral evasion strategies from TLR signaling, we report on the current knowledge of primary immunodeficiencies in TLR signaling and their consequences for viral encephalitis. Finally, we provide an outlook with examples of TLR agonist mediated intervention strategies and potentiation of vaccine responses against neurotropic virus infections.

Repetitive seizures after febrile period exclusively involving bilateral claustrum

The purpose of this study is to demonstrate the relationship between acute repetitive seizures and claustrum damage, and to provide basis for the treatment of repetitive seizures exclusively involved the bilateral claustrum.Between August 2014 and October 2015, 5 patients with repetitive seizures after a febrile period were admitted to our hospital, showing exclusive involvement of bilateral claustrum on magnetic resonance images (MRI). All patients underwent serum virology testing, autoimmune antibody test, MRI, and electroencephalograph examination.All patients were young women (16-29 years) with an unremarkable previous medical history, and 2 of them were pregnant. Similar clinical symptoms like antecedent febrile illness in the 3 to 7 days preceding seizures, psychiatric disorder, or dysautonomia occurred in 5 patients. Abnormal MRI signals exclusively confined to the bilateral claustrum appeared in 4 patients during the acute phase and in 1 patient during the chronic phase. All patients accepted empirical treatment with anti-viral and anti-seizure drugs and had good outcomes (seizure-free, though with some residual short-term memory loss) at the 3rd year follow-up.Although the clinical and associated brain imaging findings were characteristic, the etiology was still unclear. Contrary to previous studies, the patients presented here have all received a good prognosis.

Neuroinfectious Disease Emergencies

Neuroinfectious diseases can affect immunocompetent and immunosuppressed individuals and cause a variety of emergencies including meningitis, encephalitis, and abscess. Neurologic infections are frequently complicated by secondary injuries that also present emergently such as cerebrovascular disease, acute obstructive hydrocephalus, and seizure. In most cases, timely recognition and early treatment of infection can improve the morbidity and mortality of infectious neurologic emergencies.

A potential new recombinant echovirus 18 strain detected in a 4-year-old child with encephalitis in China in 2019

The species Enterovirus B includes diverse serotypes that can cause a wide spectrum of human diseases, such as aseptic encephalitis, myocarditis, and paralysis. In this study, a 4-year-old child was diagnosed with viral encephalitis, but the causative agent could not be identified using routine immunological tests. Using metagenomic RNA sequencing, a novel strain of enterovirus B, strain PC06, was identified, and its genome sequence was determined by RT-PCR and Sanger sequencing. The viral genome sequence was most similar to that of echovirus E18 strain E18-HeB15-54498/HeB/CHN/2015 (GenBank accession MG720261), with 87.73% nucleotide sequence identity, while the viral proteins shared 96.98% amino acid sequence identity with those of E18 strain Jena/AN1365/10 (GenBank accession no. KX139452). Phylogenetic analysis based on the VP1 and 3D genes revealed discrepant placement of PC06 in the two trees. In the 3D tree, PC06 formed a separate branch together with other recombinant E18 strains. Further recombination tests revealed that PC06 had possibly undergone recombination at a site between the structural and non-structural regions during its evolutionary history. Based on the analysis of VP1 phylogeny and using online genotyping tools, this potential recombinant is tentatively considered a strain of echovirus 18. This information might contribute to the diagnosis and prevention of related diseases.

From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics

Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.

Introduction to Virus Diagnosis and Treatment

Viral diagnostics is increasingly important in clinical medicine. Traditional diagnostic methods have been replaced in many places with molecular methods, but the growing number of new diseases, the expansion of specific antiviral drugs and the need for effective and safe vaccines poses challenges for the diagnostic tools available; more precise, low-cost and accessible solutions are necessary. Good communication and collaboration between laboratory personnel, researchers and clinicians is essential in battling viral infections.

Distinguishing brain inflammation from grade II glioma in population without contrast enhancement: a radiomics analysis based on conventional MRI

PURPOSE

In populations without contrast enhancement, the imaging features of atypical brain parenchyma inflammations can mimic those of grade II gliomas. The aim of this study was to assess the value of the conventional MR-based radiomics signature in differentiating brain inflammation from grade II glioma.

METHODS

Fifty-seven patients (39 patients with grade II glioma and 18 patients with inflammation) were divided into primary (n = 44) and validation cohorts (n = 13). Radiomics features were extracted from T₁-weighted images (T₁WI) and T₂-weighted images (T₂WI). Two-sample t-test and least absolute shrinkage and selection operator (LASSO) regression were adopted to select features and build radiomics signature models for discriminating inflammation from glioma. The predictive performance of the models was evaluated via area under the receiver operating characteristic curve (AUC) and compared with the radiologists' assessments.

RESULTS

Based on the primary cohort, we developed T₁WI, T₂WI and combination (T₁WI + T₂WI) models for differentiating inflammation from glioma with 4, 8, and 5 radiomics features, respectively. Among these models, T₂WI and combination models achieved better diagnostic efficacy, with AUC of 0.980, 0.988 in primary cohort and that of 0.950, 0.925 in validation cohort, respectively. The AUCs of radiologist 1's and 2's assessments were 0.661 and 0.722, respectively.

CONCLUSION

The signature based on radiomics features helps to differentiate inflammation from grade II glioma and improved performance compared with experienced radiologists, which could potentially be useful in clinical practice.

Tick-Borne Encephalitis: A Differential Pattern of Intrathecal Humoral Immune Response and Inflammatory Cell Composition Compared with Other Viral CNS Infections

To investigate whether and how cerebrospinal fluid (CSF) findings can contribute to distinguish tick-borne encephalitis (TBE) from herpes simplex virus (HSV) and varicella zoster virus (VZV) induced central nervous system (CNS) infections (HSV-I, VZV-I). Chart review and identification of TBE, HSV- I, and VZV-I was carried out, fulfilling the following criteria: (1) clinical signs of encephalitis and/or meningitis, (2) complete CSF analysis and confirmed viral etiology by either PCR or antibody testing in CSF, (3) hospitalized patients, and (4) available brain magnetic resonance imaging (MRI). Fifty-nine patients with 118 CSF/serum pairs were included. These comprised 21 with TBE (35 CSF/serum pairs), 20 (40 CSF/serum pairs) with HSV-I, and 18 (43 CSF/serum pairs) with VZV-I. In contrast to HSV-I and VZV-I, CSF cell differentiation in TBE showed more often an increased (>20%) proportion of granulocytes (p < 0.01) and a more frequent quantitative intrathecal IgM synthesis (p = 0.001 and p < 0.01, respectively), while the second was even more pronounced when follow-up CSF analyses were included (p < 0.001). CSF findings help to distinguish TBE from other viral infections. In cases with CSF pleocytosis and a positive history for a stay in or near an endemic area, TBE antibodies in CSF and serum should be determined, especially if granulocytes in CSF cell differentiation and/or an intrathecal IgM synthesis is present.

Lipid-specific IgMs induce antiviral responses in the CNS: implications for progressive multifocal leukoencephalopathy in multiple sclerosis

Progressive multi-focal leukoencephalopathy (PML) is a potentially fatal encephalitis caused by JC polyomavirus (JCV). PML principally affects people with a compromised immune system, such as patients with multiple sclerosis (MS) receiving treatment with natalizumab. However, intrathecal synthesis of lipid-reactive IgM in MS patients is associated with a markedly lower incidence of natalizumab-associated PML compared to those without this antibody repertoire. Here we demonstrate that a subset of lipid-reactive human and murine IgMs induce a functional anti-viral response that inhibits replication of encephalitic Alpha and Orthobunyaviruses in multi-cellular central nervous system cultures. These lipid-specific IgMs trigger microglia to produce IFN-β in a cGAS-STING-dependent manner, which induces an IFN-α/β-receptor 1-dependent antiviral response in glia and neurons. These data identify lipid-reactive IgM as a mediator of anti-viral activity in the nervous system and provide a rational explanation why intrathecal synthesis of lipid-reactive IgM correlates with a reduced incidence of iatrogenic PML in MS.

Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing

The long and expanding list of viral pathogens associated with causing encephalitis confounds current diagnostic procedures, and in up to 50% of cases, the etiology remains undetermined. Sequence-agnostic metagenomic next-generation sequencing (mNGS) obviates the need to specify targets in advance and thus has great potential in encephalitis diagnostics. However, the low relative abundance of viral nucleic acids in clinical specimens poses a significant challenge. Our protocol employs two novel techniques to selectively remove human material at two stages, significantly increasing the representation of viral material. Our bioinformatic workflow using open source protein- and nucleotide sequence-matching software balances sensitivity and specificity in diagnosing and characterizing any DNA viruses present. A panel of 12 cerebrospinal fluid (CSFs) from encephalitis cases was retrospectively interrogated by mNGS, with concordant results in seven of nine samples with a definitive DNA virus diagnosis, and a different herpesvirus was identified in the other two. In two samples with an inconclusive diagnosis, DNA viruses were detected and in a virus-negative sample, no viruses were detected. This assay has the potential to detect DNA virus infections in cases of encephalitis of unknown etiology and to improve the current screening tests by identifying new and emerging agents.

Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Encephalitis and Meningitis: A Large, Prospective Case Series of 213 Patients

Purpose: We assessed the performance of metagenomic next-generation sequencing (mNGS) in the diagnosis of infectious encephalitis and meningitis.

Methods: This was a prospective multicenter study. Cerebrospinal fluid samples from patients with viral encephalitis and/or meningitis, tuberculous meningitis, bacterial meningitis, fungal meningitis, and non-central nervous system (CNS) infections were subjected to mNGS.

Results: In total, 213 patients with infectious and non-infectious CNS diseases were finally enrolled from November 2016 to May 2019; the mNGS-positive detection rate of definite CNS infections was 57.0%. At a species-specific read number (SSRN) ≥2, mNGS performance in the diagnosis of definite viral encephalitis and/or meningitis was optimal (area under the curve [AUC] = 0.659, 95% confidence interval [CI] = 0.566–0.751); the positivity rate was 42.6%. At a genus-specific read number ≥1, mNGS performance in the diagnosis of tuberculous meningitis (definite or probable) was optimal (AUC=0.619, 95% CI=0.516–0.721); the positivity rate was 27.3%. At SSRNs ≥5 or 10, the diagnostic performance was optimal for definite bacterial meningitis (AUC=0.846, 95% CI = 0.711–0.981); the sensitivity was 73.3%. The sensitivities of mNGS (at SSRN ≥2) in the diagnosis of cryptococcal meningitis and cerebral aspergillosis were 76.92 and 80%, respectively.

Conclusion: mNGS of cerebrospinal fluid effectively identifies pathogens causing infectious CNS diseases. mNGS should be used in conjunction with conventional microbiological testing.

Trial Registration: Chinese Clinical Trial Registry, ChiCTR1800020442.

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.

Tick-Borne Encephalitis Virus, United Kingdom

During February 2018–January 2019, we conducted large-scale surveillance for the presence and prevalence of tick-borne encephalitis virus (TBEV) and louping ill virus (LIV) in sentinel animals and ticks in the United Kingdom. Serum was collected from 1,309 deer culled across England and Scotland. Overall, 4% of samples were ELISA-positive for the TBEV serocomplex. A focus in the Thetford Forest area had the highest proportion (47.7%) of seropositive samples. Ticks collected from culled deer within seropositive regions were tested for viral RNA; 5 of 2,041 ticks tested positive by LIV/TBEV real-time reverse transcription PCR, all from within the Thetford Forest area. From 1 tick, we identified a full-length genomic sequence of TBEV. Thus, using deer as sentinels revealed a potential TBEV focus in the United Kingdom. This detection of TBEV genomic sequence in UK ticks has important public health implications, especially for undiagnosed encephalitis.

Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology

Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies.

Rapid detection of human herpes virus by next-generation sequencing in a patient with encephalitis

BACKGROUND

The inflammatory or non-inflammatory changes caused by the virus entering the nervous system and related tissues are central nervous system virus infections. Viral infection is a common infectious disease of the central nervous system, of which herpes simplex virus encephalitis is the most common. However, conventional laboratory techniques to detect an infectious agent are difficult to achieve etiological diagnosis.

CASE PRESENTATION

Here we present a patient with severe and progressive encephalitis, requiring diagnosis of the specific pathogen to guide clinical treatments.

CONCLUSIONS

Application of next-generation sequencing provided a quick and definite diagnosis of the etiology of encephalitis and enabled our patient to be treated appropriately.

Apparent performance of metagenomic next-generation sequencing in the diagnosis of cryptococcal meningitis: a descriptive study

INTRODUCTION

In recent years, metagenomic next-generation sequencing (mNGS) has become widely used in medical microbiology to detect pathogen infection.

AIM

We aimed to assess the diagnostic performance of mNGS of cerebrospinal fluid (CSF) for prediction of cryptococcal meningitis (CM).

METHODOLOGY

A comparative evaluation of mNGS (performed on CSF samples) and conventional methods, including India ink staining, culture for fungi and cryptococcal-antigen (CrAg) detection by enzyme immunoassay, was performed on 12 consecutive non-HIV-infected patients with chronic or subacute CM.

RESULTS

India ink staining and culture of the CSF were positive for Cryptococcus in 83.33 % (10/12) of the samples; 100 % (11/11) were positive via CrAg EIA. The mNGS results of the CSF identified DNA sequences corresponding to Cryptococcus in 75 % of samples (9/12). However, the DNA of both C. neoformans s.l. and C. gattii s.l. was detected concurrently in 33.33 % (4/12).

CONCLUSION

mNGS is helpful for identifying Cryptococcus species. The application of mNGS, together with India ink staining, culture methods, and CrAg, may significantly improve the diagnostic precision in CM, thereby informing choice of appropriate antifungal treatment courses.

Outcomes with acyclovir treatment in herpes simplex encephalitis after surgery for solid CNS tumors: a case report and systematic review of the literature

Background

Herpes simplex encephalitis (HSE) occurring within 30 days after neurosurgery for solid CNS tumors is underrecognized and underreported but remains important because of high morbidity and mortality. We present the case of a 41-year-old woman who had HSE after craniopharyngioma surgery, and delayed recognition and treatment led to a poor outcome. Subsequently, we review reported HSE cases after neurosurgery for solid CNS tumors and describe outcomes after treatment with and without acyclovir.

Methods

A literature search was performed for cases meeting the above criteria. Information was gathered regarding patient demographics, tumor types, symptoms, diagnostic workup, therapy, and outcomes.

Results

Eighteen cases were studied. Encephalopathy, fever, and seizures were the most common symptoms. A majority of patients (78%) received IV acyclovir, with a 79% survival rate with treatment. Mortality rate was 100% in untreated cases. The median time to starting acyclovir was 17 postoperative days (range, 8-53 days). Most patients received steroids, but its use was not associated with a specific outcome.

Conclusions

HSE may develop following neurosurgical resection, and the threshold for suspicion of this condition should be extremely low in a patient who shows compatible symptoms (encephalopathy, fever, or seizures) or does not recover as planned. Moreover, in case of suspicion of HSE, acyclovir should be promptly started until infection can be definitely ruled out. A delay in diagnosis of HSE and failure to treat may result in severe morbidity as well as mortality. This observation may warrant further study.

Prognostic evaluation of child patients with infectious encephalitis through AEEG and REEG

This study investigated prognostic evaluation of child patients with viral encephalitis through ambulatory electroencephalogram (AEEG) and regular electroencephalogram (REEG). A total of 94 child patients who were clinically diagnosed with viral encephalitis in Yantaishan Hospital of Yantai from May 2010 to July 2014, was examined with AEEG and REEG, respectively and randomly divided into AEEG group (n=47) and REEG group (n=47). The probabilities of detecting abnormal electroencephalographic activities with two examination methods were compared. The detection rates of abnormal electroencephalographic activities with AEEG and REEG were 80.0 and 65.0%, respectively, with significant differences (P<0.05); the probabilities of detecting epileptiform discharge with AEEG and REEG were 42.5 and 6.3%, respectively, with significant differences (P<0.05). The hospitalization time and time of electroencephalogram (EEG) restoring to normal of child patients with encephalitis in the REEG group were significantly longer than those of child patients with encephalitis in the AEEG group, with statistically significant differences (P<0.05). Among child patients in the AEEG group, the incidence rate of severe illness was 2.1%, and both the incidence rates of clinical recurrence and of sequela were 0. Among child patients in the REEG group, the incidence rate, clinical recurrence rate and incidence rate of sequela were 8.5, 12.7 and 8.5%, respectively, with statistically significant differences (P<0.05). To some extent, the EEG abnormality reflects the disorder degree of brain environment of child patients with viral encephalitis. The treatment effect and prognosis of child patients with viral encephalitis can be clinically evaluated based on EEG monitoring results of child patients, which has a certain clinical guiding significance. AEEG has important significance to the auxiliary diagnosis of viral encephalitis, with higher sensitivity than REEG.

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.

Nonsuppurative (Aseptic) Meningoencephalomyelitis Associated with Neurovirulent Astrovirus Infections in Humans and Animals

Astroviruses are thought to be enteric pathogens. Since 2010, a certain group of astroviruses has increasingly been recognized, using up-to-date random amplification and high-throughput next-generation sequencing (NGS) methods, as potential neurovirulent (Ni) pathogens of severe central nervous system (CNS) infections, causing encephalitis, meningoencephalitis, and meningoencephalomyelitis. To date, neurovirulent astrovirus cases or epidemics have been reported for humans and domesticated mammals, including mink, bovines, ovines, and swine. This comprehensive review summarizes the virology, epidemiology, pathology, diagnosis, therapy, and future perspective related to neurovirulent astroviruses in humans and mammals, based on a total of 30 relevant articles available in PubMed (searched by use of the terms "astrovirus/encephalitis" and "astrovirus/meningitis" on 2 March 2018). A paradigm shift should be considered based on the increasing knowledge of the causality-effect association between neurotropic astroviruses and CNS infection, and attention should be drawn to the role of astroviruses in unknown CNS diseases.

Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality

Metagenomics approaches based on shotgun next-generation sequencing hold promise for infectious disease diagnostics. Despite substantial challenges that remain, work done over the past few years justifies excitement about the potential for these approaches to transform how clinical pathogen identification and analysis are performed. In an article in this issue of the Journal of Clinical Microbiology, M. I. Ivy et al. (J Clin Microbiol 56:e00402-18, 2018, https://doi.org/10.1128/JCM.00402-18) have applied a shotgun metagenomics approach to the diagnosis of prosthetic joint infections directly from synovial fluid. The results from this work demonstrate both the potentials and challenges of this approach applied in the clinical microbiology laboratory.

Evaluation of Clinical and Paraclinical Findings for the Differential Diagnosis of Autoimmune and Infectious Encephalitis

Background: The differential diagnosis of autoimmune and infectious encephalitis is notoriously difficult. For this study, we compare the presenting clinical symptoms and paraclinical test results of autoimmune and infectious encephalitis patients. A clinical algorithm for the diagnosis of autoimmune encephalitis has recently been published. We test these Graus criteria on our cohort for diagnostic sensitivity and specificity within the first week of presentation. Methods: We included all patients seen at our department within a 10-year-period who were diagnosed with encephalitis. The discharge diagnoses served as the reference standard for testing the clinical algorithm for two conditions: use of all the clinical information available on a patient during the first week of hospital admission assuming undefined autoantibody status and microbiological test results (C1) vs. consideration of all the information available on a patient, including the results of serological and microbiological testing (C2). Results: Eighty-four patients (33 autoimmune, 51 infectious encephalitis) were included in the study. Fifty-one (17 autoimmune, 34 infectious) had a definite clinical diagnosis. The two groups differed significantly for the presence of headache, fever, epileptic seizures, and CSF cell-count at presentation. Application of the clinical algorithm resulted in a low sensitivity (58%) and very low specificity (8%) for the diagnosis of possible autoimmune encephalitis. The latter increased considerably in the subgroups of probable and definite autoimmune encephalitis. Whereas the sensitivity of the individual diagnostic categories was clearly time-dependent, the specificity rested foremost on the knowledge of the results of microbiological testing. Anti-CASPR2- and -LGI1-associated autoimmune encephalitis and tick-borne virus encephalitis presented particular diagnostic pitfalls. Conclusions: We define clinical symptoms and paraclinical test results which prove valuable for the differentiation between infectious and autoimmune encephalitis. Sensitivity and specificity of the clinical algorithm clearly depended on the amount of time passed after hospital admission and knowledge of microbiological test results. Accepting this limitation for the acute setting, the algorithm remains a valuable diagnostic aid for antibody-negative autoimmune encephalitis or in resource-poor settings. The initiation of immune therapy however should not be delayed if an autoimmune etiology is considered likely, even if the diagnostic criteria of the algorithm are not (yet) fulfilled.

Enrichment of Viral Nucleic Acids by Solution Hybrid Selection with Genus Specific Oligonucleotides

Despite recent advances, our knowledge of potential and rare human pathogens is far from exhaustive. Current molecular diagnostic tools mainly rely on the specific amplification of marker sequences and may overlook infections caused by unknown and rare pathogens. Using high-throughput sequencing (HTS) can solve this problem; but, due to the extremely low fraction of pathogen genetic material in clinical samples, its application is only cost-effective in special, rather than routine, cases. In this study, we present a method for the semi-specific enrichment of viral conservative sequences in a HTS library by hybridization in solution with genus-specific degenerate biotinylated oligonucleotides. Nucleic acids of the test viruses (yellow fever virus and Japanese encephalitis virus) were enriched by solution hybrid selection using pan-flavivirus oligonucleotides. Moreover, enterovirus (family: Picornaviridae, genus: Enterovirus) sequences were successfully enriched using foot-and-mouth disease virus (family: Picornaviridae, genus: Aphthovirus) oligonucleotide. The enrichment factor relative to the background nucleic acid was about 1,000-fold. As hybridization has less stringent oligonucleotide match requirements than PCR, few oligonucleotides are sufficient to cover the potential sequence variation in the whole genus and may even enrich nucleic acids of viruses of other related genera. Efficient enrichment of viral sequences makes its use in diagnostics cost-efficient.