A tale of two approaches: how metagenomics and proteomics are shaping the future of encephalitis diagnostics

Mass spectrometry-based proteomic approaches for salivary protein biomarkers discovery and dental caries diagnosis: A critical review

Dental caries is a multifactorial chronic disease resulting from the intricate interplay among acid-generating bacteria, fermentable carbohydrates, and several host factors such as saliva. Saliva comprises several proteins which could be utilized as biomarkers for caries prevention, diagnosis, and prognosis. Mass spectrometry-based salivary proteomics approaches, owing to their sensitivity, provide the opportunity to investigate and unveil crucial cariogenic pathogen activity and host indicators and may demonstrate clinically relevant biomarkers to improve caries diagnosis and management. The present review outlines the published literature of human clinical proteomics investigations on caries and extensively elucidates frequently reported salivary proteins as biomarkers. This review also discusses important aspects while designing an experimental proteomics workflow. The protein-protein interactions and the clinical relevance of salivary proteins as biomarkers for caries, together with uninvestigated domains of the discipline are also discussed critically.

Evaluation of multiple consensus criteria for autoimmune encephalitis and temporal analysis of symptoms in a pediatric encephalitis cohort

Objective

To evaluate the sensitivity and specificity of current criteria for the diagnosis of autoimmune encephalitis (AE) and the temporal onset of neuropsychiatric symptoms (NP) in a pediatric encephalitis cohort.

Background

Multiple criteria for AE have been developed, including the Graus and pediatric-focused Cellucci consensus criteria, and the Determining Etiology in Encephalitis (DEE) score for patients with encephalitis. Early identification and treatment of AE is crucial to improve outcomes, but this can be difficult given the frequent overlap of clinical presentation between AE and infectious encephalitis (IE).

Design/methods

A retrospective review was conducted of patients seen at our institution from 2000 to 2021 with a final diagnosis of AE or IE. These were narrowed through multiple exclusions to etiology-confirmed IE or antibody-positive/negative AE. Time of onset or results of all symptoms and diagnostics were recorded. Sensitivity and specificity of each criterion under various clinical scenarios were calculated over the first month after initial NP symptom onset.

Results

A total of 23 antibody-positive AE, 9 antibody-negative AE and 23 IE patients were included in final analysis. Under an idealized scenario with rapid initial diagnostic evaluations, the sensitivity for pediatric AE by day 28 after onset of NP symptoms approached 90% for both Cellucci and Graus criteria. Specificity within these 28 days was low without infectious testing results, increasing the greatest with rapid PCR testing and second with infectious antibody testing-reaching ~90% with both. A DEE score of 3 provided a specificity of 100% in identifying IE, but low sensitivity (29%). Symptoms were noted to cluster within several days of onset in IE, but in AE were spread out. Personality/behavioral change, speech change, affective disorder, and sleep disturbance were noted more often in AE, while fever, elevated C-reactive protein or CSF protein, and abnormal MRI-Brain occurred more often in IE.

Conclusion

In this study, we provide the first evaluation of the Cellucci criteria and the first validation of the DEE score in the differentiation of pediatric AE and IE. Further refinement of AE criteria is needed to improve early detection and treatment of pediatric AE.

Acute viral encephalitis associated with human parvovirus B19 infection: unexpectedly diagnosed by metagenomic next-generation sequencing

We report here a case of a 17-year-old boy with viral encephalitis associated with human parvovirus B19 who presented consciousness disturbance, left hemiparesis, and focal neurologic signs. The diagnosis was based on the specific sequence reads corresponding to human parvovirus B19 (PVB19) in a CSF sample as analyzed by metagenomic next-generation sequencing (mNGS). Thus, PVB19 should be considered in the differential diagnosis of encephalitis and encephalopathy of unknown etiology. The introduction of mNGS into the diagnostic protocol of neuropathies, especially for those undiagnosed, could interrogate all genetic information in a biologic sample and facilitate the identification of the etiological agent.

Predictors of Outcome in Clinically Diagnosed Viral Encephalitis Patients: A 5-Year Prospective Study

Background

Viral encephalitis is the most common infectious disease of the central nervous system and is associated with high morbidity, mortality, and disability. The objective of this study was to analyze the clinical characteristics, auxiliary examinations, therapeutic management, and outcomes of patients clinically diagnosed with viral encephalitis and identify the outcome predictors.

Methods

We conducted a prospective observational study by collecting information from patients clinically diagnosed with viral encephalitis at the First Affiliated Hospital of Chongqing Medical University and Yongchuan Hospital of Chongqing Medical University from January 2013 to December 2018. Univariate and multivariate analyses were performed to identify factors that influenced good patient outcomes (mRS < 3) and poor patient outcomes (mRS ≥ 3) at discharge.

Results

In total, 216 patients were enrolled in the study. The multivariate analysis suggested that the following factors were associated with a poor outcome: Glasgow Coma Scale (GCS) score (OR 0.154, 95% CI (0.078-0.302), and P < 0.001), focal neurological deficits (OR 9.403, 95% CI (1.581-55.928), and P = 0.014), and total length of hospital stay (OR 1.119, 95% CI (1.002-1.250), and P = 0.045). However, neurological intensive care unit (NICU) treatment, status epilepticus, and abnormal electroencephalogram (EEG) findings did not influence the prognosis of patients.

Conclusion

Our study suggests that low GCS scores at admission, focal neurological deficits at admission, and a prolonged total hospital stay are predictors of a poor outcome at discharge in clinically diagnosed viral encephalitis patients. Whether early and effective neurological rehabilitation can improve the prognosis of viral encephalitis patients with focal neurological deficits remains to be confirmed in further studies.

Mass spectrometry-based proteomic techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections. A systematic review

OBJECTIVES

Central nervous system (CNS) infections account for considerable death and disability every year. An urgent research priority is scaling up diagnostic capacity, and introduction of point-of-care tests. We set out to assess current evidence for the application of mass spectrometry (MS) peptide sequencing in identification of diagnostic biomarkers for CNS infections.

METHODS

We performed a systematic review (PROSPEROCRD42018104257) using PRISMA guidelines on use of MS to identify cerebrospinal fluid (CSF) biomarkers for diagnosing CNS infections. We searched PubMed, Embase, Web of Science, and Cochrane for articles published from 1 January 2000 to 1 February 2019, and contacted experts. Inclusion criteria involved primary research except case reports, on the diagnosis of infectious diseases except HIV, applying MS to human CSF samples, and English language.

RESULTS

4,620 papers were identified, of which 11 were included, largely confined to pre-clinical biomarker discovery, and eight (73%) published in the last five years. 6 studies performed further work termed verification or validation. In 2 of these studies, it was possible to extract data on sensitivity and specificity of the biomarkers detected by ELISA, ranging from 89-94% and 58-92% respectively.

CONCLUSIONS

The findings demonstrate feasibility and potential of the methods in a variety of infectious diseases, but emphasise the need for strong interdisciplinary collaborations to ensure appropriate study design and biomarker validation.

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.

Autoimmune Epilepsy

The field of autoimmune epilepsy has evolved substantially in the last few decades with discovery of several neural autoantibodies and improved mechanistic understanding of these immune-mediated syndromes. A considerable proportion of patients with epilepsy of unknown etiology have been demonstrated to have an autoimmune cause. The majority of the patients with autoimmune epilepsy usually present with new-onset refractory seizures along with subacute progressive cognitive decline and behavioral or psychiatric dysfunction. Neural specific antibodies commonly associated with autoimmune epilepsy include leucine-rich glioma-inactivated protein 1 (LGI1), N-methyl-D-aspartate receptor (NMDA-R), and glutamic acid decarboxylase 65 (GAD65) IgG. Diagnosis of these cases depends on the identification of the clinical syndrome and ancillary studies including autoantibody evaluation. Predictive models (Antibody Prevalence in Epilepsy and Encephalopathy [APE2] and Response to Immunotherapy in Epilepsy and Encephalopathy [RITE2] scores) based on clinical features and initial neurological assessment may be utilized for selection of cases for autoimmune epilepsy evaluation and management. In this article, we will review the recent advances in autoimmune epilepsy and provide diagnostic and therapeutic algorithms for epilepsies with suspected autoimmune etiology.

Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children

BACKGROUND

Encephalitis is an inflammatory condition of the brain associated with long-term neurologic sequelae and even death in children. Although viruses are often implicated, an etiology is not identified in the majority of cases. Metagenomics-based next-generation sequencing (mNGS) is a high-throughput sequencing technique that can enhance the detection of novel or low-frequency pathogens.

METHODS

Hospitalized immunocompetent children aged 6 months to 18 years with encephalitis of unidentified etiology were eligible for enrollment. Demographic, historical, and clinical information was obtained, and residual blood and cerebrospinal fluid (CSF) samples were subjected to mNGS. Pathogens were identified by querying the sequence data against the NCBI GenBank database.

RESULTS

Twenty children were enrolled prospectively between 2013 and 2017. mNGS of CSF identified 7 nonhuman nucleic acid sequences of significant frequency in 6 patients, including that of Mycoplasma bovis, parvovirus B19, Neisseria meningitidis, and Balamuthia mandrillaris. mNGS also detected Cladophialophora species, tobacco mosaic virus, and human bocavirus, which were presumed to be contaminants or nonpathogenic organisms. One patient was found to have positive serology results for California encephalitis virus, but mNGS did not detect it. Patients for whom mNGS identified a diagnosis had a significantly higher CSF white blood cell count, a higher CSF protein concentration, and a lower CSF glucose level than patients for whom mNGS did not identify a diagnosis.

CONCLUSION

We describe here the results of a prospective cohort analysis to evaluate mNGS as a diagnostic tool for children with unexplained encephalitis. Although mNGS detected multiple nonpathogenic organisms, it also identified multiple pathogens successfully and was most useful in patients with a CSF abnormality.

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.

A novel cause of chronic viral meningoencephalitis: Cache Valley virus

Objective

Immunodeficient patients are particularly vulnerable to neuroinvasive infections that can be challenging to diagnose. Metagenomic next generation sequencing can identify unusual or novel microbes and is therefore well suited for investigating the etiology of chronic meningoencephalitis in immunodeficient patients.

Methods

We present the case of a 34‐year‐old man with X‐linked agammaglobulinemia from Australia suffering from 3 years of meningoencephalitis that defied an etiologic diagnosis despite extensive conventional testing, including a brain biopsy. Metagenomic next generation sequencing of his cerebrospinal fluid and brain biopsy tissue was performed to identify a causative pathogen.

Results

Sequences aligning to multiple Cache Valley virus genes were identified via metagenomic next generation sequencing. Reverse transcription polymerase chain reaction and immunohistochemistry subsequently confirmed the presence of Cache Valley virus in the brain biopsy tissue.

Interpretation

Cache Valley virus, a mosquito‐borne orthobunyavirus, has only been identified in 3 immunocompetent North American patients with acute neuroinvasive disease. The reported severity ranges from a self‐limiting meningitis to a rapidly fatal meningoencephalitis with multiorgan failure. The virus has never been known to cause a chronic systemic or neurologic infection in humans. Cache Valley virus has also never previously been detected on the Australian continent. Our research subject traveled to North and South Carolina and Michigan in the weeks prior to the onset of his illness. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. Ann Neurol 2017;82:105–114

Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance

Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear. Here, we present a robust protocol for the implementation and application of "precision metagenomics" across various sequencing platforms for clinical samples. Such a pipeline integrates DNA/RNA extraction, library preparation, sequencing, and bioinformatics analyses for taxonomic classification, antimicrobial resistance (AMR) marker screening, and functional analysis (biochemical and metabolic pathway abundance). Moreover, the pipeline has 3 tracks: STAT for results within 24 h; Comprehensive that affords a more in-depth analysis and takes between 5 and 7 d, but offers antimicrobial resistance information; and Targeted, which also requires 5-7 d, but with more sensitive analysis for specific pathogens. Finally, we discuss the challenges that need to be addressed before full integration in the clinical setting.

Systematic autoantigen analysis identifies a distinct subtype of scleroderma with coincident cancer

Scleroderma is a chronic autoimmune rheumatic disease associated with widespread tissue fibrosis and vasculopathy. Approximately two-thirds of all patients with scleroderma present with three dominant autoantibody subsets. Here, we used a pair of complementary high-throughput methods for antibody epitope discovery to examine patients with scleroderma with or without known autoantibody specificities. We identified a specificity for the minor spliceosome complex containing RNA Binding Region (RNP1, RNA recognition motif) Containing 3 (RNPC3) that is found in patients with scleroderma without known specificities and is absent in unrelated autoimmune diseases. We found strong evidence for both intra- and intermolecular epitope spreading in patients with RNA polymerase III (POLR3) and the minor spliceosome specificities. Our results demonstrate the utility of these technologies in rapidly identifying antibodies that can serve as biomarkers of disease subsets in the evolving precision medicine era.

The Clinical Approach to Encephalitis

Encephalitis has various etiologies, but viral infections and autoimmune disorders are the most commonly identified. Clinical signs, geographical clues, and diagnostic testing-including cerebrospinal fluid abnormalities and magnetic resonance imaging abnormalities-can be helpful in identifying the cause. Certain forms of encephalitis have specific treatments; hence, establishing a diagnosis rapidly and accurately is crucial. Here, we describe the clinical approach to diagnosing several common etiologies of encephalitis as well as treatment strategies.

Diagnostic and therapeutic strategies for management of autoimmune encephalopathies

INTRODUCTION

The understanding of the etio-pathogenesis of autoimmune encephalopathy syndromes has grown significantly in recent years. These are potentially reversible conditions, with variable clinical presentation and potential dramatic response to immunotherapy.

AREAS COVERED

In this article we review various diagnostic techniques and therapeutic options for management of autoimmune encephalopathy. We also review medication adverse effects and monitoring strategies. Expert commentary: Early diagnosis and immunomodulatory treatment remains the cornerstone of management, to halt the underlying neuro-inflammatory process and prevent permanent neuronal injury. The availability of serological testing and various imaging modalities has further improved detection of these immune-mediated neurological disorders. Understanding the mechanisms and potential adverse effects of immunomodulatory therapies will help physicians to choose the most favorable therapeutic strategy for each patient.

Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing

Background

Primary amoebic meningoencephalitis (PAM) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes.

Methods

In this study, we sequenced a full draft assembly of the Balamuthia mandrillaris genome (44.2 Mb in size) from a rare survivor of PAM, and recovered the mitochondrial genome from six additional Balamuthia strains. We also used unbiased metagenomic next-generation sequencing (NGS) and SURPI bioinformatics analysis to diagnose an ultimately fatal case of Balamuthia mandrillaris encephalitis in a 15-year-old girl.

Results and Discussion

Comparative analysis of the mitochondrial genome and high-copy number genes from six additional Balamuthia mandrillaris strains demonstrated remarkable sequence variation, and the closest Balamuthia homologs corresponded to other amoebae, hydroids, algae, slime molds, and peat moss. Real-time NGS testing of hospital day 6 CSF and brain biopsy samples detected Balamuthia on the basis of high-quality hits to 16S and 18S ribosomal RNA sequences present in the National Center for Biotechnology Information (NCBI) nt reference database. The presumptive diagnosis of PAM by visualization of amoebae on brain biopsy histopathology and NGS analysis was subsequently confirmed at the US Centers for Disease Control and Prevention (CDC) using a Balamuthia-specific PCR assay. Retrospective analysis of a day 1 CSF sample revealed that more timely identification of Balamuthia by metagenomic NGS, potentially resulting in a better clinical outcome, would have required availability of the complete genome sequence.

Conclusions

These results underscore the diverse evolutionary origins of Balamuthia mandrillaris, provide new targets for diagnostic assay development, and will facilitate further investigations of the biology and pathogenesis of this eukaryotic pathogen. The failure to identify PAM from a day 1 sample without a fully sequenced Balamuthia genome in the database highlights the critical importance of whole-genome reference sequences for microbial detection by metagenomic NGS.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-015-0235-2) contains supplementary material, which is available to authorized users.