Laboratory diagnosis of common viral infections of the central nervous system by using a single multiplex PCR screening assay

George K, Hoang HE, Thakur KT. Clinical and Diagnostic Features of West Nile Virus Neuroinvasive Disease in New York City

West Nile virus (WNV) neuroinvasive disease (WNND) occurs in approximately 1 percent of WNV-infected patients and typically presents as encephalitis, meningitis, or acute flaccid paralysis (AFP). WNND remains a difficult inpatient diagnosis, creating significant challenges for prognostication and therapy selection. We characterized the clinical and diagnostic features of WNND cases at two major academic medical centers in New York City in routine clinical practice. We retrospectively reviewed the charts of thirty-six patients with WNND, including twenty-six encephalitis, four meningitis, and six AFP cases. The most common presenting symptoms were fever (86.1%) and gastrointestinal symptoms (38.9%) in addition to altered mental status (72.2%), lethargy (63.9%), gait disturbances (46.2%), and headache (44.4%). Fourteen (48.3%) patients displayed acute magnetic resonance imaging (MRI) findings, particularly T2 hyperintensities in the bilateral thalami, brainstem, and deep white matter. New York State Department of Health WNV CSF IgM testing was utilized for diagnosis in 58.3% of patients; however, just 38.1% had the result by discharge, compared to 85.6% of those who underwent serum IgM testing. The median length of stay was 13.5 days, 38.9% were intubated, and three patients (8.9%) died during acute hospitalization. Our findings underscore the morbidity, mortality, and diagnostic challenges of WNND, suggesting the potential utility of serum IgM testing in combination with confirmatory CSF testing to expedite diagnosis in the acute setting.

A multicenter evaluation of the QIAstat-Dx meningitis-encephalitis syndromic test kit as compared to the conventional diagnostic microbiology workflow

PURPOSE

Rapid diagnosis and treatment of infectious meningitis and encephalitis (ME) is critical to minimize morbidity and mortality. Recently, Qiagen introduced the CE-IVD QIAstat-Dx ME panel (QS-ME) for syndromic diagnostic testing of meningitis and encephalitis. Some data on the performance of the QS-ME in comparison to the BioFire FilmArray ME panel are available. In this study, the performance of the QS-ME is compared to the current diagnostic workflow in two academic medical centers in the Netherlands.

METHODS

A total of 110 cerebrospinal fluid samples were retrospectively tested with the QS-ME. The results obtained were compared to the results of laboratory-developed real-time PCR assays (LDTs), IS-pro, bacterial culture, and cryptococcal antigen (CrAg) testing. In addition, the accuracy of the QS-ME was also investigated using an external quality assessment (EQA) panel consisting of ten samples.

RESULTS

Four of the 110 samples tested failed to produce a valid QS-ME result. In the remaining 106 samples, the QS-ME detected 53/53 viral targets, 38/40 bacterial targets, and 7/13 Cryptococcus neoformans targets. The discrepant bacterial results consisted of two samples that were previously tested positive for Listeria monocytogenes (CT 35.8) and Streptococcus pneumoniae (CT 40), respectively. The QS-ME detected one additional result, consisting of a varicella-zoster virus signal (CT 35.9), in a sample in which both techniques detected Streptococcus pyogenes. Finally, 100% concordance was achieved in testing a blinded bacterial ME EQA panel.

CONCLUSION

The QS-ME is a relevant addition to the syndromic testing landscape to assist in diagnosing infectious ME.

Human cases of lymphocytic choriomeningitis virus (LCMV) infections in Hungary

Lymphocytic choriomeningitis (LCM) is a "neglected" rodent-borne viral zoonotic disease caused by lymphocytic choriomeningitis virus (LCMV) (family Arenaviridae). The aim of this retrospective clinical and laboratory study was to detect LCMV RNA, using RT-PCR, in cerebrospinal fluid samples collected from patients with central nervous system (CNS) infections of unknown aetiology from over a 12-year period in Hungary. Between 2009 and 2020, a total of 74 cerebrospinal fluid samples were tested using an in-house LCMV-specific RT-PCR-based method at the Department of Medical Microbiology and Immunology, University of Pécs. The mean age of the 74 patients included in our study was 24 years (min. 5, max. 74), with a predominance of men (44 [59.5%]; women, 30 [40.5%]). Two (2.7%) cerebrospinal fluid samples were found to be positive for LCMV RNA by RT-PCR and sequencing. The first LCMV case was a 5-year-old preschool boy who had a hamster bite on his left-hand finger, and the second LCMV case was a 74-year-old man who was living in a village and had incipient dementia and a previous permanent functional CNS impairment. The two detected LCMV strains (MW558451 and OM648933) from the year 2020 belonged to two different genetic lineages (I and II). These two cases of CNS inflammation of unknown origin represent the first published human LCMV infections confirmed by molecular methods in Hungary.

Occurrence of Norovirus, Rotavirus, Hepatitis a Virus, and Enterovirus in Berries in Argentina

Berries have been implicated as the probable vehicle of infection in multiple outbreaks of norovirus and hepatitis A virus (HAV). These foods often receive minimal or no processing and may be exposed to virus contamination at each stage of production. In an increasingly globalized world, berries have a wide distribution and can give rise to the spread of diseases in distant parts of the world. With the aim of describing the virological quality of the berries cultivated in Argentina, a total of 184 soft fruits of different varieties (strawberries, blueberries, raspberries, blackberries, currants, pomegranate arils, cassis, and elder) were collected during the periods 2016-2018 and 2020. Viral particles were eluted and concentrated by polyethylene glycol precipitation according to ISO 15216-2:2019 guidelines. Genome detection of norovirus (NoV) genogroups I (GI) and II (GII), HAV, rotavirus, and enterovirus was performed by real-time RT-PCR with TaqMan probes. Positive samples were amplified by conventional RT-PCR and the amplicons were purified and sequenced in both directions. Phylogenetic analysis was performed using the Neighbor-Joining method based on the evolutionary model Kimura-2-parameters. NoV GII.6 was detected in 1/184 (0.5%) of the soft fruits, corresponding to a raspberry sample obtained during the fall of 2017. No presence of other human enteric viruses was found in the other berries analyzed. The collected data are the first in Argentina in relation to the prevalence of enteric viruses in berries and is useful as reference data for a risk assessment of soft fruits as vehicles of foodborne pathogenic viruses.

Assessment of a multiplex RT-PCR for Simultaneous, Rapid Screening of Common Viral Infections of Central Nervous System: A Prospective Study for Enteroviruses and Herpesviruses

Introduction

Acute meningitis is a common neurological disorder that affects both children and adults and has a high mortality rate. This study aimed to create a multiplex reverse transcriptase PCR system for screening clinical samples for the presence of the two viruses currently considered to be the most common causes of acute meningitis in Asia.

Materials and Methods

A single-tube RT multiplex PCR assay was developed and tested for sensitivity and specificity using primers that have been commonly used to screen for herpes simplex viruses 1 and 2 (HSV-1/2) and enterovirus (EV) in clinical samples. The procedure was then used to screen 303 clinical samples for the target viruses, which included 101 feces samples, 101 throat swabs, and 101 cerebrospinal fluid (CSF) samples obtained from 101 hospitalized Iranian children with suspected viral meningitis/meningoencephalitis, and the findings were compared to those of an RT monoplex PCR method.

Results

The RT-PCR approach demonstrated high precision, with no non-target virus amplification. The results of using this assay to screen clinical samples revealed that RT monoplex PCR had the same sensitivity as RT multiplex PCR for the three different types of specimens.

Conclusions

This newly developed multiplex RT-PCR method is a simple, fast diagnostic tool that can be used to screen clinical samples for viruses that cause acute meningitis/meningoencephalitis in children.

Aseptic Meningitis in Oral Medicine: Exploring the Key Elements for a Challenging Diagnosis: A Review of the Literature and Two Case Reports

Aseptic meningitis (AM) is a potentially severe and life-threatening disease characterized by meningeal inflammation, usually with mononuclear pleocytosis. It represents a challenging and controversial issue in medicine for multiple etiologies, classification, and difficult diagnosis in the face of nonspecific sets of signs and symptoms. In the area of interest of oral medicine, in specific clusters of patients, even if rare, the occurrence of aseptic meningitis can pose a diagnostic and management dilemma in the following potential etiologies: (i) systemic diseases with oral and meningeal involvement, which include Behçet’s disease and Sjögren syndrome; (ii) drug-induced aseptic meningitis; (iii) aseptic viral meningitis, mostly related to herpes simplex virus infection and hand, foot, and mouth disease, caused by enteroviruses. In this review, clinical manifestations, diagnostic methodologies, incidence, treatment, and prognosis for each of these clinical entities are provided. Furthermore, two illustrative case reports are described: a patient suffering from recurrent oral ulcers, in which a sudden onset of AM allows us to diagnose Neuro Behçet’s disease, and a patient affected by pemphigus vulgaris, manifesting a drug-induced AM. Exploring this complex clinical entity scenario, it is clear that an oral medicine specialist has a place on any multidisciplinary team in making such a challenging diagnosis.

Molecular identification and clinical characteristics of mumps virus and human herpesviruses associated with aseptic meningitis in South of Iran

Viral infections are the major etiological agent of aseptic meningitis; though, limited data exist on the prevalence and molecular epidemiology of viral pathogens responsible for the occurrence of aseptic meningitis in Iran. Therefore, this study aimed to elucidate the prevalence and clinical features of mumps virus and human herpesviruses associated with aseptic meningitis in the South of Iran. A total of 73 patients with aseptic meningitis were enrolled in this study. Cerebral spinal fluid (CSF) samples were tested for detection of HSV, CMV, VZV and mumps virus using nested PCR assay. Mumps virus, HSV-1 and VZV were found in 4 (5.5%), 4 (5.5%) and 3 (4.1%) of the CSF samples, respectively. The highest rates of mumps virus and HSV infections were observed in infants less than one year, and VZV was more prevalent in patients under 5 years of age. The majority of mumps virus and VZV infections were found among male patients, while HSV was more prevalent among female patients. The highest incidence of aseptic meningitis associated with mumps virus was observed in summer, while HSV and VZV were more prevalent during spring. Headache was the most common symptom in mumps meningitis. About HSV and VZV, the most predominant clinical symptom was fever. The results of this study indicate the importance of molecular assay in the diagnosis of etiological agents of aseptic meningitis. Prompt detection of viral pathogens provides a better chance of managing viral meningitis in health care settings.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-021-00718-y.

N-Terminal Pro-C-Type Natriuretic Peptide: The Novel Marker in Selected Disease Units

BACKGROUND

Amino-terminal pro C type natriuretic peptide (NT proCNP) is the N terminal fragment of the CNP precursor. NT proCNP occurs in an equimolar concentration with CNP in human plasma and is considered to be a marker of the extent of CNP biosynthesis. A recent study has shown associations between plasma NT proCNP and blood pressure; it is also an independent predictor of death and cardiac readmission in people with unstable angina. Beyond that, recent studies have focused on the applicability of assessing NT proCNP peptide levels in the diagnosis of diseases with different etiologies but the same denominator, i.e., inflammation.

METHODS

This study reviewed recent results on the usability of NT proCNP peptide levels in the diagnosis of diseases accompanied by statistical analysis of previously reported results.

RESULTS

The data obtained confirmed the applicability of the assessment of NT proCNP levels in biological fluids in diseases, such as Parkinson's disease, sepsis, meningitis, and asthenozoospermia.

CONCLUSION

The reported results demonstrated that NT-proCNP is helpful in a variety of diseases. Furthermore, changes in serum or CSF levels of NT-proCNP reflect only inflammatory states related to general inflammation. Local inflammation does not trigger an increase in NT proCNP level.

Arbovirus, herpesvirus, and enterovirus associated with neurological syndromes in adult patients of a university hospital, 2017-2018

INTRODUCTION:

Herpesviruses, enteroviruses, and arboviruses are important because of their clinical relevance and ability to cause meningitis, encephalitis, meningoencephalitis, and other diseases. The clinical virology associated with diagnostic technologies can reduce the morbidity and mortality of such neurological manifestations. Here we aimed to identify the genomes of agents that cause neurological syndromes in cerebrospinal fluid (CSF) samples from patients with suspected nervous system infections admitted to the University Hospital of the University of Campinas, São Paulo, Brazil, in 2017-2018.

METHODS:

CSF samples collected from adult patients with neurological syndrome symptoms and negative CSF culture results were analyzed using polymerase chain reaction (PCR), reverse transcriptase-PCR, and real-time PCR, and their results were compared with their clinical symptoms. One CSF sample was obtained from each patient.

RESULTS:

Viral genomes were detected in 148/420 (35.2%) CSF samples: one of 148 (0.2%) was positive for herpes simplex virus-1; two (0.5%) for herpes simplex virus-2; eight (1.9%) for varicella-zoster virus; four (1%) for Epstein-Barr virus; one (0.2%) for cytomegalovirus; 32 (7.6%) for human herpesvirus-6; 30 (7.1%) for non-polio enterovirus; 67 (16.0%) for dengue virus, three (0.7%) for yellow fever virus, and 21 (5%) for Zika virus.

CONCLUSIONS:

The viral genomes were found in 35.2% of all analyzed samples, showing the high prevalence of viruses in the nervous system and the importance of using a nucleic acid amplification test to detect viral agents in CSF samples.

Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

INTRODUCTION

Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.

METHODS

Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed.

RESULTS

Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection.

CONCLUSION

A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.

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.

Lessons and Considerations for the Creation of Universal Primers Targeting Non-Conserved, Horizontally Mobile Genes

Effective and accurate primer design is an increasingly important skill as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such as dsrAB and dnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a model community of six members (Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica). Using sequence alignments and in silico PCR analyses, a new approach for creating universal primers sets targeting mobile, non-conserved genes has been developed and compared to more traditional approaches used for highly conserved genes. A discussion of the potential shortfalls of the primer sets designed this way are described. The approach described here can be adapted to any unique gene set and aid in creating a wider, more robust library of primer sets to detect less conserved genes and improve the field of PCR-based screening research.IMPORTANCE Increasing use of molecular detection methods, specifically PCR and qPCR, requires utmost confidence in the results while minimizing false positives and negatives due to poor primer designs. Frequently, these detection methods are focused on conserved, core genes which limits their applications. These screening methods are being used in various industries for specific genetic targets or key organisms such as viral or infectious strains, or characteristic genes indicating the presence of key metabolic processes. The significance of this work is to improve primer design approaches to broaden the scope of detectable genes. The use of the techniques explored here will improve detection of non-conserved genes through unique primer design approaches. Additionally, the approaches here highlight additional, important information which can be gleaned during the in silico phase of primer design which will improve our gene annotations based on percent identities.

Mechanisms of Blood-Brain Barrier Disruption in Herpes Simplex Encephalitis

Herpes simplex encephalitis (HSE) is often caused by infection with herpes simplex virus 1 (HSV-1), a neurotropic double-stranded DNA virus. HSE infection always impacts the temporal and frontal lobes or limbic system, leading to edema, hemorrhage, and necrotic changes in the brain parenchyma. Additionally, patients often exhibit severe complications following antiviral treatment, including dementia and epilepsy. HSE is further associated with disruptions to the blood-brain barrier (BBB), which consists of microvascular endothelial cells, tight junctions, astrocytes, pericytes, and basement membranes. Following an HSV-1 infection, changes in BBB integrity and permeability can result in increased movement of viruses, immune cells, and/or cytokines into the brain parenchyma. This leads to an enhanced inflammatory response in the central nervous system and further damage to the brain. Thus, it is important to protect the BBB from pathogens to reduce brain damage from HSE. Here, we discuss HSE and the normal structure and function of the BBB. We also discuss growing evidence indicating an association between BBB breakdown and the pathogenesis of HSE, as well as future research directions and potential new therapeutic targets. Graphical Abstract During herpes simplex encephalitis, the functions and structures of each composition of BBB have been altered by different factors, thus the permeability and integrity of BBB have been broken. The review aim to explore the potential mechanisms and factors in the process, probe the next research targets and new therapeutic targets.

Use of multiplex PCR based molecular diagnostics in diagnosis of suspected CNS infections in tertiary care setting-A retrospective study

OBJECTIVES

CNS infections like meningitis and encephalitis pose enormous healthcare challenges due to mortality, sequelae and socioeconomic burden. In tertiary setting, clinical, microbiological, cytological and radiological investigations are not distinctive enough for diagnosing microbial etiology. Molecular diagnostics is filling this gap. We evaluated the clinical impact of a commercially available multiplex molecular diagnostic system - SES for diagnosing suspected CNS infections.

PATIENTS AND METHODS

This study was conducted in our tertiary level Neurology ICU. 110 patients admitted during Nov-2010 to April-2014 were included. CSF samples of patients clinically suspected of having CNS infections were subjected to routine investigation in our laboratory and SES test at XCyton Diagnostics. We studied the impact of SES in diagnosis of CNS infections and its efficacy in helping therapeutic management.

RESULTS

SES showed detection rate of 42.18% and clinical specificity of 100%. It had 10 times higher detection rate than conventional tests. Streptococcus pneumoniae and Mycobacterium tuberculosis were two top bacterial pathogens. VZV was most detected viral pathogen. SES results elicited changes in therapy in both positive and negative cases. We observed superior patient outcomes as measured by GCS scale. 75% and 82.14% of the patients positive and negative on SES respectively, recovered fully.

CONCLUSION

Detecting causative organism and ruling out infectious etiology remain the most critical aspect for management and prognosis of patients with suspected CNS infections. In this study, we observed higher detection rate of pathogens, target specific escalation and evidence based de-escalation of antimicrobials using SES. Institution of appropriate therapy helped reduce unnecessary use of antimicrobials.

Three cases of mumps virus and enterovirus coinfection in children with enteroviral meningitis

Several viruses are responsible for aseptic meningitis; however, in the region of Southwest Iran, the role played by each virus is still not very well known. The aim of this study is to determine the relative frequencies of mumps virus, herpes viruses, and enteroviruses, as well as coinfections among them, in patients with aseptic meningitis.In this cross-sectional study, samples of cerebrospinal fluid were collected between December 2012 and December 2013 from patients under 14 years, who were hospitalized in Abuzar Children's Hospital in Ahvaz, Southwest Iran (the only children's hospital in Khuzestan province and Southwest Iran).All 66 cerebrospinal fluid samples and corresponding clinical data were collected from patients with aseptic meningitis by specialists, and with the patients' consent. The DNA and RNA were extracted from these samples and subjected to polymerase chain reaction as well as reverse transcription polymerase chain reaction (RT-PCR) for detection of mumps virus, herpes viruses, and enteroviruses. Nine of the samples (3 mumps-positive and 6 enterovirus-positive) were sequenced. The mumps virus sequences were investigated for possible mutations in the SH and partial HN regions.Up to 39 patients (59.09%) were found to be positive for enteroviruses, 3 (4.5%) for mumps virus, and 1 (1.5%) for herpes viruses (specifically, the varicella-zoster virus). Two patients (3.03%) had a mumps virus and enterovirus coinfection. Among the 3 detected mumps virus samples, 1 belonged to genotype B, while the others belonged to genotype N. Six sequenced enteroviruses indicated the highest similarity with Echovirus 30. An amino acid substitution at position 51 (N→T) was detected in the HN region of genotype N mumps virus samples, in comparison to the reference strain.

Antiviral Activity of Hatay Propolis Against Replication of Herpes Simplex Virus Type 1 and Type 2

Background

Propolis is a bee product widely used in folk medicine and possessing many pharmacological properties. In this study we aimed to investigate: i) the antiviral activities of Hatay propolis samples against HSV-1 and HSV-2 in HEp-2 cell line, and ii) the presence of the synergistic effects of propolis with acyclovir against these viruses.

Material/Methods

All experiments were carried out in HEp-2 cell cultures. Proliferation assays were performed in 24-well flat bottom microplates. We inoculated 1×10⁵ cells per ml and RPMI 1640 medium with 10% fetal calf serum into each well. Studies to determine cytotoxic effect were performed. To investigate the presence of antiviral activity of propolis samples, different concentrations of propolis (3200, 1600, 800, 400, 200, 100, 75, 50, and 25 μg/mL) were added into the culture medium. The amplifications of HSV-1 and HSV-2 DNA were performed by real-time PCR method. Acyclovir (Sigma, USA) was chosen as a positive control. Cell morphology was evaluated by scanning electron microscopy (SEM).

Results

The replication of HSV-1 and HSV-2 was significantly suppressed in the presence of 25, 50, and 100 μg/mL of Hatay propolis. We found that propolis began to inhibit HSV-1 replication after 24 h of incubation and propolis activity against HSV-2 was found to start at 48 h following incubation. The activity of propolis against both HSV-1 and HSV-2 was confirmed by a significant decrease in the number of viral copies.

Conclusions

We determined that Hatay propolis samples have important antiviral effects compared with acyclovir. In particular, the synergy produced by antiviral activity of propolis and acyclovir combined had a stronger effect against HSV-1 and HSV-2 than acyclovir alone.

Retrospective analysis of multiplex polymerase chain reaction-based molecular diagnostics (SES) in 70 patients with suspected central nervous system infections: A single-center study

Background:

Central nervous system (CNS) infections present a grave health care challenge due to high morbidity and mortality. Clinical findings and conventional laboratory assessments are not sufficiently distinct for specific etiologic diagnosis. Identification of pathogens is a key to appropriate therapy.

Aim:

In this retrospective observational study, we evaluated the efficacy and clinical utility of syndrome evaluation system (SES) for diagnosing clinically suspected CNS infections.

Materials and Methods:

This retrospective analysis included inpatients in our tertiary level neurointensive care unit (NICU) and ward from February 2010 to December 2013. Cerebrospinal fluid (CSF) samples of 70 patients, clinically suspected of having CNS infections, were subjected to routine laboratory tests, culture, imaging, and SES. We analyzed the efficacy of SES in the diagnosis of CNS infections and its utility in therapeutic decision-making.

Results:

SES had a clinical sensitivity of 57.4% and clinical specificity of 95.6%. Streptococcus pneumoniae and Pseudomonas aeruginosa were the top two bacterial pathogens, whereas Herpes simplex virus (HSV) was the most common viral pathogen. Polymicrobial infections were detected in 32.14% of SES-positive cases. SES elicited a change in the management in 30% of the patients from initial empiric therapy. At discharge, 51 patients recovered fully while 11 patients had partial recovery. Three-month follow-up showed only six patients to have neurological deficits.

Conclusion:

In a tertiary care center, etiological microbial diagnosis is central to appropriate therapy and outcomes. Sensitive and accurate multiplex molecular diagnostics play a critical role in not only identifying the causative pathogen but also in helping clinicians to institute appropriate therapy, reduce overuse of antimicrobials, and ensure superior clinical outcomes.

Study of the Frequency of Herpesvirus Infections Among Patients Suspected Aseptic Meningitis in the West of Iran

Background:

Aseptic meningitis is the most common type of meningitis and is characterized by meningeal inflammation that is not linked to identifiable bacterial pathogens in cerebrospinal fluid (CSF).

Objectives:

This study aimed to evaluate the frequency of aseptic meningitis caused by herpesviruses, namely herpes simplex types I and II (HSV-1, HSV-2), Epstein-Barr virus (EBV), cytomegalovirus (CMV) and varicella-zoster virus (VZV).

Patients and Methods:

A total of 196 CSF samples were collected from patients with suspected meningitis. All samples were smear- and culture-negative for bacterial pathogens. The biochemical and cytological findings of CSF samples were also recorded. DNA was extracted from samples and PCR with specific primers was carried out to detect viruses.

Results:

The 196 samples derived from 100 (52%) men and 96 (48%) women ranging in age from one day to 86 years with an average age of 32.3 ± 25.3 years. Of them, 8 (4.08%) samples yielded positive results, including 5 (2.55%) cases of VZV infection and 3 (1.53%) cases of HSV-1 infection. No cases of HSV-2, CMV or EBV infection were detected. CSF protein and glucose levels among positive cases were all in the normal range.

Conclusions:

The results indicate a considerable rate of herpesvirus infection in patients with aseptic meningitis, and that VZV is the most common herpesvirus to cause infection followed by HSV-1. Our results also showed that a moderate increase in the WBC count and predominance of lymphocytes can be valuable clues in diagnosing viral meningitis. Given the different approaches of drug therapy in bacterial and viral meningitis, use of molecular methods is necessary in hospitals to rapidly discriminate between them.

Antiviral Action of Hydromethanolic Extract of Geopropolis from Scaptotrigona postica against Antiherpes Simplex Virus (HSV-1)

The studies on chemical composition and biological activity of propolis had focused mainly on species Apis mellifera L. (Hymenoptera: Apidae). There are few studies about the uncommon propolis collected by stingless bees of the Meliponini tribe known as geopropolis. The geopropolis from Scaptotrigona postica was collected in the region of Barra do Corda, Maranhão state, Brazil. The chemical analysis of hydromethanolic extract of this geopropolis (HMG) was carried out through HPLC-DAD-ESI-MS/MS and the main constituents found were pyrrolizidine alkaloids and C-glycosyl flavones. The presence of alkaloids in extracts of propolis is detected for the first time in this sample. The antiviral activity of HMG was evaluated through viral DNA quantification experiments and electron microscopy experiments. Quantification of viral DNA from herpes virus showed reduction of about 98% in all conditions and concentration tested of the HMG extract. The results obtained were corroborated by transmission electron microscopy, in which the images did not show particle or viral replication complex. The antiviral activity of C-glycosyl flavones was reported for a variety of viruses, being observed at different points in the viral replication. This work is the first report about the antiviral activity of geopropolis from Scaptotrigona postica, in vitro, against antiherpes simplex virus (HSV).

Detection of Mycobacterium tuberculosis genome in vitreous fluid of eyes with multifocal serpiginoid choroiditis

PURPOSE

To compare 3 different molecular techniques to detect the Mycobacterium tuberculosis genome in vitreous fluid of eyes with multifocal serpiginoid choroiditis (MSC).

DESIGN

Prospective, interventional case series.

PARTICIPANTS

Eleven patients (11 eyes) with active MSC in at least 1 eye underwent diagnostic pars plana vitrectomy (PPV) between October 2012 and December 2013.

METHODS

Vitreous fluid samples were subjected to multitargeted polymerase chain reaction (PCR) for a M. tuberculosis assay, the Gene Xpert MTB/RIF assay (Cepheid, Sunnyvale, CA), and a line probe assay (GenoType MTBDRplus; Hain Lifescience, GmbH, Nehren, Germany). The samples with positive results were subjected to rpoB gene sequencing to demonstrate rifampicin resistance. The clinical details, digital fundus imaging, and treatment details and outcomes also were noted.

MAIN OUTCOME MEASURES

Detection of the M. tuberculosis genome and rifampicin resistance in the vitreous samples.

RESULTS

Of the 11 eyes subjected to PPV, the multitargeted PCR results for tuberculosis were positive for 10 eyes, the MTBDRplus assay results were positive in 6 eyes, and the Gene Xpert MTB/RIF assay results were positive in 4 eyes. Rifampicin resistance was detected in 3 eyes by rpoB gene sequencing, in 3 eyes by the MTBDRplus assay, and in 1 eye by the Gene Xpert MTB/RIF assay.

CONCLUSIONS

We detected the M. tuberculosis genome in the vitreous fluid of eyes with MSC using 3 different molecular techniques. Rifampicin resistance was detected for the first time in eyes with MSC.

Etiologic agents of central nervous system infections among febrile hospitalized patients in the country of Georgia

Objectives

There is a large spectrum of viral, bacterial, fungal, and prion pathogens that cause central nervous system (CNS) infections. As such, identification of the etiological agent requires multiple laboratory tests and accurate diagnosis requires clinical and epidemiological information. This hospital-based study aimed to determine the main causes of acute meningitis and encephalitis and enhance laboratory capacity for CNS infection diagnosis.

Methods

Children and adults patients clinically diagnosed with meningitis or encephalitis were enrolled at four reference health centers. Cerebrospinal fluid (CSF) was collected for bacterial culture, and in-house and multiplex RT-PCR testing was conducted for herpes simplex virus (HSV) types 1 and 2, mumps virus, enterovirus, varicella zoster virus (VZV), Streptococcus pneumoniae, HiB and Neisseria meningitidis.

Results

Out of 140 enrolled patients, the mean age was 23.9 years, and 58% were children. Bacterial or viral etiologies were determined in 51% of patients. Five Streptococcus pneumoniae cultures were isolated from CSF. Based on in-house PCR analysis, 25 patients were positive for S. pneumoniae, 6 for N. meningitidis, and 1 for H. influenzae. Viral multiplex PCR identified infections with enterovirus (n = 26), VZV (n = 4), and HSV-1 (n = 2). No patient was positive for mumps or HSV-2.

Conclusions

Study findings indicate that S. pneumoniae and enteroviruses are the main etiologies in this patient cohort. The utility of molecular diagnostics for pathogen identification combined with the knowledge provided by the investigation may improve health outcomes of CNS infection cases in Georgia.

Discovery of a new antiviral protein isolated Lonomia obliqua analysed by bioinformatics and real-time approaches

This study presents a new recombinant protein that acts as a powerful antiviral (rAVLO—recombinant Antiviral protein of Lonomia obliqua). It was able to reduce the replication by 10⁶ fold for herpes virus and by 10⁴ fold for rubella virus. RT-PCR of viral RNA rAVLO treated infected cells also showed similar rate of inhibition in replication. The analysis of this protein by bioinformatics suggests that this protein is globular, secreted with a signal peptide and has the ability to bind to MHC class I. It was found that there are several protein binding sites with various HLA and a prevalence of α-helices in the N-terminal region (overall classified as a α/β protein type). BLAST similarity sequence search for corresponding cDNA did not reveal a similar sequence in Genbank, suggesting that it is from a novel protein family. In this study we have observed that this recombinant protein and hemolymph has a potent antiviral action. This protein was produced in a baculovirus/Sf-9 system. Therefore, these analyses suggest that this novel polypeptide is a candidate as a broad spectrum antiviral.

Viral aetiology and clinico-epidemiological features of acute encephalitis syndrome in eastern India

This study reports clinico-epidemiological features and viral agents causing acute encephalitis syndrome (AES) in the eastern Indian region through hospital-based case enrolment during April 2011 to July 2012. Blood and CSF samples of 526 AES cases were investigated by serology and/or PCR. Viral aetiology was identified in 91 (17·2%) cases. Herpes simplex virus (HSV; types I or II) was most common (16·1%), followed by measles (2·6%), Japanese encephalitis virus (1·5%), dengue virus (0·57%), varicella zoster virus (0·38%) and enteroviruses (0·19%). Rash, paresis and cranial nerve palsies were significantly higher (P < 0·05) with viral AES. Case-fatality rates were 10·9% and 6·2% in AES cases with and without viral aetiology, respectively. Simultaneous infection of HSV I and measles was observed in seven cases. This report provides the first evidence on viral aetiology of AES viruses from eastern India showing dominance of HSV that will be useful in informing the public health system.

Application of PCR technology in vaccine product development

The complex process of vaccine product development needs to be tightly controlled and closely monitored to ensure vaccine quality and consistency. Since its inception, PCR has been widely used in all stages of vaccine product development as a tool to assist in the evaluation of vaccine quality, safety and efficacy. In this review, the general principles of conventional and real-time quantitative PCR (Q-PCR) technology and its application in vaccine product development for quantitation of vaccine dose (genome quantitation assay), infectivity (Q-PCR-based potency assay), process residuals, stability, adventitious agents, safety assessment and clinical studies are described. The future outlook and the advantages and disadvantages of this technology are also discussed.

Thin-film technology for direct visual detection of nucleic acid sequences: applications in clinical research

Certain optical conditions permit the unaided eye to detect thickness changes on surfaces on the order of 20 A, which are of similar dimensions to monomolecular interactions between proteins or hybridization of complementary nucleic acid sequences. Such detection exploits specific interference of reflected white light, wherein thickness changes are perceived as surface color changes. This technology, termed thin-film detection, allows for the visualization of subattomole amounts of nucleic acid targets, even in complex clinical samples. Thin-film technology has been applied to a broad range of clinically relevant indications, including the detection of pathogenic bacterial and viral nucleic acid sequences and the discrimination of sequence variations in human genes causally related to susceptibility or severity of disease.

Meningitis, Viral

This article provides an overview of the pathogenesis, epidemiology, causes, clinical presentation, laboratory diagnosis, and treatment of the most common causes of viral meningitis in the United States. It also summarizes other infectious and noninfectious causes of lymphocytic or aseptic meningitis.

Herpes simplex virus meningitis in children in South East of caspian sea, iran

BACKGROUND

Herpes simplex virus (HSV) is a member of Herpesviridae and a leading cause of human viral diseases. Meningitis occurs as a complication of HSV-1 or HSV-2 primary infection.

OBJECTIVES

We aimed to evaluate HSV meningitis in children in Gorgan province, Iran.

PATIENTS AND METHODS

Forty-five cerebrospinal fluid samples were taken from children referred with meningitis symptoms. Samples with negative bacterial culture results were tested for viral, biochemical and cytological assays. DNA extraction and PCR were performed.

RESULTS

HSV-1 detected in 4 (8.8%) samples without any HSV-2 infections. Cases with positive results had fever and CSF pleocytosis. Vomiting, headache and higher count of WBC were observed in 3, 2 and 3 cases respectively. The cerebrospinal fluid (CSF) glucose and protein levels were normal and 3 cases showed positive C-reactive protein (CRP) results. Also erythrocyte sedimentation rate (ESR) was higher than normal in all positive cases.

CONCLUSIONS

Distribution of HSV types in children with meningitis in our area predominantly was type 1 compared with type 2, which has been reported more in other area.

Diagnostic value of a "wide-range" quantitative nested real-time PCR assay for varicella zoster virus myelitis

Myelitis is one of the rarest neurological complications of varicella zoster virus (VZV) infection. In this study, the authors remodeled the "wide-range" quantitative nested real-time (QNRT) polymerase chain reaction (PCR) assay to quantitatively detect a small amount of VZV-DNA in cerebrospinal fluid (CSF). For use as a specific internal control "calibrator," an original mutation-VZV (MZ) plasmid was developed. The initial copy number of VZV-DNA in CSF specimens was measured by the amplification rate of the MZ-plasmid. For 17 consecutive CSF specimens collected from three elderly patients with VZV myelitis, the diagnostic value of the wide-range QNRT-PCR assay was evaluated and compared with other conventional PCR assays and enzyme immunoassay (EIA). The MZ-plasmid demonstrated statistically uniform amplifications (F=1.016) against a wide range (1-100,000) of copy numbers of mimic VZV-DNA. The wide-range QNRT-PCR assay quantitatively and rapidly (within 48 hr) detected 5,863, 3,052, 958, and 6,721 copies/ml of VZV-DNA in the CSF specimens collected from all patients in the acute phase. Additionally, there was a significant difference (*P=0.023) in the copy number of VZV-DNA between before and after acyclovir treatment. Other conventional single PCR assays all revealed negative results, but were nevertheless time-consuming (7 days). The IgG EIA-value for VZV was continually elevated throughout the clinical course of all patients. The MZ-plasmid was thus regarded as an appropriate "calibrator" in the wide-range QNRT-PCR assay. This assay is a novel, rapid, accurate, quantitative, and highly sensitive technique, and will contribute as a reliable and useful clinical examination for the rapid diagnosis of VZV infection to central nervous system.

Laboratory diagnosis of CNS infections by molecular amplification techniques

The initial presentation of symptoms and clinical manifestations of CNS infectious diseases often makes a specific diagnosis difficult and uncertain, and the emergence of polymerase chain reaction-led molecular techniques have been used in improving organism-specific diagnosis. These techniques have not only provided rapid, non-invasive detection of microorganisms causing CNS infections, but also demonstrated several neurologic disorders linked to infectious pathogens. Molecular methods performed on cerebrospinal fluid are recognized as the new 'gold standard' for some of these infections caused by microorganisms that are difficult to detect and identify. Although molecular techniques are predicted to be widely used in diagnosing and monitoring CNS infections, the limitations as well as strengths of these techniques must be clearly understood by both clinicians and laboratory personnel.

Long-term valacyclovir suppressive treatment after herpes simplex virus type 2 meningitis: a double-blind, randomized controlled trial

BACKGROUND

Herpes simplex virus type 2 (HSV-2) is a common cause of acute and recurrent aseptic meningitis. Our aim was to determine the impact of antiviral suppression on recurrence of meningitis and to delineate the full spectrum of neurological complications.

METHODS

One hundred and one patients with acute primary or recurrent HSV-2 meningitis were assigned to placebo (n = 51) or 0.5 g of valacyclovir twice daily (n = 50) for 1 year after initial treatment with 1 g of valacyclovir 3 times daily for 1 week in a prospective, placebo-controlled, multicenter trial. The primary outcome was time until recurrence of meningitis. The patients were followed up for 2 years.

RESULTS

The first year, no significant difference was found between the valacyclovir and placebo groups. The second year, without study drugs, the risk of recurrence of verified and probable HSV-2 meningitis was significantly higher among patients exposed to valacyclovir (hazard ratio, 3.29 [95% confidence interval, 10.06-10.21]). One-third of the patients experienced 1-4 meningitis episodes during the study period. A considerable morbidity rate, comprising symptoms from the central, peripheral, and autonomous nervous system, was found in both groups.

CONCLUSIONS

Suppressive treatment with 0.5 g of valacyclovir twice daily was not shown to prohibit recurrent meningitis and cannot be recommended for this purpose after HSV meningitis in general. Protection against mucocutaneous lesions was observed, but the dosage was probably inappropriate for the prevention of HSV activation in the central nervous system. The higher frequency of meningitis, after cessation of active drug, could be interpreted as a rebound phenomenon.

Detection of enterovirus RNA in cerebrospinal fluid: comparison of two molecular assays

Enterovirus (EV) and human parechovirus (HPeV) are a major cause of infection in childhood. A rapid diagnostic test may improve the management of patients with EV and HPeV infection. The aim of this study is to evaluate the performance of the GeneXpert enterovirus assay (GXEA) for detection of EV RNA compared to a user-developed reverse-transcriptase (RT) quantitative real-time PCR (qPCR) in routine clinical practice. Also a RT-qPCR assay for detection of HPeV RNA in different clinical samples was developed and evaluated. Cerebrospinal fluid (CSF) from 232 patients suspected for meningitis was collected and tested for EV and HPeV using RT-qPCR assays. In parallel an aliquot of the samples was tested using the GXEA and viral culture. EV RNA was detected in 22 (19.0%) and 28 (24.1%) of 116 samples using the GXEA and RT-qPCR assay, respectively. EV was isolated from 10 of 116 (8.6%) samples by viral culture. GXEA had a sensitivity, specificity, positive predictive value and negative predictive value of 82.1%, 100%, 100% and 96.2%, respectively. In this study, molecular assays were superior to viral culture for detecting EV RNA in CSF. GXEA showed a high specificity but a lower sensitivity for the detection of EV RNA compared to the RT-qPCR assay.

Rapid virological diagnosis of central nervous system infections by use of a multiplex reverse transcription-PCR DNA microarray

Viruses are the main etiological cause of central nervous system (CNS) infections. A rapid molecular diagnosis is recommended to improve the therapeutic management of patients. The aim of this study was to evaluate the performances of a DNA microarray, the Clart Entherpex kit (Genomica, Coslada, Spain), allowing the rapid and simultaneous detection of 9 DNA and RNA neurotropic viruses: herpes simplex virus 1 (HSV-1), HSV-2, varicella-zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6), HHV-7, HHV-8, and the human enteroviruses (HEVs). This evaluation was performed with 28 samples from the European proficiency panels (Quality Control for Molecular Diagnostics [QCMD]; Glasgow, Scotland) and then with 78 cerebrospinal fluid (CSF) specimens. The majority of the QCMD results obtained by the DNA microarray were similar to those recorded by the overall QCMD participants. The main discrepant results were observed for low concentrations of HSV-2 and HEVs. From the clinical samples, the kit detected 27 of the 28 herpesvirus CNS infections and all of the 30 HEV-positive CSF samples. No false-positive result was observed among the 20 virus-negative CSF samples. The clinical sensitivity, specificity, and negative and positive predictive values of the assay were 98.3, 100, 95.2, and 100%, respectively, when the results were compared to those of commercially available PCR assays. Interestingly, HHV-7 was detected in 11 (37%) of the 30 HEV-positive CSF samples from children suffering from aseptic meningitis causing significantly longer lengths of stay at the hospital than infection with HEVs alone (2.4 versus 1.4 days; P = 0.038). In conclusion, this preliminary study showed that this DNA microarray could be a valuable molecular diagnostic tool for single and mixed DNA and RNA virus infections of the CNS.

Influence of sexual intercourse on genital tract microbiota in infertile couples

Several studies have suggested the association of disturbed genital tract microbiota with infertility. Our aim was to clarify the influence of sexual intercourse on partner's genital tract microbiota in infertile couples. Seventeen couples were studied, and in 5 men inflammatory prostatitis (IP) was diagnosed. Semen samples were collected during menstruation of the female counterpart, two self-collected vaginal samples were taken 3-5 days later - before intercourse and 8-12 h after intercourse. Ureaplasma parvum was found in 59% of women, its prevalence was higher in women whose partner had IP, as well as in half of their male partners. Sexual intercourse caused significant shifts in vaginal microbiota - increase of Nugent score and shifts in cultured microbiota (emergence and disappearance of several species). These changes were less expressed in the presence of normal vaginal microbiota but more prominent in the partners of IP men. These changes may interfere with fertilization.

Parechovirus typing in clinical specimens by nested or semi-nested PCR coupled with sequencing

BACKGROUND

The Parechovirus genus (Picornaviridae) contains two known species, Human parechovirus (HPeV) and Ljungan virus (LV). HPeVs cause a wide spectrum of disease, including meningitis, gastroenteritis, encephalitis, respiratory illness, and neonatal sepsis-like disease. LVs are associated with diabetes and myocarditis in bank voles and have been proposed to cause disease in humans. The ability to rapidly and accurately type parechoviruses is critical to understanding their role in human disease.

OBJECTIVES

For parechovirus molecular typing, we sought to develop reverse transcription, nested polymerase chain reaction (RT-PCR) assays to amplify the sequence encoding the VP1 capsid protein from all known members of the Parechovirus genus.

STUDY DESIGN

The assays consist of a two-step RT-PCR with primers flanking VP1 (PCR1), followed by semi-nested PCR2A and PCR2B reactions that produce overlapping amplicons, encompassing the complete VP1 gene, as well as a nested PCR2C that amplifies a shorter internal VP1 amplicon.

RESULTS

All primer sets are 100% sensitive and 100% specific for the 77 parechovirus culture isolates tested. The semi-nested and nested PCR primer sets are 94% sensitive and 100% specific for detection of parechovirus in original specimens. Viral genotype can be deduced from analysis of amplicon sequences. Parechoviruses of the same type share>or=77% complete VP1 nucleotide sequence identity or >or=87% amino acid identity, while those of different types share<or=73% nucleotide identity and <or=81% amino acid identity.

CONCLUSIONS

The PCR primers described here amplify VP1 sequences from all known parechoviruses, providing a sensitive, reliable system for molecular typing directly from original clinical specimens.

MPprimer: a program for reliable multiplex PCR primer design

BACKGROUND

Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in diagnostic applications of clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons with similar electrophoretic mobility.

RESULTS

A program named MPprimer was developed to help users for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR assay. In addition, MPprimer provides a virtual electrophotogram to help users choose the best PSC. The experimental validation from 2x to 5x plex PCR demonstrates the reliability of MPprimer. As another example, MPprimer is able to design the multiplex PCR primers for DMD (dystrophin gene which caused Duchenne Muscular Dystrophy), which has 79 exons, for 20x, 20x, 20x, 14x, and 5x plex PCR reactions in five tubes to detect underlying exon deletions.

CONCLUSIONS

MPprimer is a valuable tool for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex PCR assays.

Diagnostic microbiologique : du diagnostic par étiologie au diagnostic par syndrome

Objectifs

Depuis les dix dernières années, l’introduction de la biologie moléculaire et l’automatisation ont radicalement changé les pratiques dans les laboratoires de microbiologie clinique. L’amélioration de la communication entre les microbiologistes et les cliniciens ainsi que les évolutions technologiques telles que la standardisation et le développement de tests diagnostics plus rapides ont conduit à une réorganisation des laboratoires de microbiologie.

Méthodes

Jusqu’à présent la prescription des examens ciblait un diagnostic étiologique précis, actuellement l’évolution se fait vers le diagnostic par syndrome incluant un panel de tests regroupant les étiologies responsables d’un syndrome donné y compris les pathogènes émergents.

Résultats et conclusions

Dans cette revue, nous avons résumé les développements technologiques les plus récents en matière de diagnostic microbiologique adapté au diagnostic par syndrome incluant les stratégies de diagnostic exhaustif, les DNA microarray et les microarray antigéniques.