Molecular approaches to detecting herpes simplex virus and enteroviruses in the central nervous system

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

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

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

Central Nervous System Infections

This chapter provides an overview of infectious syndromes, pathogens, and diagnostic testing modalities for central nervous system infections in the immunocompromised host.

Clinical and Laboratory Findings That Differentiate Herpes Simplex Virus Central Nervous System Disease from Enteroviral Meningitis

Background. It can be difficult for clinicians to distinguish between the relatively benign enteroviral (EnV) meningitis and potentially lethal herpes simplex virus (HSV) central nervous system (CNS) disease. Very limited evidence currently exists to guide them. Objective. This study sought to identify clinical features and cerebrospinal fluid (CSF) findings associated with HSV CNS disease. Methods. Given that PCR testing often is not immediately available, this chart review study sought to identify clinical and cerebrospinal fluid (CSF) findings associated with HSV meningitis over a 6-year period. In cases where PCR was not performed, HSV and EnV were assigned based on clinical criteria. Results. We enrolled 166 consecutive patients: 40 HSV and 126 EnV patients. HSV patients had a mean 40.4 versus 31.3 years for EnV, p = 0.005, seizures 21.1% versus 1.6% for EnV, p < 0.001, altered mental status 46.2% versus 3.2% for EnV, p < 0.001, or neurological deficits 44.7% versus 3.9% for EnV, p < 0.001. CSF neutrophils were lower in HSV (median 3.0% versus 9.5%, p = 0.0002); median lymphocytes (87.0% versus 67.0%, p = 0.0004) and protein (0.9 g/L versus 0.6 g/L, p = 0.0005) were elevated. Conclusion. Our study found that HSV patients were older and more likely to have seizure, altered mental status, or neurological deficits than patients with benign EnV meningitis. HSV cases had lower CSF neutrophils, higher lymphocytes, and higher protein levels.

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.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past two decades due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, have benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods has lagged somewhat behind. The purpose of this chapter is to review and discuss the interpretation and relevance of results produced by these advanced molecular techniques. Moreover, this chapter will address the “myths” of NAATs, as these myths can markedly influence the interpretation and relevance of these results.

Surrogate markers of infection: interrogation of the immune system

Infectious diseases remain the greatest causes of morbidity and mortality in global terms. As much of the burden occurs in the developing world, limited access to diagnostic testing has hampered the diagnosis and treatment of these conditions, while, in the developed world, the cost of managing infectious diseases remains considerable. Despite the size of the problem there remains an ongoing need for tests that improve diagnostic sensitivity and specificity, provide more rapid diagnoses, are available for point-of-care testing in remote regions, and can help inform therapeutic decision-making by identifying resistance patterns or patient outcomes. This article discusses the background to biomarker development for infectious diseases, some current assays that are providing useful information regarding the host's response to infection (using examples such as Cytomegalovirus and Mycobacterium tuberculosis), as well as likely future technologies and their limitations.

Evaluation of pre-analytical variables in the quantification of dengue virus by real-time polymerase chain reaction

An accurate molecular diagnosis for viral pathogens is highly dependent on pre-analytical procedures. The efficiencies of two viral RNA extraction methods (liquid phase partition and silica-based adsorption chromatography) and the effects of handling and storage on the stability of RNA isolated from dengue virus (DENV) were studied. Viral RNA extracted from spiked sera or clinical samples characterized with DENV infection were quantified by TaqMan real-time PCR. The presence of high serum proteins severely affected the recovery of DENV RNA by the liquid phase partition, but not the silica-based method. The recovery with Trizol liquid phase partition method was significantly improved by a concomitant addition of a co-precipitant and the reduction of sera proteins, resulting in recoveries similar to that of the silica-based methods. Repeated freeze-thaw cycles did not affect the recovery of viral RNA. While intact DENV was found to be stable in serum for up to 2 hour at 25 degrees C, recovery of viral RNA from sera stored in the lysis/binding buffer was stable for up to 5 days. These data indicate that the choice of viral RNA extraction methods, the conditions for handling, and storing of clinical sera critically affect the quantification of viral nucleic acid from clinical samples. This will impact the accuracy and reproducibility of DENV diagnosis by PCR-based assays.

Prevalence and management of invalid GeneXpert enterovirus results obtained with cerebrospinal fluid samples: a 2-year study

A total of 525 cerebrospinal fluid (CSF) samples submitted during the 2007 and 2008 enteroviral seasons were included in a study to determine the prevalence of and potential risk factors for invalid Cepheid GeneXpert enterovirus assay (GXEA) results, as well as possible solutions for the problem. The invalid GXEA results were reported for 43 (8.2%) specimens and correlated with increased visibility of red blood cells (P < 0.0001) but not with CSF xanthochromia and clotting. Invalid GXEA result rates were markedly diminished by 82.1% and 96.0% and test sensitivities were minimally decreased by 1.7% and 3.6% when these specimens were tested at a 1:5 dilution and after a freeze-thaw cycle, respectively.

Qualitative and quantitative detection of Chlamydophila pneumoniae DNA in cerebrospinal fluid from multiple sclerosis patients and controls

A standardized molecular test for the detection of Chlamydophila pneumoniae DNA in cerebrospinal fluid (CSF) would assist the further assessment of the association of C. pneumoniae with multiple sclerosis (MS). We developed and validated a qualitative colorimetric microtiter plate-based PCR assay (PCR-EIA) and a real-time quantitative PCR assay (TaqMan) for detection of C. pneumoniae DNA in CSF specimens from MS patients and controls. Compared to a touchdown nested-PCR assay, the sensitivity, specificity, and concordance of the PCR-EIA assay were 88.5%, 93.2%, and 90.5%, respectively, on a total of 137 CSF specimens. PCR-EIA presented a significantly higher sensitivity in MS patients (p = 0.008) and a higher specificity in other neurological diseases (p = 0.018). Test reproducibility of the PCR-EIA assay was statistically related to the volumes of extract DNA included in the test (p = 0.033); a high volume, which was equivalent to 100 µl of CSF per reaction, yielded a concordance of 96.8% between two medical technologists running the test at different times. The TaqMan quantitative PCR assay detected 26 of 63 (41.3%) of positive CSF specimens that tested positive by both PCR-EIA and nested-PCR qualitative assays. None of the CSF specimens that were negative by the two qualitative PCR methods were detected by the TaqMan quantitative PCR. The PCR-EIA assay detected a minimum of 25 copies/ml C. pneumoniae DNA in plasmid-spiked CSF, which was at least 10 times more sensitive than TaqMan. These data indicated that the PCR-EIA assay possessed a sensitivity that was equal to the nested-PCR procedures for the detection of C. pneumoniae DNA in CSF. The TaqMan system may not be sensitive enough for diagnostic purposes due to the low C. pneumoniae copies existing in the majority of CSF specimens from MS patients.

Meningitis

* Young infants who have meningitis may present with nonspecific clinical manifestations. * S. pneumoniae and N. meningitidis remain the most common causes of bacterial meningitis in the infant and child, and GBS continues to be the most common neonatal pathogen. * Empiric therapy for suspected bacterial meningitis in a non-neonate includes a combination of parenteral vancomycin and either cefotaxime or ceftriaxone. * Children whose GCS scores are less than 8, show signs of shock or respiratory compromise, and have focal neurologic findings or clinical signs of elevated intracranial pressure should be admitted to a pediatric intensive care unit. * Sensorineural hearing loss occurs in 30% of children who have pneumococcal and 10% of those who have meningococcal meningitis.

LOMA: a fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens

BACKGROUND

Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals.

RESULTS

In this paper, we study how the efficiency of random PCR amplification affects hybridization signals. We describe a model that predicts the amplification efficiency of a given random primer on a target viral genome. The prediction allows us to filter false-negative probes of the genome that lie in regions of poor random PCR amplification and improves the accuracy of pathogen detection. Subsequently, we propose LOMA, an algorithm to generate random primers that have good amplification efficiency. Wet-lab validation showed that the generated random primers improve the amplification efficiency significantly.

CONCLUSION

The blind use of a random primer with attached universal tag (random-tagged primer) in a PCR reaction on a pathogen sample may not lead to a successful amplification. Thus, the design of random-tagged primers is an important consideration when performing PCR.

Optimization and clinical validation of a pathogen detection microarray

New design and optimization of pathogen detection microarrays is shown to allow robust and accurate detection of a range of pathogens. The customized microarray platform includes a method for reducing PCR bias during DNA amplification.

DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.

[The microbiology laboratory: a key participant in transplantation]

Together with organ rejection, infectious complications are still the most important cause of morbidity and mortality in organ transplant recipients. Many infectious complications have an exogenous origin, including those produced by organ-transmitted pathogens, whereas others are caused by latent microorganisms that become reactivated in the recipient. Accurate pre-transplantation assessment of the organ donor as well as the recipient can prevent some infectious complications or reduce their detrimental effects during the post-transplant period. A wide range of primary and opportunistic microorganisms can affect transplant recipients, and a detailed description of these pathogens is beyond the scope of this study. However, the importance of microbiology laboratories in centers with transplant programs and the need for integration and active participation of clinical microbiologists in multidisciplinary transplant teams should be emphasized. The work of these professionals is a key requisite to establish accurate diagnoses of infectious complications, which will benefit the patient and optimize the expenditure of resources.

Invader plus method detects herpes simplex virus in cerebrospinal fluid and simultaneously differentiates types 1 and 2

We report here on the development and validation of a prototype Invader Plus method for the qualitative detection of herpes simplex virus types 1 and 2 in cerebrospinal fluid (CSF). The method combines PCR and Invader techniques in a single, closed-tube, continuous-reaction format that gives an analytical sensitivity of approximately 10 copies per reaction. The clinical sensitivity and specificity were 100.0% and 98.6%, respectively, when the results of the method were validated against the results obtained with a PCR colorimetric microtiter plate system by use of clinical CSF specimens.

QIAamp MinElute virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs

Background

Nucleic acid preparation from a variety of clinical specimens requires efficient target recovery and amplification inhibitor removal and is critical for successful molecular diagnosis. The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids.

Study design

A total of 150 clinical specimens, including cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS), were used to determine the extraction efficiency of the MinElute compared to the other two methods. Nucleic acid recovery, hands-on time, turn-around-time and cost were compared across all kits.

Results

There was complete concordance between the MinElute and IsoQuick/RNAzol kits when herpes simplex virus (HSV), Epstein–Barr virus (EBV), varicella-zoster virus (VZV), influenza A virus or enteroviruses were detected using a colorimetric microtiter plate PCR system. The kits were equivalent in their ability to detect either DNA or RNA with superior ability to recover a high quality and quantity of RNA. With the potential to process larger specimen volumes, the MinElute kit can significantly shorten processing time from 2 h to 50–55 min.

Conclusions

Although relatively high test kit costs were noted, the MinElute kit provides another rapid and user-friendly specimen processing tool in the diagnostic molecular microbiology laboratory.

Defining bacterial meningitis and other infections of the central nervous system

OBJECTIVE

To define central nervous system infections of infants and children that occur as co-morbid or predisposing conditions of sepsis.

DESIGN

Standard pediatric infectious disease references and the pertinent literature in English were reviewed from 1960 to 2002 to ascertain the previous methods and definitions utilized in clinical studies of the epidemiology and treatment of bacterial infections of the central nervous system. An accepted definition of bacterial meningitis defined by the Infectious Disease Society of America was reviewed and adapted to the previous clinical definitions. The information was formulated into a proposed standard for definite, probable, and possible bacterial infections of the central nervous system.

RESULTS

The diagnosis of definite bacterial infection of the central nervous system, including bacterial meningitis, requires the isolation of the pathogen from the cerebrospinal fluid or other significant clinical site such as surgical tissue, an implanted device, or blood. Probable bacterial infection is defined by the association of a compatible clinical syndrome or cerebrospinal fluid changes associated with bacterial meningitis or other central nervous system infection, and confirmed as an anatomically defined infection by imaging or surgery, in association with positive blood cultures or bacterial antigen from cerebrospinal fluid. Possible bacterial meningitis may be defined as a compatible clinical syndrome with predefined cerebrospinal fluid changes in the absence of a confirmatory culture or antigen test from any site.

CONCLUSIONS

Bacterial meningitis and other central nervous system bacterial infections can be defined as definite, probable, and possible with a combination of a defining compatible clinical syndrome and an anatomic definition by surgery or imaging, coupled with isolation of the organism, bacterial antigen, or other defining molecular component of the organism.

Antenatal diagnosis of intrauterine infection with coxsackievirus B3 associated with live birth

BACKGROUND: Prior reported cases of stillbirth and neonates infected with enteroviruses suggest transplacental infection. We present a case of fetal infection with coxsackievirus B3, diagnosed antenatally and resulting in live birth. CASE: A pregnant woman presented at 26 weeks with fetal tachycardia and non-immune hydrops fetalis. Coxsackievirus B3 was cultured from amniotic fluid. Maternal antibody to coxsackievirus B3 was positive at 1:512. At 32 weeks, the fetus deteriorated and was delivered. Cord blood antibody to coxsackievirus B3 was positive at a higher titer. Following neonatal death, brain and placental tissues were positive for enterovirus ribonucleic acid by polymerase chain reaction. CONCLUSION: Intrauterine infection by enteroviruses should be considered in the differential diagnosis of non-immune hydrops fetalis. Antenatal diagnosis of coxsackievirus B3 infection is associated with poor outcome.

PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings

Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.

New reverse transcription-PCR assay for rapid and sensitive detection of enterovirus genomes in cerebrospinal fluid specimens of patients with aseptic meningitis

Enterovirus (EV) detection by a new commercially available reverse transcription (RT)-PCR assay (Penter RT-PCR test) was compared with EV isolation from cell cultures and with EV detection by an in-house RT-PCR assay. Of the 54 cerebrospinal fluid specimens collected during a summer outbreak of aseptic meningitis, 52% were positive by cell culture versus 76% by in-house RT-PCR assay and 80% by the new RT-PCR test (52 versus 76 versus 80%; P = 0.003). This new reliable EV RNA detection test is suitable for clinical diagnosis of EV-related meningitis and may improve the management of EV-related neurological syndromes.