Diagnosis of viral infections of the central nervous system: clinical interpretation of PCR results

Neurodevelopmental Outcomes Following Childhood Viral Meningitis in Canterbury New Zealand

BACKGROUND

Most childhood meningitis is viral in countries with widespread conjugate vaccine use. This study assessed clinical features and neurodevelopmental outcomes in preschool children following enteroviral and parechoviral meningitis.

METHODS

Children 18-42 months of age in Canterbury, New Zealand were included, who had enterovirus (EV) or parechovirus (HPEV) meningitis from 2015 to 2021. Comprehensive neurodevelopmental assessments were completed by a psychologist using the Bayley Scale for Infant Development-3 (BSID-3). Mean composite and scaled scores and proportion below the cutoff were assessed in each domain. Clinical data was analyzed.

RESULTS

There were 79 children 18-42 months old with previous EV or HPEV meningitis. BSID assessments were completed for 33 children (55% male), median age 32 months, from 2019 to 2022 including 23 with EV and 10 HPEV meningitis. At diagnosis, 32 (97%) received intravenous/intramuscular antibiotics, and 6 received a fluid bolus. Parents reported developmental speech concerns in 6 children, and delayed motor milestones in 1 child. There was no reported sensorineural hearing loss. BSID mean composite scores were in the expected range for cognition 102 (confidence interval: 98-106), language 96 (93-100) and motor 102 (98-106) domains. Overall, 12/33 (36%) children had below expected scores in 1 developmental domain, including scores 1-2 SD below the normative mean for cognition (2/33; 6%), receptive language (6/33; 18%), expressive language (5/33; 15%) and gross motor (6/33; 18%). There were no differences between scores in EV and HPEV meningitis.

CONCLUSION

Following viral meningitis, more than a third of preschool children had a mild developmental delay with comprehensive neurodevelopmental assessment, suggesting targeted follow-up should be considered.

The clinical utility of metagenomic next-generation sequencing for the diagnosis of central nervous system infectious diseases

BACKGROUND

To evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of central nervous system infections (CNSI).

METHODS

Cerebrospinal fluid (CSF) from 54 patients who were high-level clinical suspicion of CNSI was collected and sent for mNGS and conventional tests from January 2019 to March 2022.

RESULTS

Twenty out of 54 patients were diagnosed with CNSI and 34 non-CNSI. Among the 34 non-CNSI, one was false positive by mNGS. Among the 20 CNSI, 11 had presumed viral encephalitis and/or meningitis, 5 had presumed bacterial meningitis, 2 had presumed TMB, 1 had Crytococcus meningitis and 1 had neurosyphilis. The sensitivity of viral encephalitis and/or meningitis was 0.73 (8/11); 10 virus were detected; 9/10 was dsDNA; 1/10 was ssRNA. SSRN ranged from 1 to 13. The accuracy rate was 0.4, the accuracy rate was positively correlated with SSRN (r = 0.738, P = 0.015), SSRN ≥ 1, the accuracy rate was 0.4; SSRN ≥ 3, the accuracy rate was 0.66; SSRN ≥ 4, the accuracy rate was 0.75; SSRN ≥ 6, the accuracy rate was 1. The sensitivity of bacterial meningitis was 1. Seven kinds of bacteria were detected, among which 3/7 were gram positive, 3/7 were gram negative, and 1/7 was infected NTM (nontuberculous mycobacteria). The accuracy rate was 0.43 (3/7). The sensitivity of TBM was 0.66 (2/3), the accuracy rate was 1. The sensitivity of Crytococcus meningitis was 1, the accuracy rate was 0.5. PPV (positive predictive value) of mNGS was 0.94, NPV (negative predictive value) of mNGS was 0.89, specificity was 0.97 and sensitivity was 0.8. The AUG for CSF mNGS diagnosis of CNSI was 0.89 (95% CI = 0.78-0.99) Headache, meningeal irritation sign and image of meninges abnormal were correlated with the sensitivity of mNGS (r = 0.451, 0.313, 0.446; p = 0.001, 0.021, 0.001); CSF Glucose and CSF Chloride were negatively correlated with sensitivity of mNGS (r = -0.395, -0.462; p = 0.003, ＜ 0.001).

CONCLUSION

mNGS is a detection means with high sensitivity, wide coverage and strong timeliness, which can help clinicians to identify the pathogen diagnosis quickly, conduct targeted anti-infection treatment early and reduce antibiotic abuse. The pathogen which causing low CSF Glucose, low CSF Chloride or meninges infections was more likely to be detected by mNGS. It may be related to growth and structural characteristics of the pathogen and blood-brain barrier damage.

Recent Advances in Molecular and Immunological Diagnostic Platform for Virus Detection: A Review

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing coronavirus disease (COVID-19) outbreak and a rising demand for the development of accurate, timely, and cost-effective diagnostic tests for SARS-CoV-2 as well as other viral infections in general. Currently, traditional virus screening methods such as plate culturing and real-time PCR are considered the gold standard with accurate and sensitive results. However, these methods still require sophisticated equipment, trained personnel, and a long analysis time. Alternatively, with the integration of microfluidic and biosensor technologies, microfluidic-based biosensors offer the ability to perform sample preparation and simultaneous detection of many analyses in one platform. High sensitivity, accuracy, portability, low cost, high throughput, and real-time detection can be achieved using a single platform. This review presents recent advances in microfluidic-based biosensors from many works to demonstrate the advantages of merging the two technologies for sensing viruses. Different platforms for virus detection are classified into two main sections: immunoassays and molecular assays. Moreover, available commercial sensing tests are analyzed.

The epidemiology of aseptic meningitis in New Zealand children from 1991 to 2020

AIM

Aseptic meningitis, including culture negative and viral meningitis, contributes a significant health-care burden, including unnecessary antibiotic use and hospitalisation to treat possible bacterial meningitis. This study analysed aseptic meningitis hospitalisations in New Zealand (NZ) children over 29 years.

METHODS

In this population-based study, aseptic meningitis hospitalisations in NZ children <15 years old were analysed from 1991 to 2020. Incident rate ratios were calculated using Poisson regression models. Variations in hospitalisations by age, year, sex, ethnicity, geographical region and socio-economic deprivation were analysed.

RESULTS

There were 5142 paediatric aseptic meningitis hospitalisations from 1991 to 2020. Most were unspecified viral meningitis (64%), followed by enterovirus (29%). Hospitalisation rates varied annually with a median of 18.4/100 000 children including a peak in 2001 of 56.4/100 000 (51.7-61.6). From 2002 to 2019, rates increased by 8.4%/year (7.2-9.5%) in infants <90 days old but decreased in all other age groups. In 2020, a reduction in hospitalisations to 9.6/100 000 (7.9-11.8) occurred, and in infants <90 days old were 0.37 times expected. Hospitalisations were 1.50 times (1.49-1.68) higher in males than females; higher in children of Māori (P < 0.001) and Pacific (P < 0.001) versus European ethnicity; and higher for children living in the most (2.44 times, (2.16-2.75)) versus least deprived households; and in northern versus southern NZ.

CONCLUSIONS

Aseptic meningitis hospitalisations increased in young infants during 29 years of surveillance, apart from 2020 when admissions reduced during the COVID-19 pandemic. In contrast, hospitalisations decreased in children aged >1 year. Further investigation into reasons for higher admissions by ethnic group, geographical location and increased deprivation are required.

Inconsistency analysis between metagenomic next-generation sequencing results of cerebrospinal fluid and clinical diagnosis with suspected central nervous system infection

Background

Recently, with the rapid progress of metagenomic next-generation sequencing (mNGS), inconsistency between mNGS results and clinical diagnoses has become more common. There is currently no reasonable explanation for this, and the interpretation of mNGS reports still needs to be standardised.

Methods

A retrospective analysis was conducted on 47 inpatients with suspected central nervous system (CNS) infections, and clinical data were recorded. The final diagnosis was determined by an expert group based on the patient’s clinical manifestation, laboratory examination, and response to treatment. mNGS results were compared with the final diagnosis, and any inconsistencies that occurred were investigated. Finally, the credibility of mNGS results was evaluated using the integral approach, which consists of three parts: typical clinical features, positive results with the traditional method, and cerebrospinal fluid cells ≥ 100 (× 10⁶/L) or protein ≥ 500 mg/L, with one point for each item.

Results

Forty-one patients with suspected CNS infection were assigned to infected (ID, 31/41, 75.61%) and non-infected groups (NID, 10/41, 24.39%) after assessment by a panel of experts according to the composite diagnostic criteria. For mNGS-positive results, 20 of the 24 pathogens were regarded as contaminants when the final score was ≤ 1. The remaining 11 pathogens detected by mNGS were all true positives, which was consistent with the clinical diagnosis when the score was ≥ 2. For mNGS negative results, when the score was ≥ 2, the likelihood of infection may be greater than when the score is ≤ 1.

Conclusion

The integral method is effective for evaluating mNGS results. Regardless of whether the mNGS result was positive or negative, the possibility of infection was greater when the score was ≥ 2. A negative mNGS result does not necessarily indicate that the patient was not clinically infected, and, therefore, clinical features are more important.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07729-0.

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

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

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

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

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

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

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

Trial Registration: Chinese Clinical Trial Registry, ChiCTR1800020442.

Congenital viral infections in England over five decades: a population-based observational study

BACKGROUND

Congenital viral infections cause substantial long-term morbidity but population-based data about diagnosis rates are scarce. The aim of this study was to assess the long-term trends in congenital viral infections in England and to report on how the rates of these infections might have changed with improved methods for detection, the introduction of the two-dose measles-mumps-rubella (MMR) vaccine in 1996, and the implementation of the Newborn Hearing Screening Programme (NHSP) in 2006.

METHODS

For this population-based, observational cohort study, we used national and regional hospitalisation data from 1968 to 2016 in England (Hospital In-Patient Enquiry, Hospital Episode Statistics, and Oxford Record Linkage Study) to calculate annual rates of hospital discharges coded with-and individuals aged younger than 1 month diagnosed with-congenital cytomegalovirus, herpes simplex virus (HSV), varicella zoster virus (VZV), and rubella. We investigated associations of congenital cytomegalovirus, HSV, and VZV with perinatal and maternal factors (sex, mother's ethnicity, mode of delivery, gestational age, birthweight, mother's age, mother's index of multiple deprivation, and number of previous pregnancies).

FINDINGS

In 2016, discharge rates per 100 000 infant population were 22·3 (95% CI 18·8-26·1) for congenital cytomegalovirus, 17·6 (14·6-21·1) for HSV, 32·6 (28·4-37·2) for VZV, and 0·15 (0·0-0·8) for rubella. Compared with earlier years of the study, the discharge rate in 2016 was higher for congenital cytomegalovirus, HSV, and VZV, whereas it was lower for rubella. For congenital cytomegalovirus, there was a significant step-increase between 2006 and 2007 following implementation of the NHSP (rate ratio comparing the trend line post-NHSP with that pre-NHSP 1·55 [95% CI 1·12-2·14], p=0·0072). Congenital cytomegalovirus infection was associated with birthweight less than 1 kg, maternal age younger than 25 years, socioeconomically deprived households, casearean section, and mothers of black ethnicity. Congenital HSV infection was associated with maternal age younger than 20 years, gestational age less than 32 weeks, and vaginal and emergency caesarean section deliveries, while VZV infection was associated with increased parity and black and south Asian ethnicities.

INTERPRETATION

The increase in hospital discharges coded with congenital cytomegalovirus is most likely due to the introduction of sensitive diagnostic techniques and retrospective diagnoses made in infants after implementation of the NHSP. Public health strategies to improve prevention and treatment of congenital viral infections are urgently warranted. The decrease in discharges for rubella is most likely due to the MMR vaccine.

FUNDING

None.

Prevalence of herpes simplex virus-1 in hospitalized adult patients with clinical diagnosis of meningoencephalitis using real-time polymerase chain reaction: A single-center, cross-sectional study

Background

Early diagnosis of herpes simplex virus-1 (HSV-1) meningoencephalitis is very important because antiviral therapy significantly decreases mortality and morbidity. Polymerase chain reaction (PCR) is a reliable method with high sensitivity and specificity in detection of HSV-1. The aim of this study is to determine the prevalence of HSV-1 in patients with diagnosis of meningoencephalitis using real-time PCR.

Materials and Methods

The cerebrospinal fluid samples were collected from 126 patients with clinical diagnosis of HSV-1 meningoencephalitis in Alzahra Referral Hospital in Isfahan, Iran. After deoxyribonucleic acid (DNA) extraction, real-time PCR was performed by fluorescence resonance energy transfer assay and participants underwent brain magnetic resonance imaging, as well.

Results

Among 126 patients, 68.3% were male and 31.7% were female. The mean age of the participants was 41.96 ± 22.36 years. Most of the participants were in the age group of 20-29 years. Three patients (2.4%) had positive and 123 patients (97.6%) had negative HSV-1 DNA test. Among three positive cases, two were in the age group of 20-29 years and one in the age group of ≥80 years. No HSV-2 DNA was detected.

Conclusion

According to the estimated prevalence of HSV-1 meningoencephalitis in the current study, it seems that the prevalence of HSV-1 meningoencephalitis is not too high in our community; therefore, initial empiric acyclovir therapy is frequently overused.

Clinical Correlations of Positive Herpes Simplex PCR in Cerebrospinal Fluid

OBJECTIVES

Herpes simplex viruses (HSV) can produce encephalitis (HSE), which requires early detection, typically using polymerase chain reaction (PCR) in cerebrospinal fluid (CSF). However, other neurological conditions not directly caused by HSV may also present with a positive HSV PCR in the CSF (NCNHPCR+). We aimed to analyze the clinical features of both groups of patients (HSE vs. NCNHPCR+) and to consider the potential relevance of this finding in the latter.

METHODS

A retrospective analysis of clinical presentation, workup (CSF, EEG, and MRI) and outcome of patients with an HSV+ result in CSF was conducted from Jan-2007 to Sep-2015 in our institution. Patients under 18 years and those with nonencephalitic HSV associated disorders were excluded. Group comparison between HSE and NCNHPCR+ patients was conducted using parametric and nonparametric tests accordingly.

RESULTS

Sixteen HSE and 23 NCNHPCR+ patients were included. Patients with HSE presented a higher incidence of headache (87.5% vs. 43.5%; P=0.008), meningeal symptoms (50% vs. 17.4%; P=0.04), pleocytosis (75% vs. 18%; P=0.001), EEG abnormalities (46.67% vs. 22%; P=0.02) and typical MRI findings (50% vs. 0%; P<0.001), whereas 35% of patients with NCNHPCR+ had an underlying immunologic disorder (35% vs. 0%; P=0.012).

CONCLUSIONS

The pathogenic role of HSV in NCNHPCR+ is uncertain. This finding must be interpreted in the appropriate clinical, EEG, and neuroimaging context. Immunocompromise and neuroinflammation states could be related to a higher presence of HSV in CSF.

Emergency Department Approach to the Patient with Suspected Central Nervous System Infection

Central nervous system (CNS) infections require early recognition and aggressive management to improve patient survival and prevent long-term neurologic sequelae. Although early detection and treatment are important in many infectious syndromes, CNS infections pose unique diagnostic and therapeutic challenges. The nonspecific signs and symptoms at presentation, lack of characteristic infectious changes in laboratory and imaging diagnostics, and closed anatomic and immunologically sequestered space each present challenges to the emergency physician. This article proposes an approach to the clinical evaluation of patients with suspected CNS infection and highlights methods of diagnosis, treatment, and complications associated with CNS infections.

Acute recurrent lymphocytic meningitis in an immunocompetent HIV-positive African woman: Is it a Mollaret's meningitis or not?

We report a case of acute recurrent meningitis in an HIV-positive immunocompetent woman. In this case, a 34-year-old African woman with a known HIV infection presented with symptoms of acute meningitis. She was on combination antiretroviral therapy with abacavir, lamivudine, and nevirapine. Her HIV RNA level was <70 IU/mL, and CD4 counts were 640 cells/mm³. This indicates that she was not immunocompromised. She was febrile on examination, with marked neck stiffness. Her cerebrospinal fluid revealed raised white cell counts with 100% lymphocytes and mildly raised protein. Polymerase chain reaction confirmed herpes simplex type 2 meningitis. She recovered fully with aciclovir 800 mg three times a day. However, she was readmitted with a similar presentation 5 months after the initial admission. Her cerebrospinal fluid confirmed recurrent herpes simplex type 2 meningitis. This case alerts the profession to the possibility of non-opportunistic infections in an immunocompetent HIV-positive patient and of herpes simplex virus type 2 causing recurrent lymphocytic meningitis.

Detection of Toscana virus from an adult traveler returning to Australia with encephalitis

Toscana virus (TOSV) is identified in sandflies, animals, and humans around the Mediterranean Sea. TOSV has not been reported in Australia. During investigations of cerebrospinal fluid samples from patients with encephalitis, TOSV genetic sequences were identified in a traveler returning to Australia from Europe. TOSV should be considered, especially during May to October, in travelers to Australia who embarked in countries in and around the Mediterranean Sea and who subsequently present for medical care because of neurological symptoms.

Elsberg syndrome: A rarely recognized cause of cauda equina syndrome and lower thoracic myelitis

Objective:

Elsberg syndrome (ES) is an established but often unrecognized cause of acute lumbosacral radiculitis with myelitis related to recent herpes virus infection. We defined ES, determined its frequency in patients with cauda equina syndrome (CES) with myelitis, and evaluated its clinical, radiologic, and microbiologic features and outcomes.

Methods:

We searched the Mayo Clinic medical records for ES and subsequently for combinations of index terms to identify patients with suspected CES and myelitis.

Results:

Our search yielded 30 patients, 2 diagnosed with ES and an additional 28 with clinical or radiologic evidence of CES retrospectively suspected of having ES. We classified patients in 5 groups according to diagnostic certainty. MRI and EMG confirmed that 2 had only myelitis, 5 only radiculitis, and 16 both. Two had preceding sacral herpes infection and 1 oral herpes simplex. Spinal cord lesions were commonly multiple, discontinuous, not expansile, and centrally or ventrally positioned. Lesions generally spared the distal conus. Nerve root enhancement was occasionally prominent and was smooth rather than nodular. Lymphocytic CSF pleocytosis was common. Thirteen patients (43%) had viral isolation studies, which were commonly delayed; the delay may have accounted for the low rate of viral detection. Acyclovir was administered to 6 patients. Most patients recovered with sequelae; 1 patient experienced encephalomyelitis and died.

Conclusion:

ES is a definable condition likely responsible for 10% of patients with combined CES and myelitis. Radiologic findings are not entirely specific but may help in differentiating ES from some competing diagnostic considerations. We propose criteria to facilitate diagnosis.

30-year trends in admission rates for encephalitis in children in England and effect of improved diagnostics and measles-mumps-rubella vaccination: a population-based observational study

BACKGROUND

Encephalitis is a serious neurological disorder, yet data on admission rates for all-cause childhood encephalitis in England are scarce. We aimed to estimate admission rates for childhood encephalitis in England over 33 years (1979-2011), to describe trends in admission rates, and to observe how these rates have varied with the introduction of vaccines and improved diagnostics.

METHODS

We did a retrospective analysis of hospital admission statistics for encephalitis for individuals aged 0-19 years using national data from the Hospital Inpatient Enquiry (HIPE, 1979-85) and Hospital Episode Statistics (HES, 1990-2011). We analysed annual age-specific and age-standardised admission rates in single calendar years and admission rate trends for specified aetiologies in relation to introduction of PCR testing and measles-mumps-rubella (MMR) vaccination. We compared admission rates between the two International Classification of Diseases (ICD) periods, ICD9 (1979-94) and ICD10 (1995-2011).

FINDINGS

We found 16 571 encephalitis hospital admissions in the period 1979-2011, with a mean hospital admission rate of 5·97 per 100 000 per year (95% CI 5·52-6·41). Hospital admission rates declined from 1979 to 1994 (ICD9; annual percentage change [APC] -3·30%; 95% CI -2·88 to -3·66; p<0·0001) and increased between 1995 and 2011 (ICD10; APC 3·30%; 2·75-3·85; p<0·0001). Admissions for measles decreased by 97% (from 0·32 to 0·009) and admissions for mumps encephalitis decreased by 98% (from 0·60 to 0·01) after the introduction of the two-dose MMR vaccine. Hospital admission rates for encephalitis of unknown aetiology have increased by 37% since the introduction of PCR testing.

INTERPRETATION

Hospital admission rates for all-cause childhood encephalitis in England are increasing. Admissions for measles and mumps encephalitis have decreased substantially. The numbers of encephalitis admissions without a specific diagnosis are increasing despite availability of PCR testing, indicating the need for strategies to improve aetiological diagnosis in children with encephalitis.

FUNDING

None.

Diagnosis of Viral Infections

Accurate diagnosis of viral infections enhances the ability of the clinician to make decisions on appropriate treatment of patients, evaluate disease progression and prevent misuse of antibiotics. Knowledge of the pathogen involved also allow implementation of infection control and monitoring of success of antiviral treatments that may affect the prognosis of patients. Epidemiological data collected through accurate diagnostics play an important role in public health through identification and control of outbreaks, implementation of appropriate diagnostic tests, vaccination programs and treatment but also to recognize common and emerging pathogens in a community. It is key that the clinician have an understanding of appropriate specimens to send to the laboratory and the value of specific nucleic acid and serological testing for different viral pathogens. Molecular techniques have revolutionized viral diagnoses over the past decade and enhanced both the sensitivity and specificity of tests and the speed by which a diagnosis can be made and new tests be developed. The continued use of serology for viruses with a short viremia, or for chronic infections should however complement these tests. This chapter aims to provide an overview of the available tests, the principles of testing and appropriate tests to select for different viruses and syndromes. Also provided is a glimpse of new developments in diagnostics that may further enhance the capacity to make a conclusive diagnosis in the near future.

The UK joint specialist societies guideline on the diagnosis and management of acute meningitis and meningococcal sepsis in immunocompetent adults

Bacterial meningitis and meningococcal sepsis are rare conditions with high case fatality rates. Early recognition and prompt treatment saves lives. In 1999 the British Infection Society produced a consensus statement for the management of immunocompetent adults with meningitis and meningococcal sepsis. Since 1999 there have been many changes. We therefore set out to produce revised guidelines which provide a standardised evidence-based approach to the management of acute community acquired meningitis and meningococcal sepsis in adults. A working party consisting of infectious diseases physicians, neurologists, acute physicians, intensivists, microbiologists, public health experts and patient group representatives was formed. Key questions were identified and the literature reviewed. All recommendations were graded and agreed upon by the working party. The guidelines, which for the first time include viral meningitis, are written in accordance with the AGREE 2 tool and recommendations graded according to the GRADE system. Main changes from the original statement include the indications for pre-hospital antibiotics, timing of the lumbar puncture and the indications for neuroimaging. The list of investigations has been updated and more emphasis is placed on molecular diagnosis. Approaches to both antibiotic and steroid therapy have been revised. Several recommendations have been given regarding the follow-up of patients.

Human herpesvirus infections of the central nervous system: laboratory diagnosis based on DNA detection by nested PCR in plasma and cerebrospinal fluid samples

Infections of the central nervous systems (CNS) present a diagnostic problem for which an accurate laboratory diagnosis is essential. Invasive practices, such as cerebral biopsy, have been replaced by obtaining a polymerase chain reaction (PCR) diagnosis using cerebral spinal fluid (CSF) as a reference method. Tests on DNA extracted from plasma are noninvasive, thus avoiding all of the collateral effects and patient risks associated with CSF collection. This study aimed to determine whether plasma can replace CSF in nested PCR analysis for the detection of CNS human herpesvirus (HHV) diseases by analysing the proportion of patients whose CSF nested PCR results were positive for CNS HHV who also had the same organism identified by plasma nested PCR. In this study, CSF DNA was used as the "gold standard," and nested PCR was performed on both types of samples. Fifty-two patients with symptoms of nervous system infection were submitted to CSF and blood collection. For the eight HHV, one positive DNA result-in plasma and/or CSF nested PCR-was considered an active HHV infection, whereas the occurrence of two or more HHVs in the same sample was considered a coinfection. HHV infections were positively detected in 27/52 (51.9%) of the CSF and in 32/52 (61.5%) of the plasma, difference not significant, thus nested PCR can be performed on plasma instead of CSF. In conclusion, this findings suggest that plasma as a useful material for the diagnosis of cases where there is any difficulty to perform a CSF puncture.

Criteria for reducing unnecessary testing for herpes simplex virus, varicella-zoster virus, cytomegalovirus, and enterovirus in cerebrospinal fluid samples from adults

Excessive utilization of laboratory diagnostic testing leads to increased health care costs. We evaluated criteria to reduce unnecessary nucleic acid amplification testing (NAAT) for viral pathogens in cerebrospinal fluid (CSF) samples from adults. This is a single-center split retrospective observational study with a screening cohort from 2008 to 2012 and a validation cohort from 2013. Adults with available results for herpes simplex virus 1/2 (HSV-1/2), varicella-zoster virus (VZV), cytomegalovirus (CMV), or enterovirus (EV) NAAT with CSF samples between 2008 and 2013 were included (n = 10,917). During this study, 1.3% (n = 140) of viral NAAT studies yielded positive results. The acceptance criteria of >10 nucleated cells/μl in the CSF of immunocompetent subjects would have reduced HSV-1/2, VZV, CMV, and EV testing by 63%, 50%, 44%, and 51%, respectively, from 2008 to 2012. When these criteria were applied to the 2013 validation data set, 54% of HSV-1/2, 57% of VZV, 35% of CMV, and 56% of EV tests would have been cancelled. No clinically significant positive tests would have been cancelled in 2013 with this approach. The introduction of a computerized order entry set was associated with increased test requests, suggesting that computerized order sets may contribute to unnecessary testing. Acceptance criteria of >10 nucleated cells/μl in the CSF of immunocompetent adults for viral CSF NAAT assays would increase clinical specificity and preserve sensitivity, resulting in significant cost savings. Implementation of these acceptance criteria led to a 46% reduction in testing during a limited follow-up period.

Detection of human herpesvirus 7 DNA from the CSF in association with neurosarcoidosis

This study reports a previously healthy, immunocompetent adult male in whom human herpesvirus 7 (HHV-7) DNA was detected continuously from the cerebrospinal fluid (CSF). This patient developed definite sarcoidosis with primary symptomatic manifestations in the central nervous system (CNS). The initial presentation was with loss of visual acuity and papilledema. Brain MR imaging at presentation confirmed papilledema, but otherwise there were no focal abnormalities or signs of hydrocephalus. CSF investigation revealed pleocytosis and elevated protein levels. HHV-7 DNA was detected repeatedly from CSF but not from blood over 1 year follow-up. High resolution computed tomography of lungs was normal. Positron emission tomography showed several metabolically active lymph nodes in the mediastinum, and the histopathological investigation revealed granulomatous inflammation consistent with sarcoidosis. The finding of HHV-7 DNA in the CSF in the context of neurosarcoidosis has not been reported previously. The detection of HHV-7 DNA may result from the selective activation of CD4+ T-lymphocytes in the CSF caused by neurosarcoidosis. Further studies are needed to establish whether the detection of HHV-7 DNA in the CSF in association with neurosarcoidosis represents a clinically significant HHV-7 CNS infection.

Maternal and perinatal factors associated with subsequent meningococcal, Haemophilus or enteroviral meningitis in children: database study

We used a database of 248 659 births, with follow-up to subsequent disease, in the Oxford record linkage archive (1979-1999) to study the influence of family, maternal, and perinatal factors on subsequent hospital admission for meningococcal, Haemophilus, and enteroviral meningitis in the children. In this summary, we report key findings that were significant in multivariate analysis. Meningococcal meningitis was significantly associated with maternal smoking [odds ratio (OR) 2·1, 95% confidence interval (CI) 1·2-3·7]. Haemophilus meningitis was associated with having older siblings (e.g. second child compared to first-born, OR 3·3, 95% CI 2·0-5·6). Enteroviral meningitis was associated with low birth weight (OR 2·2, 95% CI 1·3-3·6) and male sex (OR 1·7, 95% CI 1·2-2·3). The mothers of six of the 312 children with enteroviral meningitis had previously had enteroviral meningitis themselves. We concluded that several maternal characteristics influence the risk of these types of meningitis.

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.

Influenza A 2009 H1N1 encephalitis in adults with viral RNA in cerebrospinal fluid

We present 3 cases of influenza A 2009 H1N1 encephalitis occurring in adults, corroborated by viral genome detection in cerebrospinal fluid (CSF) and evidence of meningeal inflammation on brain histopathology. This paper emphasizes the possibility of viral detection in CSF and stresses the lack of an effective treatment for neurological manifestations of influenza.

How appropriate are cerebrospinal fluid polymerase chain reaction requests for suspected central nervous system infections?

Cerebrospinal fluid (CSF) polymerase chain reaction (PCR) assays have become the main diagnostic tests for central nervous system viral infections in recent years. Previous studies have suggested algorithms based on CSF leukocyte count and total protein levels to determine when CSF PCR assays are indicated. Based on these criteria, 1,469 CSF PCR tests requested over a two-year period were reviewed. A proportion of positive PCR results were found in children with normal CSF, unlike in adults where such occurrences were extremely rare. The results suggest that applying a strategy of screening CSF specimens using leukocyte count, glucose and protein, at least in adults, may have avoided more than half of CSF PCR requests with little detriment to patient care and considerable cost savings. Larger prospective studies are needed to determine whether algorithms using standard CSF parameters and clinical information can optimise the use of CSF PCR assays in clinical practice.

[Acute viral and emerging viral CNS infections]

The morbidity and mortality of viral CNS infections can be reduced through early initiation of therapy, which could be specific or in most cases symptomatic. This in turn requires the physician to consider meningoencephalitis as a differential diagnosis.Increasing climate changes, global air travel and changing immune responses contribute to the emergence of rather rare viral pathogens on our continent. Thus, neurologists in Europe are facing an enormous challenge due to lacking knowledge and experience of these new germs, which needs to be taken care of.Novel therapeutic approaches with e.g. monoclonal antibodies awaken the hope of mitigating the partially lethal courses of these diseases.

The epidemiology of acute encephalitis

Encephalitis means inflammation of the brain matter. Despite being a rare condition, encephalitis is of public health importance worldwide because it has high morbidity and mortality. Yet, many details about its epidemiology have yet to be elucidated. This review attempts to summarise what is known about the epidemiology of the infective causes of encephalitis and is based on a literature search of the Medline archives. Infection is the most common cause identified, with viruses being the most important known aetiological agents. Incidence varies between studies but is generally between 3.5 and 7.4 per 100,000 patient-years. Encephalitis affects peoples of all ages; however, incidence is higher in the paediatric population. Although both sexes are affected, most studies have shown a slight predominance in males. Encephalitis occurs worldwide; some aetiologies have a global distribution (herpesviruses) while others are geographically restricted (arboviruses). Although definite epidemiological trends are evident, it is difficult to make generalisations as few population-based studies exist, most cases are not reported to health authorities, and many possible pathogens are implicated but in most cases a cause is never found. A better understanding of the epidemiology of this devastating disease will pave the way for better prevention and control strategies.

Usefulness of Herpes Consensus PCR methodology to routine diagnostic testing for herpesviruses infections in clinical specimens

The purposes of the study were to assess the usefulness of simultaneously amplifying herpes simplex virus 1 and 2, varicella-zoster virus, cytomegalovirus, Epstein-Barr virus and human herpesvirus 6 DNA in various clinical specimens and to analyze clinical events in patients presenting positive results. A total of 763 clinical samples obtained from 758 patients, including 115 cerebrospinal fluids, 102 aqueous fluids, 445 swabs from genital (152), oro-facial (138) and other (155) skin lesions, 96 eye swabs and 5 bronchoalveolar lavages, were tested by using the Consensus polymerase chain reaction methodology. The clinical files of the patients were consulted retrospectively. 171 of the 758 patients (22.5%) were positive for at least one of the six target viruses: herpes simplex virus 1 (n = 95), varicella-zoster virus (n = 40), herpes simplex virus 2 (n = 21), herpes simplex virus 1 plus herpes simplex virus 2 (n = 8), cytomegalovirus (n = 4), Epstein-Barr virus (n = 1), human herpesvirus 6 (n = 1), and herpes simplex virus 1 plus human herpesvirus 6 (n = 1). The Consensus methodology enabled the rapid and accurate detection of herpesviruses in various clinical specimens and provided a reliable tool in the diagnosis of herpetic infections.

A 12-year prospective study of childhood herpes simplex encephalitis: is there a broader spectrum of disease?

OBJECTIVE

The purpose of this study was to review the experience with herpes simplex encephalitis at the Hospital for Sick Children over the past 12 years.

METHODS

All patients who were admitted to our institution with acute encephalitis between January 1994 and December 2005 were enrolled prospectively in an encephalitis registry. Children from the registry with herpes simplex encephalitis were included in this study; we detailed the clinical presentations, laboratory findings, electroencephalographic findings, diagnostic imaging findings, treatments, and outcomes for all cases.

RESULTS

Of 322 cases of acute encephalitis, 5% were caused by herpes simplex virus. Initially negative herpes simplex virus cerebrospinal fluid polymerase chain reaction results were found in 2 cases (13%), but results became positive in repeat cerebrospinal fluid analyses. Classic clinical presentations were seen in 75% of cases, cerebrospinal fluid pleocytosis was found in 94%, elevated cerebrospinal fluid protein levels were found in 50%, electroencephalographic changes were observed in 94%, and diagnostic imaging abnormalities were noted in 88%. All patients were treated with intravenous acyclovir. Neurologic sequelae occurred in 63% of cases, including seizures in 44% and developmental delays in 25%. There were no deaths in this study group.

CONCLUSIONS

Herpes simplex encephalitis continues to be associated with poor long-term neurologic outcomes despite appropriate therapy. Cerebrospinal fluid polymerase chain reaction results may be negative early in the course of herpes simplex encephalitis; therefore, repeat cerebrospinal fluid analysis should be considered if herpes simplex encephalitis is suspected. Atypical forms of herpes simplex virus central nervous system disease may occur in children.

Encéphalites infectieuses: données et limites du PMSI pour l'étude épidémiologique, France métropolitaine 2000–2002

Many virus and bacteria can cause encephalitis but are rarely identified as the aetiological agent by individual diagnosis. In France, the only continuous source of information about encephalitis is the national hospital medical database (NHMD). Data from the VIH-negative patients recorded in mainland France between 2000 and 2002 with a diagnosis of encephalitis were extracted and analysed according to demographic, geographical and temporal distribution. Hospitalisation details were described. An average of 1200 patients was recorded each year. They were residents of all French districts and equally hospitalized in university hospitals and non university hospitals. Their mean age was 38, and most were men. The aetiological diagnosis was unknown for 80%. The most frequent aetiological diagnosis was herpes simplex virus in adults, and VZV virus in children. These results give us some clues to design a national study on encephalitis. The study will be implemented in mainland France in 2007 and will last one year. We invite all voluntary hospitals to include their encephalitic patients in our study.

Validation of laboratory screening criteria for herpes simplex virus testing of cerebrospinal fluid

Most patients with herpes simplex virus (HSV) central nervous system (CNS) infection have abnormal cerebrospinal fluid (CSF) indices. Therefore, we implemented screening criteria based on CSF values and host immune status to guide testing. All CSF samples submitted for HSV PCR analysis from January 1999 through December 2004 were included in the study. Specimens from patients with human immunodeficiency virus, a history of transplants, an age of <2 years, a CSF white blood cell count of >5 cells/mm(3), or a protein level of >50 mg/dl were tested upon request. All other samples were rejected and frozen. To validate our screening criteria, rejected specimens were pooled and tested retrospectively. Electronic medical records were also reviewed. A total of 1,659 HSV PCR requests from 1,458 patients were screened. Of the 1,296 specimens (78.1%) accepted for testing, 1,213 were negative, 7 were positive for HSV type 1 (HSV-1), 26 were positive for HSV-2, and 50 had unavailable results. Sixteen requests were rejected because an alternative microbiologic diagnosis had been established. Of the 347 samples rejected based on criteria, 222 (64.0%) remained available for pooled testing. No HSV-1-positive samples were identified in the rejected specimens. Two rejected specimens tested positive for HSV-2 DNA, but both met acceptance criteria which had not been communicated to the laboratory. Few patients (7.8%) with rejected specimens were treated with acyclovir, which suggests a low clinical concern for HSV encephalitis. Acceptance criteria based on CSF parameters and host immune status saved time and cost and did not miss patients with HSV CNS infection. Communication between the clinician and the laboratory is imperative for a successful screening program.

Appropriate use of polymerase chain reaction for detection of herpes simplex virus 2 in cerebrospinal fluid of patients at an inner-city hospital

Polymerase chain reaction (PCR) tests that detect herpes simplex virus (HSV) DNA in cerebrospinal fluid (CSF) are increasingly used to diagnose central nervous system (CNS) infections caused by HSV. To determine proper utilization of this test at an inner-city hospital, we performed a case-control study of adult patients, with HSV detected in CSF by PCR. Retrospective review of characteristics of adult patients hospitalized between 1997 and 2000 with CSF positive for HSV was done and compared to control patients with suspected CNS infection and negative CSF PCR. CSF from 1174 patients was tested; 20 (1.7%) had HSV DNA detected, 19/20 were HSV-2 and 1 was HSV-1. The HSV-2 cases were females (74%), with a median age of 41 years, of African-American ethnicity (100%). Of the cases, 90% had acute aseptic meningitis versus 13% controls (P < .001). Recurrent meningitis occurred in 42% cases and 3% controls (P < .001). CSF parameters significantly associated with HSV-2 positivity was lymphocytic pleocytosis (median leukocyte, 475 cell/mm3, 90% lymphocytes) (P < .001). In conclusion, HSV-1 was rarely detected in CSF of patients with suspected CNS infection. HSV-2 is more frequent, predominantly in young African-American women with lymphocytic aseptic meningitis, and is often recurrent. PCR testing for HSV-2 in CSF at inner-city hospitals can be greatly reduced by the application of these parameters.

A case of ramsay hunt syndrome complicated by cerebellitis

Cerebellitis associated with herpes zoster has rarely been observed. We report here a 76-year-old man who had a history of anterior resection for sigmoid colon cancer and presented during chemotherapy with vesicular rash of the left ear, neuralgic pain in the postauricular area, and ataxic gait. After a while, he developed left peripheral facial palsy, fever, aggravated gait ataxia, and prolonged nausea and vomiting. The left facial nerve was enhanced on gadolinium-enhanced brain magnetic resonance imaging. We suspected that the patient had Ramsay Hunt syndrome accompanied by cerebellitis, which has not been reported previously. Over the course of several months, during which he was treated with acyclovir and corticosteroid, his symptoms improved significantly.

Guidelines on routine cerebrospinal fluid analysis. Report from an EFNS task force

A great variety of neurological diseases require investigation of cerebrospinal fluid (CSF) to prove the diagnosis or to rule out relevant differential diagnoses. The objectives were to evaluate the theoretical background and provide guidelines for clinical use in routine CSF analysis including total protein, albumin, immunoglobulins, glucose, lactate, cell count, cytological staining, and investigation of infectious CSF. The methods included a Systematic Medline search for the above-mentioned variables and review of appropriate publications by one or more of the task force members. Grading of evidence and recommendations was based on consensus by all task force members. It is recommended that CSF should be analysed immediately after collection. If storage is needed 12 ml of CSF should be partitioned into three to four sterile tubes. Albumin CSF/serum ratio (Qalb) should be preferred to total protein measurement and normal upper limits should be related to patients' age. Elevated Qalb is a non-specific finding but occurs mainly in bacterial, cryptococcal, and tuberculous meningitis, leptomingeal metastases as well as acute and chronic demyelinating polyneuropathies. Pathological decrease of the CSF/serum glucose ratio or increased lactate concentration indicates bacterial or fungal meningitis or leptomeningeal metastases. Intrathecal immunoglobulin G synthesis is best demonstrated by isoelectric focusing followed by specific staining. Cellular morphology (cytological staining) should be evaluated whenever pleocytosis is found or leptomeningeal metastases or pathological bleeding is suspected. Computed tomography-negative intrathecal bleeding should be investigated by bilirubin detection.

Childhood encephalopathy: viruses, immune response, and outcome

This study examined children with an acute encephalopathy illness for evidence of viral infection, disordered blood-brain barrier function, intrathecal immunoglobulin synthesis, and interferon (IFN) production, and related their temporal occurrence to outcome. A prospective study of 22 children (13 males, 9 females; age range 1mo to 13y, median 2y 4mo), recorded clinical details, with serum and cerebrospinal fluid (CSF) analysis near presentation and then on convalescent specimens taken up to day 39 of the neurological illness. Outcome was assessed with standard scales between 18 months and 3 years after presentation. A history consistent with viral infection was given in 17 children but laboratory evidence of viral infection was found in only 7 (7/17). In 18 out of 21 children, an elevated CSF:serum albumin ratio indicative of impairment of the blood-CSF and blood-brain barriers was detected at some stage of the illness. In 14 of the 15 children with a raised immunoglobulin G index, and in 12 of the 14 children where the CSF was positive for oligoclonal bands, this was preceded by, or was observed at the same time as, an abnormal albumin ratio. Sixteen children (16/18) had elevated IFN-alpha levels in serum, or CSF, or in both. We conclude that these findings indicate an initial disruption of the blood-brain barrier followed by intrathecal antibody production by activated lymphocytes, clonally restricted to a few antigens. This is the first in vivo study to show this as an important pathogenetic mechanism of encephalitis in children. Poor outcome was associated with young age, a deteriorating electroencephalogram pattern from grade 1 to grade 2, and the degree of blood-brain barrier impairment, particularly when prolonged, but not with Glasgow Coma Scale score. The persistence of IFN-alpha was associated with a good prognosis.

Du diagnostic moléculaire initial prospectif des méningites à entérovirus⋯ à la lutte contre l'antibiorésistance

Meningitis initially presents with intense manifestations that are not generally specific to a given etiology. The first major question for the physician is to decide whether to initiate a probabilistic treatment. Enteroviruses are a major cause of aseptic meningitis, which is benign in immunocompetent patients. Molecular diagnosis is now becoming the gold standard and its prospective use at the time of patient admission, on the sole basis of clinical suspicion of meningitis, has yielded more reliable data. Cytological and biochemical data from CSF analyses are of low predictive value to influence the initial decision to treat with antibiotics. In addition, cases of meningitis during winter are not uncommon. Adults are concerned in about 25% of cases. Thus, if molecular diagnostic tools are not rapidly available, patient management may be inconsistent, leading to unnecessary scans, laboratory investigations and treatment (including overconsumption of antibiotics). Current progress in the automation and practicability of viral genomic detection yields the result within a few hours after admission. Rapid molecular viral diagnosis of a benign disease that does not require treatment but which is initially worrying is of unquestionable advantage. It is of benefit to both the patient and the community because of its input on health economics, the needless consumption of drugs and, as a result, resistance to antibiotics. The diagnosis of meningitis can no longer remain a retrospective diagnosis after elimination of all the possible causes, since not prescribing unnecessary laboratory tests and not treating are true therapeutic decisions.

Factors influencing PCR detection of viruses in cerebrospinal fluid of patients with suspected CNS infections

BACKGROUND

Polymerase chain reaction (PCR) is used to detect viruses in the cerebrospinal fluid (CSF) of patients with neurological disease. However, data to assist its use or interpretation are limited.

OBJECTIVE

We investigated factors possibly influencing viral detection in CSF by PCR, which will also help clinicians interpret positive and negative results.

METHODS

CSF from patients with was tested for human herpesviruses types 1-6, JC virus, enteroviruses, and Toxoplasma gondii. The likelihood of central nervous system (CNS) infection was classified as likely, possible, or unlikely. PCR findings in these categories were compared using single variable and logistic regression analysis.

RESULTS

Of 787 samples tested, 97 (12%) were PCR positive for one or more viruses. Of episodes likely to be CNS viral infections, 30% were PCR positive compared to 5% categorised as unlikely. The most frequent positive findings were Epstein Barr virus (EBV), enteroviruses, and herpes simplex virus (HSV). Enteroviruses and HSV were found predominantly in the likely CNS viral infection group, whereas EBV was found mainly in the unlikely group. Positive PCR results were more likely when there were 3-14 days between symptom onset and lumbar puncture, and when CSF white cell count was abnormal, although a normal CSF did not exclude a viral infection.

CONCLUSIONS

The diagnostic yield of PCR can be maximised by using sensitive assays to detect a range of pathogens in appropriately timed CSF samples. PCR results, in particular EBV, should be interpreted cautiously when symptoms cannot readily be attributed to the virus detected.

Viral meningitis

Viruses probably account for most cases of acute meningitis. Viral meningitis is often assumed to be a largely benign disease. For the commonest pathogens causing meningitis, enteroviruses, this is usually the case; however, for many of the other pathogens causing viral meningitis, and for common pathogens in the immunocompromised or infants, viral meningitis is frequently associated with substantial neurological complications and a significant mortality. Diagnostic methods for rapid and accurate identification of pathogens have improved over recent years, permitting more precise and earlier diagnoses. There have been fewer developments in therapies for viral meningitis, and there remain no effective therapies for most pathogens, emphasising the importance of prevention and early diagnosis. This review focuses on the presentation, diagnosis and management of viral meningitis and also covers the prevention of meningitis for pathogens where effective vaccines are available.

Real-time PCR in the microbiology laboratory

Use of PCR in the field of molecular diagnostics has increased to the point where it is now accepted as the standard method for detecting nucleic acids from a number of sample and microbial types. However, conventional PCR was already an essential tool in the research laboratory. Real-time PCR has catalysed wider acceptance of PCR because it is more rapid, sensitive and reproducible, while the risk of carryover contamination is minimised. There is an increasing number of chemistries which are used to detect PCR products as they accumulate within a closed reaction vessel during real-time PCR. These include the non-specific DNA-binding fluorophores and the specific, fluorophore-labelled oligonucleotide probes, some of which will be discussed in detail. It is not only the technology that has changed with the introduction of real-time PCR. Accompanying changes have occurred in the traditional terminology of PCR, and these changes will be highlighted as they occur. Factors that have restricted the development of multiplex real-time PCR, as well as the role of real-time PCR in the quantitation and genotyping of the microbial causes of infectious disease, will also be discussed. Because the amplification hardware and the fluorogenic detection chemistries have evolved rapidly, this review aims to update the scientist on the current state of the art. Additionally, the advantages, limitations and general background of real-time PCR technology will be reviewed in the context of the microbiology laboratory.

Stable and noncompetitive RNA internal control for routine clinical diagnostic reverse transcription-PCR

Clinical diagnostic tests based on nucleic acid amplification assist with the prompt diagnosis of microbial infections because of their speeds and extremely low limits of detection. However, the design of appropriate internal controls for such assays has proven difficult. We describe a reaction-specific RNA internal control for diagnostic reverse transcription (RT)-PCR which allows extraction, RT, amplification, and detection to be monitored. The control consists of a G+C-rich (60%) RNA molecule with an extensive secondary structure, based on a modified hepatitis delta virus genome. The rod-like structure of this RNA, with 70% intramolecular base pairing, provides a difficult template for RT-PCR. This ensures that the more favorable target virus amplicon is generated in preference to the control, with the control being detected only if the target virus is absent. The unusual structure of hepatitis delta virus RNA has previously been shown to enhance its stability and resistance to nucleases, an advantage for routine use as an internal control. The control was implemented in three nested multiplex RT-PCRs to detect nine clinically important respiratory viruses: (i) influenza A and B viruses, (ii) respiratory syncytial viruses A and B and human metapneumovirus, and (iii) parainfluenza virus types 1 to 4. The detection limits of these assays were not detectably compromised by the presence of the RNA control. During routine testing of 324 consecutive unselected respiratory samples, the presence of the internal control ensured that genuine and false-negative results were distinguishable, thus increasing the diagnostic confidence in the assay.