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

Molecular diagnostics in cerebrospinal fluid for the diagnosis of central nervous system infections

SUMMARYCentral nervous system (CNS) infections can be caused by various pathogens, including bacteria, viruses, fungi, and parasites. Molecular diagnostic methods are pivotal for identifying the different causative pathogens of these infections in clinical settings. The efficacy and specificity of these methods can vary per pathogen involved, and in a substantial part of patients, no pathogen is identified in the cerebrospinal fluid (CSF). Over recent decades, various molecular methodologies have been developed and applied to patients with CNS infections. This review provides an overview of the accuracy of nucleic acid amplification methods in CSF for a diverse range of pathogens, examines the potential value of multiplex PCR panels, and explores the broad-range bacterial and fungal PCR/sequencing panels. In addition, it evaluates innovative molecular approaches to enhance the diagnosis of CNS infections.

National Surveillance of Acute Flaccid Paralysis Cases in Senegal during 2017 Uncovers the Circulation of Enterovirus Species A, B and C

Polioviruses have been eliminated in many countries; however, the number of acute flaccid paralysis cases has not decreased. Non-polio enteroviruses are passively monitored as part of the polio surveillance program. Previous studies have shown that some enteroviruses do not grow in conventional cell lines used for the isolation of poliovirus according to the WHO guidelines. In order to evaluate the presence of enteroviruses, real-time RT-PCR was performed on Human Rhabdomyosarcoma (RD)-positive and RD-negative stool samples. A total of 310 stool samples, collected from children under the age of 15 years with acute flaccid paralysis in Senegal in 2017, were screened using cell culture and real-time RT-PCR methods. The selected isolates were further characterized using Sanger sequencing and a phylogenetic tree was inferred based on VP1 sequences. Out of the 310 stool samples tested, 89 were positive in real-time RT-PCR. A total of 40 partial VP1 sequences were obtained and the classification analysis showed that 3 (13%), 19 (82.6%), and 1 (4.4%) sequences from 23 RD-positive non-polio enterovirus isolates and 3 (17.6%), 7 (41.1%), and 7 (41.1%) sequences from 17 RD-negative stool samples belonged to the species EV-A, B, and C, respectively. Interestingly, the EV-B sequences from RD-negative stool samples were grouped into three separate phylogenetic clusters. Our data exhibited also a high prevalence of the EV-C species in RD-negative stool samples. An active country-wide surveillance program of non-polio enteroviruses based on direct RT-PCR coupled with sequencing could be important not only for the rapid identification of the involved emergence or re-emergence enteroviruses, but also for the assessment of AFP’s severity associated with non-polio enteroviruses detected in Senegal.

Evaluation of GeneXpert EV assay for the rapid diagnosis of enteroviral meningitis: a systematic review and meta-analysis

Background

GeneXpert enterovirus Assay is a PCR-based assay for Enterovirus meningitis diagnosis. However, there is currently no research about the performance of GeneXpert enterovirus assay in the diagnosis of enterovirus meningitis. Thus, a systematic review and meta-analysis is significant on the topic.

Methods

Embase, Cochrane Library, Web of Science, and PubMed were systematically reviewed with retrieval types. Some criteria were used to filter the studies. Only studies published in English, that made a comparison between GeneXpert enterovirus assay and RT-PCR, and could be formulated in a 2*2 table, were included. The quality of the included studies was evaluated by QUADAS-2. The effect of the GeneXpert enterovirus assay was assessed by the Sensitivity, Specificity, Positive Likelihood Ratio, Negative Likelihood Ratio, Diagnosis Odds Ratio, and summary receiver operating characteristic (SROC) curve. Publication bias and heterogeneity were evaluated by the Deeks' funnel test and Bivariate Box plot respectively.

Results

7 studies were recruited in the analysis. The Pooled Sensitivity was 0.96 [95% CI (0.94–0.97)], Pooled Specificity was 0.99 [95% CI (0.98–0.99)], Positive Likelihood Ratio was 130.46 [95% CI (35.79–475.58)], Negative Likelihood Ratio was 0.04 [95% CI (0.02–0.10)], and Diagnostic Odds Ratio was 3648.23 (95% CI [963.99–13,806.72)]. In SROC Curve, Area Under Curve (AUC) was 0.9980, and Q*= 0.9849. In Deeks' funnel test, the P-value was 0.807 (P > 0.05), indicating no publication bias. The Bivariate Box plot indicated no evident heterogeneity.

Conclusions

The GeneXpert enterovirus assay demonstrated high diagnostic accuracy in diagnosing enterovirus meningitis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00517-3.

Prospective case-control study of enterovirus detection differences in children's cerebrospinal fluid between multiplex PCR and real-time RT-PCR assay

Background

Viral encephalitis is common in childhood. It is an acute brain parenchymal inflammation caused by a variety of viral infection, and enterovirus accounts for the majority. Due to atypical clinical manifestations, pathogenic testing is important for assisting clinical diagnosis. The purpose of this study was to evaluate the performance of the multiplex PCR assay compared with quantitative real‐time PCR for enterovirus detection.

Methods

A prospective case‐control study was performed involving 103 pediatric patients suspected for viral encephalitis and cerebrospinal fluid (CSF) samples were collected and tested for 9 pathogens using multiplex PCR assay during April to November in 2018. In parallel, an aliquot of samples was tested for enterovirus infection by real‐time PCR assay.

Results

There were 85.4% children were confirmed as viral encephalitis on discharge, the remaining ones were diagnosed as other CNS diseases, such as epilepsy. The specificity of the two methods was the same as that of the clinical diagnosis, but the sensitivity and consistency with clinical diagnosis of multiplex PCR were both higher than the real‐time PCR. Besides of enterovirus, multiplex PCR could also detect coinfection of enterovirus with Epstein‐Barr virus and mumps virus.

Conclusion

Results of multiplex PCR method are more consistent with the clinical diagnosis and are superior to real‐time PCR for detecting enterovirus in CSF.

Rapid detection of enterovirus in cerebrospinal fluid by a fully-automated PCR assay is associated with improved management of aseptic meningitis in adult patients

BACKGROUND

Enterovirus (EV) is the most frequent cause of aseptic meningitis (AM). Lack of microbiological documentation results in unnecessary antimicrobial therapy and hospitalization.

OBJECTIVES

To assess the impact of rapid EV detection in cerebrospinal fluid (CSF) by a fully-automated PCR (GeneXpert EV assay, GXEA) on the management of AM.

STUDY DESIGN

Observational study in adult patients with AM. Three groups were analyzed according to EV documentation in CSF: group A = no PCR or negative PCR (n=17), group B = positive real-time PCR (n = 20), and group C = positive GXEA (n = 22). Clinical, laboratory and health-care costs data were compared.

RESULTS

Clinical characteristics were similar in the 3 groups. Median turn-around time of EV PCR decreased from 60 h (IQR (interquartile range) 44-87) in group B to 5h (IQR 4-11) in group C (p<0.0001). Median duration of antibiotics was 1 (IQR 0-6), 1 (0-1.9), and 0.5 days (single dose) in groups A, B, and C, respectively (p < 0.001). Median length of hospitalization was 4 days (2.5-7.5), 2 (1-3.7), and 0.5 (0.3-0.7), respectively (p < 0.001). Median hospitalization costs were $5458 (2676-6274) in group A, $2796 (2062-5726) in group B, and $921 (765-1230) in group C (p < 0.0001).

CONCLUSIONS

Rapid EV detection in CSF by a fully-automated PCR improves management of AM by significantly reducing antibiotic use, hospitalization length and costs.

Enterovirus infections in England and Wales, 2000-2011: the impact of increased molecular diagnostics

There have recently been significant changes in diagnostic practices for detecting enterovirus (EV) infections across England and Wales. Reports of laboratory-confirmed EV infections submitted by National Health Service (NHS) hospital laboratories to Public Health England (PHE) over a 12-year period (2000-2011) were analysed. Additionally, the PHE Virus Reference Department (VRD) electronic database containing molecular typing data from 2004 onwards was interrogated. Of the 13,901 reports, there was a decline from a peak of 2254 in 2001 to 589 in 2006, and then an increase year-on-year to 1634 in 2011. This increase coincided with increasing PCR-based laboratory diagnosis, which accounted for 36% of reported cases in 2000 and 92% in 2011. The estimated annual incidence in 2011 was 3.9/100,000 overall and 238/100,000 in those aged <3 months, who accounted for almost one-quarter of reported cases (n = 2993, 23%). During 2004-2011, 2770 strains were submitted for molecular typing to the VRD, who found no evidence for a predominance of any particular strain. Thus, the recent increase in reported cases closely reflects the increase in PCR testing by NHS hospitals, but is associated with a lower proportion of samples being submitted for molecular typing. The high EV rate in young infants merits further investigation to inform evidence-based management guidance.

Human parechovirus central nervous system infections in southern California children

BACKGROUND

Human parechoviruses (hPeV) are increasingly recognized as significant etiological agents for meningoencephalitis especially in young children, but testing of cerebrospinal fluid (CSF) for hPeV by PCR is not routinely performed.

METHODS

We used real-time reverse transcriptase PCR for detection of serotypes 1-6 in CSF samples of 440 children who underwent a lumbar puncture to exclude an infectious etiology of their clinical presentation. We then compared the prevalence and clinical presentation of children with hPeV-positive CSF with that of children with enterovirus (EV)-positive CSF.

RESULTS

HPeV was detected in 2.7% and EV in 10.7% of CSF samples. Many hPeV-positive patients were <3 months of age and usually had CSF parameters within the age-adjusted normal range. However, children with hPeV-positive CSF presented with neurologic symptoms more frequently than those with EV-positive CSF.

CONCLUSIONS

HPeV infections of the central nervous system occurred mainly in young infants and were more commonly associated with neurologic symptoms at presentation, despite the fact that CSF findings were within the normal range in the vast majority of these cases. HPeV should be included in the differential diagnosis of young children with central nervous system symptoms and sepsis-like illness, even in the presence of normal CSF parameters.

Atypical hand-foot-and-mouth disease associated with coxsackievirus A6 infection

BACKGROUND

Hand-foot-and-mouth disease (HFMD) is an acute viral illness commonly caused by coxsackievirus (CV)-A16 and enterovirus 71 infections. Recently, atypical HFMD has been reported in association with CV-A6, an uncommon enterovirus strain.

OBJECTIVE

We sought to describe the clinical features of atypical HFMD associated with CV-A6 infection and its diagnostic laboratory evaluation.

METHODS

Patients presenting to our institution with history and examination suggestive of atypical HFMD from January 2012 to July 2012 were identified. Morphology and distribution of mucocutaneous lesions were recorded. Enterovirus infection was assessed by reverse transcriptase polymerase chain reaction of biologic specimens. Enterovirus type was determined by viral capsid protein 1 gene sequencing.

RESULTS

Two adults and 3 children with atypical HFMD were identified. Four of 5 patients exhibited widespread cutaneous lesions. In 2 patients with a history of atopic dermatitis, accentuation in areas of dermatitis was noted. Associated systemic symptoms prompted 4 of 5 patients to seek emergency care, and both adults were hospitalized for diagnostic evaluation. Infection with CV-A6 was confirmed in all patients.

LIMITATIONS

This study is a case series from a single institution.

CONCLUSION

Consideration of the expanded range of cutaneous findings in atypical HFMD caused by CV-A6 infection may assist clinicians in diagnosis and management.

Prospective comparison of the detection rates of human enterovirus and parechovirus RT-qPCR and viral culture in different pediatric specimens

BACKGROUND

Reverse-transcriptase quantitative real-time polymerase chain reaction (RT-qPCR) has become the gold standard for the diagnosis of human enterovirus (EV) and parechovirus (HPeV) infections. The detection rate of RT-qPCR in different pediatric body specimens has not been compared prospectively in a multicentre study.

OBJECTIVES

This study compared the diagnostic detection rates of EV and HPeV RT-qPCR and viral culture in different specimens (feces, nasopharynx, blood, urine and cerebrospinal fluid (CSF)) of pediatric patients.

STUDY DESIGN

This prospective, multicenter study performed an EV and HPeV RT-qPCR on nasopharynx, blood, urine, feces and CSF specimens and a viral culture on nasopharynx, feces and CSF specimens in symptomatic children<16 years.

RESULTS

Of 285 included children EV was detected in 140 (49%) and HPeV in 44 (15%) children. Both EV and HPeV RT-qPCR had a higher sensitivity and negative predictive value than EV and HPeV viral culture, respectively. EV and HPeV RT-qPCR in feces specimen had the highest sensitivity (99.2% and 95.1%) of all specimens. Pooling results of specimens increased the detection rate for both viruses.

CONCLUSION

Of all specimens, RT-qPCR in feces had the highest detection rate for both EV and HPeV in symptomatic pediatric patients. An EV was detected in all EV positive patients if a RT-qPCR was performed on both feces and CSF specimens or in both feces and urine specimens. HPeV was detected in all HPeV positive patients if a RT-qPCR was performed on both feces and CSF specimens, feces and nasopharynx specimens or CSF and nasopharynx specimens.

A new factor influencing pathogen detection by molecular assay in children with both mild and severe hand, foot, and mouth disease

This study aimed to find novel information concerning pathogen detection and some probable coinfection factors in hand, foot, and mouth disease (HFMD). In this study, 1104 clinically diagnosed HFMD patients were included. Enterovirus 71 (EV71), coxsackievirus A16 (CA16), and 14 different respiratory pathogens were examined from nasopharyngeal swabs using polymerase chain reaction (PCR) or reverse transcriptase PCR (RT-PCR). To evaluate the immune activation in HFMD patients, 8 cytokines and IgM antibodies to EV71 and CA16 from mild and severe patients were detected. Our results indicated that the severity of HFMD may affect the pathogen detection. The lower positive rates of enterovirus and respiratory viruses in severe HFMD cases by RT-PCR were probably related to stronger immune response. Therefore, immunological tests such as ELISA are essential supplements to PCR or RT-PCR in order to increase pathogen diagnosis in HFMD, especially in severe cases.

Implementation of the Cepheid Xpert EV assay for rapid detection of enteroviral meningitis: experience of a tertiary care center and a technical review

AIMS

Rapid molecular detection of enterovirus in cerebrospinal fluid (CSF) has revolutionized the diagnosis and treatment modalities of patients with meningitis and largely affected cost of unnecessary antibiotic use and length of stay in hospitals.

MATERIALS AND METHODS

Between January 2010 and July 2012, we tested 220 CSF samples on the GeneXpert DX real-time polymerase chain reaction system (by Cepheid) using the Xpert EV kit assays. In addition, we reported 14 sample results cross-validated with an external referral laboratory as well as the results of external proficiency testing.

RESULTS

Out of all tested samples, 19% were positive for enterovirus. Furthermore, all referred and proficiency testing specimens were concordant with the peer-reviewed and tested samples.

CONCLUSION

Implementation of the Cepheid Xpert EV assay for rapid detection of enteroviral meningitis has been successful in our laboratory. This molecular diagnostic test is currently utilized by our staff physicians as a major tool in assessment and management of patients with meningitis.

Role of molecular diagnostics in the management of infectious disease emergencies

In the setting of infectious disease emergencies, rapid and accurate identification of the causative agent is critical to optimizing antimicrobial therapy in a timely manner. It is clearly evident that the age of molecular diagnostics is now upon us, with real-time PCR becoming the standard of diagnosis for many infectious disease emergencies in either monoplex or multiplex format. Other molecular techniques such as whole or partial genome sequencing, microarrays, broad-range PCR, restriction fragment length polymorphisms, and molecular typing are also being used. However, for most small clinical laboratories, implementation of these advanced molecular techniques is not feasible owing to the high cost of instrumentation and reagents. If these tests are not available in-house, samples can be sent to national reference laboratories (eg, Mayo Medical Laboratories and Quest Diagnostics) for real-time PCR assays that can be completed in 1 day. It is anticipated that over time commercial real-time PCR tests and instrumentation will become more standardized and affordable, allowing individual laboratories to conduct tests locally, thus further reducing turnaround time. Although real-time PCR has been proved to expand our diagnostic capability, it must be stressed that such molecular methodology constitutes only an additional tool in the diagnosis of infectious diseases in emergency situations. Phenotypic methodologies (staining, cultures, biochemical tests, and serology) still play a critical role in identifying, confirming, and providing antibiotic susceptibility testing for many microbial pathogens. As multiplex assays become increasingly available, there will be even greater temptation for taking a “shotgun” approach to diagnostic testing. These new technologies will not substitute for a proper history and physical examination leading to a thoughtful differential diagnosis. None the less, these new molecular tests increase the capability of the diagnostician to rapidly identify the microbiological etiology of an infection. An added advantage of rapid diagnostic tests often not emphasized is the capability to rule out certain diagnoses for which unnecessary antimicrobial therapy may otherwise be instituted and/or continued.