Diagnostic accuracy of two multiplex real-time polymerase chain reaction assays for the diagnosis of meningitis in children in a resource-limited setting

Viral meningitis in Sub-Saharan Africa: trends in prevalence, etiologies, and diagnostic approaches

Viral meningitis is a significant yet often underreported public health concern in Sub-Saharan Africa (SSA), where diagnostic limitations and surveillance gaps hinder accurate case detection. This systematic review examines epidemiological trends, etiologies, and laboratory diagnostic approaches to viral meningitis across SSA from 1987 to 2024. This data reveal that the prevalence of viral meningitis has shown an overall increasing trend, with a considerable year-to-year variability influenced by seasonal outbreaks, improved diagnostic methods, and enhanced surveillance efforts. Human enteroviruses (HEVs) were the most frequently identified causative agents, accounting for 1,164 confirmed cases, followed by the herpesvirus family, including Epstein-Barr virus (EBV) and cytomegalovirus (CMV). Other detected viral pathogens include mumps virus, adenoviruses, coxsackievirus, and arboviruses such as dengue virus. The shift from traditional viral cultures to polymerase chain reaction (PCR) and multiplex PCR has significantly improved the case detection. Despite these advancements, substantial gaps remain in diagnostic accessibility, surveillance systems, and less research focus on viral meningitis in SSA. Addressing these challenges through improved surveillance, enhanced diagnostic capacity, and targeted public health strategies is crucial for mitigating the burden of viral meningitis in the region.

Distinguishing community-acquired bacterial and viral meningitis: Microbes and biomarkers

Diagnostic tools to differentiate between community-acquired bacterial and viral meningitis are essential to target the potentially lifesaving antibiotic treatment to those at greatest risk and concurrently spare patients with viral meningitis from the disadvantages of antibiotics. In addition, excluding bacterial meningitis and thus decreasing antibiotic consumption would be important to help reduce antimicrobial resistance and healthcare expenses. The available diagnostic laboratory tests for differentiating bacterial and viral meningitis can be divided microbiological pathogen-focussed methods and biomarkers of the host response. Bacterial culture-independent microbiological methods, such as highly multiplexed nucleic acid amplification tests, are rapidly making their way into the clinical practice. At the same time, more conventional host protein biomarkers, such as procalcitonin and C-reactive protein, are supplemented by newer proteomic and transcriptomic signatures. This review aims to summarise the current state and the recent advances in diagnostic methods to differentiate bacterial from viral meningitis.

Progress in etiological diagnosis of viral meningitis

In recent years, with the rapid development of molecular biology techniques such as polymerase chain reaction and molecular biochip, the etiological diagnosis of viral encephalitis has a very big step forward. At present, the etiological examination of viral meningitis mainly includes virus isolation, serological detection and molecular biological nucleic acid detection. This article reviews the progress in etiological diagnosis of viral meningitis.

Investigation of the Etiological Causes of Central Nervous System Infection in Children with Multiplex PCR

Objective The aim of this study is to investigate the causative agents of central nervous system (CNS) infection in hospitalized pediatric patients by multiplex polymerase chain reaction.

Methods We retrospectively reviewed the medical records of children who underwent lumbar puncture with suspected CNS infection between September 2019 and September 2021. The cerebrospinal fluid (CSF) samples were evaluated by the BioFire FilmArray Meningitis/Encephalitis (ME) Panel.

Results The etiology of the infection was established in 13,02% (n = 25) cases. Human herpesvirus (HHV) type 6 was the most commonly identified pathogen 60% (n = 15), followed by enterovirus 20% (n = 5), Streptococcus pneumoniae 8% (n = 2), Streptococcus agalactiae 4% (n = 1), HHV type 1 4% (n = 1), and Listeria monocytogenes 4% (n = 1). The statistical analysis showed that the age of the group with enterovirus was younger than the age of the group with other causative microorganisms and the group with HHV-6 (respectively p: 0.032; p: 0.011). The hospitalization periods of the group with enterovirus and HHV-6 were shorter than the hospitalization periods of the other causative microorganisms (respectively p: 0.016; p: 0.000) and the absolute neutrophil count values of the group with HHV-6 were lower than the group of other causative microorganisms (p: 0.015).

Conclusion Our study identified HHV-6 as the main cause of CNS infection in Istanbul during coronavirus disease 2019 pandemic when isolation measures were taken. The duration of hospital stay was found to be shorter in CNS infection caused by viral agents. Revealing the causative agent in the CSF is a fast and effective method that prevents unnecessary antibiotic treatment and shortens the hospitalization period of patients.

Evaluation of Multiplex Real-time PCR and WHO Criteria for Diagnosing Childhood Bacterial Meningitis in a Tertiary Referral Hospital in Iran

Background: Childhood bacterial meningitis (BM) requires prompt and precise diagnosis to provide proper treatment and decline mortality and morbidity. Objectives: We aimed to evaluate the World Health Organization (WHO) criteria and polymerase chain reaction (PCR) for diagnosing BM in children admitted to a tertiary referral hospital in Shiraz, southern Iran. Materials: We included all 492 children aged one month to 17 years suspected of meningitis who had cerebrospinal fluid (CSF) leukocytosis admitted to Nemazi Hospital from August 2016 to September 2017. The CSF specimens were examined for routine analysis, Gram staining, and culture. A multiplex real-time PCR was used to identify Streptococcus pneumoniae, Haemophilus influenzae type b (Hib), and Neisseria meningitidis in the CSF samples. Seven viruses were also investigated using real-time PCR. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated using the WHO criteria and the multiplex real-time PCR results. Results: Seventy-four CSF samples had leukocytosis. Nineteen (22.9%) patients had BM caused by S. pneumoniae (n = 14), Hib (n = 2), Salmonella enterica (n = 2), and N. meningitidis (n = 1). The PCR test detected all cases, except for two with Salmonella meningitis (sensitivity 89.4%, specificity 100%, PPV 100%, and NPV 96%). The WHO criteria detected all cases, except three who received antibiotics at least four days before performing lumbar puncture (sensitivity 84.2%, specificity 98.2%, PPV 94.1%, and NPV 94.7%). Enterovirus was the most common viral etiology (6.75%). Conclusions: The WHO criteria and the multiplex real-time PCR had high accuracy in our setting, and their use could decrease the antibiotic over-prescription in febrile children suspected of meningitis.

Clinical use of multiplex-PCR for the diagnosis of acute bacterial meningitis

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Public investments in the development of GeneXpert molecular diagnostic technology

Background

The GeneXpert diagnostic platform from the US based company Cepheid is an automated molecular diagnostic device that performs sample preparation and pathogen detection within a single cartridge-based assay. GeneXpert devices can enable diagnosis at the district level without the need for fully equipped clinical laboratories, are simple to use, and offer rapid results. Due to these characteristics, the platform is now widely used in low- and middle-income countries for diagnosis of diseases such as TB and HIV. Assays for SARS-CoV-2 are also being rolled out. We aimed to quantify public sector investments in the development of the GeneXpert platform and Cepheid’s suite of cartridge-based assays.

Methods

Public funding data were collected from the proprietor company’s financial filings, grant databases, review of historical literature concerning key laboratories and researchers, and contacting key public sector entities involved in the technology’s development. The value of research and development (R&D) tax credits was estimated based on financial filings.

Results

Total public investments in the development of the GeneXpert technology were estimated to be $252 million, including >$11 million in funding for work in public laboratories leading to the first commercial product, $56 million in grants from the National Institutes of Health, $73 million from other U.S. government departments, $67 million in R&D tax credits, $38 million in funding from non-profit and philanthropic organizations, and $9.6 million in small business ‘springboard’ grants.

Conclusion

The public sector has invested over $250 million in the development of both the underlying technologies and the GeneXpert diagnostic platform and assays, and has made additional investments in rolling out the technology in countries with high burdens of TB. The key role played by the public sector in R&D and roll-out stands in contrast to the lack of public sector ability to secure affordable pricing and maintenance agreements.

Simultaneous detection of Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae by quantitative PCR from CSF samples with negative culture in Morocco

Bacteriological cultures from cerebrospinal fluids (CSF) have less sensitivity and specificity compared to quantitative PCR (RT-PCR), and multiple facts still conduct to the increase of negative culture. The aims of this study are to determine the molecular epidemiology and the simultaneous detection of bacterial meningitis in Morocco by using RT-PCR and compared this molecular approach with culture method to improve the etiological diagnosis of meningitis. The CSFs were collected over one-year period in 2018 in different hospitals covering all regions of the Kingdom of Morocco, from patients with suspected meningitis. The results showed the confirmation rate per culture recorded a rate of 33% and the RT-PCR of 70%. Molecular epidemiology is predominant of Neisseria meningitidis followed by Streptococcus pneumoniae and a dramatic reduction in meningitis due to Haemophilus influenzae following the introduction of conjugate vaccine in 2007. Also, the epidemiological profile shows a sex ratio M/F of 1.4 and a median age of 2 years. The national distribution showed a predominant of meningococcal disease followed by pneumococcal disease, especially a dominance of N. meningitidis over S. pneumoniae in two regions and a slight predominance of S. pneumoniae in the other two regions over N. meningitidis. Our research shows that culture in our country has less sensitivity and specificity than RT-PCR in diagnosis of bacterial meningitis and that molecular biology technique at bacteriology laboratories is desirable for diagnosis, early management of meningitis cases and in the context of the surveillance of meningitis in Morocco in parallel with culture.

Clinical features of bacterial meningitis among hospitalised children in Kenya

BACKGROUND

Diagnosing bacterial meningitis is essential to optimise the type and duration of antimicrobial therapy to limit mortality and sequelae. In sub-Saharan Africa, many public hospitals lack laboratory capacity, relying on clinical features to empirically treat or not treat meningitis. We investigated whether clinical features of bacterial meningitis identified prior to the introduction of conjugate vaccines still discriminate meningitis in children aged ≥60 days.

METHODS

We conducted a retrospective cohort study to validate seven clinical features identified in 2002 (KCH-2002): bulging fontanel, neck stiffness, cyanosis, seizures outside the febrile convulsion age range, focal seizures, impaired consciousness, or fever without malaria parasitaemia and Integrated Management of Childhood Illness (IMCI) signs: neck stiffness, lethargy, impaired consciousness or seizures, and assessed at admission in discriminating bacterial meningitis after the introduction of conjugate vaccines. Children aged ≥60 days hospitalised between 2012 and 2016 at Kilifi County Hospital were included in this analysis. Meningitis was defined as positive cerebrospinal fluid (CSF) culture, organism observed on CSF microscopy, positive CSF antigen test, leukocytes ≥50/μL, or CSF to blood glucose ratio <0.1.

RESULTS

Among 12,837 admissions, 98 (0.8%) had meningitis. The presence of KCH-2002 signs had a sensitivity of 86% (95% CI 77-92) and specificity of 38% (95% CI 37-38). Exclusion of 'fever without malaria parasitaemia' reduced sensitivity to 58% (95% CI 48-68) and increased specificity to 80% (95% CI 79-80). IMCI signs had a sensitivity of 80% (95% CI 70-87) and specificity of 62% (95% CI 61-63).

CONCLUSIONS

A lower prevalence of bacterial meningitis and less typical signs than in 2002 meant the lower performance of KCH-2002 signs. Clinicians and policymakers should be aware of the number of lumbar punctures (LPs) or empirical treatments needed for each case of meningitis. Establishing basic capacity for CSF analysis is essential to exclude bacterial meningitis in children with potential signs.

Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing

The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.

Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report

Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding for a partial DUF417 domain-containing protein diagnosed a non-b serotype, non-typeable H.influenzae belonging to lineage H. influenzae 22.1-21. The Oxford Nanopore metagenomic next-generation sequencing approach could be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes/serotypes.

Methods for rapid diagnosis of meningitis etiology in adults

Infectious meningitis can be caused by viral, bacterial or fungal pathogens. Despite widely available treatments, many types of infectious meningitis are still associated with significant morbidity and mortality. Delay in diagnosis contributes to poor outcomes. Cerebrospinal fluid cultures have been used traditionally but are time intensive and sensitivity is decreased by empiric treatment prior to culture. More rapid techniques such as the cryptococcal lateral flow assay (IMMY), GeneXpert MTB/Rif Ultra (Cepheid) and FilmArray multiplex-PCR (Biofire) are three examples that have drastically changed meningitis diagnostics. This review will discuss a holistic approach to diagnosing bacterial, mycobacterial, viral and fungal meningitis.

Optimizing Laboratory Diagnostic Services for Infectious Meningitis in the Meningitis Belt of sub-Saharan Africa

For longer than a century, the "meningitis belt" of sub-Saharan Africa has experienced the largest-ever global meningitis epidemic. Whereas HIV-associated immunosuppression drives higher susceptibility to environmental infectious organisms with tropism for the central nervous system (CNS), most diagnostic laboratories in the belt stick to N. meningitidis, H. influenzae, and S. pneumoniae. Cryptococcus neoformans has been the leading cause of death (incidence, 89%; death, 75%). To establish whether diagnostic services target geographically important pathogens, there is a need to know the current spectrum of etiology. Given Africa's agro-silvo-pastoralism, the One Health diagnostic approach is recommended. Considering  multipathogen detection capacity, needed speed for corticosteroid therapy decision, and susceptibility/resistance to antimicrobials with improved CNS penetration, proposed laboratory categorization will help neurologists to choose suitable services.

Multiplex-PCR for diagnosis of bacterial meningitis

Considering the great lethality and sequels caused by meningitis, rapid diagnosis and prompt treatment initiation have a great impact on patient outcome. Here, we developed a multiplex-PCR for simultaneous detection of the four most prevalent bacterial pathogens directly in CSF samples. The multiplex-PCR was designed to detect the following genes: fbsA (Streptococcus agalactiae), lytA (Streptococcus pneumoniae), crtA (Neisseria meningitidis), p6 (Haemophilus influenzae), and 16S rRNA (any bacterial agent). The multiplex-PCR showed a DNA detection limit of 1 pg/μL. Among 447 CSF samples tested, 40 were multiplex-PCR positive, in which 27 and 13 had positive and negative bacterial culture, respectively. Our multiplex-PCR is fast, reliable, and easily implementable into a laboratory routine for bacterial meningitis confirmation, especially for patients who previously started antimicrobial therapy. Our molecular approach can substantially improve clinical diagnosis and epidemiological measures of meningitis disease burden.

The GenMark ePlex®: another weapon in the syndromic arsenal for infection diagnosis

As one of the most recent additions to the syndromic testing landscape, the ePlex^® platform by GenMark Diagnostics is a system that combines the manufacturer's signature electrochemical detection technology with updated microfluidics, providing a new option for multiplex testing that is both rapid and requires minimal hands-on steps. In this review, we detail the ePlex platform and its current/future syndromic panels, with a particular focus on the respiratory pathogen panel - the platform's first assay to undergo clinical trials and receive regulatory approval in the USA. By keeping informed of these ever-expanding laboratory options, clinicians and microbiologists can stay positioned at the forefront of infectious disease diagnosis.

Impact of Cerebrospinal Fluid Multiplex Assay on Diagnosis and Outcomes of Central Nervous System Infections in Children: A Before and After Cohort Study

BACKGROUND

This study evaluated the performance of cerebrospinal fluid multiplex assay in the diagnosis of pediatric central nervous system (CNS) infection, and assessed for the effect on clinical management.

METHODS

A 15-month prospective cohort of pediatric patients with confirmed CNS infection was compared with a 15-month retrospective cohort from the Top End region of the Northern Territory, Australia. The study characterized all the CNS infections over the 30-month period and compared the time to organism identification and antibiotic management before and after the introduction of the multiplex assay.

RESULTS

Thirty-six cases of pediatric CNS infection were diagnosed before the introduction of the multiplex assay, and 29 afterwards. Multiplex assay was performed on 26/29 (90%) of the cerebrospinal fluid isolates from children with confirmed CNS infections in the prospective cohort. Enterovirus was the most common causative organism identified in 14 children, followed by human parechovirus in 4 children. The multiplex assay performed with 93.8% sensitivity and 90.0% specificity when compared with microbiologic culture or reference laboratory results. The median time to organism identification reduced from 6.0 to 2.0 days (P value <0.001), the median duration of antibiotic therapy from 3.0 to 2.0 days (P value <0.001) and median hospitalization reduced from 5.0 to 3.0 days (P value 0.016) after introduction of the multiplex assay.

CONCLUSIONS

The multiplex assay is a useful adjunct diagnostic tool enabling prompt organism identification and reducing antibiotic treatment and hospitalization duration. The assay would be of most value to hospitals that do not have access to an onsite molecular laboratory.