Evaluation of a Commercial Multiplex Molecular Panel for Diagnosis of Infectious Meningitis and Encephalitis

Unusual late presentation of cryptococcal meningitis with simultaneous CMV antigenemia in a kidney transplant recipient

Cryptococcosis is the third most common invasive fungal infection in solid-organ transplant (SOT) recipients after candidiasis and aspergillosis. These patients are at risk of disseminated cryptococcosis because of immuosuppressive therapy. The median time to disease onset after kidney transplantation is approximately 35 months and it rarely occurs more than 10 years after transplantation. Herein, we report a case of 64-year-old kidney transplant recipient suffering from coexisting disseminated cryptococcosis with brain and skin involvement, together with cytomegalovirus (CMV) antigenemia more than 20 years after transplant. She presented with frontal headache and bilateral hand tremor, in addition to multiple nodular lesions over bilateral lower limbs. The diagnosis was made after lumbar puncture and skin biopsy. She was successfully treated with a course of anti-fungal and anti-CMV regimen without any relapse of central nervous system infection. Our case illustrates that disseminated cryptococcosis can occur very late after organ transplant. It is thus important to watch out for late-onset opportunistic infections and strike the balance between risks of infections and rejections in SOT patients.

Epidemiology of pediatric meningitis and encephalitis in Japan: a cross-sectional study

Information on the epidemiology and cause-specific clinical features of pediatric meningitis and encephalitis is limited, owing to conventional laboratory methods' limitations in identifying causative pathogens. The FilmArray Meningitis/Encephalitis (FA-M/E) panel, a molecular diagnostic tool, can detect 14 pathogens within 1 hour. We investigated meningitis and encephalitis epidemiology among children in Japan and FA-M/E panels' utility in their clinical management. This cross-sectional study was conducted among children aged 0-18 years admitted to seven regional hospitals in western Japan between October 2022 and September 2023. Cerebrospinal fluid (CSF) samples were collected from 221 children and tested using the FA-M/E panel. Clinical and microbiological data were reviewed retrospectively. Fifty-eight patients tested positive using the FA-M/E panel. Viral and bacterial pathogens were detected in 49 and nine cases, respectively. Human parechovirus and enterovirus occurred mainly in epidemic clusters during the summer and were primarily detected in young infants. Patients who tested positive for human parechovirus had a significantly higher frequency of sepsis-like manifestations and a lower frequency of CSF pleocytosis than did those who tested positive for enterovirus. CSF pleocytosis was absent in 30 patients who tested positive using the FA-M/E panel. Among the patients who tested positive for bacteria, three of the nine were not diagnosed using conventional culture methods, owing to prior antimicrobial therapy. The FA-M/E panel can identify bacterial and viral pathogens causing pediatric meningitis and characterize the epidemiology in local communities.IMPORTANCECulture and polymerase chain reactions have traditionally been used to identify microorganisms causing pediatric meningitis and encephalitis. However, the methods currently used to identify the causative microorganisms are limited, particularly in general hospitals. The FilmArray Meningitis/Encephalitis (FA-M/E) panel, a fully automated genetic testing system, can detect 14 pathogens using the multiplex polymerase chain reaction method. This study described the epidemiology of pediatric meningitis and encephalitis in Japan. The microorganisms causing acute meningitis and encephalitis in children in Japan were identified using the FilmArray Meningitis/Encephalitis panel. Testing cerebrospinal fluid using the FA-M/E panel is useful for the identification of the pathogen in children with community-acquired acute meningitis and encephalitis. This increases knowledge on the epidemiology and clinical manifestations of acute meningitis and encephalitis caused by specific pathogens and can be used to facilitate optimal patient management.

Molecular Diagnostics of Cryptococcus spp. and Immunomics of Cryptococcosis-Associated Immune Reconstitution Inflammatory Syndrome

Cryptococcal infection poses a significant global public health challenge, particularly in regions near the equator. In this review, we offer a succinct exploration of the Cryptococcus spp. genome and various molecular typing methods to assess the burden and genetic diversity of cryptococcal pathogens in the environment and clinical isolates. We delve into a detailed discussion on the molecular pathogenesis and diagnosis of immune reconstitution inflammatory syndrome (IRIS) associated with cryptococcosis, with a specific emphasis on cryptococcal meningitis IRIS (CM-IRIS). Our examination includes the recent literature on CM-IRIS, covering host cellulomics, proteomics, transcriptomics, and genomics.

Hybrid capture shotgun sequencing detected unexpected viruses in the cerebrospinal fluid of children with acute meningitis and encephalitis

PURPOSE

Investigation of undiagnosed cases of infectious neurological diseases, especially in the paediatric population, remains a challenge. This study aimed to enhance understanding of viruses in CSF from children with clinically diagnosed meningitis and/or encephalitis (M/ME) of unknown aetiology using shotgun sequencing enhanced by hybrid capture (HCSS).

METHODS

A single-centre prospective study was conducted at Sant Joan de Déu University Hospital, Barcelona, involving 40 M/ME episodes of unknown aetiology, recruited from May 2021 to July 2022. All participants had previously tested negative with the FilmArray Meningitis/Encephalitis Panel. HCSS was used to detect viral nucleic acid in the patients' CSF. Sequencing was performed on Illumina NovaSeq platform. Raw sequence data were analysed using CZ ID metagenomics and PikaVirus bioinformatics pipelines.

RESULTS

Forty episodes of M/ME of unknown aetiology in 39 children were analysed by HCSS. A significant viral detection in 30 CSF samples was obtained, including six parechovirus A, three enterovirus ACD, four polyomavirus 5, three HHV-7, two BKV, one HSV-1, one VZV, two CMV, one EBV, one influenza A virus, one rhinovirus, and 13 HERV-K113 detections. Of these, one sample with BKV, three with HHV-7, one with EBV, and all HERV-K113 were confirmed by specific PCR. The requirement for Intensive Care Unit admission was associated with HCSS detections.

CONCLUSION

This study highlights HCSS as a powerful tool for the investigation of undiagnosed cases of M/ME. Data generated must be carefully analysed and reasonable precautions must be taken before establishing association of clinical features with unexpected or novel virus findings.

Utilization of a Meningitis/Encephalitis PCR panel at the University Hospital Basel - a retrospective study to develop a diagnostic decision rule

Background

The Biofire® FilmArray® Meningitis/Encephalitis (ME) PCR panel covers 14 viral, bacterial, and fungal pathogens and has been implemented in many institutions worldwide. Post-marketing studies indicate a reduced sensitivity and overutilization underscoring the need for a more targeted usage. The aim of our study is to describe the utilization of the ME panel and to develop a diagnostic-stewardship based decision rule.

Materials

Adult patients, who underwent CSF analysis with the ME panel between August 2016 and June 2021 at the University Hospital Basel, were included. Demographic, clinical, microbiological, and laboratory data were extracted from the electronic health record. Factors associated with a positive ME panel result were identified, and a decision rule was developed to potentially optimize the diagnostic yield and reduce the number of unnecessary tests.

Results

1,236 adult patients received at least one panel in the observed period, of whom 106 panels tested positive (8.6%). The most frequently observed pathogens were Varicella Zoster Virus (VZV, 27%), Streptococcus pneumoniae (19%), Enterovirus (16%), Herpes simplex Virus 1/2 (16%), and Human Herpesvirus 6 (HHV-6, 13%). Fever, vomiting, headache, and photophobia were more frequently present in test positive patients as were significantly higher CSF leukocytes and protein concentrations. When simulating a decision rule based on CSF leukocytes and protein concentration, only 35% of all patients would have qualified for a ME panel tests, thereby increasing the positivity rate to 22.7%. 10 of 106 positive ME panels would have been missed, only involving HHV-6 and VZV (6 and 4 cases, respectively). As these subjects were either severely immunocompromised or had clinical features of shingles we propose extending the testing algorithm by including those criteria.

Conclusion

The ME panel positivity rate at our institution was similar as previously published. Our results highlight the need for diagnostic-stewardship interventions when utilizing this assay by implementing a stepwise approach based on a limited number of clinical and laboratory features. This decision rule may improve the pretest probability of a positive test result, increase the quality of test utilization, and reduce costs.

Evaluating the Impact of the BioFire FilmArray in Childhood Meningitis: An Observational Cohort Study

BACKGROUND

Multiplex polymerase chain reaction assays have the potential to reduce antibiotic use and shorten length of inpatient stay in children with suspected central nervous system infection by obtaining an early microbiological diagnosis. The clinical impact of the implementation of the BioFire FilmArray Meningitis/Encephalitis Panel on the management of childhood meningitis was evaluated at the John Radcliffe Hospital in Oxford and Children's Health Ireland at Temple Street in Dublin.

METHODS

Children who had lumbar punctures performed as part of a septic screen were identified retrospectively through clinical discharge coding and microbiology databases from April 2017 to December 2018. Anonymized clinical and laboratory data were collected. Comparison of antibiotic use, length of stay and outcome at discharge was made with a historical cohort in Oxford (2012-2016), presenting before implementation of the FilmArray.

RESULTS

The study included 460 children who had a lumbar puncture as part of an evaluation for suspected central nervous system infection. Twelve bacterial cases were identified on the FilmArray that were not detected by conventional bacterial culture. Bacterial culture identified one additional case of bacterial meningitis, caused by Escherichia coli , which had not been identified on the FilmArray. Duration of antibiotics was shorter in children when FilmArray was used than before its implementation; enterovirus meningitis (median: 4 vs. 5 days), human parechovirus meningitis (median: 4 vs. 4.5 days) and culture/FilmArray-negative cerebrospinal fluid (median: 4 vs. 6 days).

CONCLUSIONS

The use of a FilmArray can identify additional bacterial cases of meningitis in children that had been negative by traditional culture methods. Children with viral meningitis and culture-negative meningitis received shorter courses of antibiotics and had shorter hospital stays when FilmArray was used. Large studies to evaluate the clinical impact and cost effectiveness of incorporating the FilmArray into routine testing are warranted.

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.

Multiplex real-time PCR FilmArray performance in the diagnosis of meningoencephalitis: lights and shadows

PURPOSE

We aimed to evaluate the performance of the FilmArray (FA) meningitis/encephalitis (ME) panel. Secondarily, we analyzed the false positive (FP) and false negative (FN) results, as well as the predictive values of the technique, regarding the cerebrospinal fluid (CSF) characteristics.

METHODS

FA is a multiplex real-time PCR detecting 14 of the most common ME pathogens in CSF. All FA performed at our hospital (2018-2022) were retrospectively reviewed. FA was compared to conventional techniques and its performance was assessed based on the final diagnosis of the episode.

RESULTS

FA was performed in 313 patients with suspicion of ME. Most patients had altered mental status (65.2%) and fever (61%). Regarding CSF characteristics, 49.8% and 53.7% presented high CSF proteins and pleocytosis, respectively. There were 84 (26.8%) positive FA results, mainly for HSV-1 (10.9%), VZV (5.1%), Enterovirus (2.6%), and S. pneumoniae (1.9%). In the 136 cases where both FA and routine methods were performed, there was a 25.7% lack of agreement. We identified 6.6% FN results, but 28.6% FP, mainly due to HSV-1. This resulted in a high negative predictive value (NPV) of 93.4%, but a positive predictive value (PPV) of 73%. Remarkably, PPV as low as 36.9%, and 70.2%, were found in cases without pleocytosis, or lack of high CSF protein levels, respectively.

CONCLUSION

FA was associated with high NPV, but frequent FP results and low PPV, particularly for HSV-1, and especially in patients without high CSF protein levels or pleocytosis.

Laboratory diagnosis of CNS infections in children due to emerging and re-emerging neurotropic viruses

Recent decades have witnessed the emergence and re-emergence of numerous medically important viruses that cause central nervous system (CNS) infections in children, e.g., Zika, West Nile, and enterovirus/parechovirus. Children with immature immune defenses and blood-brain barrier are more vulnerable to viral CNS infections and meningitis than adults. Viral invasion into the CNS causes meningitis, encephalitis, brain imaging abnormalities, and long-term neurodevelopmental sequelae. Rapid and accurate detection of neurotropic viral infections is essential for diagnosing CNS diseases and setting up an appropriate patient management plan. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis/encephalitis. However, the expansion of test menu has led to new challenges in selecting appropriate tests and making accurate interpretation of test results. There are unmet gaps in development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses. Herein we will discuss the advances and challenges in the laboratory diagnosis of viral CNS infections in children. This review not only sheds light on selection and interpretation of a suitable diagnostic test for emerging/re-emerging neurotropic viruses, but also calls for more research on development and clinical utility study of novel molecular assays. IMPACT: Children with immature immune defenses and blood-brain barrier, especially neonates and infants, are more vulnerable to viral central nervous system infections and meningitis than adults. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis and encephalitis. There are unmet gaps in the development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses.

Evaluation of pathogen from the FilmArray meningitis/encephalitis panel and recommendations on atypical findings

BACKGROUND

 Infectious meningoencephalitis is a potentially fatal clinical condition that causes inflammation of the central nervous system secondary to the installation of different microorganisms. The FilmArray meningitis/encephalitis panel allows the simultaneous detection of 14 pathogens with results in about one hour.

OBJECTIVE

 This study is based on retrospectively evaluating the implementation of the FilmArray meningitis/encephalitis panel in a hospital environment, highlighting the general results and, especially, analyzing the consistency of the test results against the clinical and laboratory conditions of the patients.

METHODS

 Data were collected through the results reported by the BioFire FilmArray system software from the meningitis/encephalitis panel. The correlated laboratory tests used in our analysis, when available, included biochemical, cytological, direct and indirect microbiological tests.

RESULTS

 In the analyzed period, there were 496 samples with released results. Of the total of 496 samples analyzed, 88 (17.75%) were considered positive, and 90 pathogens were detected, and in 2 of these (2.27%) there was co-detection of pathogens. Viruses were the agents most frequently found within the total number of pathogens detected. Of the 496 proven samples, 20 (4.03%) were repeated, 5 of which were repeated due to invalid results, 6 due to the detection of multiple pathogens and 9 due to disagreement between the panel results and the other laboratory tests and/or divergence of the clinical-epidemiological picture. Of these 20 repeated samples, only 4 of them (20%) maintained the original result after repeating the test, with 16 (80%) being non-reproducible. The main factor related to the disagreement of these 16 samples during retesting was the detection of bacterial agents without any relationship with other laboratory tests or with the patients' clinical condition.

CONCLUSION

 In our study, simply reproducing tests with atypical results from the FilmArray meningitis/encephalitis panel proved, in most cases, effective and sufficient for interpreting these results.

Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology

The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.

Application of metabolomics in diagnostics and differentiation of meningitis: A narrative review with a critical approach to the literature

Due to its high mortality rate associated with various life-threatening sequelae, meningitis poses a vital problem in contemporary medicine. Numerous algorithms, many of which were derived with the aid of artificial intelligence, were brought up in a strive for perfection in predicting the status of sepsis-related survival or exacerbation. This review aims to provide key insights on the contextual utilization of metabolomics. The aim of this the metabolomic approach set of methods can be used to investigate both bacterial and host metabolite sets from both the host and its microbes in several types of specimens - even in one's breath, mainly with use of two methods - Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR). Metabolomics, and has been used to elucidate the mechanisms underlying disease development and metabolic identification changes in a wide range of metabolite contents, leading to improved methods of diagnosis, treatment, and prognosis of meningitis. Mass spectrometry (MS) and Nuclear Magnetic Resonance (NMR) are the main analytical platforms used in metabolomics. Its high sensitivity accounts for the usefulness of metabolomics in studies into meningitis, its sequelae, and concomitant comorbidities. Metabolomics approaches are a double-edged sword, due to not only their flexibility, but also - high complexity, as even minor changes in the multi-step methods can have a massive impact on the results. Information on the differential diagnosis of meningitis act as a background in presenting the merits and drawbacks of the use of metabolomics in context of meningeal infections.

Evaluation of the QIAstat-Dx Meningitis/Encephalitis Panel, a multiplex PCR platform for the detection of community-acquired meningoencephalitis

Rapid identification of the causative pathogens of central nervous system infections is essential for providing appropriate management and improving patient outcomes. The performance of QIAstat-Dx Meningitis/Encephalitis (ME) Panel-a multiplex PCR testing platform-in detecting pathogens implicated in meningitis and/or encephalitis was evaluated using BioFire FilmArray ME Panel as a comparator method. This multicenter study analyzed 585 retrospective residual cerebrospinal fluid specimens and 367 contrived specimens. The QIAstat-Dx ME Panel showed positive percent agreement (PPA) values of 100% for Neisseria meningitidis, Streptococcus agalactiae, Escherichia coli K1, Listeria monocytogenes, and Cryptococcus gattii/neoformans on clinical samples compared to the BioFire FilmArray ME Panel. The PPA values observed for Haemophilus influenzae and Streptococcus pneumoniae were 80% and 88.24%, respectively. Negative percent agreement (NPA) values were >99.0% for each of the six bacterial targets and one fungal target tested with clinical samples. One viral target, herpes simplex virus 1, exhibited a PPA value of 100.0%, while the remaining viral targets-human parechovirus, herpes simplex virus 2, human herpes virus 6, and varicella zoster virus-were >90.0%, with the exception of enterovirus, which had a PPA value of 77.8%. The QIAstat-Dx ME Panel detected five true-positive and four true-negative cases compared to BioFire FilmArray ME Panel. The NPA values for all viral pathogens were >99.0%. Overall, the QIAstat-Dx ME Panel showed comparable performance to the BioFire FilmArray ME Panel as a rapid diagnostic tool for community-acquired meningitis and encephalitis.

Comparison of two assays to diagnose herpes simplex virus in patients with central nervous system infections

BACKGROUND

Multiplex PCR panels are frequently used for detecting the diagnosis of central nervous system infection, but have demonstrated lower sensitivity for herpes simplex virus (HSV) compared to targeted PCRs. Providers in our institution frequently order both multiplex (BioFire Meningitis/Encephalitis Panel (MEP)) and targeted HSV PCR (Diasorin Simplexa HSV-1/2 Direct), allowing comparison of assay performance in practice and a unique clinical characterization of patients with concordant positive or discordant results.

METHODS

We retrospectively analyzed all HSV testing performed using the two assays simultaneously in a large multi-center institution between 12/10/2018 and 6/6/2022. We described and compared laboratory, diagnostic and therapeutic data between patients with positive results on both assays with patients with discordant results.

RESULTS

1,387 patients were tested with both assays, of which 25 were positive on at least one assay. Eleven (44%) had discordant results; 9 were targeted-PCR-positive/MEP-negative and 2 were targeted-PCR-negative/MEP-positive. Compared with patients with concordant positive results, discordant targeted PCR-positive/MEP-negative patients had a higher PCR cycle threshold value (i.e., >35) and milder illness characterized by lower CSF WBC counts (4 vs 152; p = 0.032), fewer MRI abnormalities (37.5% vs. 87.5%; p = 0.039), HSV meningoencephalitis as primary discharge diagnosis (33% vs. 100%; p<0.0001) and were more often treated with oral medication or none at all.

CONCLUSIONS

Patients with discordant targeted PCR-positive/MEP-negative results represent a population with milder clinical disease. These findings will help clinicians and laboratorians determine when both targeted HSV and multiplex assays should be performed simultaneously and identify patients for whom a multiplex PCR may suffice, despite lower assay sensitivity.

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.

A Case of Herpes Simplex Virus Meningitis in an Immunocompromised Individual: Avoiding Common Diagnostic Pitfalls

Herpes simplex virus meningoencephalitis (HSV ME) is a severe viral infection that affects the brain and surrounding tissues. It is caused primarily by HSV type 1 (HSV-1) virus. This condition requires prompt recognition and treatment due to its potential for significant morbidity and mortality. We aim to highlight the importance of avoiding common diagnostic pitfalls in identifying HSV meningoencephalitis, especially in immunocompromised individuals. We present a case of a 34-year-old immunocompromised patient with HSV meningoencephalitis, emphasizing key clinical features and diagnostic strategies that helped us reach an accurate diagnosis. By sharing this case, we aim to enhance awareness and improve the management of HSV meningoencephalitis in similar patient populations, leading to better outcomes.

Evaluation of the Novel CE-IVD-Marked Multiplex PCR QIAstat-Dx Meningitis/Encephalitis Panel

Central nervous system (CNS) infections such as meningitis and encephalitis are life-threatening conditions that demand hospital care and prompt identification of the causative agent. Since 2015, there has been only one CE-IVD-marked rapid multiplexed diagnostic assay in cassette format for bacterial and viral detection from cerebrospinal fluid (CSF): the BioFire FilmArray meningitis/encephalitis (ME) panel. In the beginning of 2022, Qiagen introduced the QIAstat-Dx meningitis/encephalitis panel. It is a CE-IVD-marked multiplex PCR cassette test intended for the identification of suspected infectious meningitis, encephalitis, or meningoencephalitis caused by bacterial, viral, or fungal pathogens. In this study, we evaluated patient and quality control samples using the QIAstat-Dx meningitis/encephalitis panel and compared the results to those of the BioFire FilmArray meningitis/encephalitis panel and reference methods (current routine analysis methods in our laboratory, PCR, or cultivation). The combined positive percent agreement between the two panel assays was 100%, and the negative percent agreement was 94%. We further compared specifically herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) dilution series using six commercial herpesvirus assays, including the two cassette tests. The results suggested that real-time PCR methods (with separate extraction) were the most sensitive methods. When comparing the cassette tests, the BioFire FilmArray meningitis/encephalitis panel produced more positive results than the QIAstat-Dx meningitis/encephalitis panel in the herpesvirus analyses. IMPORTANCE The diagnosis of infectious meningitis and encephalitis relies mostly on specific PCR and culturing methods, but commercial syndromic panel assays are bringing a change in diagnostics. With multiplexed analysis, the identification of the pathogen is potentially faster, and less sample material is needed. The novel QIAstat-Dx meningitis/encephalitis panel assay is intended for the rapid identification of pathogens from cerebrospinal fluid for suspected central nervous system (CNS) infection, which is a life-threatening condition and difficult to diagnose. We studied the performance of this panel assay using patient samples and dilution series of selected viruses. The evaluation data for this novel meningitis/encephalitis panel assay are useful for other clinical laboratories and organizations using or considering using this test.

Clinical and Health System Impact of Biofire Filmarray Meningitis/Encephalitis Routine Testing of CSF in a Pediatric Hospital: An Observational Study

BACKGROUND

Rapid cartridge-based molecular test panels targeting multiple pathogens are increasingly available, improve pathogen detection and reduce turn-around-time but are more expensive than standard testing. Confirmation that these test panels contribute to improved patient or health service outcomes is required.

METHODS

In March 2021, our pediatric hospital laboratory implemented the BioFire Filmarray™ meningitis/encephalitis (M/E) panel as an additional routine test for all cerebrospinal fluid (CSF) samples collected from infants <90 days or from any patient in the emergency department. A retrospective chart review was done to ascertain changes in clinical outcomes, antimicrobial prescribing practices, and hospital length of stay, comparing two discrete 6-month periods: preimplementation (March-August 2019) and postimplementation (March-August 2021).

RESULTS

Both pre- and postimplementation groups were similar at baseline, except the preimplementation group had a higher proportion of infants with enterovirus and parechovirus meningitis. There was no significant difference between the groups in terms of median length of stay (2.94 vs 3.47 days, p = 0.41), duration of antibiotic treatment (2.0 vs 2.3 days, p = 0.25), need for central venous access (12.9% vs 17%, p = 0.38) or hospital-in-the-home admission (9.4% vs 9%, p = 0.92). A similar proportion of infants received aciclovir (33% vs 31%), however, a reduction in duration was observed (1.36 vs 0.90 days, p = 0.03) in the postimplementation period.

CONCLUSIONS

Introduction of the Biofire Filmarray™ M/E panel for routine testing of CSF samples reduced the duration of antiviral prescribing but had only a minor impact on antibiotic prescribing practices or health service outcomes in our pediatric hospital. The introduction of new laboratory testing needs to be supported by a comprehensive stewardship program to see optimal outcomes from new testing platforms.

Cerebrospinal fluid analysis in emergency patients with suspected infection of the central nervous system

BACKGROUND AND PURPOSE

Meningitis and encephalitis are potentially life-threatening diseases that require fast and accurate diagnostics and therapy. The value of polymerase chain reaction (PCR) multiplex testing in clinical practice is still a matter of debate. This study aims to evaluate its benefits and limitations in emergency patients.

METHODS

We assessed the value of a meningoencephalitis PCR array in the clinical routine of an emergency department.

RESULTS

Of 1578 emergency patients who received a lumbar puncture, 43% received it for a clinically suspected central nervous system (CNS) infection. After initial workup for cerebrospinal fluid (CSF) cell count, protein and glucose, a CNS infection was still considered likely in 307 patients. In these patients, further microbiologic workup was performed. A total of 230 samples were examined by PCR and a pathogen was detected in 66 of these samples. In the case of a positive microbiologic result, a comparison between PCR array and standard method was available for 59 samples, which demonstrated an overcall agreement of 80% (n = 47/59). Of interest, exclusively array-positive results were observed for patients with meningitis found to be positive for Streptococcus pneumoniae; four out of five patients had been treated with antibiotics before the lumbar puncture. In samples with normal CSF cell count only two positive array results were obtained, both for human herpesvirus 6, and these were not clinically relevant.

CONCLUSION

Our data suggest that the array substantially contributes to a detection of pathogens in patients with suspected CNS infection and seems of particular interest in patients with acute bacterial meningitis under empiric antibiotic treatment. In CSF samples with normal cell count, it might be dispensable.

Multiplex detection of meningitis and encephalitis pathogens: A study from laboratory to clinic

Introduction

Infectious meningitis and encephalitis (ME) are life-threatening conditions are caused by various pathogens. Conventional laboratory tests with low sensitivity and specificity cannot help with early diagnosis.

Methods

A prospective study using the novel multiplex PCR detection for 18 pathogens of ME (MME-18) was conducted to investigate the clinical utilization and the epidemiology characteristics of ME in southwestern China. Patients with suspected intracranial infection were recruited between May and October 2019 at West China Hospital of Sichuan University. The MME-18 was used to detect cerebrospinal fluid, and conventional experiments including cryptococcal capsular antigen detection, GeneXpert, real-time PCR, and clinical feedback were used to verify the result of MME-18.

Results

Among 581 tested patients, 139 eligible individuals were enrolled in the study. Among them, Mycobacterium tuberculosis was the most common pathogen in mono-infection. Viruses and Cryptococcus neoformans were also frequently detected. Of 139 infected patients, 12 cases were diagnosed by MME-18 only, 57 patients by conventional testing only, and 70 cases by both comparator tests and MME-18. There were 96.3% (79/82) diagnoses made by MME-18 had a favorable outcome, and two of twelve diagnoses, made solely by MME-18, had a likely unclear clinical significance.

Discussion

The MME-18 showed satisfactory consistency with expert clinical consensus for patients presenting with ME. Combined with conventional testing and clinical suspicion, MME-18 may help clinicians with the early identification of pathogens.

Evaluation and Clinical Impact of Biofire FilmArray Pneumonia Panel Plus in ICU-Hospitalized COVID-19 Patients

Microbiological diagnosis by using commercial multiplex quantitative PCR systems provides great advantages over the conventional culture. In this work, the Biofire FilmArray Pneumonia Panel Plus (FAPP+) was used to test 144 low respiratory tract samples from 105 COVID-19 patients admitted to an Intensive Care Unit (ICU), detecting 78 pathogens in 59 (41%) samples. The molecular panel was evaluated by using the conventional culture (CC) as comparator, which isolated 42 pathogens in 40 (27.7%) samples. The overall percentage of agreement was 82.6%. Values of sensitivity (93%), specificity (62%), positive predictive value (50%), and negative predictive value (96%) were obtained. The mean time elapsed from sample extraction to modification of antibiotic treatment was 7.6 h. A change in antimicrobial treatment after the FAPP+ results was performed in 27% of patients. The FAPP+ is a highly sensitive diagnostic method that can be used to significantly reduce diagnostic time and that allows an early optimization of antimicrobial treatment.

Impact of CSF Meningitis and Encephalitis Panel on Resource Use for Febrile Well-Appearing Infants

OBJECTIVES

To determine whether the BioFire FilmArray Meningitis/Encephalitis (ME) panel is associated with decreased resource use for febrile infants. The ME panel has a rapid turnaround time (1-2 hours) and may shorten length of stay (LOS) and antimicrobial use for febrile well-appearing infants.

METHODS

Retrospective cohort study of febrile well-appearing infants ≤60 days with cerebrospinal fluid culture sent in the emergency department from July 2017 to April 2019. We examined the frequency of ME panel use and its relationship with hospital LOS and initiation and duration of antibiotics and acyclovir. We used nonparametric tests to compare median durations.

RESULTS

The ME panel was performed for 85 (36%) of 237 infants. There was no difference in median hospital LOS for infants with versus without ME panel testing (42 hours, interquartile range [IQR] 36-52 vs 40 hours, IQR: 35-47, P = .09). More than 97% of infants with and without ME panel testing were initiated on antibiotics. Patients with ME panel were more likely to receive acyclovir (33% vs 18%; odds ratio: 2.2, 95%: confidence interval 1.2-4.0). There was no difference in median acyclovir duration with or without ME panel testing (1 hour, IQR: 1-7 vs 4.2 hours, IQR: 1-21, P = .10). When adjusting for potential covariates, these findings persisted.

CONCLUSIONS

ME panel use was not associated with differences in hospital LOS, antibiotic initiation, or acyclovir duration in febrile well-appearing infants. ME panel testing was associated with acyclovir initiation.

Use of the FilmArray® Meningitis/Encephalitis panel to detect pathogenic microorganisms in cerebrospinal fluid specimens: a single-center retrospective study

OBJECTIVE

Meningitis and encephalitis are neurological emergencies requiring rapid diagnosis and treatment. The performance of the FilmArray® Meningitis/Encephalitis (ME) panel, a multiplex polymerase chain reaction test, and conventional methods for diagnosing meningitis and encephalitis was compared.

METHODS

This retrospective study assessed 20 patients diagnosed with meningitis or encephalitis according to clinical symptoms and laboratory examination findings between January 2018 and December 2019. The results of the FilmArray® ME panel were compared with those of conventional methods.

RESULTS

Pathogens were identified in 11 (55%) patients using the FilmArray® ME panel and in nine (45%) patients using conventional methods. The test identified herpes simplex virus type 1 in two patients, herpes simplex virus type 2 in one, varicella-zoster virus in four, Streptococcus pneumoniae in three, and Cryptococcus neoformans in one. Furthermore, additional pathogens were detected (n = 1, S. pneumoniae and n = 1, varicella-zoster virus). The median times to pathogen identification were 2 hours using the FilmArray® ME panel and 96 hours with conventional methods.

CONCLUSIONS

The sensitivity of the FilmArray® ME panel for rapidly detecting the most common pathogens was similar to that of conventional methods. Hence, this method could decrease the time to definitive diagnosis and treatment initiation.

The Evaluation of the Diagnostic Performance of the BioFire FilmArray Meningitis/Encephalitis Panel in Children: A Retrospective Multicenter Study

Objective Acute bacterial meningitis (ABM) declined after implementing conjugate Haemophilus influenzae type B and the pneumococcal vaccines worldwide. However, it still contributes to significant morbidity and mortality. The Biofire FilmArray Meningitis Encephalitis (FAME) panel can rapidly diagnose common bacterial and viral pathogens. Several studies suggested that the use of FAME may accelerate diagnosis and decrease the time to pathogen-specific therapy. However, the clinical utility is still controversial due to scarce data and relatively high costs. Therefore, we aimed to evaluate the diagnostic performance of FAME in children.

Methods A retrospective multicenter cross-sectional study was conducted to evaluate FAME in diagnosing ABM in children with a suspected central nervous system infection between January 2017 and May 2021.

Results This study consisted of 179 children diagnosed with central nervous system infection who had parallel testing done using FAME and traditional microbiological diagnostic methods. Twenty-two FAME results were positive; 8 (36.3%) were bacterial pathogens and 14 (53.7%) were viral pathogens. The most common viral pathogen was human herpesvirus 6 (n  = 6; 27.2%), followed by herpes simplex virus 1 (n = 4; 18.1%), Enterovirus spp. (n = 2; 9%), Parechovirus (n = 2; 9%), and Cytomegalovirus (n = 1; 4.5%). Bacterial pathogens included S. pneumoniae (n = 3; 13.6%), H. influenzae (n = 3; 13.6%), Neisseria meningitidis (n = 1; 4.5%), and Streptococcus agalactiae (n = 1; 4.5%). Bacterial culture confirmed S. pneumoniae infection in only 1 of 8 (12.5%) patients, while 7 of 8 bacterial meningitis were only detected by FAME.

Conclusion FAME may also help with diagnosis and pathogen identification in patients who have already had antibiotics before cerebrospinal fluid collection. The use of FAME to detect infections quickly may minimize the improper use of medications, treatment duration, and the cost of hospitalization.

Impact of Implementing the Cerebrospinal Fluid (CSF) FilmArray Meningitis/Encephalitis Panel on Duration of Intravenous Acyclovir Treatment

Background

Herpes Simplex Virus-1 is the most common cause of sporadic encephalitis worldwide and requires prompt antiviral treatment. Traditionally, Herpes Simplex Virus-1 (HSV-1) cerebrospinal fluid (CSF) testing is conducted using standalone PCR. The BioFire CSF FilmArray Meningitis/Encephalitis Panel (BioFire ME Panel) was introduced in 2015 at our institution providing an alternative method of HSV-1 CSF testing. This study assesses the impact of the BioFire ME panel on duration of intravenous acyclovir treatment.

Methods

A retrospective review of electronic medical records between 2010 and 2019 was performed. Information on intravenous acyclovir treatment and HSV-1 CSF testing were collected and analyzed. Our descriptive analysis included Mann-Whitney tests, two proportion Z-tests, and logistic regression.

Results

Our CSF HSV-1 negative cohort included 524 BioFire patients (125 pediatric, 399 adult) and 287 standalone PCR patients (115 pediatric, 172 adult). Across both pediatric and adult groups, patients who were tested for HSV-1 with the BioFire ME panel had shorter average (SD) durations of intravenous acyclovir treatment [pediatric: 2.00 (5.71) days; adult: 3.26 (6.59) days] compared to patients tested with standalone PCR [pediatric: 4.83 (8.62) days; adult: 4.93 (8.46) days] (P &lt;0.001). Time from lumbar puncture collection to HSV-1 results was additionally faster on average for the BioFire ME panel than the standalone PCR (P &lt;0.001).

Conclusions

The implementation of the BioFire ME panel shortened CSF HSV-1 PCR result time and intravenous acyclovir duration. The shortened treatment and testing times from the BioFire ME panel implementation may reduce hospital treatment costs and unnecessary use of antiviral treatments.

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.

Noninvasive Testing and Surrogate Markers in Invasive Fungal Diseases

Invasive fungal infections continue to increase as at-risk populations expand. The high associated morbidity and mortality with fungal diseases mandate the continued investigation of novel antifungal agents and diagnostic strategies that include surrogate biomarkers. Biologic markers of disease are useful prognostic indicators during clinical care, and their use in place of traditional survival end points may allow for more rapid conduct of clinical trials requiring fewer participants, decreased trial expense, and limited need for long-term follow-up. A number of fungal biomarkers have been developed and extensively evaluated in prospective clinical trials and small series. We examine the evidence for these surrogate biomarkers in this review and provide recommendations for clinicians and regulatory authorities.

A Fatal Fungal Infection of Cryptococcus gattii (VGI) Meningitis in Texas

Cryptococcus gattii is an under-recognized cause of meningitis, especially in non-endemic regions. This report details C. gattii disease progression from admission to autopsy in an otherwise healthy 40-year-old male in Texas. It brings awareness to an often unsuspected organism that can cause severe infection requiring early recognition and treatment in immunocompetent individuals.

Evaluation of Discordant Results Between FilmArray Meningitis/Encephalitis Panel and Conventional Testing in Pediatric Patients: A Multisite Retrospective Cohort Study

BACKGROUND

The FilmArray Meningitis/Encephalitis panel (MEP) has an 11% false-positive and 2.2% false-negative rate compared with conventional testing. We describe clinical characteristics, treatment decisions, and outcomes in children with discordant results between MEP and conventional testing.

METHODS

We conducted a multisite review of patients ≤ 18 years with suspected central nervous system infection and positive results by MEP or conventional testing (cerebrospinal fluid [CSF] culture, herpes simplex virus [HSV] polymerase chain reaction (PCR), and enterovirus [EV] PCR). Descriptive results are provided for patients with discordant results. Comparison between group 1 (MEP and CSF culture positive) and group 2 (MEP positive, CSF culture negative, or showing a different pathogen) was made by Mann-Whitney test for continuous and Fisher's test for categorical variables.

RESULTS

A total of 355 patients had at least one pathogen identified. More than half of patients with bacterial pathogens identified that are included in the MEP had discordant results (30/52; 58%). There were 28 samples with bacterial pathogen identified on MEP only, 1 with different bacterial pathogens on MEP and culture, and 1 with Escherichia coli identified on CSF culture only. Patients in group 1 were more likely to have CSF pleocytosis, elevated CSF protein, and decreased CSF glucose than group 2 (P < .05). Two patients were HSV positive by MEP while HSV negative by PCR. Ten patients had discordant results between MEP and EV PCR.

CONCLUSIONS

Discordant results between MEP and conventional testing are common. Treatment decisions based on a positive MEP should be made in the appropriate clinical context.

Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Cryptococcal Meningitis in HIV-Negative Patients

Objectives

Metagenomic next-generation sequencing (mNGS) has been applied more and more widely for the diagnosis of infectious diseases, but its performance in the diagnosis of cryptococcal meningitis (CM) remains unclear.

Methods

Cerebrospinal fluid (CSF) samples from 197 HIV-negative patients with suspected central nervous system infections were tested simultaneously by mNGS and routine methods [India ink staining, fungal culture, or cryptococcal antigen (CrAg) tests]. The performance of mNGS was evaluated.

Results

Of the 197 enrolled cases, 46 (23.4%) cases were finally diagnosed with CM, including 43 (93.5%) Cryptococcus neoformans infections and 3 (6.5%) Cryptococcus gattii infections. The sensitivity, specificity, positive predictive value, negative predictive value, and concordance rate of mNGS were 93.5% [95% confidence interval (CI) at 86.4%~100.0%], 96.0% (95% CI at 92.9%~99.1%), 87.8%, 98.0%, and 95.4%, respectively. Comparing to the conventional diagnostic methods, the sensitivity and concordance rate of mNGS were slightly lower than those of CrAg tests (97.4%) but higher than those of India ink (63.0%) and culture (76.7%). Besides, mNGS had a sensitivity of 100.0% against culture. It should be noted that mNGS could identify Cryptococcus at species level; C. gattii of the 3 cases was only distinguished by mNGS.

Conclusions

CSF mNGS can be considered as a supplementary test to diagnose CM and directly distinguish C. gattii from C. neoformans in clinical specimens.

Group B Streptococcal Neonatal Meningitis

Neonatal bacterial meningitis is a devastating disease, associated with high mortality and neurological disability, in both developed and developing countries. Streptococcus agalactiae, commonly referred to as group B Streptococcus (GBS), remains the most common bacterial cause of meningitis among infants younger than 90 days. Maternal colonization with GBS in the gastrointestinal and/or genitourinary tracts is the primary risk factor for neonatal invasive disease. Despite prophylactic intrapartum antibiotic administration to colonized women and improved neonatal intensive care, the incidence and morbidity associated with GBS meningitis have not declined since the 1970s. Among meningitis survivors, a significant number suffer from complex neurological or neuropsychiatric sequelae, implying that the pathophysiology and pathogenic mechanisms leading to brain injury and devastating outcomes are not yet fully understood. It is imperative to develop new therapeutic and neuroprotective approaches aiming at protecting the developing brain. In this review, we provide updated clinical information regarding the understanding of neonatal GBS meningitis, including epidemiology, diagnosis, management, and human evidence of the disease's underlying mechanisms. Finally, we explore the experimental models used to study GBS meningitis and discuss their clinical and physiologic relevance to the complexities of human disease.

SARS-CoV-2-associated haemorrhagic encephalitis mimicking Herpes encephalitis

Although acute encephalopathy is quite commonly seen in patients of SARS-CoV-2 infection, encephalitis characterised by brain inflammation is relatively rare. Encephalitis caused by Herpes simplex type 1 is the most common cause of identified sporadic encephalitis, and early diagnosis and prompt treatment can prevent the devastating outcome. In this brief communication, we report a case of SARS-CoV-2 associated haemorrhagic encephalitis mimicking herpes encephalitis. In today's pandemic era, it is especially important to distinguish herpes encephalitis from SARS-CoV-2-associated encephalitis as treatment and prognosis of both the conditions differ greatly. This case highlights the importance of suspecting SARS-CoV-2 infection in a patient presenting with clinical symptoms and brain imaging suggestive of Herpes encephalitis.

Comparison of a Lateral Flow Assay and a Latex Agglutination Test for the Diagnosis of Cryptococcus Neoformans Infection

Infections by the basidiomycete yeast Cryptococcus neoformans are life-threatening diseases claiming more than 600,000 lives every year. The most common manifestation is cryptococcal meningitis in AIDS patients. Diagnosis primarily relies on antigen testing from serum and cerebrospinal fluid (CSF). Current guidelines recommend rapid antigen testing with a focus on point-of-care assays. Over the recent years, a range of new lateral flow assays (LFAs) was launched. There is still a lack of data evaluating the CE-certified Biosynex RDT CryptoPS LFA. We compared the performance of this LFA with a latex agglutination assay (LAA; Latex-Cryptococcus Antigen Detection System, IMMY) from blood and CSF samples. Blood and/or CSF samples of 27 patients with proven cryptococcal infections caused by different species and blood-CSF pairs of 20 controls were tested applying LFA and LAA. Upon combined analysis of blood and CSF, both assays were able to identify all C. neoformans infections. Based on CSF analysis only, the LFA and the LAA had sensitivities of 100% and 93%. Neither test gave false-positive results nor was reactive in two cases of C. non-neoformans/non-gattii species infections. Both assays have high sensitivities and specificities for the diagnosis of C. neoformans infection. Contrarily to the IMMY LAA, the RDT CryptoPS LFA is suitable as a point-of-care test but is limited in the quantification of antigen reactivity.

Polymicrobial anaerobic bacterial meningitis secondary to dermal sinus: a case report

Anaerobic bacterial meningitis is a rare infectious disease, and there are some special predisposing factors for it. We report a case of polymicrobial anaerobic bacterial meningitis in a nine-month-old boy who visited our hospital due to "fever with drowsiness and vomiting for 2 days". It was confirmed by the method of sanger sequencing after polymerase chain reaction (PCR) that the purulent meningitis was caused by a mixture of four anaerobic bacteria (Finegoldia magna, Campylobacter ureolyticus, Bacteroides fragilis and Porphyromonas bennonis). Even though there was no obvious structural abnormality on the skin surface, magnetic resonance imaging (MRI) examination suggested the presence of a sacrococcygeal dermal sinus. It was proven that anaerobic bacterial meningitis was secondary to retrograde infection of the dermal sinus. Finally, he was cured by a combination of anti-infection measures and surgical treatment. In conclusion, using appropriate molecular diagnostic techniques may quickly and accurately determine the pathogenic bacteria of anaerobic bacterial meningitis. When anaerobic bacterial meningitis occurs, the presence of structural abnormalities such as dermal sinus needs to be ruled out to avoid recurrence of the disease. In addition to anti-infective treatment, patients with dermal sinuses should undergo surgery as soon as possible to address abnormal structures and their root causes.

Impact of a Multiplex Polymerase Chain Reaction Panel on Duration of Empiric Antibiotic Therapy in Suspected Bacterial Meningitis

Background

Multiplex polymerase chain reaction (PCR) panels allow for rapid detection or exclusion of pathogens causing meningitis and encephalitis (ME). The clinical impact of rapid multiplex PCR ME panel results on the duration of empiric antibiotic therapy is not well characterized.

Methods

We performed a retrospective prepost study at our institution that evaluated the clinical impact of a multiplex PCR ME panel among adults with suspected bacterial meningitis who received empiric antibiotic therapy and underwent lumbar puncture in the emergency department. The primary outcome was the duration of empiric antibiotic therapy.

Results

The positive pathogen detection rates were similar between pre- and post-multiplex PCR ME panel periods (17.5%, 24 of 137 vs 20.3%, 14 of 69, respectively). The median duration of empiric antibiotic therapy was significantly reduced in the post-multiplex PCR ME panel period compared with the pre-multiplex PCR ME panel period (34.7 vs 12.3 hours, P = .01). At any point in time, 46% more patients in the post-multiplex PCR ME panel period had empiric antibiotic therapy discontinued or de-escalated compared with the pre-multiplex PCR ME panel period (sex- and immunosuppressant use-adjusted hazard ratio 1.46, P = .01). The median hospital length of stay was shorter in the post-multiplex PCR ME panel period (3 vs 4 days, P = .03).

Conclusions

The implementation of the multiplex PCR ME panel for bacterial meningitis reduced the duration of empiric antibiotic therapy and possibly hospital length of stay compared with traditional microbiological testing methods.

Molecular diagnosis of the central nervous system (CNS) infections

Central nervous system (CNS) infections such as meningitis and encephalitis are medical emergencies that require rapid diagnosis of the causative pathogen to guide early and adequate treatment since a delay in implementing an adequate antimicrobial therapy can lead to death. The current microbiological diagnostic methods based on culture or antigen detection have important limitations in their capacity to accurately identify the different potential pathogens causing CNS and, in the time, to obtaining results. Rapid syndromic molecular arrays have been developed. The main advantage of using a meningoencephalitis panel based in a multiplex test is that includes bacteria, viruses and fungi, covering the most prevalent microorganisms causing meningitis and encephalitis and the turn-around time is circa 1h. The use of these multiplex-PCR based tools is reviewed and the advantages and disadvantages of this technique are discussed.

A discussion of syndromic molecular testing for clinical care

Current molecular detection methods for single or multiplex pathogens by real-time PCR generally offer great sensitivity and specificity. However, many infectious pathogens often result in very similar clinical presentations, complicating the test-order for physicians who have to narrow down the causative agent prior to in-house PCR testing. As a consequence, the intuitive response is to start empirical therapy to treat a broad spectrum of possible pathogens. Syndromic molecular testing has been increasingly integrated into routine clinical care, either to provide diagnostic, epidemiological or patient management information. These multiplex panels can be used to screen for predefined infectious disease pathogens simultaneously within a 1 h timeframe, creating opportunities for rapid diagnostics. Conversely, syndromic panels have their own challenges and must be adaptable to the evolving demands of the clinical setting. Firstly, questions have been raised regarding the clinical relevance of some of the targets included in the panels and secondly, there is the added expense of integration into the clinical laboratory. Here, we aim to discuss some of the factors that should be considered before performing syndromic testing rather than traditional low-plex in-house PCR.

Update on Viral Infections Involving the Central Nervous System in Pediatric Patients

Infections of the central nervous system (CNS) are mainly caused by viruses, and these infections can be life-threatening in pediatric patients. Although the prognosis of CNS infections is often favorable, mortality and long-term sequelae can occur. The aims of this narrative review were to describe the specific microbiological and clinical features of the most frequent pathogens and to provide an update on the diagnostic approaches and treatment strategies for viral CNS infections in children. A literature analysis showed that the most common pathogens worldwide are enteroviruses, arboviruses, parechoviruses, and herpesviruses, with variable prevalence rates in different countries. Lumbar puncture (LP) should be performed as soon as possible when CNS infection is suspected, and cerebrospinal fluid (CSF) samples should always be sent for polymerase chain reaction (PCR) analysis. Due to the lack of specific therapies, the management of viral CNS infections is mainly based on supportive care, and empiric treatment against herpes simplex virus (HSV) infection should be started as soon as possible. Some researchers have questioned the role of acyclovir as an empiric antiviral in older children due to the low incidence of HSV infection in this population and observed that HSV encephalitis may be clinically recognizable beyond neonatal age. However, the real benefit-risk ratio of selective approaches is unclear, and further studies are needed to define appropriate indications for empiric acyclovir. Research is needed to find specific therapies for emerging pathogens. Moreover, the appropriate timing of monitoring neurological development, performing neuroimaging evaluations and investigating the effectiveness of rehabilitation during follow-up should be evaluated with long-term studies.

Assessment of a Multiplex LAMP Assay (Eazyplex® CSF Direct M) for Rapid Molecular Diagnosis of Bacterial Meningitis: Accuracy and Pitfalls

Background: Automated molecular panels are attractive tools for improving early meningitis diagnosis. This study assessed the Eazyplex^® CSF direct M panel (EP), a multiplex real-time Loop-Mediated Isothermal Amplification assay. Methods: From December 2016 to December 2019, cerebrospinal fluid (CSF) samples were routinely tested with the EP V1.0. CSF parameters and microbiological and clinical data were retrospectively collected. Results: Out of 230 CSF samples, the EP yielded positive, negative, and invalid results for 32 (13.9%) (16 N. meningitidis, nine S. pneumoniae, two S. agalactiae, two E. coli, two H. influenzae, one L. monocytogenes), 182 (79.1%), and 16 (7%) samples, respectively. Among the positive samples, 14 (44%) remained negative in culture (antibiotic therapy before lumbar puncture (n = 11), meningococcal meningitis (n = 3)). High CSF protein concentrations and cellularity were associated with LAMP inhibition, counteracted by centrifugation. The automated software yielded 13 false positive and five false negative results. Amplification curve analysis was necessary and enabled the attainment of positive (PPA) and negative percentage agreement and positive and negative predictive values of 91.4%, 100%, 100%, and 98.3%. Three false negative results remained (two E. coli and one N. meningitidis). E. coli presented the poorest PPA (50%). Conclusion: This work confirms the strong performance of the EP, of particular interest in cases of antibiotic therapy before lumbar puncture.

Evaluation of the BioFire® FilmArray® Meningitis/Encephalitis panel in an adult and pediatric Ugandan population

BACKGROUND

Meningitis causes significant mortality in sub-Saharan Africa and limited diagnostics exist. We evaluated the utility of the BioFire® FilmArray® Meningitis/Encephalitis multiplex PCR panel (BioFire ME) in HIV-infected adults and HIV-infected and uninfected children presenting with suspected meningitis in Uganda.

METHODS

We tested cerebrospinal fluid (CSF) using a stepwise meningitis diagnostic algorithm including BioFire ME. We determined the diagnostic performance of BioFire ME for cryptococcal meningitis, using cryptococcal antigen (CrAg) and CSF culture as reference standards, and assessed other central nervous system (CNS) pathogens identified by the panel.

RESULTS

We evaluated 328 adult and 42 pediatric CSF specimens using BioFire ME. Of the adult CSF samples tested, 258 were obtained at baseline, and 70 were obtained from repeat lumbar punctures in cryptococcal meningitis. For Cryptococcus, sensitivity was 82%, specificity was 98%, PPV was 98%, and NPV was 79% in baseline specimens using CSF CrAg as the reference standard. Among follow-up specimens, a negative BioFire ME for Cryptococcus predicted CSF culture sterility with 84% NPV. Overall sensitivity was decreased at low fungal burdens: 29% for 0-99 Cryptococcus CFU/mL compared to 94% for ≥100 CFU/mL in baseline specimens. Other pathogens detected included E. Coli, H. influenzae, S. pneumoniae, CMV, enterovirus, HSV, HHV-6, and VZV. Two specimens tested positive for S. pneumoniae and one for Cryptococcus in the pediatric population.

CONCLUSIONS

Multiplex PCR is a promising rapid diagnostic test for meningitis in adults and children in resource-limited settings. Cryptococcus at low fungal burdens in CSF may be missed by BioFire ME.

Evaluation and Management of Well-Appearing Febrile Infants 8 to 60 Days Old

This guideline addresses the evaluation and management of well-appearing, term infants, 8 to 60 days of age, with fever ≥38.0°C. Exclusions are noted. After a commissioned evidence-based review by the Agency for Healthcare Research and Quality, an additional extensive and ongoing review of the literature, and supplemental data from published, peer-reviewed studies provided by active investigators, 21 key action statements were derived. For each key action statement, the quality of evidence and benefit-harm relationship were assessed and graded to determine the strength of recommendations. When appropriate, parents' values and preferences should be incorporated as part of shared decision-making. For diagnostic testing, the committee has attempted to develop numbers needed to test, and for antimicrobial administration, the committee provided numbers needed to treat. Three algorithms summarize the recommendations for infants 8 to 21 days of age, 22 to 28 days of age, and 29 to 60 days of age. The recommendations in this guideline do not indicate an exclusive course of treatment or serve as a standard of medical care. Variations, taking into account individual circumstances, may be appropriate.

Sequential infection of Epstein-Barr virus and cryptococcal encephalitis after umbilical cord blood transplantation in a child with X-linked adrenoleukodystrophy

Dual infection with two pathogens can be found in few cases of encephalitis. Cases of sequential infection with EBV and cryptococcal encephalitis in post-transplant patients are rare. We describe a 5-year-old boy with X-linked adrenoleukodystrophy who presented sequential infection with EBV and cryptococcal encephalitis after umbilical cord blood transplant. The patient showed fever, vomiting and emotional agitation with EBV DNA detected in CSF on day 100. The child underwent 3 doses of intravenous rituximab with a good response. However, the child presented with right facial paralysis, headache, and fever on day 130 after 2 weeks of clinical stability. Brain MRI demonstrated chronic granuloma formed with ring enhancement. FilmArray ME PCR confirmed the existence of Cryptococcus neoformans/gattii in the CSF. The child underwent sequential treatment with amphotericin liposome B and flucytosine. Maintenance treatment with fluconazole was administered for 1 year. Facial paralysis was on longer present on day 260. Cryptococcus neoformans/gattii was not detected on day 310. The biochemistry and cell count of the CSF were completely normal on day 520. Follow-up 2.5 years after presentation, brain MRI changes showed near complete resolution of the lesions. The child survived for 3 years to the last following-up. Invasive cryptococcal encephalitis is rare and life-threatening complication of transplantation. It is important to recognize dual infections, and perform treatment quickly to improve the prognosis of encephalitis after transplantation.

Evaluation of FilmArray ME panel for the rapid diagnosis of meningitis-encephalitis in emergency departments

To assess the impact of a rapid diagnostic system based on nucleic acid amplification techniques (FilmArray ME) on the diagnosis and treatment of patients with meningitis or encephalitis admitted to our emergency department. Between November 2016, and June 2019 we studied 79 samples of cerebrospinal fluid from patients admitted to our emergency department with suspected diagnoses of meningitis or encephalitis. FilmArray ME panel was used routinely in addition to conventional laboratory methods for the identification of microorganisms in cerebrospinal fluid samples (CSF). A total of 46 (58%) patients had clinical and CSF results suggestive of meningitis or encephalitis, and 24 (30%) had a confirmed microbiological diagnosis. Patients' mean age was 41 years (range 2 months to 90 years) and 56% were male. Four patients had been partially treated with antibiotics. FilmArray ME identified 23 cases (1 fungal, 11 bacterial, and 11 viral). Gram staining showed microorganisms in 5 cases (1 fungal, 4 bacterial), and conventional microbiology cultures identified 8 cases (1 fungal and 7 bacterial). The time difference (95% confidence interval) between FilmArray ME and cerebrospinal fluid culture results was 3.2 days (95% CI 2.7-3.7; P < 0.001). FilmArray ME results induced modifications in antimicrobial treatment in 27 (59%) patients. The FilmArray ME panel provided a fast and reliable result in a large proportion of patients, even in those patients with culture-negative bacterial meningitis. Use of FilmArray ME can contribute to antimicrobial stewardship.

Cryptococcosis

Cryptococcosis is an invasive fungal infection of global significance caused by yeasts of the genus Cryptococcus. The prevalence of HIV in certain areas of the world and the expanding population of immunocompromised patients contribute to the ongoing global disease burden. Point-of-care serologic testing has allowed for more rapid diagnosis and implementation of screening programs in resource-limited settings. Management involves therapy aimed at reduction in fungal burden, maintenance of intracranial pressure, and optimization of host immunity. Despite diagnostic and therapeutic advances, cryptococcosis continues to be a disease with unacceptably high incidence and mortality, particularly in resource-limited settings.

Assessment of the FilmArray ME panel in 4199 consecutively tested cerebrospinal fluid samples

OBJECTIVES

In central nervous system infections, early and correct management is of utmost importance. Rapid syndromic panel testing can potentially provide valuable guidance. The FilmArray meningitis/encephalitis (ME) panel detects 14 pathogens through multiplex PCR. Our study objectives were to assess its performance compared with established diagnostic procedures, especially real-time quantitative PCR for detection of viruses, and to determine the diagnostic and clinical significance of discrepant results.

METHODS

All cerebrospinal fluid samples sent for viral diagnostics to our microbiological laboratory over 34 months were analysed with the ME panel and in-house real-time PCR for herpes simplex virus type 1 (HSV-1), HSV-2, varicella zoster virus and enteroviruses. Other pathogens detected by the panel were confirmed by routine diagnostic procedures. Discrepant results were analysed through interpretation of biological and clinical data, and performance data were calculated for individual pathogens.

RESULTS

Altogether, 315 pathogens were detected by the ME panel in 4199 cerebrospinal fluid samples (7.5%) and an additional 21 viral targets were identified using real-time PCR. Thirty-four ME panel detections were not confirmed, totalling 55 discrepant results. After discrepancy analysis, 20 false-positive and 21 false-negative ME panel results remained. Performance varied between pathogens. Sensitivity for HSV-1 was calculated at 82.4% (59.0%-93.8%) with three false-negative results. Also noteworthy were 13 false-negative enterovirus and eight false-positive Streptococcus pneumoniae results.

CONCLUSIONS

Our analysis shows good performance for the ME panel in diagnosing central nervous system infection. The risk of false-negative HSV-1 results, however, warrants additional testing when encephalitis is suspected. Uncertainties in interpretation of enterovirus and S. pneumoniae results represent other limitations.

Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review

Bacterial meningitis is a major global cause of morbidity and mortality. Rapid identification of the aetiological agent of meningitis is essential for clinical and public health management and disease prevention given the wide range of pathogens that cause the clinical syndrome and the availability of vaccines that protect against some, but not all, of these. Since microbiological culture is complex, slow, and often impacted by prior antimicrobial treatment of the patient, molecular diagnostic assays have been developed for bacterial detection. Distinguishing between meningitis caused by Neisseria meningitidis (meningococcus), Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Streptococcus agalactiae and identifying their polysaccharide capsules is especially important. Here, we review methods used in the identification of these bacteria, providing an up-to-date account of available assays, allowing clinicians and diagnostic laboratories to make informed decisions about which assays to use.