Multicenter Evaluation of BioFire FilmArray Meningitis/Encephalitis Panel for Detection of Bacteria, Viruses, and Yeast in Cerebrospinal Fluid Specimens

Diagnosis of Neurological Infections in Pediatric Patients from Cell-Free DNA Specimens by Using Metagenomic Next-Generation Sequencing

Central nervous system (CNS) infections can cause significant morbidity and mortality, especially in children. Rapid and accurate pathogenic detection in suspected CNS infections is essential for disease control at the early stage of infection. To evaluate the performance of metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) in pediatric patients, we retrospectively analyzed the efficiency of cfDNA mNGS in children with CNS infections (n = 257) or noninfectious neurological disorders (n = 81). The CSF samples of 124 random subjects were used to evaluate the accuracy between mNGS of cfDNA and whole-cell DNA (wcDNA). In total, cfDNA mNGS detected a wide range of microbes with a detection rate of 71.0%, and the sensitivity and total coincidence rate with clinical diagnosis reached 68.9% and 67.5%, respectively. Compared with wcDNA mNGS, cfDNA mNGS had a higher efficacy in detecting viruses (66 versus 13) and Mycobacterium (7 versus 1), with significantly higher reads per million. The dominant causative pathogens were bacteria and viruses in CNS infections, but these presented with different pathogen spectra in different age categories. The best timing for the mNGS test ranged from 1 to 6 days after the start of anti-infection therapy, and the earlier mNGS started, the better was identification of bacterial CNS infections. This study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in pediatric CNS infections, and it was even better than wcDNA mNGS. Furthermore, research needs to be better validated in large-scale clinical trials to improve the clinical applications of cfDNA mNGS. IMPORTANCE Our study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in CNS-infected children, and it was even better than wcDNA mNGS. cfDNA mNGS detected a wide range of pathogens with a high total coincidence rate (67.5%) against clinical diagnosis. The best timing for cfDNA mNGS detection ranged from 1 to 6 days, rather than 0 days, after the start of empirical anti-infection therapy. The earlier mNGS started, the better the identifications of bacterial CNS infections. To the best of our knowledge, this research is the first report evaluating the clinical utility of mNGS with different methods (cfDNA versus wcDNA) of extracting DNA from CSF specimens in diagnosing pediatric CNS infections. Meanwhile, this is the largest cohort study that has evaluated the performance of mNGS using cfDNA from CSF specimens in pediatric patients with CNS infections.

The Contribution of Multiplex Polymerase Chain Reaction in the Diagnosis of Central Nervous System Infections in Intensive Care Units

Introduction The aim of this study was to evaluate the contribution and limits of BioFire® FilmArray® meningitis/encephalitis panel (FA MEP) polymerase chain reaction (PCR) (bioMérieux, Marcy-l'Étoile, France) (product references: LLC RFIT-ASY-0118) coupled with bacterial and fungal culture in the diagnosis of central nervous system infections (CNSIs). Methods This was a retrospective observational study including all patients (adults and children) hospitalized in the intensive care units (ICUs) of a Moroccan university hospital, who benefited from multiplex PCR on a cerebrospinal fluid (CSF) sample. Results A total of 112 PCRs were performed, with a positivity rate of 18%. Bacterial etiology was the most frequent (70%), represented mainly by Streptococcus pneumoniae (45%), followed by viruses (25%), with four isolates of Herpes simplex virus (HSV) 1. On 94 samples, there was an agreement between the culture and PCR results. Their discordance was found in 18 cases, including 16 suspected CNSIs recovered only by PCR and two diagnoses confirmed only by bacterial culture. Conclusion This study revealed the significant impact of multiplex PCR on the early and targeted diagnostic and therapeutic management of infectious meningitis and meningoencephalitis in intensive care unit patients.

Hunting for mpox (monkeypox) mimickers: Use of the Biofire meningitis/encephalitis panel on lesion swabs to support alternative viral diagnoses

BACKGROUND

Mpox (formerly monkeypox) is an emerging zoonotic disease of public health concern that presents as a rash mimicking other common viral exanthems. Unlike traditional testing algorithms relying on several assays, the BioFire FilmArray meningitis/encephalitis (ME) panel simultaneously detects common viruses causing rashes; however, Biofire ME is only licensed for testing on cerebral spinal fluid.

OBJECTIVES

This study evaluated use of the Biofire ME panel for detection and discrimination of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), varicella zoster virus (VZV), human herpesviruses type 6 (HHV-6), enteroviruses (EVs), and human paraechoviruses (HPeVs) from a dermal or mucocutaneous swabs collected in universal transport media (UTM).

STUDY DESIGN

Results of the BioFire ME panel were compared against methods used during clinical testing. Ten-fold serial dilutions in UTM of cultured viruses were used to compare analytical sensitivity, and analytical specificity was assessed using panels of microorganisms in UTM. Clinical sensitivity and specificity were assessed using 20 positive specimens each for HHV-1, HHV-2, HHV-6, VZV, EVs, and HPeV, as well as 35 known negative specimens that included 15 mpox-positive specimens.

RESULTS

Biofire ME was as sensitive as comparator methods, and correctly discriminated all HSV-1, HSV-2, VZV, HHV-6, EVs, and HPeVs from mpox and mpox-mimickers. Cross-reaction between EV and rhinoviruses A, B, and C were noted in the specificity panel.

CONCLUSIONS

Swabs in UTM collected for mpox testing are suitable for use on the Biofire ME panel, allowing more streamlined diagnostic testing for viral exanthems in patients under investigation for mpox infection.

An Atypical Case of Enterovirus Meningitis Presenting with Unilateral Optic Disc Swelling and Minimal Optical Symptoms

PURPOSE

To report a case of unilateral disc swelling as the only presentation of enterovirus meningitis in a 43-year-old male who presented with reduction in visual quality.

METHODS

Vision was 20/20 unaided in both eyes and the only ocular finding was left optic disc edema accompanied by left relative afferent pupillary defect. Visual field examination revealed a generalized reduction in sensitivity, a paracentral scotoma and a superior and inferior arcuate defect. Apart from a marginally elevated white blood cell count, the evaluation for common diseases associated with unilateral disc swelling was negative. A comprehensive neurology and rheumatology assessment,the orbital, brain and cervical spine Magnetic Resonance Imaging (MRI), the chest and abdomen Computed Tomography (CT) and chest radiograph had no findings. However, the cerebrosipinal fluid (CSF) examination indicated the presence of enterovirus RNA.

RESULTS

A diagnosis of enterovirus meningitis was established.Patient's general health was not affected and symptoms gradually settled, with no specific anti-enteroviral treatment.

CONCLUSION

Only the CSF analysis provided interesting evidence of the site of the visual dysfunction.

Evaluation of the accuracy of multiplex polymerase chain reaction in differentiation between bacterial and viral meningitis

BACKGROUND

Meningitis is one of the most dangerous infection affecting children. The need for rapid and accurate diagnosis is mandatory for improving the outcome.

AIM OF THE WORK

To evaluate the role of multiplex polymerase chain reaction (PCR) in diagnosis of meningitis either bacterial or viral and to detect its accuracy.

PATIENTS AND METHODS

A cross-sectional study was carried out in University Children Hospital, Faculty of Medicine, between November 2019 and September 2020. The study was approved by the Ethics Review Board of Faculty of Medicine, Assiut University, and informed written consent was obtained. The committee's reference number is 17200161. Clinicaltrails.gov ID: NCT03387969. Forty-eight children aged 2 to 18 years with meningitis were included. Detailed history and examination, blood glucose level at time of admission prior to lumbar puncture, and multiplex PCR in cerebrospinal fluid (CSF) were evaluated.

RESULTS

The mean age of children was 3.27 ± 1.27 years. Thirty-five (72.9%) cases were bacterial meningitis while 13 (27.1%) cases were viral meningitis. Multiplex PCR had 94% sensitivity and 100% specificity for diagnosis of bacterial meningitis.

CONCLUSION

Multiplex PCR may help in diagnosis and differentiation of bacterial and viral meningitis with accurate and rapid results.

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.

The experience of using FilmArray Meningitis/Encephalitis Panel for the diagnosis of meningitis and encephalitis in pediatric patients

BACKGROUND/PURPOSE

Central nervous system infections can cause severe complications and even death in children. Early diagnosis of the causative pathogen can guide appropriate treatment and improve outcomes. The BioFire® FilmArray® Meningitis/Encephalitis Panel (FA-ME) is a multiplex polymerase chain reaction (PCR) assay targeting 14 pathogens. We aimed to examine FA-ME performance compared with conventional assays and its effect on antimicrobial usage.

METHODS

We prospectively enrolled 55 pediatric patients with suspected meningitis or encephalitis and simultaneously performed FA-ME and conventional assays. Sixty-three hospitalized patients with CNS infection before implementing FA-ME were considered controls. We compared the FA-ME results with conventional assays and the empiric antimicrobial usage and hospital stay between the two study groups.

RESULTS

Nine patients (16.4%) tested positive by FA-ME, four were bacterial, and five were viral. Three additional pathogens were detected by conventional assays: Enterococcus faecalis, Leptospira, and herpes simplex virus type 2. In the control group, two bacterial pathogens were detected by CSF culture and four viral pathogens by single PCRs. Compared with the control group, the FA-ME group had a shorter time for pathogen detection, but there were no significant differences in pathogen detection rate, duration of empiric antimicrobial therapy, and length of hospital stay.

CONCLUSION

Although no significant difference was found in empiric antimicrobial duration and length of stay between patients tested with FA-ME and conventional assays, FA-ME had the advantage of a shorter detection time and early exclusion of potential causative pathogens. The FA-ME results should be interpreted carefully based on the clinical presentation.

Analysis of the Clinical Impact of the BioFire FilmArray Meningitis Encephalitis Panel on Antimicrobial Use and Duration of Therapy at an Academic Medical Center

The purpose of this study was to assess the clinical impact of the BioFire FilmArray Meningitis/Encephalitis (ME) panel on antimicrobial use and clinical outcomes. This retrospective, quasi-experiment evaluated adult and pediatric patients with suspected ME, evidenced by cerebrospinal fluid (CSF) culture. Hospital-acquired meningitis patients and patients who received antimicrobials >48 h prior to lumbar puncture were excluded. The primary endpoint was days of antimicrobial therapy pre- and post-implementation of the ME panel. Secondary endpoints included total length of stay, 30-day readmission, and individual days of antimicrobial therapy. Two hundred and sixty-four total adult and pediatric patients were included. Antimicrobial days of therapy had a median of 3 days (IQR 0−5) in the pre vs. post group with a median of 2 days (2−5) (p = 0.099). Days of therapy for acyclovir were significantly decreased in the post group (median 2 days [IQR 1−3] vs. 3 days [IQR 2.5−4.5], p = 0.0002). There were no significant differences in the secondary endpoints. Overall, implementation of the ME panel impacted the duration of antimicrobials, particularly acyclovir; however, opportunities for further education regarding antimicrobial de-escalation and utilization of the panel were identified. Antimicrobial stewardship program intervention is critical to maximize benefit of this rapid diagnostic test.

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.

Current state and practice variation in the use of Meningitis/Encephalitis (ME) FilmArray panel in children

Background

The Meningitis/Encephalitis FilmArray® Panel (ME panel) was approved by the U.S. Food and Drug Administration in 2015 and provides rapid results when assessing patients with suspected meningitis or encephalitis. These patients are evaluated by various subspecialties including pediatric hospital medicine (PHM), pediatric emergency medicine (PEM), pediatric infectious diseases, and pediatric intensive care unit (PICU) physicians. The objective of this study was to evaluate the current use of the ME panel and describe the provider and subspecialty practice variation.

Methods

We conducted an online cross-sectional survey via the American Academy of Pediatrics Section of Hospital Medicine (AAP-SOHM) ListServe, Brown University PEM ListServe, and PICU Virtual pediatric system (VPS) Listserve.

Results

A total of 335 participants out of an estimated 6998 ListServe subscribers responded to the survey. 68% reported currently using the ME panel at their institutions. Among test users, most reported not having institutional guidelines on test indications (75%) or interpretation (76%). 58% of providers self-reported lack of knowledge of the test’s performance characteristics. Providers from institutions that have established guidelines reported higher knowledge compared to those that did not (51% vs. 38%; p = 0.01). More PHM providers reported awareness of ME panel performance characteristics compared to PEM physicians (48% vs. 27%; p = 0.004); confidence in test interpretation was similar between both groups (72 vs. 69%; p = 0.80).

Conclusion

Despite the widespread use of the ME panel, few providers report having institutional guidelines on test indications or interpretation. There is an opportunity to provide knowledge and guidance about the ME panel among various pediatric subspecialties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07789-2.

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.

Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France

BACKGROUND

Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis.

METHODS

A series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software.

FINDINGS

Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding > 50% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology.

INTERPRETATION

In addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis.

FUNDING

This work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.

Etiology and Risk Factors for Admission to the Pediatric Intensive Care Unit in Children With Encephalitis in a Developing Country

OBJECTIVE

To describe a cohort of pediatric patients with encephalitis and their risk factors for admission to the pediatric intensive care unit (PICU).

STUDY DESIGN

Children (<18 years old), with encephalitis evaluated by conventional microbiology and syndromic, multiplex test in cerebrospinal fluid (CSF) between July 2017 and July 2020, were recruited from 14 hospitals that comprise the Colombian Network of Encephalitis in Pediatrics. Multivariate analyses were used to evaluate risk factors associated with the need for PICU admission.

RESULTS

Two hundred two children were included, of which 134 (66.3%) were male. The median age was 23 months (IQR 5.7-73.2). The main etiologies were bacteria (n = 55, 27%), unspecified viral encephalitis (n = 44, 22%) and enteroviruses (n = 27, 13%), with variations according to age group. Seventy-eight patients (38.6%) required management in the PICU. In multivariate analysis, factors associated with admission to the PICU were the presence of generalized seizures (OR 2.73; 95% CI: 1.82-4.11), status epilepticus (OR 3.28; 95% CI: 2.32-4.62) and low leukocyte counts in the CSF (OR 2.86; 95% CI: 1.47-5.57). Compared with enterovirus, bacterial etiology (OR 7.50; 95% CI: 1.0-56.72), herpes simplex encephalitis (OR 11.81; 95% CI: 1.44-96.64), autoimmune encephalitis (OR 22.55; 95% CI: 3.68-138.16) and other viral infections (OR 5.83; 95% CI: 1.09-31.20) increased the risk of PICU admission.

CONCLUSIONS

Data from this national collaborative network of pediatric patients with encephalitis allow early identification of children at risk of needing advanced care and can guide the risk stratification of admission to the PICU.

Metagenomic next-generation sequencing of cell-free and whole-cell DNA in diagnosing central nervous system infections

Background

Central nervous system (CNS) infections pose a fatal risk to patients. However, the limited sample volumes of cerebrospinal fluid (CSF) and low detection efficiency seriously hinder the accurate detection of pathogens using conventional methods.

Methods

We evaluated the performance of metagenomics next-generation sequencing (mNGS) in diagnosing CNS infections. CSF samples from 390 patients clinically diagnosed with CNS infections were used for the mNGS of cell-free DNA (cfDNA) (n =394) and whole-cell DNA (wcDNA) (n =150).

Results

The sensitivity of mNGS using cfDNA was 60.2% (237/394, 95% confidence interval [CI] 55.1%–65.0%), higher than that of mNGS using wcDNA (32.0%, 95% [CI] 24.8%–40.2%, 48/150) and conventional methods (20.9%, 95% [CI] 16.2%–26.5%, 54/258) (P < 0.01, respectively). The accuracy of mNGS using cfDNA in positive samples was 82.6%. Most of viral (72.6%) and mycobacterial (68.8%) pathogens were only detected by the mNGS of cfDNA. Meningitis and encephalitis with Streptococcus pneumoniae infection might be more likely to result in critically ill diseases, while Human alphaherpesvirus 3 was prone to cause non-critically ill diseases.

Conclusions

This is the first report on evaluating and emphasizing the importance of mNGS using CSF cfDNA in diagnosing CNS infections, and its extensive application in diagnosing CNS infections could be expected, especially for viral and mycobacterial CNS infections.

Understanding etiology of community-acquired central nervous system infections using metagenomic next-generation sequencing

Background

Community-acquired central nervous system infections (CA-CNS infections) have the characteristics of acute onset and rapid progression, and are associated with high levels of morbidity and mortality worldwide. However, there have been only limited studies on the etiology of this infections. Here, metagenomic next-generation sequencing (mNGS), a comprehensive diagnosis method, facilitated us to better understand the etiology of CA-CNS infections.

Methods

We conducted a single-center retrospective study between September 2018 and July 2021 in which 606 cerebrospinal fluid (CSF) samples were collected from suspected CNS infectious patients for mNGS testing, and all positive samples were included in this analysis

Results

After the exclusion criteria, a total of 131 mNGS-positive samples were finally enrolled. Bacterial, viral, fungal, parasitic, specific pathogen and mixed infections were accounted for 32.82% (43/131), 13.74% (18/131), 0.76% (1/131), 2.29% (3/131) and 6.87% (9/131), respectively. A total of 41 different pathogens were identified, including 16 bacteria, 12 viruses, 10 fungi, and 1 parasite and 3 specific pathogens. The most frequent infecting pathogens are Epstein-Barr virus (n = 14), Herpes simplex virus 1 (n = 14), Mycobacterium tuberculosis (n = 13), Streptococcus pneumoniae (n = 13), and Cryptococcus neoformans (n = 8). Some difficult-to-diagnose pathogen infections were also detected by mNGS, such as Streptococcus suis, Pseudorabies virus, Bunyavirus, Orientia tsutsugamushi and Toxoplasma gondii.

Conclusion

In this study, mNGS identified a wide variety of pathogens of CA-CNS infections and many of which could not be detected by conventional methods. Our data provide a better understanding of the etiology of CA-CNS infections and show that mNGS represents a comparative screening of CSF in an unbiased manner for a broad range of human pathogens.

Herpesvirus-Associated Encephalitis: an Update

Purpose of Review

Recent Findings

Summary

Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient

There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.

Etiological Analysis of Viral Encephalitis in Children in Zhejiang Province from 2018 to 2019

Objective: To investigate the common pathogens of viral encephalitis (VE) in children, and to provide guidance for the empirical diagnosis and treatment of patients with VE. Methods: A total of 227 cerebrospinal fluid (CSF) samples were collected from pediatric patients with VE in Zhejiang province from January 2018 to December 2019. The samples were tested using multiplex and singleplex Reverse Transcription-Polymerase Chain Reaction (RT-PCR) with primers specific to enterovirus (EV), varicella-zoster virus (VZV), mumps virus (MuV), cytomegalovirus (CMV), herpes simplex virus type 1 (HSV-1)/type 2 (HSV-2), Epstein–Barr virus (EBV), and human herpesvirus 6 (HHV-6). The data of the two analyses were compared and then verified using Sanger sequencing. Results: Of the 227 CSF samples, 90 were shown to be positive for multiplex RT-PCR with a positivity rate of 39.65% and a 95% confidence interval (33.2%, 46.1%). EV was the most common cause of VE, followed by EBV, HHV-6, MuV, CMV, VZV, and HSV-1. Most included cases occurred in summer, accounting for 49.78% of all cases. For EV, EBV, and HSV-2, multiplex RT-PCR showed a positivity rate of 34.36%, which was not statistically different from that of 30.4% shown by singleplex RT-PCR. The sequences of EV, EBV, VZV, MuV, CMV, HSV-1, HHV-6, and HSV-2 were confirmed by sequencing the PCR products obtained from multiplex and singleplex PCR. Conclusions: In children, VE is more prevalent in the summer than in other seasons in Zhejiang province, and EV may be the most common causative pathogen.

Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art

Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.

A Possible Case of Varicella Zoster Virus (VZV) Meningoencephalitis in an Immunocompetent Host

The herpes zoster infection occurs in the United States, particularly targeting those who are immunocompromised, and can present with many manifestations including encephalitis. Instances of varicella zoster virus (VZV) encephalitis in immunocompetent patients have been rarely reported, but such diagnoses are becoming more frequent as detection of VZV has improved with the adoption of molecular diagnostic panels such as the BioFire Film Array meningitis panel (Salt Lake City, USA). Here, we present an interesting case of acute meningoencephalitis in an immunocompetent adult female without dermatomal neuralgia or cutaneous lesions attributable to VZV. Given many inconsistencies between the patient’s presentation and the positive polymerase chain reaction (PCR) result for VZV, we suspected our patient was infected with an undetected organism while possibly simultaneously shedding previously acquired VZV. As molecular diagnostic panels are increasingly used and have greatly improved detection of rarer etiologies of disease, we encourage clinicians to interpret results with caution.

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.

Feasibility of 16S rRNA sequencing for cerebrospinal fluid microbiome analysis in cattle with neurological disorders: a pilot study

Bacterial infection of the central nervous system (CNS) in cattle requires prompt and adequate antimicrobial treatment. The current gold standard for antemortem etiological diagnosis is cerebrospinal fluid (CSF) culture, which often yields false negative results. CSF has long been considered a sterile district in healthy patients, but this notion has been recently challenged. For this pilot study, we used 16S rRNA gene sequencing to investigate the microbial composition of CSF of cattle presenting with CNS disorders and to compare it between subjects with CNS infections and with CNS disorders of other nature. The study sample was 10 animals: 4 presenting with CNS infectious-inflammatory diseases and 6 with other CNS disorders, based on definitive diagnosis. Since the initial round of a standard 16S rRNA PCR did not yield sufficient genetic material for sequencing in any of the samples, the protocol was modified to increase its sensitivity. Bacterial genetic material was identified in 6 animals and 2 groups were formed: an infectious inflammatory (n = 3) and a noninfectious inflammatory group (n = 3). The most frequently expressed bacterial families were Pseudomonadaceae (44.61%), Moraxellaceae (19.54%), Mycobacteriaceae (11.80%); the genera were Pseudomonas (45.42%), Acinetobacter (19.91%), Mycobacterium (12.01%). There were no detectable differences in the CSF microbial composition of the samples from the two groups. Sequencing of bacterial DNA present in the CSF was possible only after increasing PCR sensitivity. The results of 16S rRNA sequencing showed the presence of a microbial community in the CSF in cattle with neurological disorders. Further studies, in which CSF samples from healthy animals and samples from the environment are included as controls, are needed.

The clinical impact of multiplex PCR panel diagnostics in paediatric meningitis/ encephalitis: a bicenter cohort study

PURPOSE

In infections of the Central Nervous System (iCNS), rapid identification of causing pathogens is crucial for survival and to avoid long-term sequelae. Targeted therapy may reduce side effects and development of antibiotic resistance. New molecular-based syndromic tests such as the "meningitis/encephalitis panel" (MEP) allow accelerated pathogen identification from cerebrospinal fluid. We conducted a clinical study to evaluate the MEP's efficacy in paediatric patients.

METHODS

Cohort study in a unique clinical setting by comparing the outcome data of two neighbouring Children's Hospitals in Germany which are comparable in size, catchment area and equipment but differ regarding availability of the MEP: study centre 1 (SC1): yes; SC2: no. The study population included 213 paediatric patients with a suspected iCNS (SC1: 106; SC2: 107), with comparable age, CRP at admission and frequency of intensive care. The primary outcome was total use of antibiotics.

RESULTS

Total antibiotic use per patient was numerically lower in SC1 than in SC2 (SC1: median 2.83 days; SC2 3.67 days; p = 0.671). Multiple linear regression analysis did not show a relevant association between MEP-availability and total antibiotic use (ß = 0.1, 95% confidence interval [-1.46; +1.67], p = 0.897). In the subcohort with suspected meningoencephalitis (SC1: 18, SC2: 17), duration of acyclovir treatment was shorter in SC1 than in SC2 (median 1.3 days vs. 2.7 days, descriptive p = 0.0397).

CONCLUSIONS

The add-on use of the MEP in paediatric patients with suspected iCNS was associated with a non-significant reduction in total antibiotic use, and with a reduced exposure to acyclovir in treated patients.

Determining an infectious or autoimmune etiology in encephalitis

Objectives

Early presentation and workup for acute infectious (IE) and autoimmune encephalitis (AE) are similar. This study aims to identify routine laboratory markers at presentation that are associated with IE or AE.

Methods

This was a multi‐center retrospective study at three tertiary care hospitals in New York City analyzing demographic and clinical data from patients diagnosed with definitive encephalitis based on a confirmed pathogen and/or autoantibody and established criteria for clinical syndromes.

Results

Three hundred and thirty‐three individuals with confirmed acute meningoencephalitis were included. An infectious‐nonbacterial (NB) pathogen was identified in 151/333 (45.40%), bacterial pathogen in 95/333 (28.50%), and autoantibody in 87/333 (26.10%). NB encephalitis was differentiated from AE by the presence of fever (NB 62.25%, AE 24.10%; p < 0.001), higher CSF white blood cell (WBC) (median 78 cells/μL, 8.00 cells/μL; p < 0.001), higher CSF protein (76.50 mg/dL, 40.90 mg/dL; p < 0.001), lower CSF glucose (58.00 mg/dL, 69.00 mg/dL; p < 0.001), lower serum WBC (7.80 cells/μL, 9.72 cells/μL; p < 0.050), higher erythrocyte sedimentation rate (19.50 mm/HR, 13.00 mm/HR; p < 0.05), higher C‐reactive protein (6.40 mg/L, 1.25 mg/L; p = 0.005), and lack of antinuclear antibody titers (>1:40; NB 11.54%, AE 32.73%; p < 0.001). CSF‐to‐serum WBC ratio was significantly higher in NB compared to AE (NB 11.3, AE 0.99; p < 0.001). From these findings, the association of presenting with fever, CSF WBC ≥50 cells/μL, and CSF protein ≥75 mg/dL was explored in ruling‐out AE. When all three criteria are present, an AE was found to be highly unlikely (sensitivity 92%, specificity 75%, negative predictive value 95%, and positive predictive value 64%).

Interpretations

Specific paraclinical data at initial presentation may risk stratify which patients have an IE versus AE.

Diagnostic accuracy of rapid one-step PCR assays for detection of herpes Simplex virus -1 and -2 in cerebrospinal fluid: A systematic Review and meta-analysis

BACKGROUND

Rapid and accurate diagnosis of HSV-1 and -2 (HSV1/2) in cerebrospinal fluid (CSF) is important for patient management.

OBJECTIVES

Summarize the diagnostic accuracy of commercial rapid sample-to-answer PCR assays (results in <90 minutes, without a separate nucleic acid extraction step) for HSV1/2 detection in CSF.

DATA SOURCES

Four databases (MEDLINE, EMBASE, Scopus and CENTRAL) and five conference abstract datasets from January 2012 to March 2022.

STUDY ELIGIBILITY CRITERIA

Diagnostic accuracy studies of FilmArray Meningitis-Encephalitis Panel™ and Simplexa™ HSV 1&2 Direct Kit compared to a PCR reference standard were included. Eligible studies provided sufficient data for the construction of a standard diagnostic accuracy two-by-two table.

PARTICIPANTS

Patients with suspected meningitis and/or encephalitis.

ASSESSMENT OF RISK OF BIAS

Two investigators independently extracted data, rated risk of bias and assessed quality using QUADAS-2.

METHODS

Accuracy estimates were pooled using Bayesian random effects models.

RESULTS

Thirty-one studies were included (27 FilmArray; 4 Simplexa), comprising 9,924 samples, with 95 HSV-1 and 247 HSV-2 infections. Pooled FilmArray sensitivities were 84.3% (95% credible interval 72.3%-93.0%) and 92.9% (95%CrI, 82.0%-98.5%) for HSV-1 and HSV-2, respectively; specificities were 99.8% (95%CrI, 99.6%-99.9%) and 99.9% (95%CrI, 99.9%-100%). Pooled Simplexa sensitivities were 97.1% (95%CrI, 88.1%-99.6%) and 97.9% (95%CrI, 89.6%-99.9%), respectively; specificities were 98.9% (95%CrI, 96.8%-99.7%) and 98.9% (95%CrI, 97.1%-99.7%). Pooled FilmArray sensitivities favored industry-sponsored studies by 10.0 and 13.0 percentage points for HSV-1 and HSV-2, respectively. Incomplete reporting frequently led to unclear risk of bias. Several FilmArray studies did not fully report true negative data leading to their exclusion.

CONCLUSION

Our results suggest Simplexa is accurate for HSV1/2 detection in CSF. Moderate FilmArray sensitivity for HSV-1 suggests additional testing and/or repeat CSF sampling is required for suspected HSV encephalitis when the HSV-1 result is negative. Low prevalence of HSV-1 infections limited summary estimates' precision. Underreporting of covariates limited exploration of heterogeneity.

Alignment of Fellowship Training with Practice Patterns for Molecular Pathologists: A Report of the Association for Molecular Pathology Training and Education Committee

In the two decades since Accreditation Council for Graduate Medical Education-accredited Molecular Genetic Pathology fellowships began, the field of clinical molecular pathology has evolved considerably. The American Board of Pathology gathered data from board-certified molecular genetic pathologists assessing the alignment of skills and knowledge gained during fellowship with current needs on the job. The Association of Molecular Pathology conducted a parallel survey of program directors, and included questions on how various topics were taught during fellowship, as well as ranking their importance. Both surveys showed that most training aligned well with the practice needs of former trainees. Genomic profiling of tumors by next-generation sequencing, bioinformatics, laboratory management, and regulatory issues were topics thought to require increased emphasis in training. Topics related to clinical genetics and microbiology were deemed less important by those in practice, perhaps reflecting the increasing subspecialization of molecular pathologists. Program directors still viewed these topics as important to provide foundational knowledge. Parentage, identity, and human leukocyte antigen testing were less important to both survey audiences. These data may be helpful in guiding future adjustments to the Molecular Genetic Pathology curriculum and Accreditation Council for Graduate Medical Education program requirements.

Clinical and Neurodevelopmental Characteristics of Enterovirus and Parechovirus Meningitis in Neonates

Background

Non-polio-enteroviruses (EV) and human parechoviruses (HPeV) are small RNA viruses, which in newborns cause infections with a wide range of severity. Today molecular biology tools allow us to diagnose viral meningitis in neonates, sparing patients from useless antibiotics. Data on neurodevelopmental outcome of children who contract enterovirus meningitis in early childhood are still limited in the literature.

Aims

To evaluate the neurodevelopmental outcome of newborns with documented enterovirus and parechovirus meningitis contracted within the first months of life.

Methods

Enterovirus and parechovirus were detected on cerebrospinal fluid (CSF) and plasma by RT-PCR. The virological typing was done according to WHO recommendations. During the hospitalization each neonate underwent many diagnostic and instrumental examinations, to evaluate any neurological lesions attributable to the infection. After the discharge children entered in an outpatient interdisciplinary assessment process, comprehensive of the administration of Bayley III scales up to 12 months old.

Results

We observed longitudinally 30 children, born at term (mean GA 39.7 ± 0.8 weeks, mean birthweight was 3,457 ± 405 grams), who contracted enterovirus and parechovirus meningitis within the first month of life (mean age at diagnosis was 15.8 ± 7.33 days). We were able to perform the genetic typing only on 15/30 (50.0%) cerebrospinal fluid (CSF) samples from 15 neonates. We found MRI anomalies in 9/26 observed neonates (34.6%): one of them presented brainstem abnormality that are specific of enteroviral central nervous system (CNS) involvement. During the follow up children displayed an overall normal neurodevelopment and no deficit in visual and hearing areas. The mean cognitive (105.19 ± 8.71), speech (100.23 ± 8.22) and motor (97.00 ± 8.98) composite scores, assessed by Bayley III, were normal in 29/30 (96.7%). Despite this, children with pathological brain magnetic resonance imaging (MRI) scored significantly lower (p = 0.01) than children with normal brain MRI on cognitive subscale at 12 months of life.

Conclusions

Early enterovirus infections can be associated to brain MRI abnormalities, more frequently the earlier the infection. Although within a normal range, our children with pathological brain MRI scored significantly lower than those with normal brain MRI on cognitive subscale at 12 months of life.

Human Herpesvirus-6 Detection in Cerebrospinal Fluid on the BioFire FilmArray Meningitis/Encephalitis Panel in a High HIV-prevalence African Setting

The prevalence and clinical relevance of human herpesvirus-6 (HHV-6) detection in cerebrospinal fluid (CSF) using multiplex polymerase chain reaction (PCR) testing in patients with suspected meningoencephalitis in high human immunodeficiency virus-prevalence African settings are not known. We describe the clinical and laboratory characteristics of 13 patients with HHV-6 CSF PCR positivity in Botswana.

How do we reduce acyclovir overuse? Impact of FilmArray meningitis/encephalitis panel tests for pediatric patients

BACKGROUND

Few Japanese hospitals can perform in-house cerebrospinal fluid (CSF) polymerase chain reaction (PCR) to screen for herpes simplex virus, leading to patients being administered acyclovir (ACV) for several days. The FilmArray Meningitis/Encephalitis Panel (ME Panel) is a multiplex PCR test that can identify 14 major pathogens within 1 h. We aimed to investigate the efficacy of the ME Panel in children admitted with central nervous system infections in Japan.

METHODS

We conducted a single-center, quasi-experimental study. The ME panel was introduced in April 2020. We outsourced the CSF samples to a laboratory during the pre-intervention period (April 2016 to March 2020) and performed the ME panel at our hospital during the post-intervention period (April 2020 to December 2021). Duration and dose of ACV and antibiotic use, length of stay (LOS) in the pediatric intensive care unit (PICU), and total LOS after testing were compared using the Mann-Whitney U test.

RESULTS

The number of cases in the pre- and post-intervention periods was 67 and 22 cases, respectively. The median duration of ACV decreased significantly from 6 days to 0 day (p < 0.001), and the median dose of ACV use decreased significantly from 14 vials to 0 vial (p < 0.001). No significant differences were noted in the total duration and dose of antibiotic use, LOS in PICU, and the total LOS after testing.

CONCLUSION

The introduction of ME panel may contribute to appropriate ACV use; however, there was no significant change in the duration and dose of antibiotic use or LOS.

Clinical and Financial Impact of a Diagnostic Stewardship Program for Children with Suspected Central Nervous System Infection

OBJECTIVE

To investigate the optimal implementation and clinical and financial impacts of the FilmArray Meningitis Encephalitis Panel (MEP) multiplex polymerase chain reaction testing of cerebrospinal fluid (CSF) in children with suspected central nervous system infection.

STUDY DESIGN

A pre-post quasiexperimental cohort study to investigate the impact of implementing MEP using a rapid CSF diagnostic stewardship program was conducted at Children's Hospital Colorado (CHCO). MEP was implemented with electronic medical record indication selection to guide testing to children meeting approved use criteria: infants <2 months, immunocompromised, encephalitis, and ≥5 white blood cells/μL of CSF. Positive results were communicated with antimicrobial stewardship real-time decision support. All cases with CSF obtained by lumbar puncture sent to the CHCO microbiology laboratory meeting any of the 4 aforementioned criteria were included with preimplementation controls (2015-2016) compared with postimplementation cases (2017-2018). Primary outcome was time-to-optimal antimicrobials compared using log-rank test with Kaplan-Meier analysis.

RESULTS

Time-to-optimal antimicrobials decreased from 28 hours among 1124 preimplementation controls to 18 hours (P < .0001) among 1127 postimplementation cases (72% with MEP testing conducted). Postimplementation, time-to-positive CSF results was faster (4.8 vs 9.6 hours, P < .0001), intravenous antimicrobial duration was shorter (24 vs 36 hours, P = .004), with infectious neurologic diagnoses more frequently identified (15% vs 10%, P = .03). There were no differences in time-to-effective antimicrobials, hospital admissions, antimicrobial starts, or length of stay. Costs of microbiologic testing increased, but total hospital costs were unchanged.

CONCLUSIONS

Implementation of MEP with a rapid central nervous system diagnostic stewardship program improved antimicrobial use with faster results shortening empiric therapy. Routine MEP testing for high-yield indications enables antimicrobial optimization with unchanged overall costs.

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.

Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study

Introduction

Rapid, sensitive, and specific laboratory assays are critical for the diagnosis and management of central nervous system (CNS) infections. The purpose of this study is to explore the intellectual landscape of research investigating methods for the detection of pathogens in patients with CNS infections and to identify the development trends and research frontier in this field.

Methods

A bibliometric study is conducted by analyzing literature retrieved from the Web of Science (WoS) Core Collection Database for the years 2000 to 2021. CiteSpace software is used for bibliometric analysis and network visualization, including co-citation analysis of references, co-occurrence analysis of keywords, and cooperation network analysis of authors, institutions, and countries/regions.

Results

A total of 2,282 publications are eventually screened, with an upward trend in the number of publications per year. The majority of papers are attributed to the disciplines of MICROBIOLOGY, INFECTIOUS DISEASES, IMMUNOLOGY, NEUROSCIENCES & NEUROLOGY, and VIROLOGY. The co-citation analysis of references shows that recent research has focused on the largest cluster “metagenomic next-generation sequencing”; the results of the analysis of the highest-cited publications and the citation burst of publications reveal that there is a strong interest stimulated in metagenomic next-generation sequencing. The co-occurrence analysis of keywords indicates that “infection”, “pathogen”, “diagnosis”, “gene”, “virus”, “polymerase chain reaction”, “cerebrospinal fluid”, “epidemiology”, and “metagenomic next-generation sequencing” are the main research priorities in the field of pathogen detection for CNS infections, and the keyword with the highest strength of burst is “metagenomic next-generation sequencing”. Collaborative network analysis reveals that the USA, the Centers for Disease Control and Prevention of USA, and XIN WANG and JENNIFER DIEN BARD are the most influential country, institution, and researchers, respectively.

Conclusions

Exploring more advanced laboratory assays to improve the diagnostic accuracy of pathogens is essential for CNS infection research. Metagenomic next-generation sequencing is emerging as a novel useful unbiased approach for diagnosing infectious diseases of the CNS.

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.

Differential Performance of the FilmArray Meningitis/Encephalitis Assay To Detect Bacterial and Viral Pathogens in Both Pediatric and Adult Populations

Meningitis/encephalitis (ME) syndromic diagnostic assays can be applied for the rapid one-step detection of the most common pathogens in cerebrospinal fluid (CSF). However, the comprehensive performance of multiplex assays is still under evaluation. In our multisite university hospital of eastern Paris, France, ME syndromic testing has been gradually implemented since 2017 for patients with neurological symptoms presenting to an adult or pediatric emergency unit. We analyzed the results from the BioFire FilmArray ME panel versus standard routine bacteriology and virology techniques, together with CSF cytology and clinical data, over a 2.5-year period to compare the diagnostic accuracy of the FilmArray ME panel to that of the reference methods. In total, 1,744 CSF samples from 1,334 pediatric and 336 adult patients were analyzed. False-positive (mostly bacterial) and false-negative (mostly viral) cases were deciphered with the help of clinical data. The performance of the FilmArray ME panel in our study was better for bacterial detection (specificity >99%, sensitivity 100%) than viral detection (specificity >99%, sensitivity 75% for herpes simplex virus 1 [HSV-1] and 89% for enterovirus), our study being one of the largest, to date, concerning enteroviruses. The use of a threshold of 10 leukocytes/mm³ considerably increased the positive agreement between the results of the FilmArray ME panel and the clinical features, especially for bacterial pathogens, for which agreement increased from 58% to 87%, avoiding two-thirds of inappropriate testing. Based on this analysis, we propose an algorithm for the use of both syndromic and specific assays for the optimal management of suspected meningitis/encephalitis in adult and pediatric patients.

IMPORTANCE Based on our comparative analysis of performances of the diagnostic assays, we propose an algorithm for the use of both syndromic and specific assays, for an optimal care of the meningitis/encephalitis threat in adult and pediatric patients.

FilmArray® Meningoencephalitis panel in the diagnosis of central nervous system infections: stewardship and cost analysis in a paediatric hospital in Chile

BACKGROUND

Central nervous system (CNS) infection has been an ongoing concern in paediatrics. The FilmArray® Meningoencephalitis (FAME) panel has greater sensitivity in identifying the aetiology of CNS infections. This study's objective was to compare the aetiological identification and hospitalization costs among patients with suspected CNS infection before and after the use of FAME.

METHODS

An analytical observational study was carried out using a retrospective cohort for the pre-intervention (pre-FAME use) period and a prospective cohort for the post-intervention (post-FAME use) period in children with suspected CNS infection.

RESULTS

A total of 409 CSF samples were analysed, 297 pre-intervention and 112 post-intervention. In the pre-intervention period, a total of 85.5% of patients required hospitalization, and in the post-intervention period 92.7% required hospitalization (p < 0.05). Median of ICU days was significantly lower in the post-intervention period than it was in the pre-intervention period. The overall positivity was 9.4 and 26.8%, respectively (p < 0.001). At ages 6 months and below, we found an increase in overall positivity from 2.6 to 28.1%, along with an increased detection of viral agents, S. agalactiae, S. pneumoniae, and N. meningitidis. The use of this diagnostic technology saved between $2916 and $12,240 USD in the cost of ICU bed-days. FAME use provided the opportunity for more accurate aetiological diagnosis of the infections and thus the provision of adequate appropriate treatment.

CONCLUSIONS

The cost/benefit ratio between FAME cost and ICU bed-day cost savings is favourable. Implementation of FAME in Chilean public hospitals saves public resources and improves the accuracy of aetiological diagnosis.

Reassessing the Value of CSF Protein and Glucose Measurement in Pediatric Infectious Meningitis

OBJECTIVES

Infectious meningitis (IM) in US children is increasingly rare and new rapid multiplex PCR-based testing is increasingly available. We evaluated the added value of cerebrospinal fluid (CSF) protein and glucose tests to predict IM when compared with information provided by CSF white blood cell count (WBC) and multiplex polymerase chain reaction (PCR).

METHODS

We retrospectively reviewed CSF results from October 2015 to August 2017 in patients 0 to 18 years at a US children's hospital. Noninfectious evaluations were excluded. Test characteristics were calculated for CSF WBC, protein, and glucose in isolation and in parallel for prediction of microbiologically confirmed IM. Chart review was performed to identify consideration of protein and glucose in medical decision-making (MDM).

RESULTS

We identified 735 patients including 446 <2 months; 45 (6.1%) had microbiologically-confirmed IM, including 23 (5.2%) age <2 months. Multiplex PCR and/or CSF WBC identified all IM patients. When added to CSF WBC, measurement of glucose made no contribution to sensitivity, specificity, positive predictive value (PPV) or negative predictive value (NPV), and protein had no impact on sensitivity and decreased the specificity, PPV, and NPV compared with CSF WBC alone. Abnormal protein was documented in MDM in 6 (0.8%) patients, all of whom had elevated WBC counts also cited. Glucose was not mentioned in MDM.

CONCLUSIONS

Multiplex PCR testing and WBC may be sufficient to predict meningitis in children in low incidence settings. Protein and glucose did not contribute significant additional information. More intentional use of protein and glucose testing in patients with suspected IM may achieve higher value care.

Comparison and development of a metagenomic next-generation sequencing protocol for combined detection of DNA and RNA pathogens in cerebrospinal fluid

BACKGROUND

The purpose of this study was to evaluate different pretreatment, extraction, amplification, and library generation methods for metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) and to develop an efficient procedure for the simultaneous detection of DNA and RNA pathogens.

METHODS

We generated thirteen mock CSF samples with four representative pathogens of encephalitis. Each sample was subjected to ten different methods by varying sample pretreatment/nucleic acid extraction (microbial DNA, total DNA, total NA, total RNA, Whole Transcriptome Amplification (WTA)) and library generation (Illumina or NEB). Negative extraction controls (NECs) were used for each method variation.

RESULTS

We found that the quality of mNGS sequencing reads was higher from the NEB kit for library generation. Microbial DNA and total RNA increased microbial deposition by depleting the host DNA. Methods total NA and total RNA can detect gram-positive, gram-negative, RNA and DNA pathogens. We applied mNGS, including total NA and NEB library generation, to CSF samples from five patients diagnosed with infectious encephalitis and correctly determined all pathogens identified in clinical etiological tests.

CONCLUSIONS

Our findings suggested that total nucleic acid extraction combined with NEB library generation is the most effective mNGS procedure in CSF pathogen detection. The optimization of positive criteria and databases can improve the specificity and sensitivity of mNGS diagnosis.

TRIAL REGISTRATION

Chinese Clinical Trial Registry, ChiCTR1800015425 (29/03/2018), https://www.chictr.org.cn/edit.aspx?pid=26292&htm=4 .

Multicenter Evaluation of the Simplexa VZV Direct Assay for Detection of Varicella-Zoster Virus in Cerebrospinal Fluid and Lesion-Swab Specimens

Varicella-zoster virus (VZV) is the etiologic agent of varicella (chickenpox) and herpes zoster (shingles) infections commonly involving skin, mucous membranes, and less frequently the central nervous system. Traditional methods for the laboratory diagnosis of these infections are time-consuming, labor-intensive, and often insensitive. As such, these tests are being replaced by more sensitive and rapid molecular methods. This study evaluated the performance of two different molecular assays, the Simplexa VZV Direct and Simplexa VZV Swab Direct, to detect VZV DNA in cerebrospinal fluid (CSF) and lesion-swab specimens, respectively. The Simplexa VZV Direct and Simplexa VZV Swab Direct assays were compared against individual composite reference methods that varied depending on the sample cohort examined. A total of 883 CSF and 452 cutaneous and mucocutaneous prospective, retrospective, and contrived specimens were evaluated in this multicenter study. The results of this study showed that the Simplexa assays demonstrated near perfect agreement (k = 0.98) compared to the composite reference methods for the detection of VZV in CSF and lesion swab specimens. A further comparison between the standard of care molecular assays employed at the site of specimen collection and the Simplexa assays demonstrated excellent agreement (k = 1.0). The Simplexa assays offer rapid and reliable alternatives for the detection of VZV in certain clinical specimens without the need for nucleic acid extraction.

A Review: The Manifestations, Mechanisms, and Treatments of Musculoskeletal Pain in Patients With COVID-19

The outbreak of COVID-19 poses a serious threat to global health. Musculoskeletal (MSK) pain is the most frequent symptom in patients with COVID-19 besides fever and cough. There are limited studies addressing MSK symptoms in patients with COVID-19. This review aims to provide an overview of current studies related to MSK pain in patients with COVID-19, summarize the possible mechanisms of myalgia, and describe the current management options. In addition to acute respiratory manifestations, COVID-19 might also affect neurological systems which include skeletal manifestations and muscular injury. A possible mechanism of MSK pain and myalgia in COVID-19 may be related to the distribution of angiotensin-converting enzyme 2 (ACE-2) and the occurrence of cytokine storms. ACE-2 has been shown to be the receptor of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV2). Moreover, studies have shown that inflammatory cytokines could cause myalgia by inducing prostaglandin E2 (PGE2) production. In addition, it was also found that the plasma levels of IL2, IL7, IL10, IL-6, TNFα, and e lymphopenia were higher in patients with COVID-19. In general, the treatment of MSK pain in patients with COVID-19 falls into pharmacological and non-pharmacological interventions. Various treatments of each have its own merits. The role of vaccination is irreplaceable in the efforts to prevent COVID-19 and mitigates its subsequent symptoms.

COVID-19 and its impact on the brain and Mind- A conceptual model and supporting evidence

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus that is causing the ongoing coronavirus disease 2019 (COVID-19) pandemic, was first reported in late 2019. Since then, an unprecedented amount of new knowledge has emerged about this virus and its treatment. Although the reported symptoms of COVID-19 are primarily respiratory with acute respiratory distress syndrome, SARS-CoV-2 has also been shown to affect other organs, including brain, and there are growing reports of neuropsychiatric symptoms due to COVID-19. There are two suggested pathways for how COVID-19 can affect the brain and mind: the direct impact on the brain and impact mediated via stress. Direct impact on the brain is manifested as encephalitis/encephalopathy with altered mental status (AMS) and delirium. In this paper, we summarize evidence from studies of previous outbreaks and current data from the COVID-19 pandemic that describe how COVID-19 is associated with an increased prevalence of anxiety, stress, poor sleep quality, obsessive-compulsive symptoms, and depression among the general population during the pandemic. In addition, we summarize the current evidence that supports how COVID-19 can also impact the CNS directly and result in delirium, cerebrovascular events, encephalitis, unspecified encephalopathy, AMS, or peripheral neurologic disorders.

Evaluation of the Utilization of FilmArray Meningitis/Encephalitis in Children With Suspected Central Nervous System Infection: A Retrospective Case Series

BACKGROUND

The etiology of central nervous system infections is often difficult to establish. FilmArray meningitis/encephalitis (ME) panel is a multiplex polymerase chain reaction for rapid identification of 14 pathogens. The aim of this study was to evaluate potential real-life contributions of the use of this method in the pediatric population.

METHODS

We herein report the results obtained with FilmArray ME in a retrospective case series of 367 children with suspected central nervous system infection. We identified viral and bacterial agents by FilmArray, and we evaluated the potential diagnostic contributions of the use of the panel taking into account the cytological, biochemical, and microbiological results of the cerebrospinal fluid (CSF) analysis.

RESULTS

The FilmArray ME panel detected a viral infection in 186 cases (50.7%) and a bacterial infection in 12 cases (3.3%). Fifty-three cases (28.4%) of viral infection had at least 1 CSF finding that could be mistaken for bacterial meningitis. Enterovirus was identified in 2 cases with normal CSF findings. Among 12 bacterial infection cases, only 6 (50%) had a positive result with conventional microbiology analysis (Gram stain and culture). The CSF findings suggestive of bacterial meningitis were found in all 6 cases in which FilmArray was the only method to identify bacterial etiological agent.

CONCLUSIONS

FilmArray ME panel identified an etiological agent in cases in which conventional CSF analysis failed, providing potential clinical contributions to the management of such cases.

Biofire FilmArray Meningitis/Encephalitis panel for the aetiological diagnosis of central nervous system infections: A systematic review and diagnostic test accuracy meta-analysis

BACKGROUND

The FilmArray Meningitis/Encephalitis(FA/ME) panel brings benefits in clinical practice, but its diagnostic test accuracy (DTA) remains unclear. We aimed to determine the DTA of FA/ME for the aetiological diagnostic in patients with suspected central nervous system(CNS) infection.

METHODS

We performed a systematic review with DTA meta-analysis (PROSPERO: CRD42020139285). We searched Embase, Medline (Ovid), and Web of Science from inception until September 1st, 2021. We assessed the study-level risk of bias with the QUADAS-2 tool and applied the GRADE approach to assess the certainty of the synthesised evidence. We included studies that simultaneously measured the reference test (CSF/blood culture for bacteria, and specific polymerase chain reaction for viruses) and the FA/ME in patients with suspected CNS infection. We performed random-effects bivariate meta-analysis models of combined sensitivity and specificity using CSF/blood cultures(reference test 1) and a final diagnosis adjudication based on clinical/laboratory criteria (reference test 2).

FINDINGS

We included 19 studies (11,351 participants). For all bacteria with reference test 1 (16 studies/6183 patients) sensitivity was estimated at 89·5% (95%CI 81·1-94·4), and specificity at 97·4% (95%CI 94-98·9). With reference test 2 (15 studies/5,524 patients), sensitivity was estimated at 92·1%(95%CI 86·8-95·3) and specificity at 99.2(95%CI 98·3-99·6) For herpes simplex virus-2(HSV-2), enteroviruses, and Varicella-Zoster virus (VZV), we obtained sensitivities between 75·5 and 93·8%, and specificities above 99% (reference test 1). Certainty of the evidence was low.

INTERPRETATION

FA/ME may have acceptable-to-high sensitivities and high specificities for identifying bacteria, especially for S.pneumoniae, and viruses, especially for HSV-2, and enteroviruses. Sensitivities for L.monocytogenes, H.influenzae, E.coli, and HSV-1 were suboptimal.

FUNDING

None.

Quality Management to Improve CSF Gram Stain Turnaround Time

BACKGROUND

With appropriate turnaround time (TAT), cerebrospinal fluid (CSF) Gram stains can provide rapid, clinically actionable information in patients with meningitis. Monitoring CSF Gram stain TAT at our institution revealed workflow gaps that were causing result reporting delays. We then implemented a new quality management program to improve TAT.

METHODS

We reviewed the TAT of all CSF specimens submitted for bacterial culture received between August 1, 2016, and July 31, 2020, and began prospectively monitoring CSF Gram stain TAT in January 2019. We then implemented the following changes in April 2019: (i) monthly reviews of TAT with staff, (ii) hand-off sheets for shift transitions, and (iii) pre- and post-shift walk throughs including centrifuge checks.

RESULTS

A total of 6913 samples were included in the analysis. CSF samples with TAT > 60 min decreased from 27.3% to 9.89% (P < 0.0001), and median TAT decreased by 9 min (P < 0.0001) with significantly reduced variability. These changes were sustained throughout the follow-up period across all shifts and shift transitions.

CONCLUSIONS

A new monthly quality metric allowed us to track CSF Gram stain TAT, identify barriers to TAT goals, and implement workflow changes that significantly improved TAT without the need for costly interventions.

Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection

The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.

Approach to fever in patients with neutropenia: a review of diagnosis and management

Febrile neutropenia (FN) is associated with mortality rates as high as 40%, highlighting the importance of appropriate clinical management in this patient population. The morbidity and mortality of FN can be attributed largely to infectious processes, with specific concern for infections caused by pathogens with antimicrobial resistance. Expeditious identification of responsible pathogens and subsequent initiation of empiric antimicrobial therapy is imperative. There are four commonly used guidelines, which have variable recommendations for empiric therapy in these populations. All agree that changes could be made once patients are stable and/or with an absolute neutrophil count (ANC) over 500 cells/mcL. Diagnostic advances have the potential to improve knowledge of pathogens responsible for FN and decrease time to results. In addition, more recent data show that rapid de-escalation or discontinuation of empiric therapy, regardless of ANC, may reduce days of therapy, adverse effects, and cost, without affecting clinical outcomes. Antimicrobial and diagnostic stewardship should be performed to identify, utilize, and respond to appropriate rapid diagnostic tests that will aid in the definitive management of this population.