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.

Acompanhamento do comportamento do HIV através de exames laboratoriais em portadora do vírus: relato de caso / Monitoring of HIV behavior through laboratory tests in a virus carrier: case report

O vírus da imunodeficiência humana é o agente etiológico da AIDS, doença crônica que destrói o sistema imunológico e é caracterizada pela baixa contagem de células TCD4, alta contagem de partículas virais no sangue e manifestações clínicas da doença. O diagnóstico se dá com o aparecimento de infecções oportunistas, que levam a contagem de TCD4 a níveis menores que 200 céls/mm³. Os exames laboratoriais para o diagnóstico do HIV foram os principais avanços para o início do tratamento, reduzindo a transmissão. Detecção de anticorpos, detecção de antígenos e amplificação do genoma do vírus são alguns dos exames laboratoriais utilizados para diagnóstico. Os dois principais biomarcadores são os exames de contagem de células TCD4, que verifica o sistema imune, e a quantificação de carga viral, que informa a quantidade de partículas virais, mostrando a progressão da infecção. Quanto maior a carga viral, maior o dano ao sistema imune. Uma carga viral indetectável é inferior a 50 cópias/mL, mas valores menores ou iguais a 200 cópias/mL também impedem a transmissão. Uma declaração de consenso afirma que Indetectável é igual a Intransmissível. Portanto, quando indetectável, a transmissão inexiste. O presente estudo relata e discute o caso clínico de uma paciente diagnosticada com HIV/AIDS aos 28 anos, que sobreviveu, apesar do diagnóstico tardio, e sob presença de doença oportunista com um grave grau de diminuição de células TCD4 (22 cél/mm³). Por meio do diagnóstico, introdução e adesão correta da terapia antirretroviral e monitorização de exames laboratoriais, conseguiu evitar a morte e ter uma vida semelhante à de um HIV negativo. Ultrapassou a expectativa de vida que na descoberta era de 10 anos, com uma qualidade de vida considerável, não sendo transmissora do vírus, diminuindo assim o estigma e preconceito. O biomédico é peça fundamental nesse contexto, considerando que deve fornecer informações precisas e fidedignas, tão necessárias ao acompanhamento de pessoas vivendo com HIV, para que autoridades e profissionais de saúde adotem medidas adequadas, tanto na prevenção, quanto no diagnóstico e monitoramento da doença.

The human immunodeficiency virus is the etiological agent of AIDS, a chronic disease that destroys the immune system and is characterized by low TCD4 cell count, high viral particle count in blood and clinical manifestations of the disease. The diagnosis is due to the appearance of opportunistic infections, which lead to TCD4 counts below 200 cells / mm³. Laboratory tests for the diagnosis of HIV were the main advances in starting treatment, reducing transmission. Antibody detection, antigen detection and virus genome amplification are some of the laboratory tests used for diagnosis. The two main biomarkers are the TCD4 cell count tests, which checks the immune system, and viral load quantification, which reports the number of viral particles, showing the progression of infection. The higher the viral load, the greater the damage to the immune system. An undetectable viral load is less than 50 copies / mL, but values less than or equal to 200 copies / mL also prevent transmission. A consensus statement states that Undetectable equals Non-Transmissible. Therefore, when undetectable, transmission does not exist. The present study reports and discusses the clinical case of a patient diagnosed with HIV / AIDS at age 28, who survived despite late diagnosis and under the presence of opportunistic disease with a severe degree of TCD4 cell reduction (22 cells / mm³). Through the diagnosis, introduction and correct adherence of antiretroviral therapy and monitoring of laboratory tests, she was able to avoid death and have a life similar to that of an HIV negative. Exceeded the life expectancy that in the discovery was 10 years, with a considerable quality of life, not transmitting the virus, thus reducing the stigma and prejudice. The biomedical is a key player in this context, considering that he must provide accurate and reliable information, which is so necessary for the monitoring of people living with HIV, so that authorities and health professionals adopt appropriate measures, both in prevention, diagnosis and monitoring of the disease.

Frequency of serious bacterial infections in young infants with and without viral respiratory infections.

BACKGROUND: The goal of our investigation was to describe the incidence of serious bacterial infection (SBI, defined as bacteremia, urinary tract infection (UTI), or meningitis) in young infants with and without documented viral pathogens. METHODS: This was a retrospective cross-sectional study (1/2016-12/2017) in 3 emergency departments (EDs). Previously healthy 0-60-day-old infants were included if at least respiratory viral testing and a blood culture was obtained. The frequency of SBI, the primary outcome, was compared among infants with/without respiratory viral infections using the Pearson Chi-square test (or Fisher's Exact Test) and unadjusted odds ratios (OR). RESULTS: The median age of the 597-infant cohort was 32 days (interquartile range: 20-45 days); 42% were female. Eighty-three percent were well appearing in the ED and 72% were admitted. ED triage vitals commonly revealed tachypnea (68%), pyrexia (45%), and tachycardia (28%); hypoxemia (5%) was uncommon. Twenty-eight percent had positive viral testing, most commonly RSV (93/169, 55%), parainfluenza (29, 17%), and influenza A (23, 14%). Eighty-three infants (13.9%) had SBI: 8.4% (n = 50) had UTI alone, 2.8% (n = 17) had bacteremia alone, 1.2% (n = 7) had bacteremia + UTI, 1.0% (n = 6) had bacteremia + meningitis, and 0.5% (n = 3) had meningitis alone. Infants with documented respiratory viral pathogens were less likely to have any SBI (OR: 0.23; 95% CI: 0.11-0.50), UTI (OR 0.22, 95% CI: 0.09-0.56), or bacteremia (OR 0.27, 95% CI: 0.08-0.9) than infants with negative viral testing. There was no difference in meningitis frequency based on viral status (OR: 0.13, 95% CI: 0.008-2.25). CONCLUSIONS: The frequency of bacteremia and UTI was lower in young infants with respiratory viral infections compared to infants with negative respiratory viral testing.

Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis.

Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.

Impact of the FilmArray meningitis/encephalitis panel on antimicrobial duration among patients with suspected central nervous system infection.

Ten controlled studies evaluated antimicrobial use following implementation of the FilmArray meningitis and encephalitis panel versus usual care. Only one-half of studies identified significant reductions in antibiotic duration, with 8/10 reporting modest reductions for acyclovir. Coupling the FilmArray meningitis and encephalitis panel with interventions by antimicrobial stewardship programs may help enhance its clinical impact.

Antiviral Cytokine Response in Neuroinvasive and Non-Neuroinvasive West Nile Virus Infection.

Data on the immune response to West Nile virus (WNV) are limited. We analyzed the antiviral cytokine response in serum and cerebrospinal fluid (CSF) samples of patients with WNV fever and WNV neuroinvasive disease using a multiplex bead-based assay for the simultaneous quantification of 13 human cytokines. The panel included cytokines associated with innate and early pro-inflammatory immune responses (TNF-α/IL-6), Th1 (IL-2/IFN-γ), Th2 (IL-4/IL-5/IL-9/IL-13), Th17 immune response (IL-17A/IL-17F/IL-21/IL-22) and the key anti-inflammatory cytokine IL-10. Elevated levels of IFN-γ were detected in 71.7% of CSF and 22.7% of serum samples (p = 0.003). Expression of IL-2/IL-4/TNF-α and Th1 17 cytokines (IL-17A/IL-17F/IL-21) was detected in the serum but not in the CSF (except one positive CSF sample for IL-17F/IL-4). While IL-6 levels were markedly higher in the CSF compared to serum (CSF median 2036.71, IQR 213.82-6190.50; serum median 24.48, IQR 11.93-49.81; p < 0.001), no difference in the IL-13/IL-9/IL-10/IFN-γ/IL-22 levels in serum/CSF was found. In conclusion, increased concentrations of the key cytokines associated with innate and early acute phase responses (IL-6) and Th1 type immune responses (IFN-γ) were found in the CNS of patients with WNV infection. In contrast, expression of the key T-cell growth factor IL-2, Th17 cytokines, a Th2 cytokine IL-4 and the proinflammatory cytokine TNF-α appear to be concentrated mainly in the periphery.

Whole-Exome Sequencing of Patients With Recurrent HSV-2 Lymphocytic Mollaret Meningitis.

Recurrent lymphocytic meningitis, also referred to as Mollaret meningitis, is a rare neurological disease characterized mainly by reactivation of herpes simplex virus 2 (HSV-2) from sensory ganglia. However, the underlying host immune determinants and viral factors rendering some individuals unable to maintain HSV-2 latency are largely unknown. We collected a cohort of 15 patients diagnosed with Mollaret meningitis. By whole-exome sequencing we identified rare host genetic variants predicted to be deleterious in molecules involved in (1) ubiquitin-proteasome pathways, (2) the autophagy machinery, and (3) cell proliferation/apoptosis. Moreover, infection of patient cells with HSV-2 or stimulation by virus-derived double-stranded DNA ligands revealed reduced antiviral interferon responses in most patients. These findings may contribute to a better understanding of disease pathogenesis and protective immunity to HSV in the central nervous system, and may ultimately be of importance for identification of targets for development of improved prophylaxis and treatment of this disease.

Tick-Borne Encephalitis: A Differential Pattern of Intrathecal Humoral Immune Response and Inflammatory Cell Composition Compared with Other Viral CNS Infections.

To investigate whether and how cerebrospinal fluid (CSF) findings can contribute to distinguish tick-borne encephalitis (TBE) from herpes simplex virus (HSV) and varicella zoster virus (VZV) induced central nervous system (CNS) infections (HSV-I, VZV-I). Chart review and identification of TBE, HSV- I, and VZV-I was carried out, fulfilling the following criteria: (1) clinical signs of encephalitis and/or meningitis, (2) complete CSF analysis and confirmed viral etiology by either PCR or antibody testing in CSF, (3) hospitalized patients, and (4) available brain magnetic resonance imaging (MRI). Fifty-nine patients with 118 CSF/serum pairs were included. These comprised 21 with TBE (35 CSF/serum pairs), 20 (40 CSF/serum pairs) with HSV-I, and 18 (43 CSF/serum pairs) with VZV-I. In contrast to HSV-I and VZV-I, CSF cell differentiation in TBE showed more often an increased (>20%) proportion of granulocytes (p < 0.01) and a more frequent quantitative intrathecal IgM synthesis (p = 0.001 and p < 0.01, respectively), while the second was even more pronounced when follow-up CSF analyses were included (p < 0.001). CSF findings help to distinguish TBE from other viral infections. In cases with CSF pleocytosis and a positive history for a stay in or near an endemic area, TBE antibodies in CSF and serum should be determined, especially if granulocytes in CSF cell differentiation and/or an intrathecal IgM synthesis is present.

COVID-19 and the nervous system.

A pandemic due to novel coronavirus arose in mid-December 2019 in Wuhan, China, and in 3 months' time swept the world. The disease has been referred to as COVID-19, and the causative agent has been labelled SARS-CoV-2 due to its genetic similarities to the virus (SARS-CoV-1) responsible for the severe acute respiratory syndrome (SARS) epidemic nearly 20 years earlier. The spike proteins of both viruses dictate tissue tropism using the angiotensin-converting enzyme type 2 (ACE-2) receptor to bind to cells. The ACE-2 receptor can be found in nervous system tissue and endothelial cells among the tissues of many other organs.Neurological complications have been observed with COVID-19. Myalgia and headache are relatively common, but serious neurological disease appears to be rare. No part of the neuraxis is spared. The neurological disorders occurring with COVID-19 may have many pathophysiological underpinnings. Some appear to be the consequence of direct viral invasion of the nervous system tissue, others arise as a postviral autoimmune process, and still others are the result of metabolic and systemic complications due to the associated critical illness. This review addresses the preliminary observations regarding the neurological disorders reported with COVID-19 to date and describes some of the disorders that are anticipated from prior experience with similar coronaviruses.

Point-of-care multiplexed diagnosis of meningitis using the FilmArray® ME panel technology.

Infectious meningitis is a medical urgency and rapid detection of the causative pathogen into the cerebrospinal fluid (CSF) is mandatory to guide the management of patients. We compared the performances of the multiplexed PCR FilmArray® ME panel with standard microbiological analyses, for rapid diagnosis of infectious meningitis. All the CSF samples received in our routine laboratory for the diagnosis of infectious meningitis were prospectively analyzed by the FilmArray® ME panel for the detection of fourteen targets in parallel to standard routine real-time PCR assays and bacterial culture. We reviewed clinical and biological records of patients for whom a discrepant result was obtained to achieve a definite diagnosis. Among 1124 CSF samples tested over a 43-week period, 113 (10.1%) and 87 (7.74%) were positive using the FilmArray® ME panel and the standard techniques, respectively. Among 40 CSF samples which yielded discrepant results, 34 were positive only using the FilmArray® ME panel and 6 were positive only using standard techniques. A total of 16/34 (47.1%) FilmArray® ME panel-positive CSF, and 6/6 (100%) of standard technique-positive CSF were interpreted as true positive. We were able to estimate the sensitivity, the specificity, the positive predictive value, and the negative predictive value of the FilmArray® ME panel at 94.2%, 98.2%, 84.3%, and 99.4%, respectively. The FilmArray® ME panel is an efficient tool for the rapid diagnosis of infectious meningitis at the point-of-care. Its higher sensitivity compared with that of standard molecular biology and culture techniques yields an increase of true positive diagnosis.

Jamestown Canyon virus in Massachusetts: clinical case series and vector screening.

Jamestown Canyon virus (JCV) is a neuroinvasive arbovirus that is found throughout North America and increasingly recognized as a public health concern. From 2004 to 2012, an average of 1.7 confirmed cases were reported annually in the United States, whereas from 2013 to 2018 this figure increased over seventeen-fold to 29.2 cases per year. The rising number of reported human infections highlights the need for better understanding of the clinical manifestations and epidemiology of JCV. Here, we describe nine patients diagnosed with neuroinvasive JCV infection in Massachusetts from 2013, the year of the first reported case in the state, to 2017. Because current diagnostic testing relies on serology, which is complicated by cross-reactivity with related orthobunyaviruses and can be negative in immunosuppressed patients, we developed and evaluated an RT-qPCR assay for detection of JCV RNA. We tested this on the available archived serum from two patients, but did not detect viral RNA. JCV is transmitted by multiple mosquito species and its primary vector in Massachusetts is unknown, so we additionally applied the RT-qPCR assay and confirmatory RNA sequencing to assess JCV prevalence in a vector candidate, Ochlerotatus canadensis. We identified JCV in 0.6% of mosquito pools, a similar prevalence to neighboring Connecticut. We assembled the first Massachusetts JCV genome directly from a mosquito sample, finding high identity to JCV isolates collected over a 60-year period. Further studies are needed to reconcile the low vector prevalence and low rate of viral evolutionary change with the increasing number of reported cases.

Predictors of infectious meningitis or encephalitis: the yield of cerebrospinal fluid in a cross-sectional study.

BACKGROUND: Cerebrospinal fluid (CSF) analyses are recommended in patients with meningitis and/or encephalitis, but evidence regarding its diagnostic yield is low. We aimed to determine predictors of infectious pathogens in the CSF of adult patients presenting with meningitis, and/or encephalitis. METHODS: Consecutive patients with meningitis and/or encephalitis form 2011-17 at a Swiss academic medical care center were included in this cross-sectional study. Clinical, neuroradiologic, and laboratory data were collected as exposure variables. Infectious meningitis and/or encephalitis were defined as the composite outcome. For diagnosis of bacterial meningitis the recommendations of the European Society of Clinical Microbiology and Infectious Diseases were followed. Viral meningitis was diagnosed by detection of viral ribonucleic or deoxyribonucleic acid in the CSF. Infectious encephalitis was defined according to the International Encephalitis Consortium (IEC). Meningoencephalitis was diagnosed if the criteria for meningitis and encephalitis were fulfilled. Multinomial logistic regression was performed to identify predictors of the composite outcome. To quantify discriminative power, the c statistic analogous the area under the receiver-operating curve (AUROC) was calculated. An AUROC between 0.7-0.8 was defined as "good", 08-0.9 as "excellent", and > 0.9 as "outstanding". Calibration was defined as "good" if the goodness of fit tests revealed insignificant p-values. RESULTS: Among 372 patients, infections were diagnosed in 42.7% presenting as meningitis (51%), encephalitis (32%), and meningoencephalitis (17%). Most frequent infectious pathogens were Streptococcus pneumoniae, Varicella zoster, and Herpes simplex 1&2. While in multivariable analysis lactate concentrations and decreased glucose ratios were the only independent predictors of bacterial infection (AUROCs 0.780, 0.870, and 0.834 respectively), increased CSF mononuclear cells were the only predictors of viral infections (AUROC 0.669). All predictors revealed good calibration. CONCLUSIONS: Prior to microbiologic workup, CSF data may guide clinicians when infection is suspected while other laboratory and neuroradiologic characteristics seem less useful. While increased CSF lactate and decreased glucose ratio are is the most reliable predictors of bacterial infections in patients with meningitis and/or encephalitis, only mononuclear cell counts predicted viral infections. TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT03856528. Registered on February 26th 2019.

Central nervous system infections produced by varicella zoster virus.

PURPOSE OF REVIEW: Varicella zoster virus (VZV) causes varicella, establishes latency, then reactivates to produce herpes zoster. VZV reactivation can also cause central nervous system (CNS) disease with or without rash. Herein, we review these CNS diseases, pathogenesis, diagnosis, and treatment. RECENT FINDINGS: The most common CNS manifestation of VZV infection is vasculopathy that presents as headache, cognitive decline, and/or focal neurological deficits. VZV vasculopathy has also been associated with cerebral amyloid angiopathy and moyamoya syndrome. Rarely, VZV will produce a meningitis, encephalitis, cerebellitis, and myelopathy. Pathogenic mechanisms include direct VZV infection of affected tissue, persistent inflammation, and/or virus-induced hypercoagulability. Diagnosis is confirmed by the temporal association of rash to disease onset, intrathecal synthesis of anti-VZV antibodies, and/or the presence of VZV DNA in CSF. Most cases respond to intravenous acyclovir with corticosteroids. SUMMARY: VZV produces a wide spectrum of CNS disorders that may be missed as some cases do not have an associated rash or a CSF pleocytosis. Clinicians must be vigilant in including VZV in their differential diagnosis of CNS infections as VZV is a ubiquitous pathogen; importantly, VZV CNS infections are treatable with intravenous acyclovir therapy and corticosteroids.

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

Purpose: We assessed the performance of metagenomic next-generation sequencing (mNGS) in the diagnosis of infectious encephalitis and meningitis. Methods: This was a prospective multicenter study. Cerebrospinal fluid samples from patients with viral encephalitis and/or meningitis, tuberculous meningitis, bacterial meningitis, fungal meningitis, and non-central nervous system (CNS) infections were subjected to mNGS. Results: In total, 213 patients with infectious and non-infectious CNS diseases were finally enrolled from November 2016 to May 2019; the mNGS-positive detection rate of definite CNS infections was 57.0%. At a species-specific read number (SSRN) ≥2, mNGS performance in the diagnosis of definite viral encephalitis and/or meningitis was optimal (area under the curve [AUC] = 0.659, 95% confidence interval [CI] = 0.566-0.751); the positivity rate was 42.6%. At a genus-specific read number ≥1, mNGS performance in the diagnosis of tuberculous meningitis (definite or probable) was optimal (AUC=0.619, 95% CI=0.516-0.721); the positivity rate was 27.3%. At SSRNs ≥5 or 10, the diagnostic performance was optimal for definite bacterial meningitis (AUC=0.846, 95% CI = 0.711-0.981); the sensitivity was 73.3%. The sensitivities of mNGS (at SSRN ≥2) in the diagnosis of cryptococcal meningitis and cerebral aspergillosis were 76.92 and 80%, respectively. Conclusion: mNGS of cerebrospinal fluid effectively identifies pathogens causing infectious CNS diseases. mNGS should be used in conjunction with conventional microbiological testing. Trial Registration: Chinese Clinical Trial Registry, ChiCTR1800020442.

Implementation of the FilmArray ME panel in laboratory routine using a simple sample selection strategy for diagnosis of meningitis and encephalitis.

BACKGROUND: Infectious meningitis is a serious disease and patient outcome relies on fast and reliable diagnostics. A syndromic panel testing approach like the FilmArray ME can accelerate diagnosis and therefore decrease the time to pathogen specific therapy. Yet, its clinical utility is controversial, mainly because of a remaining uncertainty in correct interpretation of results, limited data on its performance on clinical specimens and its relatively high costs. The aim of this study was to analyze clinical performance of the assay in a real life setting at a tertiary university hospital using a pragmatic and simple sample selection strategy to reduce the overall cost burden. METHODS: Over a period of 18 months we received 4623 CSF samples (2338 hospitalizations, 1601 individuals). FilmArray ME analysis was restricted to CSF-samples with a high pretest probability of infectious meningitis, e.g. positive Gram-stain, samples in which leukocytes and/or bacteria were evident or urgent suspicion of infection was communicated by clinicians. N = 171 samples matched to our risk criteria and were subjected to FilmArray ME analysis. Those samples were also analyzed by reference methods: culture only (n = 45), PCR only (n = 20) or both methods (n = 106). RESULTS: 56/171 (32.75%) were FilmArray ME positive. Bacterial pathogens were detected in 30/56 (53.57%), viral pathogens were detected in 27/56 (48.21%) and yeast DNA was detected in 1/56 (1.79%) of positive samples. Double detection occurred in 2/56 samples. In 52/56 (92.86%) FilmArray ME positive samples, results could be confirmed by the reference assays (sensitivity = 96.30%, specificity =96.58%). CONCLUSION: The FilmArray ME assay is a fast and reliable diagnostic tool for the management of infectious meningitis and can easily be implemented in routine diagnostic workflows. However, correlation of test results and underlying clinical symptoms requires experienced users and the awareness of potentially false negative or false positive results. Moreover, considering the need for antimicrobial susceptibility testing, the use of molecular tests as a stand-alone diagnostic cannot be recommended.

Cerebrospinal Fluid Findings Are Poor Predictors of Appropriate FilmArray Meningitis/Encephalitis Panel Utilization in Pediatric Patients.

Molecular testing of cerebrospinal fluid (CSF) using the BioFire FilmArray meningitis/encephalitis (FA-M/E) panel permits rapid, simultaneous pathogen detection. Due to the broad spectrum of targeted organisms, FA-M/E testing may be restricted to patients with abnormal CSF findings. We sought to determine if restriction is appropriate in our previously healthy and/or immunocompromised pediatric patients. FA-M/E was ordered on 1,025 CSF samples from 948 patients; 121 (11.8%) specimens were FA-M/E positive. Of these, 89 (73.6%) were virus positive, and 30 (24.8%) were bacterium positive. The most common targets detected were enterovirus (n = 38), human herpesvirus 6 (HHV-6) (n = 30), and Streptococcus pneumoniae (n = 14). Pleocytosis with white blood cell (WBC) levels of ≥5 cells/mm3 and ≥10 cells/mm3 were found in 33.1% and 24.3% of all specimens, respectively. Using WBC levels of ≥5 cells/mm3, 63.4% (59/93) of positive specimens exhibited pleocytosis, compared to 29.5% (233/789) of negative specimens. Among positive specimens, 54.4% (37/68) of viral and 87% (20/23) of bacterial cases had pleocytosis. The use of a pleocytosis cutoff of ≥10 cells/mm3 would have missed an additional enterovirus, one cytomegalovirus (CMV), and two HHV-6 diagnoses. CSF glucose and protein levels were normal for 83/116 (75.2%) and 51/116 (44%) positive specimens. Abnormal glucose in combination with WBC levels of ≥10 cells/mm3 showed high specificity (94.5%) and was a better predictor of FA-M/E positivity than abnormal protein. Sensitivity and positive predictive values were <90% for all biomarkers. CSF pleocytosis and abnormal glucose/protein were poor predictors of FA-M/E. Restricting FA-M/E orders based on pleocytosis or other abnormal parameters would have resulted in missed diagnostic opportunities, particularly for the detection of viruses in both previously healthy and immunocompromised patients.

Impact of a multiplex PCR assay (FilmArray®) on the management of patients with suspected central nervous system infections.

Microbiological diagnosis of central nervous system (CNS) infections is challenging due to limited access to CNS samples, overlap between meningitis and encephalitis, and the multiplicity of pathogens potentially involved. We aimed to estimate the impact of a commercial multiplex PCR assay (FilmArray® meningitis/encephalitis) on the management of patients with suspicion of meningitis or encephalitis, in terms of time to diagnosis, antimicrobial agents use, duration of hospitalization, and costs. This prospective observational study was conducted at Saint Joseph Hospital (Paris, France) from December 2016 to December 2017. All CSF samples sent to the microbiology laboratory for suspicion of meningitis and/or encephalitis, with CSF cells count > 5 cells/µL, were tested by meningitis/encephalitis multiplex PCR assay. One hundred thirty patients were included. The multiplex PCR assay was positive in 33 patients (25%). Main pathogens found were Enterovirus (n = 12), Varicella-Zoster virus (n = 7), Herpes simplex virus-2 (n = 6), and Listeria monocytogenes (n = 3) as main pathogens. The multiplex PCR assay reduced time to microbiological diagnosis by 3.3 ± 1.6 days and allowed an earlier discontinuation of empirical anti-infective drugs in 42 patients (32%) and an earlier hospital discharge in 23 patients (18%), with an estimated saving of 82 hospital days overall, and a management cost reduction of 26,242 € (201 €/patient). The systematic use of the FilmArray® meningitis/encephalitis multiplex PCR assay may allow earlier diagnosis, earlier discontinuation of empirical treatment, reduced duration of stay, and costs reduction.