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

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.

Pathogen or Bystander: Clinical Significance of Detecting Human Herpesvirus 6 in Pediatric Cerebrospinal Fluid

Human herpesvirus 6 (HHV-6) is an important cause of meningitis and meningoencephalitis. As testing for HHV-6 in cerebrospinal fluid (CSF) is more readily available using the FilmArray Meningitis/Encephalitis panel (FA-ME; BioFire Diagnostics, Salt Lake City, UT), we aimed to determine the clinical significance of detecting HHV-6 in order to identify true infections and to ensure appropriate antiviral initiation. Chart review on 25 patients positive for HHV-6 by FA-ME was performed to determine clinical presentation, comorbidity, treatment, and outcome. The presence of chromosomally integrated HHV-6 (ciHHV-6) DNA was also investigated. Of 1,005 children tested by FA-ME, HHV-6 was detected in 25 (2.5%). Five patients were diagnosed with either HHV-6 meningitis or meningoencephalitis based on HHV-6 detection in CSF, clinical presentation, and radiographic findings. Detection of HHV-6 by FA-ME led to discontinuation of acyclovir within 12.0 h in all 12 patients empirically treated with acyclovir. Six of the 12 patients were started on ganciclovir therapy within 6.8 h; 4 of these were treated specifically for HHV-6 infection, whereas therapy was discontinued in the remaining 2 patients. CSF parameters were not generally predictive of HHV-6 positivity. The presence of ciHHV-6 was confirmed in 3 of 18 patients who could be tested. Five of the 25 patients included in the study were diagnosed with HHV-6 meningitis/meningoencephalitis. FA-ME results led to discontinuation of empirical antiviral treatment in 12 patients and appropriate initiation of ganciclovir in 4 patients. In our institution, detection of HHV-6 using FA-ME led to faster establishment of disease etiology and optimization of antimicrobial therapy.

Development of a Mobile Laboratory for Sudden Onset Disasters

OBJECTIVES

Clinical diagnostics in sudden onset disasters have historically been limited. We set out to design, implement, and evaluate a mobile diagnostic laboratory accompanying a type 2 emergency medical team (EMT) field hospital.

METHODS

Available diagnostic platforms were reviewed and selected against in field need. Platforms included HemoCue301/WBC DIFF, i-STAT, BIOFIRE FILMARRAY multiplex rt-PCR, Olympus BX53 microscopy, ABO/Rh grouping, and specific rapid diagnostic tests. This equipment was trialed in Katherine, Australia, and Dili, Timor-Leste.

RESULTS

During the initial deployment, an evaluation of FilmArray tests was successful using blood culture identification, gastrointestinal, and respiratory panels. HemoCue301 (n = 20) hemoglobin values were compared on Sysmex XN 550 (r = 0.94). HemoCue WBC DIFF had some variation, dependent on the cell, when compared with Sysmex XN 550 (r = 0.88-0.16). i-STAT showed nonsignificant differences against Vitros 250. Further evaluation of FilmArray in Dili, Timor-Leste, diagnosed 117 pathogens on 168 FilmArray pouches, including 25 separate organisms on blood culture and 4 separate cerebrospinal fluid pathogens.

CONCLUSION

This mobile laboratory represents a major advance in sudden onset disaster. Setup of the service was quick (< 24 hr) and transport to site rapid. Future deployment in fragmented health systems after sudden onset disasters with EMT2 will now allow broader diagnostic capability.

Methods for rapid diagnosis of meningitis etiology in adults

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

HHV-6-Associated Neurological Disease in Children: Epidemiologic, Clinical, Diagnostic, and Treatment Considerations

Human herpesviruses 6A and 6B, often referred to collectively as human herpesvirus 6, are a pair of beta-herpesviruses known to cause a variety of clinical syndromes in both immunocompetent and immunocompromised individuals. Most humans are infected with human herpesvirus 6B, and many with human herpesvirus 6A. Primary infection typically occurs in early childhood, although large-scale reviews on the topic are limited. Herein, the authors explore the clinical manifestations of human herpesvirus 6-associated disease in both immunocompetent and immunocompromised pediatric patients, the risk factors for development of human herpesvirus 6-associated neurological disease, the risk of autoimmunity associated with development of active or latent infection, the relevance of human herpesvirus 6-specific diagnostic tests, and the medications used to treat human herpesvirus 6. The goal of this review is to improve the current understanding of human herpesvirus 6 in pediatric populations and to examine the most effective diagnostic and therapeutic interventions in this disease state.

Rapid Diagnosis of Meningococcal Meningitis in a Patient With Familial Mediterranean Fever by the FilmArray Meningitis/Encephalitis Panel: A Case Report

Familial Mediterranean fever (FMF) is a rare autoinflammatory disorder of the innate immune system. Patients with innate immune system defects are at a high risk of meningococcal disease, although it is unclear if patients with FMF also have increased susceptibility to invasive infection. Herein, we present a diagnostically challenging case of a male adolescent with a past medical history of FMF stabilized on colchicine who presented with some of the early clinical features of community-acquired bacterial meningitis. To our knowledge, this is the first case of meningococcal meningitis in a patient with FMF diagnosed with the FilmArray Meningitis/Encephalitis (ME) Panel. This case report demonstrates that rapid detection of Neisseria meningitidis by the ME Panel can aid in the early diagnosis and prompt treatment of patients with suspected meningitis and may be the only positive test in patients with early presentation and/or prior antimicrobial therapy.

Delirium in Meningitis and Encephalitis: Emergence and Prediction in a 6-Year Cohort

BACKGROUND/OBJECTIVE

Data regarding delirium in patients presenting with infections of the central nervous system, such as meningitis and/or encephalitis (ME), are scarce. We aimed to determine the frequency and early predictors of delirium in the acute phase of ME.

METHODS

We assessed clinical, radiologic, and laboratory data of patients with ME at a Swiss academic medical center from 2011 to 2017. The highest Intensive Care Delirium Screening Checklist (ICDSC) score was assessed within 24 hours around lumbar puncture. Multivariable logistic regression was performed to identify predictors of delirium (ICDSC ≥4).

RESULTS

Among 330 patients with ME, infectious pathogens were identified in 41%. An ICDSC >1 was found in 28% with and 19% without identified infectious pathogens. Delirium was diagnosed in 18% with and 14% without infectious pathogens and significantly associated with prolonged in-hospital treatment and mechanical ventilation, more frequent administration of neuroleptics and anesthetics (in 96% with delirium vs 35% without), complications, and less recovery to premorbid functional baseline. Low serum albumin at presentation was the only independent predictor of delirium (area under the receiver-operating curve [AUROC] = 0.792) in patients with pathogens. In patients with infections, the AUROC was smallest for encephalitis (AUROC = 0.641) and larger for patients with meningeal infections (meningitis AUROC = 0.807; meningoencephalitis AUROC = 0.896).

CONCLUSIONS

Delirium in the context of ME is seen in almost every fifth patient and linked to prolonged treatment, complications, and incomplete recovery. Among clinical, radiologic, and laboratory parameters, the good calibration and discrimination of low albumin serum concentrations for the prediction of delirium in patients with ME seem promising, especially if meninges are affected.

Economic Evaluation: Onsite HSV PCR Capabilities for Pediatric Care

Objective:

Herpes simplex virus (HSV) encephalitis has an overall mortality rate of 11%–29% with treatment. Although rare, HSV encephalitis is frequently tested for and empirically treated, especially in the neonatal population. HSV infection can be diagnosed with polymerase chain reaction (PCR) testing, although this frequently requires sending samples to reference laboratories. The inherent delay in results may lead to prolonging empiric treatment and hospital stay, resulting in increased costs. This study investigates whether onsite HSV PCR testing decreases hospitalization duration, acyclovir treatment duration, and financial cost on an institution.

Project design:

This single-center project utilized the IHI model for improvement to evaluate third-party HSV PCR processing versus an implemented onsite PCR-based meningitis–encephalitis panel for HSV central nervous system evaluation. The primary outcome was hospital cost differential with secondary outcomes, including duration of acyclovir administration and time to result.

Results:

We identified 96 children age 0–18 from 2010 to 2016, 74 patients utilizing offsite third-party testing, and 22 patients utilizing onsite. We observed a per-patient cost savings of $428 ($618.43–$190.43, P = 0.029) upon the implementation of onsite testing. The mean duration of acyclovir therapy decreased from 3.7 to 0.26 days per patient (P < 0.001). Time to result decreased from 4.6 to 0.13 days (P < 0.001).

Conclusions:

Acquisition of real-time local HSV PCR capabilities significantly decreased time to result and empiric medication use while significantly reducing hospital costs in a military treatment facility.

Molecular and Histologic Diagnosis of Central Nervous System Infections

Infections of the central nervous system cause significant morbidity and mortality in immunocompetent and immunocompromised individuals. A wide variety of microorganisms can cause infections, including bacteria, mycobacteria, fungi, viruses, and parasites. Although less invasive testing is preferred, surgical biopsy may be necessary to collect diagnostic tissue. Histologic findings, including special stains and immunohistochemistry, can provide a morphologic diagnosis in many cases, which can be further classified by molecular testing. Correlation of molecular, culture, and other laboratory results with histologic findings is essential for an accurate diagnosis, and to minimize false positives from microbial contamination.

Genomic and serologic characterization of enterovirus A71 brainstem encephalitis

Objective

In 2016, Catalonia experienced a pediatric brainstem encephalitis outbreak caused by enterovirus A71 (EV-A71). Conventional testing identified EV in the periphery but rarely in CSF. Metagenomic next-generation sequencing (mNGS) and CSF pan-viral serology (VirScan) were deployed to enhance viral detection and characterization.

Methods

RNA was extracted from the CSF (n = 20), plasma (n = 9), stool (n = 15), and nasopharyngeal samples (n = 16) from 10 children with brainstem encephalitis and 10 children with meningitis or encephalitis. Pathogens were identified using mNGS. Available CSF from cases (n = 12) and pediatric other neurologic disease controls (n = 54) were analyzed with VirScan with a subset (n = 9 and n = 50) validated by ELISA.

Results

mNGS detected EV in all samples positive by quantitative reverse transcription polymerase chain reaction (qRT-PCR) (n = 25). In qRT-PCR-negative samples (n = 35), mNGS found virus in 23% (n = 8, 3 CSF samples). Overall, mNGS enhanced EV detection from 42% (25/60) to 57% (33/60) (p-value = 0.013). VirScan and ELISA increased detection to 92% (11/12) compared with 46% (4/12) for CSF mNGS and qRT-PCR (p-value = 0.023). Phylogenetic analysis confirmed the EV-A71 strain clustered with a neurovirulent German EV-A71. A single amino acid substitution (S241P) in the EVA71 VP1 protein was exclusive to the CNS in one subject.

Conclusion

mNGS with VirScan significantly increased the CNS detection of EVs relative to qRT-PCR, and the latter generated an antigenic profile of the acute EV-A71 immune response. Genomic analysis confirmed the close relation of the outbreak EV-A71 and neuroinvasive German EV-A71. A S241P substitution in VP1 was found exclusively in the CSF.

Rapid diagnostic tests for infectious diseases in the emergency department

Background

Rapid diagnostic tests (RDTs) for infectious diseases, with a turnaround time of less than 2 hours, are promising tools that could improve patient care, antimicrobial stewardship and infection prevention in the emergency department (ED) setting. Numerous RDTs have been developed, although not necessarily for the ED environment. Their successful implementation in the ED relies on their performance and impact on patient management.

Objectives

The aim of this narrative review was to provide an overview of currently available RDTs for infectious diseases in the ED.

Sources

PubMed was searched through August 2019 for available studies on RDTs for infectious diseases. Inclusion criteria included: commercial tests approved by the US Food and Drug Administration (FDA) or Conformité Européenne (CE) in vitro diagnostic devices with data on clinical samples, ability to run on fully automated systems and result delivery within 2 hours.

Content

A nonexhaustive list of representative commercially available FDA- or CE-approved assays was categorized by clinical syndrome: pharyngitis and upper respiratory tract infection, lower respiratory tract infection, gastrointestinal infection, meningitis and encephalitis, fever in returning travellers and sexually transmitted infection, including HIV. The performance of tests was described on the basis of clinical validation studies. Further, their impact on clinical outcomes and anti-infective use was discussed with a focus on ED-based studies.

Implications

Clinicians should be familiar with the distinctive features of each RDT and individual performance characteristics for each target. Their integration into ED work flow should be preplanned considering local constraints of given settings. Additional clinical studies are needed to further evaluate their clinical effectiveness and cost-effectiveness.

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.

Validation of multiplex PCR for the diagnosis of acute bacterial meningitis in culture negative cerebrospinal fluid

INTRODUCTION

This study evaluated the operational characteristics of the multiplex polymerase chain reaction (PCR) for cerebrospinal fluid (CSF) from patients with cellular and biochemical characteristics of acute bacterial meningitis and positive or negative CSF cultures.

METHODS

Multiplex PCR was performed for 36 CSF samples: culture-proven acute bacterial meningitis (n = 7), culture-negative acute bacterial meningitis (n = 17), lymphocytic meningitis (n = 8), and normal CSF (n = 4). The operational characteristics of multiplex PCR were evaluated with definite and probable bacterial meningitis, using culture positive, cytological and biochemical CSF characteristics as the gold standard.

RESULTS

Multiplex PCR for CSF was efficient in the group with CSF cellular and biochemical characteristics of acute bacterial meningitis but with a negative CSF culture. This group demonstrated high specificity, positive predictive value, and efficiency.

CONCLUSIONS

Multiplex PCR for CSF can improve the speed and accuracy of acute bacterial meningitis diagnosis in a clinical setting as a complement to classical immunological and bacteriological assays in CSF. It is also useful for CSF culture-negative acute bacterial meningitis.

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.

Immunomodulatory Strategies in Herpes Simplex Virus Encephalitis

Herpes simplex virus 1 (HSV-1) can be responsible for life-threatening HSV encephalitis (HSE). The mortality rate of patients with HSE who do not receive antiviral treatment is 70%, with most survivors suffering from permanent neurological sequelae. The use of intravenous acyclovir together with improved diagnostic technologies such as PCR and magnetic resonance imaging has resulted in a reduction in the mortality rate to close to 20%. However, 70% of surviving patients still do not recover complete neurological functions. Thus, there is an urgent need to develop more effective treatments for a better clinical outcome. It is well recognized that cerebral damage resulting from HSE is caused by viral replication together with an overzealous inflammatory response. Both of these processes constitute potential targets for the development of innovative therapies against HSE. In this review, we discuss recent progress in therapy that may be used to ameliorate the outcome of patients with HSE, with a particular emphasis on immunomodulatory agents. Ideally, the administration of adjunctive immunomodulatory drugs should be initiated during the rise of the inflammatory response, and its duration should be limited in time to reduce undesired effects. This critical time frame should be optimized by the identification of reliable biomarkers of inflammation.

Evaluation of a commercial multiplex PCR for diagnosis of central nervous system (CNS) nosocomial infections

Nosocomial Central Nervous System (CNS) infections are often serious complications of neurosurgical procedures. Their diagnosis is complex and frequently based on microbiological culture. The aim of this work was to evaluate the effectiveness of the FilmArray® Blood Culture Identification (BCID) panel, a multiplex PCR designed to identify the most common etiologic agents of sepsis involved with nosocomial CNS infections. A total of ninety samples were analyzed with the BCID panel. The sensitivity and specificity achieved were 77.4% and 100% respectively, when compared with the reference method (culture). Based on the analysis of the melting curves, another cut-off was established improving sensitivity to 83.9% whilst maintaining 98.3% specificity. The BCID panel seems to be a helpful tool for the prompt diagnosis of CNS nosocomial infections. The cut-off proposed here can increase sensitivity, but further studies are required to confirm its effectiveness and its applicability in clinical microbiology laboratories.

Assessment of the FilmArray® multiplex PCR system and associated meningitis/encephalitis panel in the diagnostic service of a tertiary hospital

Rapid and accurate diagnosis of meningitis/encephalitis (M/E) is essential for successful patient outcomes. The FilmArray® meningitis/encephalitis Panel (MEP) is a multiplexed PCR test for simultaneous, rapid detection of pathogens directly from cerebrospinal fluid (CSF) samples. 94 prospectively collected CSF specimens from patients with clinical suspicion of infective M/E underwent testing for 14 pathogens simultaneously, including Escherichia coli, Haemophilus influenzae, Neisseria meningitidis, and Varicella zoster. MEP demonstrated 95% agreement with current PCR methods, resulting in 16 diagnosed cases of M/E. Typically, the FilmArray® MEP results were delivered within approximately one hour, contrasting with current practices taking up to 5.6 days. Given the significant morbidity and mortality associated with delayed diagnosis of central nervous system infections, the FilmArray® MEP is a useful addition to the diagnostic capabilities of a clinical microbiology department.

Small Molecular Contaminant and Microorganism Can Be Simultaneously Detected Based on Nanobody-Phage: Using Carcinogen Aflatoxin and Its Main Fungal Aspergillus Section Flavi spp. in Stored Maize for Demonstration

Simultaneous detection technology has become a hot topic in analytical chemistry; however, very few reports on how to simultaneously detect small molecular contaminants and microorganisms have been in place. Aflatoxins are a group of highly toxic and carcinogenic compounds, which are produced mainly by Aspergillus flavus and Aspergillus parasiticus from section Flavi responsible for aflatoxin accumulation in stored cereals. Both aflatoxins and Aspergillus section Flavi were used to demonstrate the duplex real-time RCR method of simultaneously detecting small molecular contaminants and microorganisms. The detection of aflatoxins and Aspergillus section Flavi was carried out depending on the anti-idiotypic nanobody-phage V_2–5 and aflatoxin-synthesis related gene nor-1 (=aflD), respectively. The quantitative standard curves for simultaneous detection of aflatoxins and Aspergillus section Flavi were constructed, with detection limits of 0.02 ng/ml and 8 × 10² spores/g, respectively. Naturally contaminated maize samples (n = 25) were analyzed for a further validation. The results were in good agreement between the new developed method and the referential methods (high-performance liquid chromatography and the conventional plating counts).

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Purpose of Review

Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients.

Recent Findings

Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies.

Summary

The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.

Comparison of antibiotic and acyclovir usage before and after the implementation of an on-site FilmArray meningitis/encephalitis panel in an academic tertiary pediatric hospital: a retrospective observational study

BACKGROUND

Prompt initiation of empiric therapy is common practice in case of suspected meningitis or encephalitis. However, in children the most common pathogens are viruses that usually do not require and are not covered by the applied anti-infective treatment. Novel multiplex PCR (mPCR) panels provide rapid on-site diagnostic testing for a variety of pathogens. This study compared empiric antibiotic and acyclovir usage before and after the introduction of an on-site FilmArray Meningitis/Encephalitis Panel (FA ME Panel).

METHODS

We retrospectively compared data for empiric antibiotic and acyclovir usage between pediatric patients with suspected central nervous system (CNS) infection receiving mPCR testing and a matched historical control group. Patients were matched by age and suspected CNS infection. We included all patients for whom empiric antibiotics and/or acyclovir were prescribed.

RESULTS

Each study group consisted of 46 patients with 29 (63.0%) infants and 17 (37.0%) older children. A viral pathogen was diagnosed in 5/46 (10.9%) patients in the control group (all enteroviruses) and in 14/46 (30.4%) patients in the mPCR group (enterovirus n = 9; human herpesvirus 6 (HHV-6) n = 5), (p = 0.038)). Length of Therapy (LoT) and Days of Therapy (DoT) for antibiotics were significantly lower for infants (4.0 vs. 3.0, p = 0.038 and 8.0 vs. 6.0, p = 0.015, respectively). Acyclovir therapy was significantly shorter for both, infants and older children (3.0 vs. 1.0 day, p < 0.001 for both age groups).

CONCLUSION

The findings of our study suggest that the introduction of a FA ME Panel into clinical routine procedures is associated with a significantly reduced LoT and DoT of empiric anti-infective treatment in children with suspected meningoencephalitis. The largest effect was observed in infants.

Clinical characteristics of enterovirus A71 neurological disease during an outbreak in children in Colorado, USA, in 2018: an observational cohort study

BACKGROUND

In May, 2018, Children's Hospital Colorado noted an outbreak of enterovirus A71 (EV-A71) neurological disease. We aimed to characterise the clinical features of EV-A71 neurological disease during this outbreak.

METHODS

In this retrospective observational cohort study, children (younger than 18 years) who presented to Children's Hospital Colorado (Aurora, CO, USA) between March 1 and November 30, 2018, with neurological disease (defined by non-mutually exclusive criteria, including meningitis, encephalitis, acute flaccid myelitis, and seizures) and enterovirus detected from any biological specimen were eligible for study inclusion. The clinical characteristics of children with neurological disease associated with EV-A71 were compared with those of children with neurological disease associated with other enteroviruses during the same period. To explore the differences in clinical presentation of acute flaccid myelitis, we also used a subgroup analysis to compare clinical findings in children with EV-A71-associated acute flaccid myelitis during the study period with these findings in those with enterovirus D68 (EV-D68)-associated acute flaccid myelitis at the same hospital between 2013 and 2018.

FINDINGS

Between March 10 and Nov 10, 2018, 74 children presenting to Children's Hospital Colorado were found to have enterovirus neurological disease; EV-A71 was identified in 43 (58%) of these children. The median age of the children with EV-A71 neurological disease was 22·7 months (IQR 4·0-31·9), and most of these children were male (34 [79%] children). 40 (93%) children with EV-A71 neurological disease had findings suggestive of meningitis, 31 (72%) children showed evidence of encephalitis, and ten (23%) children met our case definition of acute flaccid myelitis. All children with EV-A71 disease had fever and 18 (42%) children had hand, foot, or mouth lesions at or before neurological onset. Children with EV-A71 disease were best differentiated from those with other enteroviruses (n=31) by the neurological findings of myoclonus, ataxia, weakness, and autonomic instability. Of the specimens collected from children with EV-A71, this enterovirus was detected in 94% of rectal, 79% of oropharyngeal, 56% of nasopharyngeal, and 20% of cerebrospinal fluid specimens. 39 (93%) of 42 children with EV-A71 neurological disease who could be followed up showed complete recovery by 1-2 months. Compared with children with EV-D68-associated acute flaccid myelitis, children with EV-A71-associated acute flaccid myelitis were younger, showed neurological onset earlier after prodromal symptom onset, had milder weakness, showed more rapid improvement, and were more likely to completely recover.

INTERPRETATION

This outbreak of EV-A71 neurological disease, the largest reported in the Americas, was characterised by fever, myoclonus, ataxia, weakness, autonomic instability, and full recovery in most patients. Because EV-A71 epidemiology outside of Asia remains difficult to predict, identification of future outbreaks will be aided by prompt recognition of these distinct clinical findings, testing of non-sterile and sterile site specimens, and enhanced enterovirus surveillance.

FUNDING

None.

Towards Predicting Progression to Severe Dengue

There is an urgent need for prognostic assays to predict progression to severe dengue infection, which is a major global threat. While the majority of symptomatic dengue patients experience an acute febrile illness, 5-20% progress to severe infection associated with significant morbidity and mortality. Early monitoring and administration of supportive care reduce mortality and clinically usable biomarkers to predict severe dengue are needed. Here, we review recent discoveries of gene sets, anti-dengue antibody properties, and inflammatory markers with potential utility as predictors of disease progression. Upon larger scale validation and development of affordable sample-to-answer technologies, some of these biomarkers may be utilized to develop the first prognostic assay for improving patient care and allocating healthcare resources more effectively in dengue endemic countries.

Etiology of Central Nervous System Infections in a Rural Area of Nepal Using Molecular Approaches

The etiology of infections of the central nervous system (CNS) in Nepal often remains unrecognized because of underdeveloped laboratory facilities. The aim of this study was to investigate the etiology of CNS infections in a rural area of Nepal using molecular methods. From November 2014 to February 2016, cerebrospinal fluid (CSF) was collected from 176 consecutive patients presenting at United Mission Hospital in Tansen, Nepal, with symptoms of possible CNS infection. After the CSF samples were stored and transported frozen, polymerase chain reaction (PCR) was performed in Sweden, targeting a total of 26 pathogens using the FilmArray^® ME panel (BioFire, bioMerieux, Salt Lake City, UT), the MeningoFinder^® 2SMART (PathoFinder, Maastricht, The Netherlands), and an in-house PCR test for dengue virus (DENV), Japanese encephalitis virus (JEV), and Nipah virus (NiV). The etiology could be determined in 23%. The bacteria detected were Haemophilus influenzae (n = 5), Streptococcus pneumoniae (n = 4), and Neisseria meningitidis (n = 1). The most common virus was enterovirus detected in eight samples, all during the monsoon season. Other viruses detected were cytomegalovirus (n = 6), varicella zoster virus (n = 5), Epstein–Barr virus (n = 3), herpes simplex virus (HSV) type 1 (HSV-1) (n = 3), HSV-2 (n = 3), human herpes virus (HHV) type 6 (HHV-6) (n = 3), and HHV-7 (n = 2). Cryptococcus neoformans/gatti was found in four samples. None of the samples were positive for DENV, JEV, or NiV. Of the patients, 67% had been exposed to antibiotics before lumbar puncture. In conclusion, the etiology could not be found in 77% of the samples, indicating that the commercial PCR panels used are not suitable in this setting. Future studies on the etiology of CNS infections in Nepal could include metagenomic techniques.

Evaluation of the Biofire FilmArray meningitis/encephalitis assay for the detection of Cryptococcus neoformans/gattii

OBJECTIVES

Cryptococcal meningitis (CM) remains an important cause of morbidity and mortality among immunocompromised patients. Laboratory diagnostics for CM includes antigen detection, staining and culture. Data on the performance of the Biofire® FilmArray® meningitis/encephalitis (ME) panel for detecting Cryptococcus neoformans/gattii is limited, with several reports describing false negativity for this target.

METHODS

A retrospective analysis of 1384 physician-ordered ME panel tests ordered between January 2017 to October 2018 was performed. ME panel results were compared to cerebrospinal fluid (CSF) cryptococcal antigen (CrAg) and CSF culture testing and clinical significance of cryptococcal detection was determined.

RESULTS

There were 34 patients positive for cryptococcal detection by either ME panel, CSF CrAg or CSF culture in 2.7% of CSF specimens tested (38/1384). Of the 34 patients positive for cryptococcal detection, 85.3% were human immunodeficiency virus positive (29/34). The ME panel detected 32/38 (84.2%) cryptococcal-positive specimens, culture detected 28/38 (73.7%) and CSF CrAg was positive in 37/38 specimens (97.4%). The ME panel had a sensitivity and specificity of 96.4% (95% CI 81.7-99.9%) and 99.6% (95% CI 99.2-99.9%) compared with culture, and 83.8% (95% CI 68.0-93.8%) and 99.9% (95% CI 99.6-100.0%) compared to CSF CrAg testing, respectively. CrAg titres were lower among ME panel-negative, culture-negative specimens compared with ME panel-positive, culture-negative specimens (reciprocal median end-point titres of 128 ± 60 vs. 1920 ± 1730, p 0.04). All five CrAg-positive, ME panel- and culture-negative specimens were obtained from previously treated CM patients.

DISCUSSION

The ME panel had high correlation with CSF culture and a somewhat lower correlation with CSF CrAg testing. The potential utility of using negative ME panel test results to predict culture sterility among patients undergoing treatment for CM warrants further study.

Impact of decreasing cerebrospinal fluid enterovirus PCR turnaround time on costs and management of children with suspected enterovirus meningitis

To estimate the impact of implementing in-hospital enterovirus (EV) polymerase chain reaction (PCR) testing of cerebrospinal fluid (CSF) with same-day turn-around-time (TAT) on length-of-stay (LOS), antibiotic use and on cost per patient with suspected EV meningitis, compared with testing at an outside reference laboratory. A model-based analysis using a retrospective cohort of all hospitalized children with CSF EV PCR testing done between November 2013 and 2017. The primary outcome measured was the potential date of discharge if the EV PCR result had been available on the same day. Patients with positive EV PCR were considered for potential earlier discharge once clinically stable with no reason for hospitalization other than intravenous antibiotics. Descriptive statistics and cost-sensitivity analyses were performed. CSF EV PCR testing was done on 153 patients, of which 44 (29%) had a positive result. Median test TAT was 5.3 days (IQR 3.9–7.6). Median hospital LOS was 5 days (IQR 3–12). Most (86%) patients received intravenous antibiotics with mean duration of 5.72 ± 6.51 days. No patients with positive EV PCR had a serious bacterial infection. We found that same-day test TAT would reduce LOS and duration of intravenous antibiotics by 0.50 days (95%CI 0.33–0.68) and 0.67 days (95%CI 0.42–0.91), respectively. Same-day test TAT was associated with a cost reduction of 342.83CAD (95%CI 178.14–517.00) per patient with suspected EV meningitis. Compared with sending specimens to a reference laboratory, performing CSF EV PCR in-hospital with same-day TAT was associated with decreased LOS, antibiotic therapy, and cost per patient.

Childhood Infectious Encephalitis: An Overview of Clinical Features, Investigations, Treatment, and Recent Patents

BACKGROUND

Infectious encephalitis is a serious and challenging condition to manage. This overview summarizes the current literature regarding the etiology, clinical manifestations, diagnosis, management, and recent patents of acute childhood infectious encephalitis.

METHODS

We used PubMed Clinical Queries as a search engine and used keywords of "encephalitis" AND "childhood" Patents were searched using the key term "encephalitis" in google.patents.- com and patentsonline.com.

RESULTS

Viral encephalitis is the most common cause of acute infectious encephalitis in children. In young children, the clinical manifestations can be non-specific. Provision of empiric antimicrobial therapy until a specific infectious organism has been identified, which in most cases includes acyclovir, is the cornerstone of therapy. Advanced investigation tools, including nucleic acid-based test panel and metagenomic next-generation sequencing, improve the diagnostic yield of identifying an infectious organism. Supportive therapy includes adequate airway and oxygenation, fluid and electrolyte balance, cerebral perfusion pressure support, and seizure control. Recent patents are related to the diagnosis, treatment, and prevention of acute infectious encephalitis.

CONCLUSION

Viral encephalitis is the most common cause of acute infectious encephalitis in children and is associated with significant morbidity. Recent advances in understanding the genetic basis and immunological correlation of infectious encephalitis may improve treatment. Third-tier diagnostic tests may be incorporated into clinical practice. Treatment is targeted at the infectious process but remains mostly supportive. However, specific antimicrobial agents and vaccines development is ongoing.

Antimicrobial Stewardship Program in Critical Care-Need of the Hour

Maximum antibiotic usage within hospitals occurs in critical care areas. Reasons for this usage are the moribund state of patients, invasive devices, and protocol based necessity for empiric antibiotic initiation in most critical conditions. Although unavoidable, prudent use of antibiotics (empiric and therapeutic) should be tailored based on national or if available, unit-based hospital antibiogram. This forms the footstool of every antibiotic policy formulated at tertiary care hospitals. Strict adherence to antibiotic policy formulated based on hospital antibiogram largely benefits patients and hospital-wide antimicrobial stewardship is ensured. The necessity, benefits, key targets, and usefulness of antimicrobial stewardship program (AMSP) in critical care has been elaborated in this review. How to cite this article: Vadala R, Princess I. Antimicrobial Stewardship Program in Critical Care-Need of the Hour. Indian J Crit Care Med 2020;24(9):847-854.

Clinical microbiology

The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory.

After reviewing this chapter, the reader will be able to:•

List key considerations for specimen collection for microbiology testing.

•

Discuss the advantages and limitations of automation in the clinical microbiology laboratory.

•

Describe the evolution of microorganism identification methods.

•

Discuss the benefits and limitations of molecular microbiology point-of-care testing.

•

Summarize currently available multiplex molecular microbiology testing options.

Diagnostic challenges of central nervous system infection: extensive multiplex panels versus stepwise guided approach

BACKGROUND

Cerebrospinal fluid (CSF) testing is a key component for the diagnosis of central nervous system (CNS) infections. Current meningitis and encephalitis management guidelines agree on the need for CSF molecular testing in combination with other direct and indirect biological testing, both in CSF and blood. Multiplex molecular tests have been developed to reduce turnaround times and facilitate the diagnostic approach.

OBJECTIVES

We aim to discuss the role of multiplex molecular panels in the management of CNS infections.

SOURCES

The MEDLINE database and the grey literature have been searched for relevant articles.

CONTENT

New molecular multiplex panels are being developed to simultaneously detect a large array of neuropathogens in CSF. Although one of these assays has been US Food and Drug Administration-approved, extensive analytical and clinical validation is still missing, and suboptimal performance related issues have been raised. Its use has been associated with decreased costs, reduced length of hospital stay and reduced antiviral therapy administration in retrospective, industry-sponsored studies. The pros and cons of this multiplex syndromic approach are discussed in this narrative review.

IMPLICATIONS

Molecular multiplex CNS infection diagnosis panels have been developed and present several attractive features, including ease of use and low turnaround time. However, suboptimal analytical performances render these tests difficult to use without additional confirmatory tests. Such panels are not comprehensive nor adapted to all situations, depending on the epidemiological or clinical context. Overall, available data in the literature currently do not support the use of a multiplex PCR panel in clinical routine as a 'stand-alone' molecular assay. Except in restricted laboratory capacity settings where such easy-to-use multiplex panels offer the diagnostic means that would otherwise not be available, the stepwise testing approach remains a more rational option. Serological testing both in blood and CSF should not be neglected, but it represents essential complementary tools regarding some neuropathogens.

Development and validation of a multiplex-PCR based assay for the detection of 18 pathogens in the cerebrospinal fluid of hospitalized children with viral encephalitis

BACKGROUND

The Applied Biosystems 3500 Genetic Analyzer (ABI3500) allows for automated capillary electrophoresis on multiple targets. So far, the application of this method for detecting cerebrospinal fluid pathogens has hardly been reported.

METHODS

To assess the performance of multiplex-PCR assay for 18 pathogens detection, 127 CSF samples from hospitalized children with suspected viral encephalitis were prospectively collected from April to November 2018. The Sanger sequencing was applied to verify this assay.

RESULTS

All of the 18 target pathogens can be identified by multiplex-PCR assay at 10⁴ copies (or CFU/mL) of each virus, bacterium and fungus. In contrast, 10 control microorganisms failed to be amplified. Approximately 68.5 % of the cases tested had positive results, the enterovirus accounted for the majority of the positive cases (63.8 %). Agreement between multiplex-PCR and sequencing was 91.49 %.

CONCLUSIONS

Our findings suggest that the ABI3500-based multiplex-PCR detection kit could be a valuable diagnostic tool for pathogen detection in CSF of children with suspected viral encephalitis.

Collaborative Antimicrobial Stewardship: Working with Microbiology

There have been tremendous advances in methodologies available for detection and identification of organisms causing infections. Providers can now obtain identification results and antimicrobial susceptibility results in a shorter period of time. However, declining health care resources highlight the importance of selecting the right test at the right time to maximize diagnostic benefits. Therefore, the role of the antimicrobial stewardship team in the clinical microbiology laboratory has expanded to include diagnostic stewardship and provision of guidance on test selection for diagnosis and management of infection. This review focuses on the experience of our group in collaborative stewardship, emphasizing successes and challenges.

Molecular Diagnostic Advances in Transplant Infectious Diseases

PURPOSE OF REVIEW

The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases.

RECENT FINDINGS

Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.

Performance of a multiplex PCR pneumonia panel for the identification of respiratory pathogens and the main determinants of resistance from the lower respiratory tract specimens of adult patients in intensive care units

Background

Timely diagnostic investigation to establish the microbial etiology of pneumonia is essential to ensure the administration of effective antibiotic therapy to individual patients.

Methods

We evaluated a multiplex PCR assay panel, the FilmArray® pneumonia panel (FilmArray PP, BioFire Diagnostics), for detection of 35 respiratory pathogens and resistance determinants and compared the performance of the standard-of-care test in intensive care unit patients with lower respiratory tract infections.

Results

Among the 59 endotracheal aspirates and bronchoalveolar lavage specimens obtained from 51 adult patients, FilmArray PP was effective in detecting respiratory bacterial pathogens with an overall positive percent agreement of 90% (95% confidence interval [CI], 73.5–97.9%) and negative percent agreement of 97.4% (95% CI, 96.0–98.4%). FilmArray PP semi-quantitative reporting demonstrated a concordance rate of 53.6% for the culture-positive specimens and 86.3% for the culture-negative specimens. FilmArray PP detected 16 viral targets, whereas the conventional viral isolation failed, except influenza A, which showed 100% concordance with PCR. Coinfections were detected in 42.3% of the specimens. Substantial discrepancies were observed in identifying antimicrobial resistance gene targets and in the susceptibility testing. However, FilmArray PP may still be useful at the early stage of pneumonia before culture and susceptibility test reports are available. Consequently, the results of FilmArray PP might alter the antibiotic prescription in 40.7% of the patients.

Conclusions

FilmArray PP offers a rapid and sensitive diagnostic method for lower respiratory tract infections. However, clinical correlation is advised to determine its significance in interpreting multiple pathogens and detection of genes involved in antimicrobial resistance.

Diagnostic test accuracy of the BioFire® FilmArray® meningitis/encephalitis panel: a systematic review and meta-analysis

BACKGROUND

The FilmArray® meningitis/encephalitis (ME) panel is a multiplex PCR assay which can detect the most commonly identified pathogens in central nervous system infections. It significantly decreases the time to diagnosis of ME and data has yielded several positive outcomes. However, in part, reports of both false positive and false negative detections have resulted in concerns about adoption.

OBJECTIVES

The aim was to evaluate the ME panel in a diagnostic test accuracy review.

DATA SOURCES

The PubMed and EMBASE databases were systematically searched through May 2019.

STUDY ELIGIBILITY CRITERIA

Eligible studies were those providing sensitivity and specificity data for the ME panel compared with a reference standard. Studies providing details on false positive and false negative results of the panel as well as further investigation (adjudication) of the discordant results between the panel and comparator assays were included and assessed separately.

PARTICIPANTS

Patients with suspected ME for whom a panel was ordered were included.

METHODS

The ME panel was compared to reference standard methods for diagnosing community-acquired ME. We performed a meta-analysis and calculated the summary sensitivity and specificity of the ME panel. Moreover, we evaluated the false positive and false negative results of the panel.

RESULTS

Thirteen studies (3764 patients) were included in the review and 8 of them (3059 patients) were pooled in a meta-analysis. The summary estimates of sensitivity and specificity with 95% confidence intervals (CI) was 90% (95% CI 86-93%) and 97% (95% CI 94-99%), respectively. When we looked specifically at studies that assessed further the false positive and false negative results, false positive detections were 11.4% and 4% before and after adjudication, respectively. The highest proportion of false positive was observed for Streptococcus pneumoniae followed by Streptococcus agalactiae. False negative isolates were 2.2% and 1.5% before and after adjudication, respectively. Herpes simplex virus 1 and 2, enterovirus and Cryptococcus neoformans/gattii had the highest proportions of false negative determinations. False negative C. neoformans/gattii were mostly patients with positive antigen titres, on treatment or cleared disease.

CONCLUSIONS

The currently available literature suggests that the ME panel has high diagnostic accuracy. However, the decision for implementation should be individualized based on the needs of the patient population, the capabilities of the laboratory, and the knowledge of the healthcare providers that will utilize the test.

Strategies used by bacterial pathogens to cross the blood-brain barrier

The skull, spine, meninges, and cellular barriers at the blood-brain and the blood-cerebrospinal fluid interfaces well protect the brain and meningeal spaces against microbial invasion. However, once in the bloodstream, a range of pathogenic bacteria is able to reach the brain and cause meningitis. Despite advances in antibacterial therapy, bacterial meningitis remains one of the most important infectious diseases worldwide. The most common causative bacteria in children and adults are Streptococcus pneumoniae and Neisseria meningitidis associated with high morbidity and mortality, while among neonates, most cases of bacterial meningitis are due to group B Streptococcus and Escherichia coli. Here we summarise our current knowledge on the strategies used by these bacterial pathogens to survive in the bloodstream, to colonise the brain vasculature and to cross the blood-brain barrier.

FilmArray Meningitis/Encephalitis (ME) panel in the diagnosis of bacterial meningitis

The precise diagnosis of bacterial meningitis is essential. Cytological and biochemical examination of cerebrospinal fluid (CSF) are not specific. Conventional methods for bacterial meningitis lack sensitivity or take too long for a final result. Therefore, other methods for rapid and accurate diagnosis of central nervous system infections are required. FilmArray meningitis/encephalitis (ME) panel is a PCR multiplex for simultaneous and rapid identification of 14 pathogens, including 6 bacteria, 7 viruses, and Cryptococcus. We evaluated 436 CSF samples submitted to FilmArray ME Panel. Among them, 25 cases were positive for bacteria, being Streptococcus pneumonia the most frequent (48 %). Among positive cases for bacteria, 60 % were positive only with FilmArray. All the bacterial meningitis cases in which the only positive test was FilmArray had CSF findings suggestive of bacterial meningitis, including neutrophilic pleocytosis, increased CSF protein and lactate, and decreased CSF glucose. These findings suggest that FilmArray may increase the diagnostic sensitivity for bacterial meningitis.

Clinical, laboratory and immune aspects of Zika virus-associated encephalitis in children

OBJECTIVE

To evaluate the clinical, laboratory, and immune characteristics of Zika virus (ZIKV)-associated encephalitis in pediatric patients after the epidemic in Huila, southern Colombia.

METHODS

A pediatric neuro-surveillance hospital study was conducted in a referral health center in southern Colombia, from October 2016 to October 2017. Cases of encephalitis were confirmed by nucleic acid amplification tests and serological methods in cerebrospinal fluid (CSF), plasma, and/or urine. Levels of six cytokines were evaluated by flow cytometry. Patients underwent daily clinical and laboratory follow-up.

RESULTS

Twenty children with probable encephalitis were included for further studies and 16 of them were confirmed. Four cases of bacterial meningoencephalitis (Streptococcus pneumoniae, group B Streptococcus, Staphylococcus epidermidis, and Escherichia coli) and 12 cases of viral encephalitis were identified, six of them associated with ZIKV infection. Other viral encephalitis cases were caused by herpes viruses (n=3), enterovirus (n=2), and dengue virus type 2 (DENV-2; n=1) infections. ZIKV-associated encephalitis symptoms subsided faster than those of patients with encephalitis caused by other agents. CSF analysis revealed lymphocytic pleocytosis. Compared to healthy controls, children with ZIKV-associated encephalitis presented modest plasma interleukin (IL)-10 but not IL-2, IL-4, IL-6, interferon gamma (IFN-γ), or tumor necrosis factor alpha (TNF-α). Cytokine expression was differentially regulated, as dramatically elevated IL-6, IL-10, and IFN-γ levels were observed in CSF but not in paired plasma samples in one of the patients with ZIKV detectable in CSF.

CONCLUSIONS

This study provides evidence that ZIKV is responsible for pediatric encephalitis in endemic areas, and the local presence of the virus may induce cephalic but not systemic expression of cytokines.

Early clinical management of acute CNS infections: a prospective cohort study

Aim: To explore early management and clinical predictors of patients with suspected CNS infections. Methods: In a prospective cohort study of 125 adult patients with suspected CNS infections, clinical features and early management time points were compared between groups with and without confirmed CNS infections. Results: The door-to-lumbar puncture time was associated with the initial Glasgow Coma Scale score, the confirmed diagnosis and the time to change empirical treatment. Multivariate analysis indicated that the initial Glasgow Coma Scale score was an independent risk factor for prognosis. Conclusion: Lumbar puncture plays a crucial role in early management of CNS infections. Patients with CNS infection who have disturbances of consciousness should receive particular attention.

A review of a 13-month period of FilmArray Meningitis/Encephalitis panel implementation as a first-line diagnosis tool at a university hospital

Early diagnosis and treatment of meningitis and encephalitis is essential for reducing both their morbidity and mortality. The FilmArray® Meningitis/Encephalitis (FA-M/E) panel is a recently available molecular tool allowing the simultaneous detection of 14 pathogens in about one hour. We evaluated its routine use over a 13-month period at Nîmes University Hospital, France. Cerebrospinal fluid (CSF) specimens were prospectively analyzed, independently of cell count; results were retrospectively analyzed and positive results compared to clinical and microbiological data. Among the 708 patients included (734 CSF samples), 89 (12.6%) had a positive FA-M/E panel, 71 (80%) for a viral pathogen and 18 (20%) for a bacterial pathogen. Enterovirus and HHV-6 were the main detected pathogens. Mean time-to-results was 1h46mn. Four non-clinically relevant results were detected (3 HHV-6 and 1 Haemophilus influenzae) on the basis of inconsistent clinical and/or biological data, and/or after visualization of melting curves. No CSF pleocytosis was observed in 11% of the patients with a positive FA-M/E panel. For the 18 patients with a positive FA-M/E panel for a bacterial pathogen, five (28%) had CSF samples showing a positive Gram stain allowing an early diagnosis of bacterial infection and 67% had CSF displaying a positive culture. Altogether the panel detected 5 cases of bacterial M/E (29%) not diagnosed by culture. Despite undeniable advantages, mainly ease of use, quick result availability, and an extremely low rate of invalid results, measures should be implemented to limit false-positive results due to contamination and a careful interpretation based on the overall data for each patient is required.

Biomarkers of Infection and Sepsis

The role of biomarkers for detection of sepsis has come a long way. Molecular biomarkers are taking front stage at present, but machine learning and other computational measures using bigdata sets are promising. Clinical research in sepsis is hampered by lack of specificity of the diagnosis; sepsis is a syndrome with no uniformly agreed definition. This lack of diagnostic precision means there is no gold standard for this diagnosis. The final conclusion is expert opinion, which is not bad but not perfect. Perhaps machine learning will displace expert opinion as the final and most accurate definition for sepsis.

Enterovirus-Associated Hand-Foot and Mouth Disease and Neurological Complications in Japan and the Rest of the World

Enteroviruses (EVs) are responsible for extremely large-scale, periodic epidemics in pediatric cohorts, particularly in East and Southeast Asia. Clinical presentation includes a diverse disease spectrum, including hand-foot and mouth disease (HFMD), aseptic meningitis, encephalitis, acute flaccid paralysis, and acute flaccid myelitis. HFMD is predominantly attributable to EV-A types, including the major pathogen EV-A71, and coxsackieviruses, particularly CV-A6, CV-A16, and CV-A10. There have been multiple EV-A71 outbreaks associated with a profound burden of neurological disease and fatal outcomes in Asia since the early 1980s. Efficacious vaccines against EV-A71 have been developed in China but widespread pediatric vaccination programs have not been introduced in other countries. Encephalitis, as a consequence of complications arising from HFMD infection, leads to damage to the thalamus and medulla oblongata. Studies in Vietnam suggest that myoclonus is a significant indicator of central nervous system (CNS) complications in EV-A71-associated HFMD cases. Rapid response in HFMD cases in children is imperative to prevent the progression to a CNS infection; however, prophylactic and therapeutic agents have not been well established internationally, therefore surveillance and functional studies including development of antivirals and multivalent vaccines is critically important to reduce disease burden in pediatric populations.

Acute Bacterial Meningitis

PURPOSE OF REVIEW

While acute bacterial meningitis is becoming less common in developed countries because of the widespread use of vaccines against Streptococcus pneumoniae, Neisseria meningitides, and Haemophilus influenzae, bacterial meningitis still occurs worldwide, with peak incidence in young children and the elderly. Bacterial meningitis is usually lethal unless appropriate antibiotics that cross the blood-brain barrier are given. Clinical suspicion of bacterial meningitis begins when patients present with the abrupt onset of fever, headache, and meningismus.

RECENT FINDINGS

New technologies are being developed for more rapid identification of the bacterial species causing meningitis. When appropriate, administration of adjunctive dexamethasone with the antibiotics often lessens neurologic sequelae in survivors, which may include aphasia, ataxia, paresis, hearing loss, and cognitive impairment.

SUMMARY

Confirmation of the diagnosis of bacterial meningitis comes mainly from examination and culture of CSF obtained from a lumbar puncture. Typically, the CSF shows an elevated neutrophil count, elevated protein, depressed glucose, positive Gram stain, and growth of the bacteria on appropriate culture media. Antibiotic sensitivities of the bacteria determine the appropriate antibiotics, although an educated guess of the best antibiotics to be given promptly must be made until the antibiotic sensitivities return, usually in a few days.

Association of the FilmArray Meningitis/Encephalitis Panel With Clinical Management

OBJECTIVES

To determine the association of the use of the multiplex assay meningitis/encephalitis panel with clinical management of suspected meningitis.

METHODS

A cross-sectional study was conducted with children 0 to 18 years of age who received a lumbar puncture within 48 hours of admission for an infectious workup. Patient demographic and presenting information, laboratory studies, and medication administration were collected. The primary measure was length of stay (LOS) with secondary measures: time on antibiotics, time to narrowing antibiotics, and acyclovir doses. LOS and antibiotic times were stratified for outcomes occurring before 36 hours. Logistic regression analysis was used to account for potential confounding factors associated with both the primary and secondary outcomes. A value of P < .05 was considered statistically significant.

RESULTS

Meningitis panel use was associated with a higher likelihood of a patient LOS <36 hours (P = .04; odds ratio = 1.7; 95% confidence interval [CI]: 1.03-2.87), a time to narrowing antibiotics <36 hours (P = .008; odds ratio = 1.89; 95% CI: 1.18-2.87), and doses of acyclovir (P < .001; incidence rate ratio = 0.37; 95% CI: 0.26-0.53). When controlling for potential confounding factors, these associations persisted.

CONCLUSIONS

Use of the meningitis panel was associated with a decreased LOS, time to narrowing of antibiotics, and fewer acyclovir doses. This likely is a result of the rapid turnaround time as compared with cerebrospinal fluid cultures. Additional studies to examine the outcomes related to this change in management are warranted.