Use of multiplex PCR based molecular diagnostics in diagnosis of suspected CNS infections in tertiary care setting-A retrospective study

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

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

Impact of a Multiplex Polymerase Chain Reaction Assay on the Clinical Management of Adults Undergoing a Lumbar Puncture for Suspected Community-Onset Central Nervous System Infections

Patients admitted from the community with a suspected central nervous system (CNS) infection require prompt diagnostic evaluation and correct antimicrobial treatment. A retrospective, multicenter, pre/post intervention study was performed to evaluate the impact that the BioFire^® FilmArray^® meningitis/encephalitis (ME) panel run in-house had on the clinical management of adult patients admitted from the community with a lumbar puncture (LP) performed for a suspected CNS infection. The primary outcome was the effect that this intervention had on herpes simplex virus (HSV) polymerase chain reaction (PCR) turnaround time (TAT). Secondary outcomes included the effect that this intervention had on antiviral days of therapy (DOT), total antimicrobial DOT, and hospital length of stay (LOS). A total of 81 and 79 patients were included in the pre-intervention and post-intervention cohorts, respectively. The median HSV PCR TAT was significantly longer in the pre-intervention group (85 vs. 4.1 h, p < 0.001). Total antiviral DOT was significantly greater in the pre-intervention group (3 vs. 1, p < 0.001), as was total antimicrobial DOT (7 vs. 5, p < 0.001). Pre-intervention hospital LOS was also significantly longer (6.6 vs. 4.4 days, p = 0.02). Implementing the ME panel in-house for adults undergoing an LP for a suspected community-onset CNS infection significantly reduced the HSV PCR TAT, antiviral DOT, total antimicrobial DOT, and hospital LOS.

Epidemiology and Etiology of Severe Childhood Encephalitis in The Netherlands

BACKGROUND

Limited data are available on childhood encephalitis. Our study aimed to increase insight on clinical presentation, etiology, and clinical outcome of children with severe encephalitis in the Netherlands.

METHODS

We identified patients through the Dutch Pediatric Intensive Care Evaluation database and included children diagnosed with encephalitis <18 years of age admitted to 1 of the 8 pediatric intensive care units (PICU) in the Netherlands between January 2003 and December 2013. We analyzed demographic characteristics, clinical symptoms, neurologic imaging, etiology, treatment and mortality.

RESULTS

We included 121 children with a median age of 4.6 years (IQR 1.3-9.8). The most frequently described clinical features were headache (82.1%), decreased consciousness (79.8%) and seizures (69.8%). In 44.6% of the children, no causative agent was identified. Viral- and immune-mediated encephalitis were diagnosed in 33.1% and 10.7% of the patients. A herpes simplex virus infection (13.2%) was mainly seen in children <5 years of age, median age, 1.73 years (IQR 0.77-5.01), while immune-mediated encephalitis mostly affected older children, median age of 10.4 years (IQR, 3.72-14.18). An age of ≥ 5 years at initial presentation was associated with a lower mortality (OR 0.2 [CI 0.08-0.78]). The detection of a bacterial (OR 9.4 [CI 2.18-40.46]) or viral (OR 3.7 [CI 1.16-11.73]) pathogen was associated with a higher mortality.

CONCLUSIONS

In almost half of the Dutch children presenting with severe encephalitis, a causative pathogen could not be identified, underlining the need for enhancement of microbiologic diagnostics. The detection of a bacterial or viral pathogen was associated with a higher mortality.

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.

Clinical impact of cerebrospinal fluid Gram stain and culture testing: A retrospective cohort study

BACKGROUND

Stewardship of microbiological tests can improve laboratory efficiency. One indicator of appropriate test stewardship is test impact on patient management decisions. We sought to assess the impact of cerebrospinal fluid (CSF) Gram stain and culture results on treatment decisions. Our hypothesis was that CSF Gram stain and culture have low impact on patient management.

METHODS

CSF specimens received at a tertiary microbiology laboratory between January 1, 2013, and December 31, 2013, were included. Clinical information and data on antibiotic treatment before CSF collection, antibiotic treatment after CSF Gram stain results, and antibiotic treatment after CSF culture results were collected. Ethics approval for secondary use of data was obtained.

RESULTS

We received 242 CSF specimens for Gram stain and culture during the study period; 120 were excluded (84 from children, 2 from indwelling ventricular drains, 12 collected at outside hospitals, 21 data missing, 1 duplicate). No Gram stains or cultures were positive among patients not already treated empirically. The number needed to test to influence treatment was 17 for Gram stain (11 for abnormal cytochemistry, 29 for normal cytochemistry) and 6 for culture (3 for abnormal cytochemistry, 6 for normal cytochemistry).

CONCLUSIONS

CSF Gram stain and culture are rarely positive and are being performed on inappropriate specimens. CSF results never prompt physicians to start treatment, so results are affecting not outcome but antibiotic stewardship. Negative CSF culture often leads to discontinuation of antibiotics. Labs could consider rejecting CSF Gram stain if cytochemistry is normal.

Syndrome Evaluation System for Simultaneous Detection of Pathogens Causing Acute Encephalitic Syndrome in India, Part-2: Validation Using Well Characterized Clinical Samples

Diagnosis of the aetiological agent in case of acute encephalitic syndrome (AES) continues to pose a challenge in clinical practice as a variety of pathogens are known to cause AES. Here, we report the validation of a Syndrome Evaluation System (SES) developed for simultaneous detection of multiple AES pathogens using a well characterized set of Cerebrospinal fluid (CSF) samples. The validation of the SES was carried out in two phases. In the first phase, the SES was validated using 51 CSF samples obtained from autopsy proven cases and 50 samples obtained from apparently healthy individuals undergoing spinal anesthesia for minor surgeries served as "controls." The SES detected etilogical agent in 48/51 (94.11 %) samples obtained from autopsy proven AES cases while all the 50 CSF samples obtained from "controls" were negative. In the second phase, the SES was validated using well characterized CSF samples obtained from AES patients fulfilling the WHO case definition of AES (Group I; n = 207) and samples that were collected from patients with non-infectious neurological disorder (Group II; n = 90). All the samples were tested using multiple conventional/serological assays and categorized into various groups. Amongst the AES cases fulfilling WHO case definition, the SES detected AES pathogens in 160/207 (77.29%) cases while conventional serological/molecular assays were able to detect AES pathogens only in 77/207 (37.1%) of cases. Further, in 12/83 CSF samples that were positive by SES and negative by conventional serological/molecular tests, the results were additionally confirmed by sequencing the PCR products to rule out non-specific amplification in the SES. In patients with non-infectious neurological disorders the SES detected latent viruses 12/90 CSF samples. These results indicate that the SES, apart being a rapid, sensitive, specific, and cost-effective method provides the major advantage of simultaneous detection of multiple pathogens using as single specimen of CSF.

New molecular tools for meningitis diagnostics in Ethiopia - a necessary step towards improving antimicrobial prescription

BACKGROUND

Meningitis remains a top cause of premature death and loss of disability-adjusted life years in low-income countries. In resource-limited settings, proper laboratory diagnostics are often scarce and knowledge about national and local epidemiology is limited. Misdiagnosis, incorrect treatment and overuse of antibiotics are potential consequences, especially for viral meningitis.

METHODS

A prospective study was conducted over three months in a teaching hospital in Ethiopia with limited laboratory resources. Cerebrospinal fluid (CSF) samples from patients with suspected meningitis were analysed using a multiplex PCR-based system (FilmArray, BioFire), in addition to basic routine testing with microscopy and culture. Clinical data, as well as information on treatment and outcome were collected.

RESULTS

Two hundred and eighteen patients were included; 117 (54%) neonates (0-29 days), 63 (29%) paediatrics (1 month-15 years) and 38 (17%) adults (≥16 years). Of 218 CSF samples, 21 (10%) were PCR positive; 4% in neonates, 14% in paediatrics and 18% in adults. Virus was detected in 57% of the PCR positive samples, bacteria in 33% and fungi in 10%. All CSF samples that were PCR positive for a bacterial agent had a white cell count ≥75 cells/mm³ and/or turbid appearance. The majority (90%) of patients received more than one antibiotic for treatment of the meningitis episode. There was no difference in the mean number of different antibiotics received or in the cumulative number of days with antibiotic treatment between patients with a microorganism detected in CSF and those without.

CONCLUSIONS

A rapid molecular diagnostic system was successfully implemented in an Ethiopian setting without previous experience of molecular diagnostics. Viral meningitis was diagnosed for the first time in routine clinical practice in Ethiopia, and viral agents were the most commonly detected microorganisms in CSF. This study illustrates the potential of rapid diagnostic tests for reducing antibiotic usage in suspected meningitis cases. However, the cost of consumables for the molecular diagnostic system used in this study limits its use in low-income countries.