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

Abstract

BackgroundMeningitis 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.MethodsA 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.ResultsTwo 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.ConclusionsA 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.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3589-4) contains supplementary material, which is available to authorized users.

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

“…Despite the small number of studies on FA-M/E use currently available (42 studies retrieved with the Mesh terms “FilmArray” and “meningitis” on 17 July, 2019), their comparison is limited by highly diverse study designs, e.g., CSF selection criteria [11,12]; focus on CSF specimens positive or negative by other methods [13,14], on specific population defined by age or clinical condition [15–20], on specific pathogens [17,21–24]; result comparison with other approaches for all or specific discordant results [9,18] or no comparison (most studies). Most of these studies were retrospective, and our literature review only identified four large prospective studies [8,11,25,26]. We present the fifth study on prospective CSF testing with the FA-M/E panel and show an overall positive rate of 12% after exclusion of non-clinically relevant results, consistent with the aforementioned studies.…”

“…The FilmArray system automatically interprets the three results obtained as three independent melting curves to give a unique final result. Despite high-level miniaturized technology, use of the system does not require any specific skills in molecular-based methods [8] requiring only microbiological safety precautions. Handling time and time-to-results reported by the manufacturer are 2 minutes and 1 hour, respectively.…”

Molecular diagnosis of meningitis and meningoencephalitis with an automated real-time multiplex polymerase chain reaction in a tertiary reference complex in Medellín, Colombia

“…Briefly, a total of 200 µL of each CSF sample were required to run the assay; the test process includes a nucleic acid extraction/purification stage, a first round of highly multiplexed amplification of all targets, followed by a nested-amplification of each target triplicated tested on the array. The FilmArray ® software system automatically interprets the three results obtained as three independent melting curves to give a unique final result 7 . The master list includes: E. coli K1, H. influenzae, L.monocytogenes, N. meningitidis, S.agalactiae, S. pneumoniae, CMV (Cytomegalovirus), EV (Enterovirus), Herpes Simplex Virus 1 and 2 (HSV-1 and HSV-2), Human Herpes virus 6 (HHV-6), Human Parechovirus (HPeV), Varicella-Zoster Virus (VZV) and C. neoformans/gatti.…”

“…This is a molecular tool that allows the simultaneous detection of 14 pathogens (bacteria, viruses and one fungus). The entire process is fully automated and takes approximately one hour to release the results 7 . In this study, we have documented the performance of FA-M/E in CSF samples of patients with suspected meningitis or meningoencephalitis infections in the context of a tertiary referral hospital, comparing the results obtained by this molecular method with traditional testing.…”

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

“…10,11 These techniques could be of special importance for both clinical routine and surveillance purposes in settings where culture of the cerebrospinal fluid (CSF) is not available. 12 A rapid molecular multiplex polymerase chain reaction (PCR) panel for CNS infections has been studied in low- and middle-income countries with a positivity rate of 10% in a general population 13,14 and a higher detection rate in a cohort of HIV-infected patients. 15…”