Development and validation of an advanced fragment analysis-based assay for the detection of 22 pathogens in the cerebrospinal fluid of patients with meningitis and encephalitis

Multiplex detection of meningitis and encephalitis pathogens: A study from laboratory to clinic

Introduction

Infectious meningitis and encephalitis (ME) are life-threatening conditions are caused by various pathogens. Conventional laboratory tests with low sensitivity and specificity cannot help with early diagnosis.

Methods

A prospective study using the novel multiplex PCR detection for 18 pathogens of ME (MME-18) was conducted to investigate the clinical utilization and the epidemiology characteristics of ME in southwestern China. Patients with suspected intracranial infection were recruited between May and October 2019 at West China Hospital of Sichuan University. The MME-18 was used to detect cerebrospinal fluid, and conventional experiments including cryptococcal capsular antigen detection, GeneXpert, real-time PCR, and clinical feedback were used to verify the result of MME-18.

Results

Among 581 tested patients, 139 eligible individuals were enrolled in the study. Among them, Mycobacterium tuberculosis was the most common pathogen in mono-infection. Viruses and Cryptococcus neoformans were also frequently detected. Of 139 infected patients, 12 cases were diagnosed by MME-18 only, 57 patients by conventional testing only, and 70 cases by both comparator tests and MME-18. There were 96.3% (79/82) diagnoses made by MME-18 had a favorable outcome, and two of twelve diagnoses, made solely by MME-18, had a likely unclear clinical significance.

Discussion

The MME-18 showed satisfactory consistency with expert clinical consensus for patients presenting with ME. Combined with conventional testing and clinical suspicion, MME-18 may help clinicians with the early identification of pathogens.

Diagnostic Yield of Multiplex PCR Method in Cerebrospinal Fluid for the Diagnosis of Purulent Meningitis in Children

Objective To evaluate the diagnostic yield of the multiplex polymerase chain reaction (PCR) method in cerebrospinal fluid (CSF) for the diagnosis of purulent meningitis (PM) in children.

Methods PM was diagnosed according to the European Society for Clinical Microbiology and Infectious Diseases guideline (2016). Patients with PM between May 2015 and October 2018 were included. The multiplex PCR method was used to detect eight common identified bacteria in PM. Its sensitivity and specificity were compared with bacteria culture.

Results A total of 106 cases were enrolled. Pathogenic bacteria were identified in 27 (25.5%) cases by culture and in 37 (34.9%) cases by multiplex PCR assay. The top three bacteria were Streptococcus pneumoniae, Escherichia coli K1, and Streptococcus agalactiae. When using culture as the gold standard, the multiplex PCR assay showed a sensitivity of 100, 88.9, and 75.0% for S. agalactiae, S. pneumoniae, and E. coli K1, respectively, and a specificity of more than 91.3% for all three bacteria. For detectable bacteria, the positive rate of the multiplex PCR assay (36.6%, 37/101) was significantly higher than that of the bacteria culture (21.8%, 22/101). When combining the two methods, etiology was identified in 42.5% (45/106) of the patients.

Conclusion Streptococcus pneumoniae, E. coli K1, and S. agalactiae were the predominant pathogens causing pediatric PM. As a rapid method with high sensitivity and specificity, the multiplex PCR assay in CSF could be used as an adjunctive approach with bacteria culture for the pathogen identification of PM.

Development and validation of an advanced fragment analysis-based assay for the detection of 22 pathogens in the cerebrospinal fluid of patients with meningitis and encephalitis

Background

Meningitis and encephalitis (ME) are central nervous system (CNS) infections mainly caused by bacteria, mycobacteria, fungi, viruses, and parasites that result in high morbidity and mortality. The early, accurate diagnosis of pathogens in the cerebrospinal fluid (CSF) and timely medication are associated with better prognosis. Conventional methods, such as culture, microscopic examination, serological detection, CSF routine analysis, and radiological findings, either are time‐consuming or lack sensitivity and specificity.

Methods

To address these clinical needs, we developed an advanced fragment analysis (AFA)‐based assay for the multiplex detection of 22 common ME pathogens, including eight viruses, 11 bacteria, and three fungi. The detection sensitivity of each target was evaluated with a recombinant plasmid. The limits of detection of the 22 pathogens ranged from 15 to 120 copies/reaction. We performed a retrospective study to analyze the pathogens from the CSF specimens of 170 clinically diagnosed ME patients using an AFA‐based assay and compared the results with culture (bacteria and fungi), microscopic examination (fungi), polymerase chain reaction (PCR) (Mycobacterium tuberculosis), and Sanger sequencing (virus) results.

Results

The sensitivity of the AFA assay was 100% for 10 analytes. For Cryptococcus neoformans, the sensitivity was 63.6%. The overall specificity was 98.2%. The turnaround time was reduced to 4‐6 hours from the 3‐7 days required using conventional methods.

Conclusions

In conclusion, the AFA‐based assay provides a rapid, sensitive, and accurate method for pathogen detection from CSF samples.