Diagnostic Performance of Complementary Serum and Cerebrospinal Fluid Multiplex PCR for Acute Bacterial Meningitis

Abstract

Background: Developing molecular tools for the diagnosis of bacterial meningitis is crucial for improving the diagnosis and initiation of prompt treatment of patients. This study aimed to evaluate the diagnostic performance of cerebrospinal fluid and serum multiplex PCR compared with conventional diagnostic methods for detecting bacterial pathogens among patients clinically suspected of bacterial meningitis. Methods: A cross-sectional study was conducted at Tikur Anbessa Specialized Hospital and Yekatit 12 Hospital Medical College from August 2023 to February 2024. A total of 202 patients who were suspected of having meningitis were included in the study. Conventional laboratory analysis, including Gram staining and bacterial culture from CSF, was performed. CSF and serum PCR for the detection of Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, Streptococcus agalactiae, Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, and Klebsiella pneumoniae were performed. The agreement between tests used to detect etiologic agents of bacterial meningitis was determined by McNemar’s Test and Cohen’s kappa statistic. Results: Of the 202 study participants, 109 (54.0%) were male, and 178 (88.1%) were pediatric, with the majority being infants (mean age: 1.45 ± 0.69 years). Poor feeding was the most common clinical presentation at 151/202 (74.8%), followed by high fever at 144/202 (71.3%), and loss of consciousness at 134/202 (66.3%). Among the 202 CSF samples, nine (4.5%) and 11 (5.4%) tested positive for culture and Gram stain, respectively. Bacterial DNA was detected in 54/202 (26.7%) of the CSF samples and 93/202 (46.0%) of the serum samples. E. coli was detected in 30/54 (55.5%) of CSF samples and 57/93 (61.2%) of serum samples, followed by S. pneumoniae, which was detected in 8/54 (14.8%) of CSF samples and 27/93 (29.0%) of serum samples. The overall agreement between CSF and serum PCR is 60.9% (123/202), with a positive percent agreement of 62.96% (34/54), and a negative percent agreement of 60.14% (89/148). McNemar’s test indicated a significant difference between the two tests (p < 0.0001), and Cohen’s kappa statistic showed slight agreement (κ = 0.188, 95% CI: 0.109–0.293). Conclusions: Bacterial DNA was detected more often in serum multiplex PCR than CSF PCR or culture, suggesting its potential role as a complementary diagnostic tool for epidemiological surveillance, particularly in resource-limited settings where lumbar puncture may not always be feasible. However, serum PCR should not replace CSF analysis for definitive diagnosis; rather, it can serve as a screening or surveillance tool, with positive results requiring clinical correlation and, where possible, CSF confirmation. A relatively small sample size, reliance on conventional PCR, absence of comparison with quantitative PCR, potential blood contamination, lack of sequencing, and lack of long-term outcome data limit the generalizability of our findings. Future investigations should include a large sample size in conjunction with confirmatory culture techniques to enhance the robustness and validity of the findings.