A refined, controlled 16S rRNA gene sequencing approach reveals limited detection of cerebrospinal fluid microbiota in children with bacterial meningitis

Advances in both laboratory and computational components of high-throughput 16S amplicon sequencing (16S HTS) have markedly increased sensitivity and specificity. Additionally, these refinements have better delineated the limits of sensitivity, and contributions of contamination to these limits, for 16S HTS that are particularly relevant for samples with low bacterial loads such as human cerebrospinal fluid (CSF). The objectives of this work were to (1) optimize the performance of 16S HTS in CSF samples with low bacterial loads by defining and addressing potential sources of error; and (2) perform refined 16S HTS on CSF samples from children diagnosed with bacterial meningitis and compare results with those from microbiological cultures.