University College London
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The Streptococcus pneumoniae transcriptome in patient cerebrospinal fluid identifies novel virulence factors required for meningitis

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posted on 2024-04-30, 09:58 authored by Emma WallEmma Wall, Jeremy BrownJeremy Brown, Jose Afonso Guerra Martins Dos Santos Assuncao, Robert HeydermanRobert Heyderman

Abstract: To better understand Streptococcus pneumoniae pathogenesis we performed RNA sequencing on cerebrospinal fluid (CSF) from meningitis patients to identify bacterial genes expressed during invasion of the central nervous system. Comparison to transcriptome data for serotype 1 S. pneumoniae cultured in ex vivo human CSF defined a subset of 57 genes with high expression during human meningitis. Deletion of two of the most highly expressed genetic loci, bgaA (encodes for a ß-galactosidase) or the SP_1801-5 putative stress response operon, resulted in S. pneumoniae strains still able to transmigrate the blood brain barrier but which were more susceptible to complement opsonisation and unable to maintain brain infection in a murine meningitis model. In 1144 meningitis patients, infection with bgaA containing S. pneumoniae strains was associated with a higher mortality (22% versus 14% p=0.02). These data demonstrate that direct bacterial RNAseq from CSF can identify previously undescribed S. pneumoniae virulence factors required for meningitis pathogenesis.

Data available:

Tab 1: Summary transcripts/million reads (TPM) per human meningitis sample, annotated by gene name and gene number (TIGR4 annotation) across the entire mapped pneumococcal transcriptome.

Tab 2: Summary differential gene expression of S. pneumoniae in vitro between THY, CSF and CSF + neutrophils. Median TPM for each sample type from 8 replicates are given, with the fold change and statistical significance. Gene numbers are given for the original human mapped S. pneumoniae serotype 1 strain gamPNI0373 (genbank CP001845.1) for ease of comparison with the human meningitis data.

Tab 3: Mapped alignment of the meningitis reads from human samples against a range of pneumococcal serotypes. Heatmap colours indicate higher alighment rates.


This study was funded by a Clinical Lecturer Starter Grant from the Academy of Medical Sciences (UK) and Wellcome Trust Institutional Strategic Support Funding (ISSF) with the Robin Weiss Fund to EW. The Bundles for Adult Meningitis (BAM) study was funded by a PhD Fellowship in Global Health to EW from the Wellcome Trust (089671/B/09/Z). Additional funding included a Postdoctoral Clinical Research Fellowship to EW from the Francis Crick Institute. . The Malawi-Liverpool-Wellcome Trust Clinical Research Programme is supported by a core grant from the Wellcome Trust (101113/Z/13/Z). The laboratory work was undertaken in part at UCLH/UCL who received a proportion of funding from the National Institute for Health Research University College London Hospitals Department of Health’s NIHR Biomedical Research Centre. ECW, RH and JSB are supported by the Centre’s funding scheme. RJW, AP and EW were supported by the Francis Crick Institute which receives funding from Wellcome (CC2112), Cancer Research UK (FC2112) and UK Research and Innovation: Medical Research Council (FC2112). The human foetal material was provided by the Joint MRC/Wellcome Human Developmental Biology Resource ( (project#200511). RSH is a NIHR Senior Investigator. Additional laboratory work at UCL and LSHTM was funded by an Investigator award to JSB and BW from the Wellcome Trust.


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