Inflammation induced by influenza virus impairs innate control of human pneumococcal carriage

Simon P. Jochems; Fernando Marcon; Beatriz F. Carniel; Mark Holloway; Elena Mitsi; Emma Smith; Jenna F. Gritzfeld; Carla Solórzano; Jesús Reiné; Sherin Pojar; Elissavet Nikolaou; Esther L. German; Angie Hyder-Wright; Helen Hill; Caz Hales; Wouter A.A de Steenhuijsen Piters; Debby Bogaert; Hugh Adler; Seher Zaidi; Victoria Connor; Jamie Rylance; Helder I. Nakaya; Daniela M. Ferreira

Quality control of raw sequencing data was done using fastQC. Mapping to a human reference 365 genome assembly (GRCh38) was done using STAR 2.5.0a 55 . Read counts from the resulting 366 BAM alignment files were obtained with featureCounts using a GTF gene annotation from the The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/347161 doi: bioRxiv preprint 16 (https://bioconductor.org/packages/release/bioc/html/CEMiTool.html) 39 . This package unifies the 377 discovery and the analysis of coexpression gene modules, evaluating if modules contain genes 378 that are over-represented by specific pathways or that are altered in a specific sample group. A p-379 value = 0.05 was applied for filtering lowly expressed genes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. Heatmap showing for each cytokine the median log2 fold-change compared to baseline for the timepoints 0/2/7/9, n = 19 per group. c) The delta in median log fold change (FC) following LAIV vaccination just prior to inoculation with Spn for subjects becoming carriage+ or carriage-(excluding subjects becoming positive by PCR only, who resemble subjects that become carriage+ by All rights reserved. No reuse allowed without permission.