Rapid increase of oral bacteria in nasopharyngeal microbiota after antibiotic treatment in children with invasive pneumococcal disease

This project contains raw 16S rRNA gene sequencing data from the nasopharyngeal samples of children with Invasive Pneumococcal Disease (IPD) previous to antibiotic exposure (n=27) and children with IPD after antibiotic exposure (n=54). These samples are included in the paper: "Rapid increase of oral bacteria in nasopharyngeal microbiota after antibiotic treatment in children with invasive pneumococcal disease ". This project also includes the sequencing data of negative controls. Bacterial DNA was extracted from samples by the automated system NucliSENS easyMag (BioMérieux, Marcy-l'Étoile, France) and 16S rRNA gene was amplified by using gene-specific primer sequences that target the hypervariable V3-V4 regions, of approximately 465 bp in length: 5'-CCTACGGGNGGCWGCAG-3' (S-D-Bact-0341-b-S-17) and 5'-GACTACHVGGGTATCTAATCC-3' (S-D-Bact-0785-a-A-21). A second amplification step attached dual index barcodes and Illumina sequencing adapters to the amplicons previously generated using the Nextera Index kit (Illumina, San Diego, California, USA). Amplicons from each sample were pooled in equimolar amounts and sequenced with Illumina Miseq platform (Illumina, San Diego, California, USA) with paired-end sequencing technology generating 2 x 300 bp reads.