Nasopharyngeal microbiota and genus Enterovirus infection in children

This project contains 16S rRNA gene sequencing data from nasopharyngeal aspirate samples of 104 children included in the paper: "Impact of the bacterial nasopharyngeal microbiota on the severity of genus enterovirus lower respiratory tract infection in children: a case-control study”. This cross-sectional study included 17 children without viral infection (healthy controls), 34 children with either mild or asymptomatic rhinovirus/enterovirus infection (infected controls) and 53 rhinovirus/enterovirus infected children that required pediatric intensive care unit stay (cases). Sequencing data for 15 negative controls (extraction and PCR controls) is also included. Total DNA was extracted from nasopharyngeal aspirates using the automated system NucliSENS easyMag (BioMérieux, Marcy-l'Étoile, France) following manufacturer's instructions. The 16S rRNA gene amplicons covering the hypervariable regions V3-V4 (~465bp in length) were produced using region specific primers: 5'-CCTACGGGNGGCWGCAG-3' (S-D-Bact-0341-b-S-17) and 5'-GACTACHVGGGTATCTAATCC-3' (S-D-Bact-0785-a-A-21'. Next-generation sequencing library was built using Nextera XT v2 DNA Library Preparation kit (Illumina) according to the manufacturer's instructions and was further sequenced using Illumina MiSeq 2x300 bp reads.