Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco

Abstract Background Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective this study, which is part the Pneumococcal African Genome project (PAGe), was to determine phylogenetic relationships isolates recovered from children patients Casablanca (Morocco), compared these other countries; and investigate contribution accessory genes recombination events genetic diversity serotype. Results genome average size six-pneumococcus 2,227,119 bp, content coding sequences 2113, ranging 2041 2161. Pangenome analysis 80 genomes used study revealed 1685 core 1805 genes. tree based on hierarchical bayesian clustering five sublineages phylogeographic structure by country. Moroccan strains cluster two different lineages, clusters altogether divergent clade distantly related non-invasive strain, that all Africa. Conclusions whole sequencing provides increased resolution highly virulent Casablanca, Morocco. Our results are concordant previous works, showing phylogeography S. structured country, despite small (six isolates) sample, our shows cohesion isolates.