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

Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenzae isolates associated with paediatric otitis media and upper respiratory infection

“…While traditional phenotyping and PCR / multilocus sequence typing (MLST)-based methods are often used for clinical pathogen diagnostics and molecular epidemiology, whole genome sequencing (WGS) -based workflows can provide a comprehensive pathogen phylogenetic affiliation, gene content, and predict resistance genes or mutations. WGS-based workflows offer high-resolution pathogenomic profiling and have been critical for genomic epidemiological studies of H. influenzae [ 31 , 32 ] and S. pneumoniae [ 33 – 35 ]. WGS also have several advantages over traditional approaches including the ability to determine the taxonomic identity of a pathogen more accurately or identify novel genes and genomic features that are not tested for using traditional diagnostic approaches.…”