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

Néhémie Nzoyikorera,Kaotar Nayme,Idrissa Diawara,Chrispin Chaguza,Mossaab Maaloum,Khalid Katfy,Naima Elmdaghri,Jennifer Cornick,Khalid Zerouali,Mohammed Timinouni,Pablo Fresia,Houria Belabess,Fakhreddine Maaloum

doi:10.1186/s12864-020-07316-0

Abstract

BackgroundStreptococcus 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.ResultsThe 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.ConclusionsThe 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.

Highlights

Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with pneumococcal conjugated vaccines (PCV)-10/PCV-13 vaccine implementation
Characteristics of pneumococcal serotype 1 isolates from Casablanca, Morocco We analyzed six strains of S. pneumoniae serotype 1 isolated among ≤5 years children (Table 1)
Five isolates were from invasive infections while the remaining strain was isolated from the protected distal bronchial sample (PDBS) in the pneumonia context

Summary

Introduction

Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. Streptococcus pneumoniae, an encapsulated commensal bacterium of the human nasopharynx, remains a major cause of mortality and morbidity worldwide, that frequently infects children under 2 years old with immature immune system and elderly with a decrease of the immune response, as well as people with underlying diseases [1, 2]. This pathogen is the well-known agent of non-invasive infections such as sinusitis and otitis media, and invasive infections such as meningitis, bacteraemia and bacteraemic pneumonia [1]. In African countries, serotype 1 remains a leading cause of IPDs, even in countries with pneumococcal conjugated vaccines (PCV), PCV-10/PCV-13 [5]

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Discussion

Conclusion