Néhémie Nzoyikorera1,2, Idrissa Diawara3, Pablo Fresia4,5, Fakhreddine Maaloum6,7, Khalid Katfy6,7, Kaotar Nayme8, Mossaab Maaloum9,10, Jennifer Cornick11,12, Chrispin Chaguza13, Mohammed Timinouni8, Houria Belabess6,7, Khalid Zerouali6,7, Naima Elmdaghri6,7. 1. Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco. nzoyikorera@yahoo.fr. 2. Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco. nzoyikorera@yahoo.fr. 3. Faculty of Sciences and Health Techniques, Mohammed VI University of Health Sciences (UM6SS) of Casablanca, Casablanca, Morocco. 4. Institut Pasteur de Montevideo, Pasteur + INIA Joint Unit (UMPI), Montevideo, Uruguay. 5. Institut Pasteur de Montevideo, Microbial Genomics Laboratory, Montevideo, Uruguay. 6. Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco. 7. Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco. 8. Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco. 9. Laboratory of Biology and Health, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco. 10. Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France. 11. Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. 12. Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. 13. Wellcome Trust Sanger Institute, Cambridge, UK.
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.
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 childrenpatients 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.
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