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

- Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1.
- 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;.
- 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.
- Conclusions: The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco.
- 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..
- Keywords: Streptococcus pneumoniae , Serotype 1, Whole genome sequencing, Comparative genomic analysis.
- Full list of author information is available at the end of the article.
- Streptococcus pneumoniae, an encapsulated commensal bacterium of the human nasopharynx, remains a major cause of mortality and morbidity worldwide, that fre- quently infects children under 2 years old with immature immune system and elderly with a decrease of the im- mune response, as well as people with underlying dis- eases [1, 2].
- According to the World Health Organization (WHO) in 2015, of the estimated 5.83 million globally deaths among <.
- The objectives of this study, as part of the Pneumococcal African Genome project (PAGe), were to determine the phylogenetic relationships of.
- The average length of the six pneumococcus serotype 1 genomes analyzed was 2,227,119 bp.
- The minimum and maximum CDS content were of the strain from CSF and PDBS respectively..
- The maximum likelihood reconstruction of the phylo- genetic relationships among the African isolates of S..
- pneu- moniae serotype 1, we reconstructed the pangenome of the 80 genomes.
- 1c based on the dis- criminant analysis of principal components (DAPC) using the accessory genes that sublineage 1 is highly dif- ferent from the remaining sublineages.
- The tips of the tree are colored by country, and beside there are two bars that are the result of the clustering analysis with hierBaps.
- 95%, which value is indicative of the same species of pneumococcus (Fig.
- The recombination events on the core genome align- ment of the 80 isolates were examined to investigate their contributions to the phylogenetic diversity of sero- type 1.
- We also corre- lated the Jaccard distance, as a measure of the dynamic and similarty of the accessory genome, with the nucleo- tide diversity based on the synonymous polymorphisms (neutral evolution).
- pneumoniae serotype 1 isolates Table 2 Pangenome analysis of 80 genomes of S.
- In African countries, serotype 1 is one of the top three of most common vaccine serotypes causing IPD among children [14, 15]..
- This could be associated with the short duration of this serotype in asymptomatic colonization of the human nasopharynx, where exchange of genetic elements through recombination with other Streptococci took place [16–18]..
- The average length of the genome of the serotype 1 strains from Morocco was 2,227,119 bp.
- This genome size is greater than the size of the reference strain of serotype 1, S.
- In our study, 1685 CDS were highlighted as core gen- ome in all 80 isolates analyzed which corresponds on 79.7% of the total genome translation.
- The quantification of the bacterial core genome may vary among different isolates collections.
- The accessory genome of the serotype 1 isolates studied was highly variable..
- 3 Recombination and accessory genome analysis of S.
- pneumoniae serotype 1 isolates.
- b Linear regression analysis of genomic fluidity (accessory genome) against synonym diversity (core genome).
- Those genes are mainly associ- ated with evasion of the host immune system and viru- lence factors [21].
- The study on phylogenetic analysis in South Africa by du Plessis et al the global invasive serotype 1 population was grouped in 9 clusters and showed a strong phylogeographic structure.
- As published by Chaguza et al..
- [28], the identified sequence Clusters (SCs) in African pneumococcal serotype 1 population matched the phylo- genetic clades from the phylogeny and were predomin- antly associated with geographical origin of the isolates..
- The ST306 is a worldwide distributed pneumococcal serotype 1, suspected to be an important pathogen behind the increase of the serotype 1 IPD ex- pansion and is responsible for more than 80% of cases of serotype 1diseases [29, 30]..
- This finding could suggest that the strain was probably carried for long periods enough to result in extensive genetic exchanges with other closely related species as Streptococcus mitis as reported in the large study of Lessa et al.
- mitis clones were found highly similar to wzy1 of the serotype 1 S.
- This study constitutes the first pneumococcal genome analysis by whole genome sequencing in Morocco, pro- viding increased resolution on the analysis of the highly virulent serotype 1.
- pneumoniae serotype 1 despite the small size of the Moroccan sample, and showed it basal position on the phylogenetic tree of Afri- can isolates.
- pneumoniae serotype 1 causing infections among children under 5 years, were randomly selected from the data bank of the microbiology laboratory of IR-UHC of Casablanca, to perform the WGS analysis.
- The genomic DNA of the six strains selected for this surveillance was purified with the QIAamp DNA Mini Kit (Hilden, Germany) following the manufacturer’s rec- ommendations.
- DNA quality and quantity were esti- mated by measuring the absorbance of the sample using NanoVue™ Plus Spectrophotometer (GE Healthcare UK Limited, UK) at wavelengths 260 nm and 280 nm follow- ing the manufacturer’s instructions.
- The DNAs of the six strains were whole-genome-sequenced using an Illumina HiSeq 2500 platform at the Wellcome Trust Sanger Institute, as part of the PAGe project.
- The quality of the generated reads from high throughput NGS was assessed using FastQC v0.11.8 [15].
- In the study of by Chaguza et al.
- [28], the phylo- genic analysis of the global population structure of serotype 1 in Africa showed that all isolates were grouped in five distinct clades.
- For the inference of the phylogenetic re- lationships among the 80 isolates, Maximum Likeli- hood (ML) phylogenetic analyses were performed by using RAxML v based on core genome obtained with progressiveMauve (recombinations were filtered out with Gubbins), with 1000 bootstrap iterations.
- To accurately reconstruct the pangenome of the whole dataset, all 80 assembled and annotated ge- nomes (6 genomes from Morocco and 74 public ge- nomes) were analyzed by Roary v3.11.2 [42].
- Finally, we did a linear regression of the Jaccard dis- tance based on the accessory genes and the nucleotide diversity of synonym sites of core genes for each pair of genomes to provide insights of accessory genome ada- taptive evolution.
- DAPS: Discriminant analysis of principal components.
- This study is a part of the Pneumococcal African Genome project (PAGe) project.
- Sequence information of the 6 Moroccan pneumococcal serotype 1 genomes are available in the European Nucleotide Archive (ENA) database under the accession number given in Additional file 1.
- This study was approved by the Ethical committee for biomedical research of the University Mohammed V-Soussi, Faculty of Medicine, Pharmacy and Dental Medicine of Rabat, Morocco (No.
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