Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13

Hanachi, Mariem, Kiran, Anmol ORCID: 0000-0003-2680-2303, Cornick, Jennifer, Harigua-Souiai, Emna, Everett, Dean, Benkahla, Alia and Souiai, Oussama (2020) Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13. Bioinformatics and Biology Insights, 14. p. 117793222096210.

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Official URL: http://dx.doi.org/10.1177/1177932220962106

Abstract

<jats:p> Streptococcus pneumoniae serotype 1 is a common cause of global invasive pneumococcal disease. In New Caledonia, serotype 1 is the most prevalent serotype and led to two major outbreaks reported in the 2000s. The pneumococcal conjugate vaccine 13 (PCV13) was introduced into the vaccination routine, intending to prevent the expansion of serotype 1 in New Caledonia. Aiming to provide a baseline for monitoring the post-PCV13 changes, we performed a whole-genome sequence analysis on 67 serotype 1 isolates collected prior to the PCV13 introduction. To highlight the S. pneumoniae serotype 1 population structure, we performed a multilocus sequence typing (MLST) analysis revealing that NC serotype 1 consisted of 2 sequence types: ST3717 and the highly dominant ST306. Both sequence types harbored the same resistance genes to beta-lactams, macrolide, streptogramin B, fluoroquinolone, and lincosamide antibiotics. We have also identified 36 virulence genes that were ubiquitous to all the isolates. Among these virulence genes, the pneumolysin sequence presented an allelic profile associated with disease outbreaks and reduced hemolytic activity. Moreover, recombination hotspots were identified in 4 virulence genes and more notably in the cps locus ( cps2L), potentially leading to capsular switching, a major mechanism of the emergence of nonvaccine types. In summary, this study represents the first overview of the genomic characteristics of S. pneumoniae serotype 1 in New Caledonia prior to the introduction of PCV13. This preliminary description represents a baseline to assess the impact of PCV13 on serotype 1 population structure and genomic diversity. </jats:p>

Item Type:	Article
Uncontrolled Keywords:	Streptococcus pneumoniae, serotype 1, whole-genome sequencing, recombination, virulence factors, antibiotics resistance genes, pneumolysin, New Caledonia
Depositing User:	Symplectic Admin
Date Deposited:	05 Nov 2020 11:01
Last Modified:	18 Jan 2023 23:23
DOI:	10.1177/1177932220962106
Open Access URL:	https://doi.org/10.1177/1177932220962106
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3106091