Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing

PloS One
Walter H B DemczukMichael R Mulvey

Abstract

Since implementation of the 13-valent polyvalent conjugate vaccine (PCV13) in Canada during 2010, the proportion of PCV13 serotypes causing invasive pneumococcal disease (IPD) has declined from 55% (n = 1492) in 2010 to 31% (n = 764) in 2014. A concurrent increase of non-PCV13 serotypes has occurred and 22F has become the most prevalent serotype in Canada increasing from 7% (n = 183) to 11% (n = 283). Core single nucleotide variant phylogenetic analysis was performed on 137 Streptococcus pneumoniae serotype 22F isolates collected across Canada from 2005-2015. Six phylogenetic lineages (n = 117) were identified among a serotype 22F/ST433 clonal complex (CC), including a recently expanding erythromycin-resistant clone. Erythromycin-resistance was observed in 25 isolates possessing ermB, mef or a 23S rRNA A2061G point mutation; 2 penicillin-resistant isolates had recombinant pbp1a, pbp2a and/or pbp2x; 3 tetracycline-resistant isolates contained tetM; and 1 isolate was multidrug-resistant. Virulence factor analysis indicated a high level of homogeneity among the 22F/ST433 clonal complex strains. A group of 6 phylogenetic outlier strains had differing MLST, antimicrobial resistance and molecular profiles suggestive of capsule switch...Continue Reading

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Citations

Jul 10, 2018·The Journal of Antimicrobial Chemotherapy·Alyssa R GoldenUNKNOWN Canadian Antimicrobial Resistance Alliance (CARA)
May 23, 2020·Applied Microbiology and Biotechnology·Yolanda Torres-Corral, Ysabel Santos
Sep 11, 2019·The Journal of Antimicrobial Chemotherapy·Alyssa R GoldenUNKNOWN Canadian Antimicrobial Resistance Alliance (CARA) and CANWARD
Jul 1, 2021·Diagnostic Microbiology and Infectious Disease·Alyssa R GoldenUNKNOWN Canadian Antimicrobial Resistance Alliance (CARA)

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Datasets Mentioned

BETA
PRJEB10893
PRJNA347910
AKU19949.1
AKU19950.1
ACA37579.1
ACA35669.1
ACA36344.1
ACA36574.1

Software Mentioned

PubMLST
SAMtools mpileup
Mummer
Neptune DNA signature discovery software
GView
ClusterPicker
FLASH
BLAST
Prokka
SPAdes

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