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Volume 27, Number 6—June 2021
Dispatch

Serotype-Switch Variant of Multidrug-Resistant Streptococcus pneumoniae Sequence Type 271

Erin M. Scherer1, Bernard BeallComments to Author , and Benjamin Metcalf
Author affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia, USA

Main Article

Figure

Streptococcus pneumoniae serotype 3/ST271 lineage resulting from a recombination event between a 19F/ST271 recipient and 3/ST700 donor. A) Phylogenetic tree showing progeny serotype 3/ST271 isolates 20155315-S-ABC, 20170822-S-ABC, and 20182806-S-ABC (red arrow) most closely related to the putative recipient 19F/ST271 isolates 6299-05 and 2012214924 (blue arrows). The most closely related ST271 single contig reference is A026 (also indicated with blue arrow). Branch colors: yellow, additional 19F/ST271 Active Bacterial Core surveillance (ABCs) isolates and single contig references; red, single-locus variant single contig references or ABCs isolates; orange, double-locus variant single contig reference or ABCs isolates; blue, ST320 ABCs isolates. Zero-, single-, and double-locus variant, single contig references were identified by using the PubMLST database (https://pubmlst.org). Scale bar corresponds to 1,062 single nucleotide polymorphisms. B) Phylogenetic alignment of the 3 recombinant serotype 3/ST271 isolates and closest known genomic matches of the ST271 recipient lineage and a schematic of recombinant genome fragments, represented by rectangular blocks, that were predicted by Gubbins (10). Block locations and sizes are relative to the aligned genomes; red blocks represent sites in common between >2 isolates (1 site, <150 bp in length, was not counted among the 17 total shown), blue blocks sites unique to a given isolate, and gray blocks the serotype-switch fragment that replaced the corresponding cps19F region within the recipient 19F/ST271 strain. The cps3 locus was not identified using Gubbins because of its complete divergence from cps19F and instead was identified using ProgressiveMauve (12) within the encompassed 55.9 kb fragment (panel C). Gray block contains cps3, pbp1a (PBP1A-17), trigger factor, and choline binding protein G genes. C) Schematic illustrating ancestral recombination event between the 3/ST700 donor (B20605) and 19F/ST271 recipient (A026) to yield the 3/ST271 progeny (20155315-S-ABC). Deduced crossover points, including coordinates in the progeny, are shown. luxS and spsB genes are shown as blue/red hybrids. The minimum genes of the cps3 operon required for polysaccharide capsuale biosynthesire shown in gray (ugd, wchE, gtaB). Genes with arrows in black differ between B20605 and 73D36881 and are absent in the 3/ST271 isolates. ST, sequence type.

Figure. Streptococcus pneumoniae serotype 3/ST271 lineage resulting from a recombination event between a 19F/ST271 recipient and 3/ST700 donor. A) Phylogenetic tree showing progeny serotype 3/ST271 isolates 20155315-S-ABC, 20170822-S-ABC, and 20182806-S-ABC (red arrow) most closely related to the putative recipient 19F/ST271 isolates 6299-05 and 2012214924 (blue arrows). The most closely related ST271 single contig reference is A026 (also indicated with blue arrow). Branch colors: yellow, additional 19F/ST271 Active Bacterial Core surveillance (ABCs) isolates and single contig references; red, single-locus variant single contig references or ABCs isolates; orange, double-locus variant single contig reference or ABCs isolates; blue, ST320 ABCs isolates. Zero-, single-, and double-locus variant, single contig references were identified by using the PubMLST database (https://pubmlst.org). Scale bar corresponds to 1,062 single nucleotide polymorphisms. B) Phylogenetic alignment of the 3 recombinant serotype 3/ST271 isolates and closest known genomic matches of the ST271 recipient lineage and a schematic of recombinant genome fragments, represented by rectangular blocks, that were predicted by Gubbins (10). Block locations and sizes are relative to the aligned genomes; red blocks represent sites in common between >2 isolates (1 site, <150 bp in length, was not counted among the 17 total shown), blue blocks sites unique to a given isolate, and gray blocks the serotype-switch fragment that replaced the corresponding cps19F region within the recipient 19F/ST271 strain. The cps3 locus was not identified using Gubbins because of its complete divergence from cps19F and instead was identified using ProgressiveMauve (12) within the encompassed 55.9 kb fragment (panel C). Gray block contains cps3, pbp1a (PBP1A-17), trigger factor, and choline binding protein G genes. C) Schematic illustrating ancestral recombination event between the 3/ST700 donor (B20605) and 19F/ST271 recipient (A026) to yield the 3/ST271 progeny (20155315-S-ABC). Deduced crossover points, including coordinates in the progeny, are shown. luxS and spsB genes are shown as blue/red hybrids. The minimum genes of the cps3 operon required for polysaccharide capsuale biosynthesire shown in gray (ugd, wchE, gtaB). Genes with arrows in black differ between B20605 and 73D36881 and are absent in the 3/ST271 isolates. ST, sequence type.

Main Article

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1Current affiliation: Emory University, Atlanta, Georgia, USA.

Page created: April 13, 2021
Page updated: May 18, 2021
Page reviewed: May 18, 2021
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