A novel invasive Streptococcus pyogenes variant sublineage derived through recombinational replacement of the emm12 genomic region

• Published in: Scientific reports Vol. 13; no. 1; pp. 21510 - 15
• Main Authors: Unoarumhi, Yvette, Davis, Morgan L., Rowe, Lori A., Mathis, Saundra, Li, Zhongya, Chochua, Sopio, Li, Yuan, McGee, Lesley, Metcalf, Benjamin J., Lee, Justin S., Beall, Bernard
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06-12-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/326; 631/337; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antigens, Bacterial - genetics; Antimicrobial agents; Bacterial Outer Membrane Proteins - genetics; Cardiovascular disease; Disease control; Drug Resistance, Bacterial - genetics; Genes; Genomes; Genomics; Genotype; Humanities and Social Sciences; Humans; Impetigo; Infections; M protein; multidisciplinary; Opacity; Pediatrics; Phenotypes; Phylogenetics; Phylogeny; Proteins; Respiratory diseases; Science; Science (multidisciplinary); Serum opacity factor; Single-nucleotide polymorphism; Streptococcal Infections - drug therapy; Streptococcus infections; Streptococcus pyogenes; Vaccines; Virulence
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-48035-2

Group A streptococcal strains potentially acquire new M protein gene types through genetic recombination (
emm
switching). To detect such variants, we screened 12,596 invasive GAS genomes for strains of differing
emm
types that shared the same multilocus sequence type (ST). Through this screening we detected a variant consisting of 16 serum opacity factor (SOF)-positive,
emm
pattern E,
emm82
isolates that were ST36, previously only associated with SOF-negative,
emm
pattern A,
emm12
. The 16
emm82/
ST36 isolates were closely interrelated (pairwise SNP distance of 0–43), and shared the same
emm82-
containing recombinational fragment.
emm82/
ST36 isolates carried the
sof12
structural gene, however the
sof12
indel characteristic of
emm12
strains was corrected to confer the SOF-positive phenotype. Five independent
emm82/
ST36 invasive case isolates comprised two sets of genetically indistinguishable strains. The
emm82/
ST36 isolates were primarily macrolide resistant (12/16 isolates), displayed at least 4 different core genomic arrangements, and carried 11 different combinations of virulence and resistance determinants. Phylogenetic analysis revealed that
emm82/
ST36 was within a minor (non-clade 1) portion of ST36 that featured almost all ST36 antibiotic resistance. This work documents emergence of a rapidly diversifying variant that is the first confirmed example of an
emm
pattern A strain switched to a pattern E strain.