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Published on: September 11, 2020

Sudden re-emergence of Streptococcus pyogenes subtype emm3.93 in Spain, 2023-2024

Villalón Pilar1, Medina-Pascual María José1, Garrido Noelia1

  • 1Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220, Spain.

New Microbes and New Infections
|June 26, 2026
PubMed
Abstract

Insights

The rare Streptococcus pyogenes emm3.93 subtype caused a 2023-2024 outbreak in Spain, leading to re-emergence of emm3 genotype. This hypervirulent clone shows global dissemination and specific genetic features.

Area of Science:

  • Microbiology
  • Genomics
  • Epidemiology

Background:

  • Streptococcus pyogenes emm3 genotype re-emerged in Spain post-COVID-19 pandemic.
  • Expansion of the rare emm3.93 subtype drove an outbreak from November 2023 to June 2024.

Purpose of the Study:

  • Characterize microbiological features of emm3 isolates from 2020-2024.
  • Incorporate clinical and epidemiological data for emm3 strains.

Main Methods:

  • Studied 138 emm3 strains, typing emm and exotoxin genes via PCR-sequencing.
  • Assessed antimicrobial susceptibility using E-test.
  • Performed whole genome sequencing and LA-PCR on ten emm3.93 genomes.

Main Results:

  • emm3 strains were linked to sepsis, with children and the elderly most vulnerable.
  • emm3.93 was detected in 114/138 strains and remained susceptible to common antibiotics.
  • Genomes belonged to ST315, carried characteristic prophages, and showed a predominant chromosomal inversion; phylogenetic analysis revealed a Spanish clade and international clusters.

Conclusions:

  • The 2023-2024 outbreak was driven by the emergent clone emm3.93/speA-speG-speK-smeZ-ssa/ST315.
  • This clone represents contemporary hypervirulent emm3 lineages.
  • The findings indicate global dissemination of the emergent emm3.93 subtype.
Keywords:
Chromosomal arrangementExotoxinOutbreakProphageStreptococcus pyogenesSubtype emm3.93Type emm3

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