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

ABSTRACT Background The re-emergence of Streptococcus pyogenes genotype emm 3 in Spain after the COVID-19 pandemic was driven by the expansion of the rare subtype emm 3.93 which caused an outbreak between November 2023 and June 2024. This study aimed to characterize the microbiological features of emm3 isolates recovered during 2020–2024, incorporating clinical and epidemiological data. Methods A total of 138 emm 3 strains were studied. emm and exotoxin genes were typed by PCR-sequencing. Antimicrobial susceptibility was undertaken by E-test. Ten emm 3.93 genomes were further investigated by whole genome sequencing, and chromosomal arrangements were determined by long acute LA-PCR. Results Type emm 3 was associated with sepsis, and children and elderly people were the most vulnerable. Subtype emm 3.93 was detected in 114/138 emm 3 strains. The emm 3 population was susceptible to penicillin G, tetracycline, erythromycin and clindamycin. All genomes belonged to the sequence type ST315 and carried the six characteristic prophages Φ315.1, Φ315.2, Φ315.3, Φ315.4, Φ315.5 and Φ315.6; and 4/10 genomes also harboured ΦspeC-spd1. The predominant chromosomal arrangement (8/10 genomes) displayed an inversion around the terminus of replication, and 2/10 genomes were like the emm 3 reference genome MGAS315. Phylogenetic study grouped 7/10 genomes into the “Spanish clade”; and 3/10 genomes clustered with international strains, which evidenced global dissemination of the emergent emm 3.93 subtype. Conclusions The 2023-2024 outbreak was caused by the emergent clone emm 3.93/ spe A- spe G- spe K- sme Z- ssa /ST315, representative of contemporary hypervirulent emm 3 lineages.