Evolutionary dynamics and virulence factor variability in invasive Streptococcus pyogenes in Norway, 2017−2023

TL;DR

This study analyzed Streptococcus pyogenes infections in Norway from 2017 to 2023 to understand how virulence factors and antibiotic resistance have changed over time.

Contribution

The study identifies new phages carrying virulence factors and highlights the dynamic nature of phage integration and excision in S. pyogenes.

Findings

15.6% of isolates showed antibiotic resistance, with tetracycline resistance being the most common.

Dominant emm types included emm1, emm12, emm89, emm28, emm4, and emm87, with emm1 largely belonging to the M1UK lineage.

Four new phages carrying virulence factors speC and spd1 were identified, showing rapid turnover and genomic variability.

Abstract

Invasive infections caused by Streptococcus pyogenes (iGAS) have increased in Europe over the past decade, with a marked upsurge after the COVID-19 pandemic. Here, we examined whether the increase in iGAS infections in Norway was associated with the spread of variants that had acquired new virulence factors. A collection of 1,163 iGAS isolates submitted to the National Reference Laboratory between January 2017 and April 2023, representing 87% of all cases recorded by the Norwegian Surveillance System for Infectious Diseases, was analyzed by whole genome sequencing. Resistance to one or more antibiotics was found in 15.6% of the isolates: 14.1% were resistant to tetracycline, 6.4% to erythromycin, and 4.0% to clindamycin. Resistance to other antibiotics was < 1%. The dominating emm types were emm1 (30.9%), emm12 (13.8%), emm89 (9.3%), emm28 (8.3%), emm4 (6.0%), and emm87 (4.5%), with the remaining isolates belonging to 55 other emm types; 62.3% of emm1 belonged to the hypervirulent lineage M1UK. Genetic characterization of the virulence factors of the dominant six emm types demonstrated extensive competition between related phages, leading to phage switching and interplay between integration and excision of temperate phages carrying virulence factors. Bacteriophages carrying virulence factors speC and spd1 displayed a particularly high turnover rate, with several pairs of otherwise genomically identical isolates exhibiting different phage-carrying status. We identified and characterized four new speC and spd1-carrying phages. The rapid turnover pattern of these, as well as other phages carrying superantigens and DNAses suggests an important role in pathogenesis.

This analysis of 1,163 iGAS isolates collected between January 2017 and April 2023 aimed to map virulence factor content to understand the observed increased incidence of iGAS in Norway. Our findings indicate that 15.6% of the isolates were resistant to at least one antibiotic, with tetracycline resistance being the most common. The dominant emm types were emm1, emm4, emm12, emm28, emm87, and emm89, which together accounted for 72.7% of the isolates. The study highlights the dynamic nature of virulence factor-carrying temperate phages, particularly the ones carrying speC and spd1, which frequently integrate and excise within emm types. Four previously unseen phages carrying speC and spd1 were identified and characterized. This research underscores the complexity of iGAS epidemiology and the need for continuous surveillance to understand the evolving landscape of bacterial virulence factors, antibiotic resistance, and circulating emm types.

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