Characteristics of Streptococcus pyogenes causing invasive infections among adults in Portugal, 2016-2019: Pre-COVID-19 expansion of the M1UK sublineage

Abstract

Background: Genome-based epidemiological surveillance of Streptococcus pyogenes (Lancefield Group A Streptococcus, GAS) infections facilitated the detection of emergent successful lineages, such as the M1_UK sublineage. This sublineage dominated the post-COVID-19 upsurge of invasive GAS infections (iGAS) in multiple countries, including Portugal. Here, we characterized the genetic lineages causing iGAS in Portugal during 2016-2019 to evaluate possible temporal trends and compare them with internationally circulating lineages.

Methods: Whole-genome sequencing and antimicrobial susceptibility testing were performed for 273 iGAS isolates.

Results: The dominant emm types were emm1 (n = 87), emm3 (n = 37), and emm89 (n = 26), collectively comprising 55 % of all isolates (n = 273). Throughout the study, the M1_UK sublineage increased in prevalence, accounting for 48 % of all emm1 isolates. Core-genome multilocus sequence typing supports multiple introductions of M1_UK in Portugal pre-COVID-19, and a limited relatedness to the M1_UK isolates recovered during the post-COVID-19 surge in pediatric iGAS. Several internationally disseminated lineages expressing various emm types were identified. Mutations inactivating key regulators of virulence (CovRS and RopB) and in the capsule locus were found in a significant fraction of isolates. Macrolide resistance was primarily associated with the erm(A) and erm(B) genes and remained low (4 %), highlighting differences between Europe and North America.

Conclusions: Despite adult iGAS in Portugal being caused by geographically widespread, successful GAS lineages that may be repeatedly introduced in the country, including M1_UK, there was no apparent increase in disease. This is consistent with upsurges of iGAS post-COVID-19 not being driven primarily by the emergence or introduction of novel GAS clones.