Background: The emergence of intra-emm sublineages of Streptocccus pyogenes (Group A Streptococcus, GAS) identified using whole-genome data has been correlated with infection upsurges. This study aimed at identifying clonal changes among invasive GAS (iGAS) circulating in Portugal.
Methods: A total of 355 iGAS isolated during 2016-2019 were sequenced with Illumina MiSeq or NextSeq. The emm-types and 7-gene multilocus sequence types (STs) were predicted using emmTyper and MLST, respectively. Genetic relatedness was evaluated by core-genome multilocus sequence typing (cgMLST) using minimum spanning trees.
Results: The isolates comprised 42 emm-types and 62 STs, but 6 emm-types accounted for 75% of all isolates, namely emm1 (n=112), emm3 (n=57), emm89 (n=27), emm6 (n=25), emm12 (n=25), and emm4 (n=20). The emm-types included in the 30-valent vaccine under development represented 91% of the isolates. The prevalence of emm3 increased relative to 2010-2015 (p=0.004). During 2016-2019, emm1 presented an increasing trend, while emm3, emm6, and emm89 presented a decreasing trend (p<0.01). Among 112 emm1 isolates, 53 were grouped with the M1UK clone by cgMLST, increasing throughout the study period (p=0.0006). High-expression variants of the nga promoter occurred in 76% of the isolates, including all emm89 isolates, which grouped with the reference genomes of emm89-clade 3.
Conclusions: During 2016-2019, although there was an upsurge of emm3, emm1 remained the major cause of iGAS disease in Portugal, with an increasing trend in both overall emm1 and in the recently described M1UK clone. In contrast, emm89 was decreasing, despite the continued dominance of clade 3.