ICESp1109, a novel hybrid Integrative-Conjugative Element of macrolide-resistant Streptococcus pyogenes serotype M77 collected between 2003 and 2017 in Poland

Abstract

Background. The antibiotic resistance determinants and associated mobile genetic elements (MGEs) were detected among Streptococcus pyogenes (group A streptococci [GAS]) clinical isolates of an M77 serotype collected in Poland between 2003 and 2017. Methods. The genomes of 136 M77 GAS isolates were sequenced using short- and selected with long-read approach; whole genome sequences were analyzed to determine the genetic context of macrolide resistance determinants. Results. The analysed strains were collected from in- and outpatients. Sequencing data analysis revealed that all strains carried the tet(O) gene. They were classified as a single sequence type, ST63. The unique erythromycin-resistance determinant, the erm(TR), was detected in 76.5% (n = 104) of isolates. It was found predominantly (n = 74) within a novel hybrid integrative conjugative element composed of the ICESp1108-like sequence and ICESp2906 variant, which was then named ICESp1109. However, in strains isolated before 2008, erm(TR) was located within ICESp2905 (n = 27) and in 3 strains - within stand-alone ICESp1108-like sequences. Conclusions. Based on phylogenetic analysis results, the clonal dissemination of the macrolide-resistant S pyogenes M77/ST63 strain with hybrid ICESp1109 was observed between 2008 and 2017. ICESp1109 is the novel hybrid ICE in gram-positive bacteria.