Deciphering mobile genetic elements disseminating macrolide resistance in Streptococcus pyogenes over a 21 year period in Barcelona, Spain. (20th May 2021) - Berbel, Dàmaris
Abstract: Objectives: To phenotypically and genetically characterize the antibiotic resistance determinants and associated mobile genetic elements (MGEs) among macrolide-resistant (MR) Streptococcus pyogenes [Group A streptococci (GAS)] clinical isolates collected in Barcelona, Spain. Methods: Antibiotic susceptibility testing was performed by microdilution. Isolates were emm and MLST typed and 55 were whole-genome sequenced to determine the nature of the macrolide resistance (MR) determinants and their larger MGE and chromosomal context. Results: Between 1998 and 2018, 142 of 1028 GAS (13.8%) were MR. Among 108 isolates available for molecular characterization, 41.7% had cMLSB, 30.5% iMLSB and 27.8% M phenotype. Eight erm (B)-containing strains were notable in having an MDR phenotype conferred by an MGE encoding several antibiotic resistance genes. MR isolates were comprised of several distinct genetic lineages as defined by the combination of emm and ST. Although most lineages were only transiently present, the emm 11/ST403 clone persisted throughout the period. Two lineages, emm 9/ST75 with erm (B) and emm 77/ST63 with erm (TR), emerged in 2016–18. The erm (B) was predominantly encoded on the Tn 916 family of transposons (21/31) with different genetic contexts, and in other MGEs (Tn 6263, ICE SpHKU372 and one harbouring an MDR cluster called ICE Sp1070HUB ). The erm (TR) was found in ICE Sp2905 (8/17), ICE Sp1108 -like (4/17), ICE SpHKU165 (3/17) and two structures described in this study (IME Sp316HUB and ICE Sp3729HUB ). The M phenotype [ mef (A)- msr (D)] was linked to phage φ1207.3. Eight integrative conjugative element/integrative mobilizable element (ICE/IME) cluster groups were classified on the basis of gene content within conjugation modules. These groups were found among MGEs, which corresponded with the MR-containing element or the site of integration. Conclusions: We detected several different MGEs harbouring erm (B) or erm (TR). This is the first known description of Tn 6263 in GAS and three MGEs [IME Sp316HUB, ICE Sp3729HUB and ICE Sp1070HUB ] associated with MR. Periods of high MR rates in our area were mainly associated with the expansion of certain predominant lineages, while in low MR periods different sporadic and low prevalence lineages were more frequent.