Increase of macrolide resistance among Streptococcus pyogenes pharyngitis driven by a mef (A)- msr (D)/ emm 2-ST55 lineage in Portugal (2014–2019)

Increases in macrolide resistance occurred recently among Streptococcus pyogenes (Group A Streptococcus , GAS) in some countries. While the importance of monitoring the clinical and molecular epidemiology of non-invasive GAS is increasingly recognized, most surveillance focuses on invasive infections, since culture is rarely performed in tonsillo-pharyngitis. We determined the antimicrobial susceptibility and characterized the macrolide-resistant lineages of 2,002 pharyngeal isolates recovered in a Portuguese hospital in 2014–2019. There were seasonal variations in the numbers of recovered isolates, with peaks shifting between March–July and October–December, but consistently low numbers in August and September. Macrolide-resistant and macrolide-susceptible GAS presented independent seasonal and clonal dynamics, with resistant isolates showing lower genetic diversity and minimal overlap with susceptible lineages. Overall, 84 (4%), 77 (4%), and 52 (3%) isolates were resistant to erythromycin, clindamycin, and tetracycline, respectively. Until 2018, macrolide resistance was mainly due to an internationally disseminated emm 77-ST63 lineage carrying erm (A) and tet (O) in ICE Sp2905 and an emm 75-ST49 lineage carrying mef (A)- msr (D) in a novel ɸ1207.3 variant. In 2019, resistance peaked at 9% due to the rapid expansion of mef (A)- msr (D)-positive emm 2-ST55 isolates, replacing previous lineages. Other minor resistant lineages carried mostly erm (B) in a diversity of mobile genetic elements, including emm 75-ST150, emm 9-ST75, emm 11-ST403, emm 12-ST36, emm 76-ST50, and emm 77-ST399 [ erm (T)]. Tetracycline resistance was associated with the genes tet (M) and tet (O), in most cases co-located in the same genetic elements as the erm genes. This study reveals clonal changes among macrolide-resistant GAS driving fluctuations in macrolide resistance and associated phenotypes.