Background: The CDC designated macrolide-resistant GAS a ‘concerning threat’ (2019).
Methods: Methods include whole genome sequencing, bioinformatics and phenotype measures.
Results: Global analysis identified 105 distinct ‘strains’ of macrolide-resistant GAS, wherein ‘strain’ is defined by the unique combination of emm type, pilin type, R-gene and integration site. Macrolide resistance genes include: (i), mef(A/O)/msr(D) on (conjugative) phage (20 GAS strains) with 75% of the elements integrating at one locus (comEC); (ii) erm(A) on ICEs/IMEs (36 strains) with 92% of integration sites limited to two loci (rlmD/rumA, hsdM); (iii), erm(B) on ICEs/IMEs (47 strains) with a diverse set of >16 different integration sites; and (iv), erm(T) (plasmid; 2 strains). Among the complete set of unique macrolide-resistant strains, >40% of elements integrate at/near loci that may impact cell-cell interactions and/or acquisition of foreign DNA: comEC (DNA internalization-related competence protein), hsdM (type I restriction-modification system, DNA-methyltransferase), blpM (bacteriocin-like peptide M) and rplL/pbp (D-alanyl-D-alanine carboxypeptidase). RNA-seq analysis of isogenic GAS pairs generated by transfer of a mef(O) element, with site-specific integration within comEC, reveals slightly skewed RNA transcript levels for numerous genes involved in quorum sensing. emm49 strains from a regional sampling [erm(A)/rlmD, erm(B)/hsdM] exhibit alterations in colony morphology and/or biofilm formation compared to susceptible emm49 isolates differing by a few detectable SNPs.
Conclusions: The 105 unique macrolide-resistant GAS strains likely emerged via distinct horizontal transfer events. Acquisition of genetic elements conferring macrolide resistance appears to alter non-resistance-related phenotypes. It seems plausible that the chromosomal integration step has pleiotropic effects on the host cell.