Ultrastructural, metabolic and genetic characteristics of determinants facilitating the acquisition of macrolide resistance by Streptococcus pneumoniae

To investigate the molecular events associated with acquiring macrolide resistance genes [ mefE / mel (Mega) or ermB ] in Streptococcus pneumoniae ( Spn ) during nasopharyngeal colonization. Genomic analysis of 128 macrolide-resistant Spn isolates revealed recombination events in genes of the conjugation apparatus, or the competence system, in strains carrying Tn 916 -related elements. Studies using confocal and electron microscopy demonstrated that during the transfer of Tn 916 -related elements in nasopharyngeal cell biofilms, pneumococcal strains formed clusters facilitating their acquisition of resistance determinants at a high recombination frequency (rF). Remarkably, these aggregates comprise both encapsulated and nonencapsulated pneumococci that span extracellular and intracellular compartments. rF assessments showed similar rates regardless Mega was associated with large integrative and conjugative elements (ICEs) (>23 kb) or not (∼5.4 kb). The rF for Mega Class IV(c) insertion region (∼53 kb) was three orders of magnitude higher than the transformation of the capsule locus. Metabolomics studies of the microenvironment created by colonization of human nasopharyngeal cells revealed a link between the acquisition of ICEs and the pathways involving nicotinic acid and sucrose. Pneumococcal clusters, both extracellular and intracellular, facilitate macrolide resistance acquisition, and ICEs were acquired at a higher frequency than the capsule locus. Metabolic changes could serve as intervention targets. • Recombination hotspots were identified within the Tn 2010 conjugation machinery of Spn CC271 strains. • Extracellular and intracellular clusters of pneumococci facilitate macrolide resistance acquisition. • Macrolide resistance acquisition via recombination is more frequent than classic capsule locus transformation events. • Pneumococci and nasopharyngeal create a microenvironment altering host metabolites, linked to increased macrolide resistance acquisition.