Macrolide resistance associated with macrolide efflux (mef) has rapidly increased in Streptococcus pneumoniae. We defined the genetic structure and dissemination of a novel mefE-containing chromosomal insertion element. The mefE gene was found on the 5' end of a 5.5- or 5.4-kb insertion designated as the macrolide efflux genetic assembly (mega), which is found in > or =4 distinct sites of the pneumococcal genome. The element was transformable and conferred macrolide resistance to susceptible S. pneumoniae. The first 2 open-reading frames (ORFs) of the element formed an operon composed of mefE and a predicted adenosine triphosphate-binding cassette homologous to msrA. Convergent to this efflux operon were 3 ORFs with homology to stress response genes of Tn5252. Mega was related to the recently described mefA-containing element Tn1207.1 but lacked the genes necessary for transposition and had unique termini and insertion sites. In metropolitan Atlanta, macrolide resistance due to mega rapidly increased in S. pneumoniae by clonal expansion and horizontally by transformation.