Phi m46.1, the Main Streptococcus pyogenes Element Carrying mef(A) and tet(O) Genes

Phi m46.1, the recognized representative of the most common variant of mobile, prophage-associated genetic elements carrying resistance genes mef(A) (which confers efflux-mediated erythromycin resistance) and tet(O) (which confers tetracycline resistance) in Streptococcus pyogenes, was fully characterized. Sequencing of the Phi m46.1 genome (55,172 bp) demonstrated a modular organization typical of tailed bacteriophages. Electron microscopic analysis of mitomycin-induced Phi m46.1 revealed phage particles with the distinctive icosahedral head and tail morphology of the Siphoviridae family. The chromosome integration site was within a 23S rRNA uracil methyltransferase gene. BLASTP analysis revealed that the proteins of Phi m46.1 had high levels of amino acid sequence similarity to the amino acid sequences of proteins from other prophages, especially Phi 10394.4 of S. pyogenes and lambda Sa04 of S. agalactiae. Phage DNA was present in the host cell both as a prophage and as free circular DNA. The lysogeny module appears to have been split due to the insertion of a segment containing tet(O) (from integrated conjugative element 2096-RD.2) and mef(A) (from a Tn1207.1-like transposon) into the unintegrated phage DNA. The phage attachment sequence lies in the region between tet(O) and mef(A) in the unintegrated form. Thus, whereas in this form tet(O) is similar to 5.5 kb upstream of mef(A), in the integrated form, tet(O), which lies close to the right end of the prophage, is similar to 46.3 kb downstream of mef(A), which lies close to the left end of the prophage.