The Cfr rRNA Methyltransferase Confers Resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A Antibiotics

Abstract

A novel multidrug resistance phenotype mediated by the Cfr rRNA methyltransferase is observed in Staphylococcus aureus and Escherichia coli. The cfr gene has previously been identified as a phenicol and lincosamide resistance gene on plasmids isolated from Staphylococcus spp. of animal origin and recently shown to encode a methyltransferase that modifies 23S rRNA at A2503. Antimicrobial susceptibility testing shows that S. aureus and E. coli strains expressing the cfr gene exhibit elevated MICs to a number of chemically unrelated drugs. The phenotype is named PhLOPS A for resistance to the following drug classes: Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics. Each of these five drug classes contains important antimicrobial agents that are currently used in human and/or veterinary medicine. We find that binding of the PhLOPS A drugs, which bind to overlapping sites at the peptidyl transferase center that abut nucleotide A2503, is perturbed upon Cfr-mediated methylation. Decreased drug binding to Cfr-methylated ribosomes has been confirmed by footprinting analysis. No other rRNA methyltransferase is known to confer resistance to five chemically distinct classes of antimicrobials. In addition, the findings described in this study represent the first report of a gene conferring transferable resistance to pleuromutilins and oxazolidinones.The bacterial ribosome is the site of protein synthesis and the target for many chemically diverse classes of antimicrobial agents. The antimicrobial drugs target important functional centers of the ribosome and most often bind to rRNA. Recently, a new phenicol and clindamycin resistance phenotype was found to be caused by an RNA methyltransferase designated Cfr. A detailed analysis by drug footprinting studies and matrix-assisted laser desorption-ionization time of flight/tandem mass spectrometry showed that Cfr adds an additional methyl group at position A2503 of 23S rRNA (9). Since A2503 is located in close proximity to the overlapping ribosomal binding sites of phenicols and clindamycin, it was concluded that the Cfr-mediated methylation confers resistance to these two classes of antimicrobial agents by interfering with the positioning of the drugs (9).The cfr gene was first discovered in 2000 during a surveillance study for florfenicol resistance among staphylococci from animals. It was initially detected on the 17.1-kb multiresistance plasmid pSCFS1 from a bovine strain of Staphylococcus sciuri (24) and has also been found in bovine strains of Staphylococcus simulans (6). In addition to cfr, the pSCFS1 plasmid carries the rRNA methylase gene erm(33), the aminocyclitol phosphotransferase gene spc, and the ABC transporter gene lsa(B), which confer resistance to macrolide-lincosamide-streptogramin B (MLS B ) antibiotics, spectinomycin, and lincosamides, respectively. The cfr gene was recently detected on the 35.7-kb plasmid, pSCFS3, from a porcine Staphylococcus aureus strain, together with the chloramphenicol/florfenicol exporter gene f...

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

“…Methylation of the C8 position of A2503 in S. aureus by the Cfr enzyme leads to multidrug resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A (PhLOPS A ) (26,66,67). The A2503 nucleotide interacts with linezolid and is ∼98% conserved throughout all kingdoms (52); nevertheless, it can be modified without interfering with protein biosynthesis.…”

Identification and characterization of cfr-positive Staphylococcus aureus isolates from community-onset infectious patients in a county hospital in China

“…The rRNA methyltransferase coded by the cfr gene modifies the adenine residue at position 2503 of the 23S rRNA, resulting in resistance to antibiotics including lincosamides, phenicols, pleuromutilins and streptogramin A (Long et al, 2006). Among the 14 cfr-positive isolates, 12, 11 and 10 isolates exhibited altered resistance to erythromycin, chloramphenicol and clindamycin, respectively, whereas all isolates were susceptible to vancomycin and teicoplanin.…”

Determination of Risk Factors Associated With Isolation of Linezolid-Resistant Strains of Vancomycin-Resistant Enterococcus

“…Lastly, exposures to antibiotics that acted on the bacterial ribosome were pooled together in the risk analysis because of a recent study that identified a plasmid-mediated transferable rRNA methyltransferase in Staphylococcus aureus. 26 Although this has not been identified in Enterococcus species, the transfer of other genetic material between these 2 bacteria has been described.…”