The New Macrolide-Lincosamide-Streptogramin B Resistance Gene erm (45) Is Located within a Genomic Island in Staphylococcus fleurettii

Abstract

Genome alignment of a macrolide, lincosamide, and streptogramin B (MLS B )-resistant Staphylococcus fleurettii strain with an MLS B -susceptible S. fleurettii strain revealed a novel 11,513-bp genomic island carrying the new erythromycin resistance methylase gene erm(45). This gene was shown to confer inducible MLS B resistance when cloned into Staphylococcus aureus. The erm(45)-containing island was integrated into the housekeeping gene guaA in S. fleurettii and was able to form a circular intermediate but was not transmissible to S. aureus. Staphylococcus fleurettii is a commensal bacterium of various animal species and an occasional cause of bovine mastitis (1-3). It naturally contains the methicillin resistance gene mecA within its chromosome and is therefore suspected to have been the source of the mecA gene found in staphylococcal cassette chromosome mec (SCCmec) of methicillin-resistant staphylococci, including methicillin-resistant Staphylococcus aureus (MRSA) (4).Due to this intrinsic resistance to ␤-lactams, other antibiotic classes such as macrolides or lincosamides are being used for the treatment of mastitis caused by S. fleurettii (5, 6).S. fleurettii strain JW205, recently isolated from bovine milk in Switzerland, exhibited resistance to erythromycin and inducible resistance to clindamycin (3). This suggested the presence of a macrolide, lincosamide, and streptogramin B (MLS B ) resistance methylase (Erm) (7). However, none of the erm genes commonly occurring in staphylococci were detected by microarray analysis (8, 9). We therefore examined S. fleurettii strain JW205 for a novel MLS B resistance mechanism by genome comparison with MLS Bsusceptible S. fleurettii strain JW404 (Table 1).Detection and characterization of erm(45). Genomes of strain JW205 and JW404 were sequenced using Ion Torrent (Life Technologies, Grand Island, NY) at the UZH/ETH Functional Genomics Center (Zurich, Switzerland) and Illumina MiSeq (Illumina, San Diego, CA) at the Department of Clinical Microbiology at Hvidovre Hospital (Hvidovre, Denmark), respectively. Contigs of the sequenced strains were aligned using the progressive Mauve algorithm (10). This revealed an 11,513-bp integrated genomic island in JW205, which was absent in strain JW404. The island contained 18 open reading frames (ORFs) (Fig. 1), which were identified by the Prokaryotic Dynamic Programming Genefinding Algorithm (Prodigal) (11) and compared to protein sequences and conserved domains in the BLASTp program (http: //blast.ncbi.nlm.nih.gov/Blast.cgi) and the Swiss Institute of Bioinformatics PROSITE database (http://prosite.expasy.org/). The rightmost ORF of the island encoded a 245-amino-acid (aa) protein, which contained the rRNA adenine dimethylase PROSITE signature PS01131, which is present in nearly all Erm 23S rRNA methylases (12). Of all 36 currently described Erm determinants, this methylase exhibited the highest similarity to Erm(B), with 64% aa and 67% nucleotide (nt) identity (Fig. 2).The novel gene was assigned the name erm(45) according to th...

Diversity and Evolution of the Tn 5801-tet (M)-Like Integrative and Conjugative Elements among Enterococcus, Streptococcus, and Staphylococcus

“…All Tn5801 platforms identified in enterococci in this study were chromosomally located at the 3= end of guaA, as previously observed for three emblematic Tn5801 elements of staphylococci, Clostridium, and S. agalactiae (13,28). In the available sequences of the Tn5801 variants was the 11-bp sequence described previously as direct repeats (DRs) situated within the 3= end of guaA (13). All guaA sequences within the same species had high similarity (99 to 100%), which was somewhat lower (70 to 80%) when comparing isolates from different species.…”

“…Tn5801 has a site-specific tyrosine recombinase that recognizes the 3= end of the GMP synthase gene (guaA) (10,11), an insertion hot spot of genomic islands coding for pathogenicity or antibiotic resistance in different Firmicutes (12)(13)(14). Tn5801 was originally detected in the vancomycin-resistant Staphylococcus aureus (VRSA) clinical strain Mu50 recovered in Japan in 1997 (15), but several studies have documented the presence of platforms highly similar to Tn5801 in early isolates of Streptococcus agalactiae (France, 1953) (1), S. aureus (Denmark, 1963; designated Tn6014) (3), and Clostridium perfringens (United States, 1977; a truncated element designated CW459tet(M)] (16).…”

Characterization of Novel Broad-Host-Range Bacteriophage DLP3 Specific to Stenotrophomonas maltophilia as a Potential Therapeutic Agent

“…Further investigation into gp69 with HHblits revealed high sequence identity to Erm(45) of Staphylococcus fleurettii (HHblits: 100% probability, 2.4e-104 E -value). Researchers identified Erm(45) as the enzyme responsible for increased erythromycin resistance in some strains of S. fleuretti ( Wipf et al, 2015 ). The erm gene ( e rythromycin r ibosome m ethylase) encodes a methylase enzyme that provides macrolide resistance by methylating the erythromycin target-site on the ribosome ( Prunier et al, 2002 ).…”

New Macrolide-Lincosamide-Streptogramin B Resistance Gene erm (48) on the Novel Plasmid pJW2311 in Staphylococcus xylosus

“…Along with the erm(44) and erm(45) genes, which were also recently identified in staphylococci from bovine mastitis milk (9,22,23), the discovery of erm(48) highlights the role of dairy cows as a source of new MLS B resistance genes. Accession number(s).…”