Detection of the macrolide-lincosamide-streptogramin B resistance gene erm(44) and a novel erm(44) variant in staphylococci from aquatic environments

Resistance to macrolides, lincosamides and streptogramin B antibiotics (MLSB) is not restricted to staphylococci from clinical samples but can also be present in staphylococci from the aquatic environment. Two coagulase-negative staphylococci – Staphylococcus xylosus and Staphylococcus saprophyticus were obtained from sewage and receiving river water samples and were investigated for the genetic basis of inducible MLSB resistance by whole genome sequencing. Two rRNA methylases, encoded by erm(44) and a novel Erm(44) variant were identified, which had only 84% amino acid identity. While fragments of phage DNA were found in the vicinity of the erm(44) gene of S. xylosus, no relics of mobile genetic elements were detected in the sequences flanking the erm(44) variant gene in the S. saprophyticus strain. The functionality of the erm genes was confirmed by cloning and transformation experiments. Based on the obtained sequences, specific PCR assays for both erm genes were developed and used to identify erm(44) in another seven S. xylosus and 17 S. saprophyticus isolates from aquatic environments.