Characterization of a prophage and a defective integrative conjugative element carrying the optrA gene in linezolid-resistant Streptococcus dysgalactiae subsp. equisimilis isolates from pigs, Italy

Abstract Objectives To investigate the optrA-carrying genetic elements and their transferability in two linezolid-resistant Streptococcus dysgalactiae subsp. equisimilis (SDSE) strains of swine origin. Methods SDSE strains (V220 and V1524) were phenotypically and genotypically characterized. Transferability of oxazolidinone resistance genes (filter mating), genetic elements and relatedness between isolates (WGS) were analysed. Excision of the genetic elements was assayed by inverse PCR. Results SDSE isolates were resistant to chloramphenicol, florfenicol and linezolid, but susceptible to tedizolid and both carried the optrA gene. In SDSE V220 optrA was located on a 72.9-kb ICESdyV220 inserted in the 3′ end of the chromosomal rum gene. It was 94%–96% identical (coverage, from 31% to 61%) to other optrA-carrying ICEs. In-depth ICESdyV220 sequence analysis revealed that optrA was carried by an IMESdyV220 (17.9 kb), also containing the tet(O/W/32/O) gene. Inverse PCR assays excluded the ICESdyV220 mobility. In SDSE V1524, optrA was carried by the ΦSdyV1524 prophage, integrated near the 5′ end of the chromosomal had gene, showing a genetic organization similar to that of other streptococcal phage. Conjugation and transduction assays failed to demonstrate the optrA transferability to streptococcal recipients. V220 and V1524 belonged to two novel sequence types (ST704 and ST634, respectively). Conclusions To the best of our knowledge, this is the first identification of the optrA gene on a prophage and an ICE in SDSE isolates from swine brain. These findings are consistent with the current belief in the key role of bacteriophages and ICEs in the streptococcal evolution and adaptation.