Isolation of a Sphingomonas strain able to degrade the pleuromutilin antibiotic tiamulin: in vitro characterization of the antibiotic transformation capacity and pathway elucidation via comparative genomics, transcriptomics, and metabolomics.

Tiamulin (TIA) is a commonly used veterinary antibiotic. It is persistent in the animal digestive system, its excreta and receiving environments, posing environmental and public health concerns due to potential selection for microbial TIA resistance. We isolated a TIA-degrading bacterium with potential use in mitigating TIA environmental pressure. The isolate degraded up to 100 µg/mL of TIA, with pH and temperature optima of 6.5-7.5 and 16-25 °C respectively. Phylogenomics deemed the isolate to be a new Sphingomonas strain, which we named Candidatus Sphingomonas perruchoniana. Genomics and transcriptomics revealed antibiotrophy-relevant putative features like (i) TIA-detoxifying transporters and (ii) oxygenases and hydrolases possibly contributing to TIA transformation. The latter along with LC-QTOF-MS/MS analysis data suggest a monooxygenase mediated primary oxidation of the tricyclic moiety of TIA to a mono-hydroxylated derivative (OH-TIA), further bio-oxidized to di-OH-TIA or bio-hydrolysed to 2-diethylamino-ethyl-thio acetic acid. This study enforces the prospects of antibiotrophy in treating antibiotic polluted environments.