Isolation of a novel Sphingomonas strain able to degrade the pleuromutilin tiamulin: omic analysis reveals its transformation pathway

Tiamulin (TIA) is a commonly used veterinary antibiotic, persistent in the animal digestive system and downstream receiving environments like soil after manuring. We aimed to isolate and characterize TIA-degrading bacteria for bioaugmentation strategies towards mitigating TIA environmental pressure. A strain able to degrade TIA and use it as sole C source was isolated from a soil exhibiting enhanced biodegradation of the antibiotic. The isolate degraded TIA at concentrations up to 100 μg ml ^-1 , with pH and temperature optima of 6.5-7.5 and 16-25°C respectively. Phylogenomic analysis deemed the isolate to be a new Sphingomonas species (83.87 % ANI with S. laterariae, ≤ 95 %), which was named Candidatus Sphingomonas perruchonii. Genomics and transcriptomics revealed the TIA-driven induction of features conducive with its antiotrophic character; genes encoding for drug efflux pumps and the catabolism of xenobiotics. These included ribosome protective ABC-F transporters and efflux pumps able to protect the ribosome and microbial cells from TIA, oxygenases (e.g. P450 cytochrome) and hydrolases (e.g. alpha/beta hydrolases and amidohydrolases) possibly contributing to its degradation. LC-MS/MS analysis detected putative transformation products (TPs) of TIA, leading us to propose a transformation pathway. This involved a primary oxidation of the tricyclic moiety of TIA to a mono-hydroxylated derivative (TIA-O), potentially mediated by the highly upregulated monoxygenases, which was either further oxidized to TIA-O ₂ or hydrolysed, by the upregulated hydrolase or amidohydrolases, to 2-diethylamino-ethyl-thio acetic acid, both not degrading further. Further tests and in vitro functional analysis will verify the role of these genes in the transformation of TIA.