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 {micro}g ml-1, with pH and temperature optima of 6.5-7.5 and 16-25{degrees}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-O2 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. IMPORTANCEAnthropogenic antibiotic pressure in environmental settings has been acknowledged as a major threat for the public health and the environment, through the: (i) associated ecotoxicological impact; and (ii) the increase of antibiotic resistance dispersal among non-pathogenic and pathogenic bacteria, restricting available choices for treating infections in health care. In situ microbial biotransformation of antibiotics and eventual removal is an environmentally friendly method currently under intense investigation, which was recently proposed for the reduction of antibiotic selective pressure. The present study provides mechanistic insights on the genomic constituents of antibiotrophy, namely, the tolerance against and the biodegradation/transformation of the antibiotic in question. We characterize the capacity of a bacterial isolate to transform tiamulin, a heavily used antibiotic in pig farming, and propose associated biotransformation mechanisms, through an integrated approach of standard microbiological methods combined with and multi-omics (genomics, transcriptomics, metabolomics).