Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Effective simultaneous removal of 17β-estradiol and tetracycline by a novel Alkalibacterium strain: characteristics, mechanisms, and application in livestock wastewater treatment

The environmental risk posed by 17β-estradiol (E2) and tetracycline (TC) contamination within livestock wastewater has been widely concerned. Especially, the co-occurrence of these pollutants poses a tremendous challenge to their efficient bioremediation, highlighting the need for strains capable of simultaneous E2 and TC removal. In this study, a novel strain of Alkalibacterium sp. AEPI-S25 was successfully isolated from the sediments of Qinghai Lake, demonstrating the ability to remove 89.91% of 20 mg L-1 E2 and nearly 100% of 20 mg L-1 TC simultaneously within 5 days. AEPI-S25 exhibited remarkable environmental adaptability and maintained high simultaneous removal efficiency under various stress conditions and the presence of two typical livestock wastewater samples. Based on Ultra-Performance Liquid Chromatography coupled with Orbitrap High-Resolution Mass Spectrometry (UPLC-Orbitrap-HRMS) analysis, dehydrogenation and monooxygenation were identified as the key steps in the removal pathways of E2 and TC, respectively. Whole-genome sequencing further identified the potential E2/TC removal genes, and the detected potential E2-dehydrogenation (S25_gene0393) and TC-monooxygenation (S25_gene0878) genes were subsequently validated through transcription analysis and heterologous expression. Notably, S25_gene0878 exhibited significant differences from the well-characterized TC removal gene TetX, extending a new understanding of the bacterial TC removal mechanism. Overall, this study provides the first report of a single microbial strain capable of simultaneously removing E2 and TC, offering valuable insights for the application of microbial technologies in addressing typical E2-TC combined pollution in livestock wastewater. KEY POINTS: • AEPI-S25 can remove nearly 90% and 100% of 20 mg L-1 E2 and TC within 5 days • Key E2 (S25_gene0393) and TC (S25_gene0878) removal genes were cloned and expressed • A novel TC-monooxygenase gene distinct from TetX was discovered within the strain.

Binding assays enable discovery of Tet(X) inhibitors that combat tetracycline destructase resistance

The Tet(X) flavin-dependent monooxygenases enable tetracycline antibiotic resistance by catalysing inactivating hydroxylation, so preventing inhibition of bacterial ribosomes. Tet(X) resistance is growing rapidly, threatening the efficacy of important last-resort tetracyclines such as tigecycline. Tet(X) inhibitors have potential to protect tetracyclines in combination therapies, but their discovery has been hampered by lack of high-throughput assays. We report the development of an efficient fluorescence polarisation Tet(X) binding assay employing a tetramethylrhodamine-glycyl-minocycline conjugate that enables inhibitor discovery. The assay was applied to tetracycline substrates and reported inhibitors, providing insight into their binding modes. Screening of a bioactive molecule library identified novel Tet(X) inhibitors, including psychoactive phenothiazine derivatives and the 5-HT4 agonist tegaserod, the activities of which were validated by turnover assays. Crystallographic studies of Tet(X4)-inhibitor complexes reveal two new inhibitor binding modes, importantly providing evidence for active site binding of Tet(X) inhibitors that do not share structural similarity with tetracycline substrates. In some cases, potentiation of tigecycline activity was observed in bacteria expressing Tet(X4). The combined results provide non-tetracycline scaffolds for development of potent Tet(X) inhibitors and highlight the need to evaluate the impact of non-antibiotics on antimicrobial resistance.

C10-Benzoate Esters of Anhydrotetracycline Inhibit Tetracycline Destructases and Recover Tetracycline Antibacterial Activity

Tetracyclines (TCs) are an important class of antibiotics threatened by enzymatic inactivation. These tetracycline-inactivating enzymes, also known as tetracycline destructases (TDases), are a subfamily of class A flavin monooxygenases (FMOs) that catalyze hydroxyl group transfer and oxygen insertion (Baeyer-Villiger type) reactions on TC substrate scaffolds. Semisynthetic modification of TCs (e.g., tigecycline, omadacycline, eravacycline, and sarecycline) has proven effective in evading certain resistance mechanisms, such as ribosomal protection and efflux, but does not protect against TDase-mediated resistance. Here, we report the design, synthesis, and evaluation of a new series of 22 semisynthetic TDase inhibitors that explore D-ring substitution of anhydrotetracycline (aTC) including 14 C10-benzoate ester and eight C9-benzamides. Overall, the C10-benzoate esters displayed enhanced bioactivity and water solubility compared to the corresponding C9-benzamides featuring the same heterocyclic aryl side chains. The C10-benzoate ester derivatives of aTC were prepared in a high-yield one-step synthesis without the need for protecting groups. The C10-esters are water-soluble, stable toward hydrolysis, and display dose-dependent rescue of tetracycline antibiotic activity in E. coli expressing two types of tetracycline destructases, represented by TetX7 (Type 1) and Tet50 (Type 2). The best inhibitors recovered tetracycline antibiotic activity at concentrations as low as 2 μM, producing synergistic scores <0.5 in the fractional inhibitory concentration index (FICI) against TDase-expressing strains of E. coli and clinical P. aeruginosa. The C10-benzoate ester derivatives of aTC reported here are promising new leads for the development of tetracycline drug combination therapies to overcome TDase-mediated antibiotic resistance.

The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation

The history of clinical resistance to tetracycline antibiotics is characterized by cycles whereby the deployment of a new generation of drug molecules is quickly followed by the discovery of a new mechanism of resistance. This suggests mechanism-specific selection by each tetracycline generation; however, the evolutionary dynamics of this remain unclear. Here, we evaluate 24 recombinant Escherichia coli strains expressing tetracycline resistance genes from each mechanism (efflux pumps, ribosomal protection proteins, and enzymatic inactivation) in the context of each tetracycline generation. We employ a high-throughput barcode sequencing protocol that can discriminate between strains in mixed culture and quantify their relative abundances. We find that each mechanism is preferentially selected for by specific antibiotic generations, leading to their expansion. Remarkably, the minimum inhibitory concentration associated with individual genes is secondary to resistance mechanism for inter-mechanism relative fitness, but it does explain intra-mechanism relative fitness. These patterns match the history of clinical deployment of tetracycline drugs and resistance discovery in pathogens.