Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance

Nyerges, Ákos and Csörgő, Bálint and Draskovits, Gábor and Kintses, Bálint and Szili, Petra and Ferenc, Györgyi and Révész, Tamás and Ari, Eszter and Nagy, István and Bálint, Balázs and Vásárhelyi, Bálint and Bihari, Péter and Számel, Mónika and Balogh, Dávid and Papp, Henrietta and Kalapis, Dorottya and Papp, Balázs and Pál, Csaba (2018) Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115 (25). E5726-E5735. ISSN 0027-8424

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Abstract

Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology.

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