Genome-wide screening of antibiotic survival genes in Escherichia coli MG1655

BACKGROUND: The widespread usage and exposure to non-lethal concentrations of antibiotics has made antibiotic resistance one of the top global health threats. Besides studying bacterial responses towards antibiotic treatment, identifying preexisting genes in bacterial genomes that could protect cells from antibiotics is another important approach to understanding the mechanisms of resistance. In this study, we tested each of the ~4,200 strains in the ASKA library, which is an overexpression library of Escherichia coli K-12 open reading frames, to identify potential antibiotic survival genes in E. coli against 12 types of commonly used antibiotics. RESULTS: In total, we identified 172 candidate genes, whose overexpression increased minimum inhibitory concentrations (MICs) by at least 3-fold against one or multiple antibiotics. These identified genes are mainly involved in metabolism, stress responses, protein synthesis, and transporters, and many of them have not been shown to be associated with antibiotic resistance before. CONCLUSIONS: This study provides a broad profile of antibiotic survival genes in the E. coli MG1655 strain, implying potential mechanisms for adaptation to antibiotic exposure.