Transcriptome-based design of antisense inhibitors re-sensitizes CRE E. coli to carbapenems

Carbapenems are a powerful class of antibiotics, often used as a last-resort treatment to eradicate multidrug-resistant infections. In recent years, however, the incidence of carbapenem-resistant Enterobacteriaceae (CRE) has risen substantially, and the study of bacterial resistance mechanisms has become increasingly important for antibiotic development. Although much research has focused on genomic contributors to carbapenem resistance, relatively few studies have examined CRE pathogens through changes in gene expression. In this research, we used transcriptomics to study a CRE Escherichia coli clinical isolate that is sensitive to meropenem but resistant to ertapenem, to both explore carbapenem resistance and identify novel gene knockdown targets for carbapenem re-sensitization. We sequenced total and small RNA to analyze gene expression changes in response to treatment with ertapenem or meropenem, as compared to an untreated control. Significant expression changes were found in genes related to motility, maltodextrin metabolism, the formate hydrogenlyase complex, and the general stress response. To validate these transcriptomic findings, we used our labs Facile Accelerated Specific Therapeutic (FAST) platform to create antisense peptide nucleic acids (PNA), gene-specific molecules designed to inhibit protein translation. FAST PNA were designed to inhibit the pathways identified in our transcriptomic analysis, and each PNA was then tested in combination with each carbapenem to assess its effect on the antibiotics minimum inhibitory concentrations. We observed significant treatment interaction with five different PNAs across six PNA-antibiotic combinations. Inhibition of the genes hycA, dsrB, and bolA were found to re-sensitize CRE E. coli to carbapenems, whereas inhibition of the genes flhC and ygaC was found to confer added resistance. Our results identify new resistance factors that are regulated at the level of gene expression, and demonstrate for the first time that transcriptomic analysis is a potent tool for designing antibiotic PNA.