W27.00009. Transcriptome-based design of antisense inhibitors re-sensitizes CRE E. coli to carbapenems

Presented by: Thomas Aunins


In recent years, 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 resistance factors, relatively few studies have examined CRE pathogens through changes in gene expression. Here 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 the gene expression response to ertapenem or meropenem treatment, and found significant expression changes in genes related to motility, maltodextrin metabolism, the formate hydrogenlyase complex, and the general stress response. To validate these findings, we used our lab’s Facile Accelerated Specific Therapeutic (FAST) platform to create antisense peptide nucleic acids (PNA), gene-specific molecules designed to inhibit protein translation. 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 PNA-antibiotic interaction with five different PNAs across six combinations. Inhibition of the genes hycA, dsrB, and bolA re-sensitized CRE E. coli to carbapenems, whereas inhibition of the genes flhC and ygaC conferred added resistance. Our results identify new resistance factors and demonstrate for the first time that transcriptomic analysis is a potent tool for designing antibiotic PNA.


  • Thomas Aunins
  • Keesha Erickson
  • Anushree Chatterjee


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