Mechanisms of Polymyxin Resistance in Acid-Adapted Enteroinvasive Escherichia coli NCCP 13719 Revealed by Transcriptomics

Acid adaptation in <i>Escherichia coli</i> can induce antimicrobial resistance (AMR), posing challenges to global public health. We investigated the effects of acid adaptation on antimicrobial susceptibility, gene expression, zeta potential, and the outer membrane (OM) properties of <i>Escherichia coli</i> NCCP 13719. The acid-adapted (AA) strain exhibited increased resistance to multiple antimicrobials, with minimum inhibitory concentrations for colistin and polymyxin B increasing eight- and two-fold, respectively. Transcriptomic analysis identified 2225 differentially expressed genes, including upregulated genes associated with resistance to cationic antimicrobial peptides such as <i>arnCTE</i>, <i>marA</i>, and <i>tolC</i>. The upregulation of the <i>arn</i> operon suggests modifications in lipid A of lipopolysaccharides (LPS), reducing the negative charge of the OM and decreasing polymyxin binding affinity. Zeta potential measurements indicated a shift toward a less negative surface charge in the AA strain, which is consistent with LPS modifications. The AA strain also showed decreased OM permeability, which correlated with increased resistance to antimicrobials that penetrate the OM. These mechanisms collectively diminish the efficacy of polymyxins and highlight the potential for environmental factors to drive antimicrobial resistance. In conclusion, the acid adaptation of <i>E. coli</i> NCCP 13719 enhances AMR through changes in gene expression and OM modifications, highlighting the need for careful control of acidic environments during the treatment of medical devices and wastewater from food processing to prevent the emergence of resistant strains.