BackgroundAbuse of β-lactam antibiotics and its spread of drug resistance challenged the applicability of antimicrobial agents, enabling polymyxins as a last-line treatment for anti-infections of multi-drug resistant (MDR) pathogen. Polymyxin is applicable to herb breeding/growth prompting and combatting Gram-negative bacteria by combining other antimicrobials by membrane dysfunction, permeability damage, vesicle–vesicle contacts and oxidative stress, with its increasingly ubiquitous resistance. However, the complex mechanisms and high transmission risk of polymyxin resistance pose a severe threat to public health, such as improved colonization advantages and infection risks of Escherichia coli.MethodsIn this study, a polymyxin-resistant Escherichia coli strain capable of producing extended-spectrum β-lactamase (ESBL), thereafter designated as EcE.ESBL.COL, was isolated from a urine sample. Antimicrobial susceptibility testing and whole-genome sequencing revealed that this strain likely harbors multiple antibiotic resistance determinants.ResultsTherefore, these candidates were found on one chromosome [an integron-like MDR region not detected in another ST1485 representative strain (O83:H42)] and three plasmids (including blaTEM − 1B and blaCTX − M−55) in this strain, pertaining to multi-locus sequence type (MLST) 1485 and serotype O25:H42. Interestingly, this genomic region of plasticity with similar arrangements located on either chromosome or plasmid in other distantly-related strains [for example, the chromosome of E. coli strain LWY24 (previously as ST93, reclassified into ST457 in our study) and plasmid pFXCREC004-1, harbored by E. coli strain FXCREC004 (ST101)]. Next, an arnBCADTEF operon and no mcr-like determinant was found on EcE.ESBL.COL chromosome, facilitating the 4-amino-4-deoxy-L-arabinose (L-Ara4N) modification of lipid A in lipopolysaccharide (LPS). Interestingly, polymyxin resistance conferred by arn was augmented by additional polysaccharides retrieved from Lycium barbarum (LBP) and antioxidant N-acetylcysteine (NAC), while no significant antimicrobial coordination was observed if combined with colistin. In addition, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and comparative transcriptomics demonstrated that the LPS production and morphology significantly varied in response to polymyxin stress, indicating that polymyxin can induce the transcription of arnBCADTEF, thereby promoting L-Ara4N modification and polymyxin resistance.ConclusionOverall, our finding indicates that the co-occurrence of antibiotic resistance factors (such as MDR candidates and LPS architectural variation in this isolate) involves both chromosomal recombination and plasmid dissemination, thereby highlighting important implications for antimicrobial resistance surveillance, molecular epidemiological retrospection, and precision clinical anti-infection.