Species-dependent in polymyxin B heteroresistance: genomic insights into adaptive evolution in Enterobacteriaceae

Polymyxin heteroresistance poses a growing challenge in antimicrobial resistance management, yet its epidemiological features and molecular basis across different bacterial species and environments remain poorly understood. This study aimed to systematically evaluate the prevalence and genomic mechanisms of heteroresistance in Escherichia coli and Klebsiella pneumoniae.

A total of 416 isolates (272 E. coli and 144 K. pneumoniae) were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Polymyxin heteroresistance was characterized using population analysis profiling (PAP) with stability validation. All isolates underwent antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS) for genomic analysis. An in vitro induction model was used to track resistance evolution.

Heteroresistance prevalence was significantly higher in animal-derived than human-derived E. coli (17.83% vs. 2.10%, p < 0.01). Animal-derived resistant subpopulations carried distinct mutations in the two-components systems (TCSs) phoPQ-pmrAB/D. Structural modeling indicated that a PmrB T156M substitution disrupts kinase domain integrity, potentially triggering heteroresistance. Community-associated K. pneumoniae showed lower heteroresistance rates than clinical strains (34.03% vs. 76.62%, p < 0.01), with divergent insertion sequence (IS) distributions in the mgrB gene (IS903B/ISKpn74 vs. ISKpn26/ISKpn14). When challenged with polymyxin pressure, K. pneumoniae exhibited a significantly faster progression to polymyxin resistance than E. coli.

This study emphasizes the persistent influence of historical agricultural polymyxin use on the development of heteroresistance among E. coli and K. pneumoniae with diverse sources. The complexity of heteroresistance requires more cautious antibiotic selection and tailored therapeutic strategies in clinical practice to combat antimicrobial resistance.