Population structure, antimicrobial resistance, and virulence factors of diabetic foot-associated Escherichia coli

ABSTRACT Diabetic foot infections (DFIs) are a major complication of diabetes, often leading to lower limb amputations. Escherichia coli is a predominant Gram-negative pathogen in DFI, yet its genomic and pathogenic features remain poorly characterized. Here, we present a whole-genome sequence-based analysis of diabetic foot-associated E. coli (DFEC) isolates from diverse geographical locations. Phylogenetic reconstruction revealed substantial diversity, with strains spanning 7 phylogroups and 28 sequence types. Capsule biosynthesis loci linked to invasive infections, such as K1, K2ab, and K5, were also detected. The DFEC pangenome comprised 18,263 gene clusters, indicating high genomic plasticity. The plasmid repertoire was also varied and contributed to the genomic diversity of the strains. Approximately 78% of isolates were multidrug-resistant or extensively drug-resistant, with resistance to last-resort antibiotics such as colistin and carbapenems also observed. High frequencies of virulence factors involved in host cell adherence, iron metabolism, serum survival, as well as toxins and type 3 secretion system genes were also detected. In contrast, metabolic modeling showed conserved biochemical profiles. Clustering based on accessory metabolic functions did not mirror phylogeny, suggesting metabolic convergence among distinct lineages. Collectively, these findings reveal that DFEC are versatile pathogens with a repertoire of antimicrobial resistance and virulence determinants. These traits make them functionally distinct from commensal E. coli strains and highlight the potential of DFEC to cause severe and invasive infections. IMPORTANCE This study presents the first multisite genomic characterization of diabetic foot-associated Escherichia coli (DFEC). Our findings reveal that DFEC strains are phylogenetically diverse and span multiple lineages. The high prevalence of multidrug-resistant and extensively drug-resistant genotypes underscores the underestimated antimicrobial resistance (AMR) threat posed by DFEC. We detect high frequencies of virulence factors commonly associated with extraintestinal pathogenic E. coli , which indicates that DFEC might have the potential to cause severe complications, such as sepsis. The large accessory genome and evidence of metabolic convergence across distinct lineages highlight the adaptive versatility of DFEC in the polymicrobial and inflammatory environment of chronic wounds. These insights advance our understanding of DFEC pathobiology and support the development of targeted diagnostics, AMR surveillance, and therapeutic strategies to improve clinical outcomes for diabetic patients.