Abstract
<jats:p>Background. Escherichia coli is a common inhabitant of the human gastrointestinal tract but can also act as an opportunistic pathogen responsible for a wide range of clinical infections. Its genomic plasticity, facilitated by horizontal gene transfer and mobile genetic elements, enables adaptation to diverse host environments. This study aimed to characterize structural and accessory genomic features contributing to strain-level diversity among selected clinical E. coli isolates. Methods. A total of 1,000 clinical specimens were examined using standard microbiological methods, yielding 125 non-duplicate E. coli isolates. Following molecular confirmation, six representative isolates were selected for whole-genome sequencing based on the presence of a clear specific PCR amplicon, adequate DNA concentration and purity, and variation in antimicrobial susceptibility profiles. Genomic analyses investigated assembly characteristics, prophage regions, pathogenicity islands, and clustered regularly interspaced short palindromic repeat-associated systems. Results. Escherichia coli was recovered from 125 of the 1,000 clinical specimens examined (12.5%). Urine specimens showed the highest recovery rate (22.75%). The analyzed genomes exhibited a relatively conserved GC content of approximately 50%, whereas accessory genomic elements varied substantially among isolates. Between six and 14 prophage regions were identified per genome, with differences in their predicted completeness. PAIs associated with adhesion/fimbrial functions and siderophore-mediated iron acquisition were the most frequently represented functional categories. Type III secretion system-associated islands were detected only in isolate E63. In contrast, a Type I-E CRISPR–Cas system was identified in all six isolates, although the numbers of CRISPR arrays and spacers varied. Conclusion. The analyzed E. coli isolates exhibited considerable structural genomic variability, mainly driven by differences in prophage content and pathogenicity islands. These mobile genetic elements play an important role in shaping genome plasticity, strain-level diversification, and the evolutionary adaptation of clinical E. coli isolates, whereas the CRISPR–Cas system was relatively conserved. Overall, these findings provide genomic insights into clinically relevant E. coli lineages and support the potential integration of whole-genome sequencing into surveillance programs.</jats:p>