Detection of Colibactin-Encoding Genes (clbA, clbQ) and C-Terminal Sequence Analysis of ClbA and ClbQ Among MDR Gram-Negative Uropathogens from an Egyptian Tertiary-Care Hospital

Uropathogenic Gram-negative bacteria are increasingly resistant to multiple antimicrobials and frequently form biofilms. The genotoxin colibactin, encoded by the pks genomic island genes clbA and clbQ, causes DNA damage and has been linked to colorectal cancer, but its prevalence and molecular diversity in Egyptian uropathogens are unknown. This study aimed to determine the prevalence and molecular diversity of clbA and clbQ among MDR Gram-negative uropathogens from an Egyptian tertiary-care hospital and to assess their relationship with hemolytic activity, biofilm formation, and antimicrobial resistance. Sixty-nine Gram-negative uropathogenic isolates collected between November 2024 and October 2025 were characterized for antimicrobial susceptibility, biofilm formation, and hemolytic activity. clbA and clbQ were detected by PCR in selected isolates; amplicons from representative isolates were Sanger-sequenced, translated, and used for homology modelling (SWISS-MODEL) and phylogenetic analysis. Escherichia coli was most prevalent (52.2%), followed by Klebsiella pneumoniae (20.3%), Pseudomonas aeruginosa (14.5%), Acinetobacter baumannii (10.1%), and Proteus mirabilis (2.9%). All 69 isolates were MDR; pooled resistance was highest to ceftazidime (100.0%, 66/66), cefixime (98.5%, 66/67), and gentamicin (98.5%, 64/65), and lowest to imipenem (33.3%, 19/57). Biofilm formation occurred in 68.1% (strong 36.2%, moderate 2.9%, weak 29.0%); no significant association was detected between biofilm category and resistance, and subgroup comparisons were exploratory because of small species numbers. β-Hemolysis occurred in 29.0% of isolates, predominantly in P. aeruginosa (90%). Among β-hemolytic E. coli available for PCR, 5 carried both clbA and clbQ; the remaining isolate was not tested. Sequencing revealed that ClbA from isolate 88FE carries a C-terminal sequence variant (…YQLIHSSN, positions 236–241) of equal length to the 241-aa reference, whereas ClbA from isolate 104FE matched the reference. ClbQ from isolate 104FE included both a reference- and template-matched QR form (…QTIESLEIVG) and a distinct QF form (…QTMNHSKIV). Homology modelling predicted that the ClbA C-terminal extension is surface-exposed; the functional significance of these variants was not experimentally validated. MDR was universal and biofilm formation was frequent but not associated with resistance in this collection. clbA/clbQ carriage was common among β-hemolytic E. coli, and predicted C-terminal variants in ClbA and ClbQ highlight the genetic plasticity of the pks island. Functional studies are required to determine whether these variants affect colibactin synthesis or activity.