Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and High-Risk Escherichia coli CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Algeria

Background: High-risk Escherichia coli clones, such as Sequence Type (ST)131 and ST1193, along with multidrug-resistant (MDR) Klebsiella pneumoniae, are globally recognized for their significant role in urinary tract infections (UTIs). This study investigates the characteristics of these pathogens in the Tebessa re-gion of Algeria. Methods: Forty E. coli and 17 K. pneumoniae isolates exhibiting extended-spectrum cephalosporin (ESC)-resistance were phenotypically and genotypically characterized. Whole genome sequencing (WGS) was performed on the ST1193 clone. Results: Among K. pneumoniae isolates, all except one har-bored CTX-M-15, with a single isolate carrying blaCTX-M-194. Additionally, two K. pneumoniae isolates co-harboring blaCTX-M-15 and blaNDM exhibited both phenotypic and genotypic hypervirulence traits. Fluoroquinolone resistance (FQR) was de-tected in 94.1% of K. pneumoniae isolates. The E. coli isolates carried diverse ESC-resistance genes, including CTX-M-15 (87.5%), CTX-M-27 (5%), CTX-M-1, CMY-59, and CMY-166 (2.5% each). Co-carriage of blaESC and blaOXA-48 was identi-fied in three E. coli isolates, while 62.5% exhibited FQR. Phylogenetic analysis revealed that 52.5% of E. coli belonged to phylogroup B2, including the high-risk clonal complex (CC)131 CH40-30 (17 isolates) and ST1193 (one isolate). The vir-ulence profile indicated that 72.5% of isolates met the criteria for extraintestinal pathogenic E. coli (ExPEC), while 47.5% were classified as uropathogenic E. coli (UPEC). Characterization of CC131 clone showed that virotypes F and E ac-counted for 59% of isolates. In silico analysis of the ST1193 genome determined O75:H5-B2 (CH14-64), and the carriage of IncI1-I(Alpha) and IncF [F-:A1:B10] plasmids. Notably, core genome single-nucleotide polymorphism (SNP) analy-sis demonstrated high similarity between the Algerian ST1193 isolate and a previously annotated genome from a hospital in Northwest Spain. Conclusions: This study highlights the spread and genetic diversity of E. coli CC131 CH40-30 and hypervirulent K. pneumoniae clones in Algeria. Additionally, it represents the first report of a CTX-M-15-carrying E. coli ST1193 in the country. These findings emphasize the urgent need for surveillance programs and optimized antibiotic stewardship to curb the dissemination of high-risk clones that pose an increas-ing public health threat in Algeria.