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

BACKGROUND

High-risk clones, such as sequence type (ST)131 and ST1193, along with multidrug-resistant (MDR) , are globally recognized for their significant role in urinary tract infections (UTIs). This study aimed to provide an overview of the virulence factors, clonal diversity, and antibiotic resistance profiles of extended-spectrum cephalosporin (ESC)- and causing UTIs in humans in the Tebessa region of Algeria.

METHODS

Forty and 17 isolates exhibiting ESC-resistance were recovered (July 2022-January 2024) from urine samples of patients at three healthcare facilities to be phenotypically and genotypically characterized. Whole genome sequencing (WGS) was performed on the ST1193 clone.

RESULTS

Among isolates, all except one harbored CTX-M-15, with a single isolate carrying . Additionally, two isolates co-harboring and exhibited phenotypic and genotypic hypervirulence traits. Fluoroquinolone resistance (FQR) was detected in 94.1% of isolates. The 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 and was identified in three isolates, while 62.5% exhibited FQR. Phylogenetic analysis revealed that 52.5% of belonged to phylogroup B2, including the high-risk clonal complex (CC)131 CH40-30 (17 isolates) and ST1193 (one isolate). 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) analysis 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 CC131 CH40-30 and hypervirulent clones in Algeria. It represents the first report of a CTX-M-15-carrying ST1193 in the region. The findings emphasize the urgent need for antibiotic optimization programs and enhanced surveillance to curb the dissemination of high-risk clones that pose an increasing public health threat in Algeria. A simplified method based on virulence traits for and is proposed here for antimicrobial resistance (AMR) monitoring.