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 Human Patients in Algeria

Abstract

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 aimed to provide an overview of the virulence factors, clonal diversity, and antibiotic resistance profiles of extended-spectrum cephalosporin (ESC)-E. coli and K. pneumoniae causing UTIs in humans in the Tebessa region of Algeria.

Methods: Forty E. coli and 17 K. pneumoniae 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 K. pneumoniae isolates, all except one harbored CTX-M-15, with a single isolate carrying bla_CTX-M-194. Additionally, two K. pneumoniae isolates co-harboring bla_CTX-M-15 and bla_NDM exhibited phenotypic and genotypic hypervirulence traits. Fluoroquinolone resistance (FQR) was detected 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 bla_ESC and bla_OXA-48 was identified 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). 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 E. coli CC131 CH40-30 and hypervirulent K. pneumoniae clones in Algeria. It represents the first report of a CTX-M-15-carrying E. coli 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 E. coli and K. pneumoniae is proposed here for antimicrobial resistance (AMR) monitoring.

Keywords: Algeria; ESBL; Escherichia coli; Klebsiella pneumoniae; ST1193; ST131; carbapenemases; urinary tract infection (UTI).

Figure 1

Prevalence of antimicrobial resistance among the 40 E. coli isolates analysed in this study. Minimum inhibitory concentrations (MICs) were interpreted according to EUCAST 2025 and CLSI 2024 clinical breakpoints. Abbreviations: AMP, ampicillin; AMC, amoxicillin/clavulanic acid; CXM, cefuroxime; FOX, cefoxitin; CTX, cefotaxime; CAZ, ceftazidime; ETP, ertapenem; AZT, aztreonam; NAL, nalidixic acid; CIP, ciprofloxacin; GEN, gentamicin; TOB, tobramycin; AMI, amikacin; D, doxycycline; TGC, tigecycline; NIT, nitrofurantoin; FOS, fosfomycin; TMP-SXT, trimethoprim-sulfamethoxazole; CL, colistin; CHL, chloramphenicol; FQR, fluoroquinolone resistance.

Figure 2

Phylogenetic dendrogram based on whole-genome SNP analysis. (A) Phylogenetic dendrogram based on SNP counts per substitution within the core genome of the Algerian and Spanish ST1193 isolates. The WGS comparison resulted in a core genome covering 95.65% of the reference genome LREC-269 (5.4 Mb). (B) Phylogenetic dendrogram incorporating the Algerian, Spanish, and ESC_RA5887AA ST1193 isolates, showing SNP counts per substitution. The WGS comparison resulted in a core genome covering 82.6% of the reference genome LREC-269 (5.4 Mb).

Figure 3

Prevalence of antimicrobial resistance among the 17 K. pneumoniae analysed in this study. MICs were interpreted according to EUCAST 2025 and CLSI 2024 clinical breakpoints. Abbreviations: AMP, ampicillin; AMC, amoxicillin/clavulanic acid; CXM, cefuroxime; FOX, cefoxitin; CTX, cefotaxime; CAZ, ceftazidime; ETP, ertapenem; AZT, aztreonam; NAL, nalidixic acid; CIP, ciprofloxacin; GEN, gentamicin; TOB, tobramycin; AMI, amikacin; D, doxycycline; TGC, tigecycline; NIT, nitrofurantoin; FOS, fosfomycin; TMP-SXT, trimethoprim-sulfamethoxazole; CL, colistin; CHL, chloramphenicol; FQR, fluoroquinolone resistance.