Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria

Abstract

Urinary tract infections (UTIs) caused by Escherichia coli represent a significant public health concern due to the high virulence and antimicrobial resistance exhibited by these pathogens. This study aimed to analyze the phylogenetic diversity and antibiotic resistance profiles of Uropathogenic E. coli (UPEC) strains isolated from UTI patients in Algeria, focusing on virulence factors such as extended β-lactamase (ESBL) production, biofilm formation, and hemolytic activity. Phylogenetic grouping of 86 clinical imipenem resistant E. coli isolates showed the prevalence of group B2 (48.9%), followed by groups E (22.1%), unknown (12.8%), A (8.1%), and B1 (4.7%), and Clade I, D, Clade I, or Clade II (1.2%). The highest resistance rates were observed towards amoxicillin (86.04%), ticarcillin (82.55%), piperacillin (73.25%), nitrofurantoin (84.88%), and trimethoprim-sulfamethoxazole (51.16%). Notably, 69.8% of UPEC strains were multidrug-resistant (MDR) and 23.2% were extensively drug-resistant (XDR). Additionally, 48.9%, 42%, and 71% of strains demonstrated ESBL production, hemolytic activity, and weak biofilm production, respectively. Continuous monitoring and characterization of UPEC strains are essential to track the spread of the most resistant and virulent phylogenetic groups over time, facilitating rapid therapeutic decisions to treat infections and prevent the emergence of new resistant organisms, helping choose the most effective antibiotics and reducing treatment failure.

Keywords: Escherichia coli; antibiotic resistance; biofilm; hemolysin; imipenem; phylogenetic groups; urinary tract infections.

Figure 1

Frequency distribution of the 86 E. coli clinical isolates in seven phylogroups (A, B1, B2, D, E, Unknown, Clade I, and Clade I or Clade II).

Figure 2

Antibiotic resistance profile of E. coli isolates towards 25 antibiotics belonging to nine classes. *: p < 0.05; **: p < 0.01; ***: p < 0.0001. AMX: amoxicillin, AMC: amoxicillin + clavulanic acid, TC: ticarcillin, TCC; ticarcillin + clavulanic acid, PRL: piperacillin, TPZ: piperacillin + tazobactam, CN: cephalexin, CX: cefoxitin, CFM: cefixime, CAZ: ceftazidime, CTX: cefotaxime, FEP: cefipime, IMP: imipenem, GEN: gentamycin, AK: amikacin, TOB: tobramycin, NA: nalidixic acid, CIP: ciprofloxacin, OF: ofloxacin, C: chloramphenicol, ATM: aztreonam, NIT: nitrofurantoin, SXT: trimethoprim-sulfamethoxazole, FF: fosfomycin, CS: colistin, ND: not determined.

Figure 3

MIC of sensitive E. coli isolates. C Concentration stands for Critical Concentration; EUCAST RBp stands for EUCAST Resistant Break point; *: signification (p < 0.05); **: signification (p < 0.01); ***: signification (p < 0.001). AMX: amoxicillin, AMC: amoxicillin + clavulanic acid, TC: ticarcillin, PRL: piperacillin, TPZ: piperacillin + tazobactam, CN: cephalexin, CFM: cefixime, CAZ: ceftazidime, CTX: cefotaxime, GEN: gentamycin, TOB: tobramycin, NA: nalidixic acid, CIP: ciprofloxacin, OF: ofloxacin, C: chloramphenicol, ATM: aztreonam, SXT: trimethoprim/sulfamethoxazole.

Figure 4

Distribution of ESBL-producing strains according to phylogenetic groups.

Figure 5

Relative frequencies of resistant (R), multidrug-resistant (MDR), and extensively drug resistant (XDR) strains among non-producers and weak, moderate, and strong biofilm producers.

Figure 6

Comparison of OD values of biofilm formation between resistant, intermediate, and susceptible strains. *: p value < 0.05, TOB: tobramycin, FEP: cefipime, CAZ: ceftazidime, SXT: trimethoprim-sulfamethoxazole, C: chloramphenicol, CTX: cefotaxime, CIP: ciprofloxacin, OF: ofloxacin, NA: nalidixic acid, AK: amikacin, GEN: gentamycin, ATM: aztreonam, NIT: nitrofurantoin.

Figure 6

Comparison of OD values of biofilm formation between resistant, intermediate, and susceptible strains. *: p value < 0.05, TOB: tobramycin, FEP: cefipime, CAZ: ceftazidime, SXT: trimethoprim-sulfamethoxazole, C: chloramphenicol, CTX: cefotaxime, CIP: ciprofloxacin, OF: ofloxacin, NA: nalidixic acid, AK: amikacin, GEN: gentamycin, ATM: aztreonam, NIT: nitrofurantoin.