Characterization and genome analyses of the novel phages targeting extraintestinal Escherichia coli clones ST131 and ST410.

The rise of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC) poses a severe healthcare threat, necessitating alternative treatment strategies such as bacteriophage therapy. In this study, four lytic phages (EC.W2-9, EC.W5-4, EC.W8-1, and EC.W14-2) were isolated from hospital wastewater and characterized for their efficacy against MDR ExPEC isolates. A total of 44 ExPEC isolates were analyzed, with 41% belonging to sequence type (ST) 131 and 59% to ST410, all exhibiting MDR phenotypes. Among these, 49% produced extended-spectrum β-lactamases (ESBLs), and 86% were identified as carbapenem-resistant E. coli (CREC). Phages EC.W2-9, EC.W8-1, and EC.W14-2 displayed high lytic activity against ST131 (≥ 90% lysis) but were significantly less effective against ST410 (≤ 30% lysis). Phage EC.W5-4 exhibited intermediate efficacy, lysing 78% of ST131 and 23% of ST410 isolates. Morphological and phylogenetic analyses classified EC.W2-9, EC.W5-4, and EC.W14-2 within the Tequatrovirus genus of the Straboviridae family, while EC.W8-1 belonged to the Kuravirus genus of the Podoviridae family. These phages demonstrated favorable biological properties, including short latent periods (10-25 min), high burst sizes (115-158 pfu/cell), and stability across a broad temperature (≤ 70 °C) and pH range (3-10). Genomic analysis (46,328-116,943 bp, 35.2-39.9% G + C content) confirmed the absence of virulence and antibiotic resistance genes. Furthermore, combined phage therapy effectively reduced planktonic and biofilm growth of MDR-ExPEC. These findings demonstrate the potential of these phages as effective therapeutic agents against MDR ExPEC, particularly ST131 and ST410, in combating antibiotic-resistant infections.