Isolation and characterization of bacteriophages for carbapenem resistant Enterobacter cloacae complex strains

Abstract

Abstract There has been an increased interest in phage therapy for the treatment of antimicrobial resistant bacterial infections due to the decreasing effectiveness of antibiotics. While phage therapy has been successful, it often requires time to isolate and characterize phages suitable for phage therapy. Here, we isolated and characterized three phages against carbapenem-resistant Enterobacter cloacae complex (ECC) strains to potentially be applied in phage therapy. ECC strains commonly cause sepsis and urinary tract infections in hospitals and are designated as a pathogen of critical importance for its global prevalence and high instance of antimicrobial resistance. Initially, a total of 96 phages were isolated using a collection of diverse clinical ECC strains. Three phages were selected for genome sequencing and additional characterization based on their broad host range and lytic activity. Based on average nucleotide identity (ANI), vB_ECC_YI837 and vB_ECC_MY742 were considered strains of previously isolated phages vB_CsaM_leN and Entb_45, respectively. One phage had an ANI of 92.65% and was therefore considered novel and named vB_ECC_CW742. Furthermore, none of the phages carried toxin, antimicrobial resistance, or lysogeny-related genes. Collectively, the phages covered 82% (108/131) of our carbapenem-resistant ECC strain library. These findings suggest that the three phages are promising candidates for phage therapy against carbapenem-resistant ECC infections.