Genomic characterization of three bacteriophages targeting multidrug resistant clinical isolates of Escherichia, Klebsiella and Salmonella

Application of bacteriophages (phages) to treat complex multidrug-resistant bacterial infection is gaining traction because of its efficacy and universal availability. However, as phages are specific to their host, a diverse collection of locally isolated phage from various geographical locations is required to formulate a wide host range phage cocktail. Here, we report morphological and genomic features of three newly isolated phages from river water of the urban region in Kathmandu, Nepal, targeting three different bacteria (Escherichia coli, Klebsiella pneumoniae and Salmonella enterica.) from the Enterobacteriaceae family. Morphological identification and genome analysis indicated that two phages (Escherichia phage vB_EcoM_TU01 and Klebsiella phage vB_KpnP_TU02) were strictly lytic and free from integrases, virulence factors, toxins and known antimicrobial resistance genes, whereas Salmonella phage vB_SalS_TU03 was possibly a temperate phage. The genomic features of these phages indicate that natural phages are capable of lysing pathogenic bacteria and may have potential in bacterial biocontrol. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00203-022-02948-0.