Phenotypic and genomic characterization of three lytic bacteriophages against MDR Escherichia coli from livestock in India.

backgroundAntimicrobial resistance (AMR) in Escherichia coli, particularly among animal-derived isolates, poses a major threat to public and veterinary health. With conventional antibiotics becoming increasingly ineffective against multidrug-resistant (MDR) strains, alternative solutions are urgently needed. Lytic bacteriophages, known for their host specificity and potent antibacterial activity, are promising therapeutic options. However, limited genomic data on phages from diverse ecological contexts hinder a comprehensive understanding of their diversity and functional potential.

methodsThis study aimed to isolate, characterize, and assess the therapeutic potential of lytic bacteriophages targeting MDR E. coli isolated from livestock. Phages were enriched from the sewage samples using an MDR E. coli host. Plaque morphology was assessed for lytic characteristics, and Transmission Electron Microscopy (TEM) was used for morphological identification. The thermal and pH stabilities were assessed under controlled incubation conditions. The host range was determined using 20 MDR E. coli strains from cattle, buffalo, and goats. One-step growth experiments were performed to determine the latent period and burst size of the phages. Whole-genome sequencing and annotation were performed to determine the genetic features, taxonomic classification, safety, and phylogenetic relationships.

resultsThree lytic Escherichia phage BASUE2, BASUE7, and BASUE10, were isolated, producing clear plaques indicative of strong lytic activity. All phages remained viable between 25 °C and 42°C and within pH 6–9, but were inactivated at 80°C and at highly acidic or alkaline conditions. BASUE7 exhibited the broadest host range, lysing 75% of MDR E. coli isolates, followed by BASUE2 (65%) and BASUE10 (55%), while none of the phages were active against K. pneumoniae, S. aureus, or Salmonella spp. Genome analysis revealed double-stranded DNA genomes of approximately 157 kb (BASUE2), 50 kb (BASUE7), and 48 kb (BASUE10), with G + C contents ranging from 44.62% to 45.47%. Taxonomically, BASUE2 was classified under Ackermannviridae, whereas BASUE7 and BASUE10 belonged to Siphoviridae, all within Caudovirales. All phages were predicted to be strictly lytic and lacked genes associated with lysogeny, antibiotic resistance, or virulence. Phylogenetic analysis revealed a distinct cluster of BASUE2, suggesting a divergent evolutionary origin from BASUE7 and BASUE10.

conclusionThis study presents the isolation of genetically safe, environmentally stable, and broadly active lytic phages effective against MDR E. coli of animal origin. These findings highlight the potential of these phages for use in veterinary therapy. However, further in vivo validation and development of phage cocktails are necessary to advance their clinical applications.