Biocontrol potential and genomic analysis of novel lytic bacteriophage CABI-SEA 2302 against multidrug-resistant avian pathogenic Escherichia coli associated with colibacillosis

Abstract

Multidrug-resistant avian pathogenic Escherichia coli (MDR-APEC) causes critically high first-week mortality in chickens, resulting in substantial economic losses in the global poultry industry. This study aimed to isolate and characterize a novel bacteriophage as an effective safe alternative for the control of colibacillosis. A lytic bacteriophage CABI-SEA 2302 was obtained from E. coli lesion samples collected from commercial poultry farms. The selected phage was classified as a new species in the genus Tunavirus, subfamily Tunavirinae. Genomic analysis revealed that the phage contains 49,550 base pairs of double-stranded DNA genome with 55% GC content, no toxin, virulence, and antimicrobial resistance genes. Phage CABI-SEA 2302 exhibited lytic activity against 24% of MDR-APEC clinical isolates (12/50) obtained from broiler and layer chicken lesions. An adsorption rate of 87% to the bacterial host was observed within 10 min. One-step growth analysis showed that phage CABI-SEA 2302 had a latent period of 20 min and a burst size of 458 PFU/cell. At the lowest multiplicity of infection of 0.001, a representative MDR-APEC isolate was significantly reduced at 3 h post-infection. Cellular abnormality of the MDR-APEC isolate exposed to the novel phage was confirmed by scanning electron microscopy. More importantly, phage CABI-SEA demonstrated potent inhibition of bacterial biofilm formation. Notably, the phage survived under simulated chicken gastrointestinal conditions (99.00 ± 3.61%) and remained stable at temperatures between -80–60 °C and pH 2–12. By specifically targeting bacterial host cells and inhibiting biofilms, this approach could reduce the reliance on traditional antibiotics in the commercial poultry industries.