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Background The major problem in the management of burn wounds are infections. Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major cause of infection in burn wounds. Antibiotic resistant bacteria around the world has become a major therapeutic challenge. Bacteriophages and their lysine are suggested as an antimicrobial alternative agent. Phage display technique is suggested for production of recombinant lysine by Nano carrier technology. The approach of this study was to evaluate the potential of recombinant Nano phage efficacy in MRSA burn wound infection in vivo. Materials and methods The 3rd degree burn wounds were induced in 54 rats and infected with MRSA ATCC 33591 via the topical route in four groups. Burn wound size was measured in 0, 14, 21, 28 days. The efficacy of Nano phage gel was assessed on the basis of percentage collagen deposition, granulation tissue, neovascularization, fibroblastic maturity, re-epithelization, and scar formation in rats following treatment in 14, 21, 28 days. Results The results showed that the percentage of wound size were 3 cm on base line day and the average macroscopic wound healing rates were increased in the prevention groups receiving the recombinant Nano phage gel and natural phage gel, in the treatment groups with secondary infection receiving the recombinant Nano phage gel and the natural phage gel, and in the two control groups respectively. The average microscopic wound healing rates were increased in the prevention groups receiving the recombinant Nano phage gel and natural phage gel, in the treatment groups with secondary infection receiving the recombinant Nano phage gel and the natural phage gel, and in the two control groups respectively. Conclusions In conclusion the recombinant Nano phage gel is efficacy to treat and prevent MRSA burn wound infection.