A method for treating shell eggs with a gas includes subjecting the eggs to lower than atmospheric pressure for a period of time, heat for a period of time, and a treatment gas for a period of time. The treatment gas may be ozone at about 8-12% concentration by weight, the treatment temperature may be between 55° C. and 60° C. for about 2-25 minutes, and the atmospheric pressure may be from about 60-81 kPa for about 33 minutes or less. Eggs treated using this method showed a reduction in the concentration of Salmonella Enteritidis of at least log 5.