Improved, low cost vaccines for administration to living subjects such as mammals and birds are provided, which include killed recombinantly modified microorganisms (whole cell recombinant bacterin vaccine), the latter including recombinant DNA encoding at least one protective protein (e.g., an antigenic protein) which has been expressed by the microorganisms prior to killing thereof. The protective protein(s) are operable to prevent or reduce the severity of a disease of the subject. The vaccine preparations of the invention do not require separation of the protective protein(s) from the host recombinant microorganism(s), thereby materially decreasing the complexity and cost of the vaccine formulations. A preferred vaccine against kennel cough includes recombinantly modified microorganisms which express protective antigens containing pertactin and filamentous hemagglutinin protein products.