P. multocida is the causative agent of a wide range of animal disease syndromes, including fowl cholera in birds, haemorrhagic septicaemia in ungulates, atrophic rhinitis in pigs and shipping fever in livestock animals. The high morbidity and mortality of these diseases causes a severe economic impact on agricultural industries. P. multocida can also cause zoonotic infections in humans, commonly causing animal bite wound infections, as well as pneumonia, meningitis, peritonitis, and bloodstream infections. Although P. multocida causes a range of animal and human diseases, the pathogenic mechanisms that underly each disease are poorly understood, with almost nothing known about P. multocida strains that cause disease in humans. We have utilised comparative genomics and transposon-directed insertion site sequencing (TraDIS) to investigate P. multocida pathogenesis. We sequenced 22 human and 14 cat P. multocida isolates and performed comparative genomics to identify differences in P. multocida strains that cause different diseases. Phylogenetic analysis showed human and cat isolates were distinct from animal isolates, and accessory genome analysis identified genes likely important for human disease, and for haemorrhagic septicaemia. We also performed TraDIS to investigate genes required for hyaluronic acid capsule production in P. multocida strain VP161. This analysis identified the stringent response as a novel regulator of P. multocida type A capsule biosynthesis genes.