Infectious disease outbreaks and epidemics are a significant burden on health systems. Understand what constitutes epidemic potential, how epidemics emerge and their subsequent evolution can inform surveillance and reduce future epidemics. New Zealand experienced a prolonged meningococcal epidemic between 1991 and 2008. We have a unique opportunity to analyse and understand a large-scale meningococci epidemic using genome sequencing. We will use genomics to understand epidemic strain emergence and diversification, discover any strain adaptation to vaccination plus immune evasion and virulence strategies by integrate disease case metadata with genome variation. In addition we will analyse current disease causing meningococci in NZ, greatly increasing the quality of surveillance. The proposed project will be one of the most comprehensive analyses of a major, prolonged meningococcal epidemic to date. It will aid our understanding of how an epidemic starts and spreads as well as discover possible immune evasion and virulence factors.