Now the genes are known, it is possible that vaccines could be produced to alert the immune system to the body chemicals to which each gene is linked.
Researchers hope their discovery will help produce a vaccine for a type of meningitis which is responsible for the majority of cases in the UK each year.
But in a small number of cases it invades the bloodstream and causes immense and often life-threatening damage.
Approximately 3,000 people get meningitis each year - 10% of these will die from the infection.
A vaccine has been produced for the other common form of the bacterium, meningitis C, but a completely successful B vaccination has not yet been produced.
Even before the introduction of the C vaccine, 60% of all cases were caused by meningitis B.
Scientists at Oxford University have used the latest genome technology to identify what they believe are the genes responsible for transforming the bacterium from a harmless resident into a dangerous invader.
Seventy-five genes
Dr Christoph Tang, who headed the study, said: "The spread of the bacterium through the body in the bloodstream is a critical step in the disease process.
"Without this septicaemic stage the bacterium does not cause any harm in people, and our work pinpoints 75 genes in the meningococcus that are essential to this stage."
Now the genes are known, it is possible that vaccines could be produced to alert the immune system to the body chemicals to which each gene is linked.
So the body might leave the meningitis B bacterium alone as long as it was doing no harm - but spot the danger immediately it began to turn nasty.
A spokesman for the Meningitis Research Foundation said an effective vaccine for the B strain was one of the most eagerly sought advances, with many teams of scientists using different methods in an effort to develop it.
The B strain differs from meningitis C because its coat is made up of proteins which do not trigger an immune response.
'Working towards a vaccine'
While vaccines have been developed, they only appear to work against strains in certain parts of the world, rather than all B strain bacteria.
The spokesman said: "The number of people infected with the B strain has actually been rising slightly.
"Everybody's working towards a vaccine, but it is going to be far more difficult to produce than the meningitis C vaccine.
"Using these virulence genes as a target could be one way of doing it."
The research was published in the journal Nature Medicine.