Even people who aren't big fans of spy shows seem to love scenes where agents disguised with latex masks, slip past their adversaries and then give us the big reveal.

It's a great analogy for microbes that use this game of disguise and attack.

Consider the bacterium Streptococcus pneumonia or S. pneumoniae for short. It's the number one cause of community acquired pneumonia, meningitis and ear infections in children. This wily microbe has now learned to outwit vaccines.

The vaccines are Pneumovax and Prevnar which have been quite effective against common strains of S. pneumoniae. They do not protect against rarer strains of the bacteria, which can end up causing disease after the vaccine gets rid of the common strains.

That's what happened when Alaskan children were first vaccinated. Their infection rates plummeted but returned within three years, when rarely seen strains began infecting kids. This is called replacement disease.

So, how is the virus getting around the vaccine? Well, recall we said the vaccine had eliminated the common strains – well, scientists began seeing them again. How?

By sequencing the whole genomes of these common strains, molecular epidemiologists are finding evidence of something called horizontal gene transfer.

Just like the mission impossible agents putting on latex masks, these bacteria are swapping genomic sequences with a rare strain, changing the way they look so that they can avoid the vaccines. They're constantly swapping genes, which is how they found a way around the vaccines. And now some are even resistant to the antibiotics used to treat them.

What we're seeing is evolution at work, and the changes are rapid. This study shows microbiologists like us just how hard it will be to eliminate disease causing microbes with this same ability to adapt.