Presumably, the bacteria are still immunogenic and capable of creating an immune response and being recognized by the immune system.

However, the vaccine is now outdated because it is not a good match to these new strains. The vaccine is not creating an immune response against these new strains.

However, the problems we are seeing with B. pertussis are far more complicated than just getting everyone vaccinated.  They are forcing researchers to rethink how they are designing, implementing and monitoring vaccine regimes.

The problem is children don’t get the same kind of immunity that they would with a whole-cell vaccine as their immune system is only building a response to specific proteins that we have identified as being associated with the virulent bacterium.

What the NEJM letter is indicating is that the specific proteins we target with modern acellular vaccines (namely pertactin) are undergoing selective pressure to either become removed from the bacterium or mutated. This means that the immunity we receive from the vaccine does not necessarily allow our immune systems to detect/target the bacterium.

Research groups are looking at and have added additional proteins specific to B. pertussis to the current vaccines but whenever we are targeting something specific we are always going to run the risk that the organism we are targeting will mutate to become resistant. Life has a funny way of trying to outsmart us as we solve these problems with novel solutions.

With something like the flu, say, it moves sufficiently fast that they’ve gotten reformulating down to a routine, with the major challenge being guessing the hit strain of the year far enough in advance to start the process.

With other pathogens, years of research have failed to produce a vaccine that works against any flavor of the bug.