For my blood pressure I choose not to read the anti-vax site spin on the results, but go straight to the article (thanks for the link).
Emmy526 - I notice you didn't include this quote from it:
The reemergence of pertussis has been attributed to various factors, including increased awareness, improved diagnostics, decreased vaccination coverage, suboptimal vaccines, waning vaccine-induced immunity, and pathogen adaptation.
It's quite interesting actually - they are suggesting that by making infants immune to pertussis this selects for strains which can better deal with immune systems which have had more practice at fighting a variety of toxins (ie. adults). In their words:
We propose that the crucial event, which shifted the competitive balance between ptxP1 and ptxP3strains, was the removal by vaccination of immunologically naive infants as the major source for transmission, selecting for strains, which are more efficiently transmitted by primed hosts.
Also I found this interesting:
Pertussis among recently vaccinated children is rare, indicating that pathogen adaptation does not play a role unless immunity has waned. Thus, we propose that waning immunity and pathogen adaptation have contributed to the resurgence of pertussis, although other factors such as increased awareness and improved diagnostics have also played a role.
And their conclusions about the best way to solve the problem are:
suggest that an effective way to control pertussis is the improvement of current vaccines to induce Ptx-neutralizing antibodies which persist longer.
I personally see interesting parallels with anti-biotic resistent bacteria. It's an unfortunate side effect of our ability to kill bacteria with anti-biotics that we are selecting for bacteria which can survive this. But I don't think many people would suggest this means we should completely stop using anti-biotics against any bacteria - we just have to be a bit more clever and keep working on the problem.