That article is terribly misleading.
This article is good:
http://www.medscape.com/viewarticle/815247
The original research paper is here:
http://www.pnas.org/content/early/2013/11/20/1314688110
A subscription is required for the full article, but if you really want it, PM me and I'll email it to you.
Now, the real point of interest
(Sidenote - Tod Merkel is the corresponding author, but not actually the lead author. He's 3rd of three authors.)
I don't know if Tod Merkel mis-spoke, was misquoted, or if I'm really getting something wrong, but I can't see how his quote is supported by the research conducted.
Administering the acellular pertussis vaccine does not, and can not, directly make someone an asymptomatic carrier, because it does not contain the whole pertussis virus.
The issue revealed by the research is that vaccinated baboons (and potentially people) can
become asymptomatic carriers
if they are exposed to the virus (ie contact with an individual with a pertussis infection.) Note that they are not an asymptomatic carrier forever - the aP vaccinated baboons who acquired an asymptomatic infection cleared the infection in a few weeks, as did the unvaccinated baboons who acquired an infection (the vaccinated ones actually took a longer by perhaps a week, although the small study size makes this uncertain.)
This is a problem, because if the baboon findings are true for people, it means that pertussis infections could still spread through a vaccinated community, and thus the virus would not confer herd immunity.
As for the recent outbreaks, trying to pin blame on someone is pretty pointless, and can lead only to acrimony. Try to focus on how to move forward, rather than pointing fingers.