Vaccinations give us all a false sense of security. A universal mantra that vaccines are safe and effective has trumped any attempt to have a conversation about it without being attacked and ridiculed. But are vaccines really safe? Are they always, indefinitely effective? Why are asking these very basic questions met with such hostility and fear, even though time has shown us that science is evolving and a truth or fact at one moment in history is not predictive of its potential to remain true. Do we really want to threaten this conversation from being indexed, and simply blame the unvaccinated for every disease that upticks, or could we use our naturally inquisitive minds to collectively push vaccines to be even safer, and even more effective?

When it comes to the topic of infectious disease and vaccines our brains filter information in black and white: A vaccinated person is absolved from getting sick and spreading disease; whereas an unvaccinated person is an overflowing petri dish of infection, spreading disease to the most vulnerable. But this highly emotive and irrational dichotomy is not scientific at all.

Vaccines do not inherently, indefinitely protect you from disease. Outbreaks and re-emergence of disease is not solely because of the unvaccinated, which in regards to children, represents much less than 5% of the school-aged population, in most cases closer to 2%. To understand what is happening with the “re-emergence” of infections, we need to remember what we are dealing with. If you believe in science, then you believe in adaptation.

Case in point: Bordetella pertussis, often called Whooping Cough, has outsmarted her vaccines, DTaP and TDaP. Researchers have known for about 10 years that this bacterium is mutating.

A highly vaccinated population is just the kind of incentive for a bacterium like B. pertussis to adapt in order to survive. An outer membrane protein, pertactin, is a key antigen component of the acellular pertussis vaccine, and in response to the vaccine, B. pertussis is mutating without pertactin, also known as pertactin-deficient. We have seen outbreaks of whooping cough amongst heavily vaccinated populations and what is the usual conclusion is the vaccine is waning, meaning another booster shot is needed. But what scientists are finding more recently, is that the bacterium is mutating.

Back in 2014, scientists warned the public that B. Pertussis was “mutating at a faster rate than other surface proteins not included in the vaccine. This could mean that the bacteria is changing to get around the immune system’s defenses created by the vaccine.”

A more recent study from earlier this year assesses how “emerging B. pertussis strains have evolved to dampen the vaccine-induced inflammatory response, which would benefit survival and transmission of this pathogen.”

While this study, which looked at 263 cases and 726 controls to determine DTaP and TDaP vaccine effectiveness concluded that 90% of whooping cough isolates tested were pertactin-deficient strains:

“More specifically, several recent studies indicate pertactin deficiency may especially benefit the bacteria among a highly immunized population. For instance, pertactin-deficient strains were found to colonize mice primed with acellular pertussis vaccine more effectively than pertactin-expressing strains; a separate study found that acellular vaccinated individuals had two- to fourfold greater odds of being infected with a pertactin-deficient rather than a pertactin-expressing B pertussis strain.18,22 Pertactin deficiency may also facilitate transmission by supporting longer infections: acellular-vaccinated mice infected with pertactin-deficient pertussis sustained longer infections than those infected with pertactin-expressing strains.34 In addition, pertactin deficiency may result in improved transmission by avoidance of pertactin-specific vaccine-induced host immune responses. This would be especially relevant to acellular vaccine–primed individuals, in whom it has been demonstrated that antibodies to pertactin correlated with protection.42 Through these mechanisms, pertactin deficiency may be amplifying the pertussis disease resurgence, especially in the setting of exclusive use of acellular vaccines that are associated with waning immunity and that fail to prevent B pertussis colonization and transmission.4345

We see this sort of viral and bacterial adaptation in response to vaccines or medications all the time, for example antibiotics. This is why they produce a new influenza vaccine every year, in an attempt to guess what group of strains might be predominant. They mutate and change from natural infections, but also the vaccines themselves.

The original Gardasil vaccine targeted four strains of human papillomavirus (HPV), specifically, types 16, 18, 6 and 11. This study of 600 women found that after being vaccinated with Gardasil they had a higher risk of infection of the strains not included in the vaccine than unvaccinated women.

We see mutation with polio virus as well. In the Congo in 2010 there was an outbreak of polio amongst a primarily fully vaccinated population and the doctors discovered that the polio virus had mutated beyond the vaccine’s reach, and resulted in 445 infections and 209 deaths.

No one wants any disease to come back, or proliferate, ever, but vaccinations are not the cure all, end all everyone wants them to be. If you believe in science, then you believe in questions.

Pediatricians around the country are pushing pregnant women to get their TDaP, and I wonder if any of those doctors are sharing with their patients that B. pertussis is mutating, and the vaccine might not be as effective as it was during its own clinical trials. We see cyclical and continual outbreaks of infectious disease caused by vaccine effectiveness waning over time, vaccine failure, as well as viral and bacterial mutations in response to vaccine’s selectiveness.

Just because you are vaccinated against B. pertussis does not mean you will not get sick and transmit disease, so regardless of if you are unvaccinated or vaccinated: If you’re sick, do us all a favor and stay home. Quarantine is still the most effective way at preventing diseases from spreading.