There’s a heated discussion of vaccinations on a Facebook thread of mine, on which Pedram made such informative comments in response to a claim that whooping cough was coming back because of “over use of vaccination” that I requested and got permission to quote them here. The rest is Pedram.
No, high vaccination rates in the population means that a pathogen cannot replicate as quickly–many fewer hosts will be available. Vaccination is just a way of inducing a regular adaptive immune response (the adaptive immune cells are exposed to antigens that mark the dead or inactivated pathogen used in the vaccine, without the danger of an infection). If this is done extensively enough, the pathogen can quickly be suppressed or even (mostly) eradicated. Preventing new infections is a very fast way of stopping a disease in a population.
And, those few people who cannot get vaccinated (those with severely weakened immune systems, lymphoma, or very rare autoimmune conditions) can be protected by the ‘herd immunity’–if others aren’t being infected, no one can spread it to them. Now if vaccination rates are low, the pathogen has a chance to replicate again, starting with the unvaccinated people. After enough rounds of new infections, that suddenly expanding, once-small population of pathogen strains would be carrying a *lot* of low-frequency new mutations, and gradually, increased exposure of vaccinated individuals to non-vaccinated individuals (who are basically walking microbial culture vats at this point) means more chances for the resurgent pathogen to spread to them. That in turn gives a significant selection pressure–those variants among the myriad low-frequency mutants which differ in key antigens will slip unnoticed past the vaccine-primed immune systems (which were adapted to the old strains), and the fast spread will begin anew. **And even worse, those low-frequency mutants will still be among a whole bunch of medium-frequency ‘freak’ mutants, since the previously severely contracted population of pathogen would have left various strains that possibly differ substantially from the wild type of the past, just by sampling error (i.e. genetic drift), but now supplemented with this explosion of new mutants.
Antibiotic overuse is totally different. It is most often the problem when they’re being misused–‘stretched’ in low doses, or the dosing is terminated prematurely. Most mutations which confer resistance to an antibiotic (or antivirals, for that matter) are also costly in terms of replicative fitness, since they involve changes in structure of key receptors or overactivity of some metabolic enzyme, so fully-resistant strains are extremely rare. Strong, sustained antibiotic dosing regimens kill off infections. But decreased antibiotic concentration means that partially-resistent strains (shitty replicators, but better against antibiotics than the wild type strain) can outcompete their nonresistant counterparts. Once enough of them survive, more replicative generations means more chance for some other mutation to appear which compensate for the resistance traits’ effects on replication, or complete the resistance without further reproductive cost, so the resistant strain takes off. Vaccines on the other hand aren’t killing off robust and diverse populations of pathogens–rather, they prevent new infections by small founding populations, which are overwhelmed by the vaccine-primed immune system’s fast adaptive response.
Nature doesn’t choose how to adapt. Adaptations happen because of changes in average genetic variants in the population, due to some variants replicating more frequently than other variants.