Van Loo IH, van der Heide HG, Nagelkerke NJ, Verhoef J, Mooi FR. Eijkman-Winkler Institute for Medical Microbiology, University Hospital Utrecht, The Netherlands. Temporal trends in the population structure of Bordetella pertussis during 1949-1996 in a highly vaccinated population. J Infect Dis. 1999 Apr;179(4):915-23.

The population structure of Bordetella pertussis in The Netherlands in 5 successive periods, encompassing 1949-1996, was analyzed by DNA typing ("fingerprinting"). In 10 years following the introduction of wide-scale vaccination in 1953, a decrease in genotypic diversity (GD) was observed, suggesting clonal expansion of strains that were adapted to vaccine-induced immunity. In subsequent periods, GD increased to prevaccination levels, probably reflecting a gradual adaptation of the B. Pertussis population involving many lineages. In the 1990s, GD decreased again. This decrease coincided with an antigenic shift in the surface protein pertactin. No evidence was found for changes in DNA types or GD in 1996, when a large pertussis epidemic occurred. Thus, gradual changes in the bacterial population previous to 1996 were probably the cause of the 1996 epidemic. The results herein suggest that vaccination has selected for strains that are adapted to a highly vaccinated population. Similar changes may have occurred in other countries, explaining the reemergence of pertussis in vaccinated populations.

The CDC also touches on this subject:

Frits R. Mooi, Inge H. M. van Loo, and Audrey King. National Institute for Public health and the Environment (RIVM) Bilthoven, The Netherlands. Adaptation of Bordetella pertussis to Vaccination: A Cause for Its Reemergence? Presentation from the 2000 Emerging Infectious Diseases Conference in Atlanta, Georgia.

In The Netherlands, as in many other western countries, pertussis vaccines have been used extensively for more than 40 years. Therefore, it is conceivable that vaccine-induced immunity has affected the evolution of B. pertussis. Consistent with this notion, pertussis has reemerged in The Netherlands, despite high vaccination coverage. Further, a notable change in the population structure of B. Pertussis was observed in The Netherlands subsequent to the introduction of vaccination in the 1950s. Finally, we observed antigenic divergence between clinical isolates and vaccine strains, in particular with respect to the surface-associated proteins pertactin and pertussis toxin. Adaptation may have allowed B. Pertussis to remain endemic despite widespread vaccination and may have contributed to the reemergence of pertussis in The Netherlands.

We have had antibiotic resistant bacteria, now we are getting vaccine resistant strains in vaccines ...