Research into outbreaks of whooping cough has uncovered that the bacteria responsible for causing the illness, B.Pertussis, are becoming resistant to the vaccine. The antigen pertactin (contained in the current vaccine), is responsible for initiating the immune response that stimulates antibody production in the human body. The new bacterial strain does not have this antigen, which effectively renders the vaccine useless.
Pertactin-negative pertussis bacteria have already been identified in Japan, France and Finland. Researchers in France have begun more regular testing for this strain in order to monitor bacterial mutations. These same researchers report that the proportion of pertactin negative samples has increased from 2% in 2005 to 14% in 2012.
The US Food & Drug Administration (FDA) openly admitted in 2013 that the whooping cough vaccine does not prevent infection, and may only reduce the symptoms. They also admit that those who have been vaccinated may actually spread the disease, if they carry the bacteria.
Polio virus also showing signs of resistance
A mutant strain of the polio virus has been discovered that renders that vaccine ineffective too. There have been several outbreaks of this new strain of polio internationally. One of those outbreaks occurred in the Republic of Congo, and showed an exceptionally high fatality rate.
This new evidence is strikingly similar to the behaviour of antibiotic resistant bacteria and poses a very real threat for a society reliant on immunisation to avoid outbreaks of contagious disease.
 Edmundson, L. First cases of vaccine resistant whooping cough found in the United States. Feb 8th, 2013 http://www.healthmap.org/site/diseasedaily/article/first-cases-vaccine-resistant-whooping-cough-found-united-states-2813
 Parch, L. Why Whooping Cough is Rising Despite a New Vaccine. WebMD, 2015.