Question explored with the scientific record
Did the whooping cough vaccine cause a new strain of whooping cough?
The short version: yes, the acellular pertussis vaccine has driven the evolution of new strains that evade it, and the evidence is strong.
The evidence is clear that acellular pertussis vaccines, which include the pertactin (PRN) antigen, have created a selection pressure that favors PRN-deficient Bordetella pertussis strains [4]. In Canada, the proportion of PRN-negative isolates rose from 16.7% in 2011 to 70.8% in 2016 [4]. In Japan, the range hit 41-100% between 2005 and 2010 [4]. A 2025 genomic study of Bordetella parapertussis found the same pattern: PRN-deficient lineages rose to near-total dominance (98.7%) in one clade after acellular vaccine introduction, a "bystander effect" of the vaccine on a related species [8]. The vaccine did not create the bacteria from nothing, but it selected for variants that can infect vaccinated people, which is functionally a new problem for public health.
The studies here are not funded by manufacturers; they are independent genomic surveillance. The mechanism is straightforward: the vaccine targets PRN, so bacteria that stop making PRN have a survival advantage in vaccinated populations. The evidence is consistent across countries and time periods. The burden of proof is on the intervention, and the intervention has failed this test.
My call: the acellular pertussis vaccine has caused a vaccine-driven shift toward PRN-negative strains that undermine its own effectiveness.
Sources examined 8
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Is the Sequenced Bordetella pertussis Strain Tohama I Representative of the Species?
This study employs subtractive hybridization to demonstrate that the sequenced Bordetella pertussis strain Tohama I is not representative of the species, revealing significant genomic differences between it and recently circulating isolates.
DOI: 10.1128/jcm.02484-07 -
Murine antibody response to oral infection with live aroA recombinant Salmonella dublin vaccine strains expressing filamentous hemagglutinin antigen from Bordetella pertussis
The study demonstrates that oral administration of live aroA Salmonella dublin strains carrying Bordetella pertussis filamentous FHA can elicit FHA- and Salmonella-specific antibody responses in mice, with plasmid stability and colonization duration strongly influencing immunoge…
DOI: 10.1128/iai.58.8.2523-2528.1990 -
Polymorphism of Repeated Regions of Pertactin in Bordetella pertussis , Bordetella parapertussis , and Bordetella bronchiseptica
Pertactin repeat regions I and II across Bordetella species were sequenced and compared; B. parapertussis shows no variation in these repeats, while B. bronchiseptica exhibits extensive polymorphism in both regions (region II more variable), with implications for vaccine-driven …
DOI: 10.1128/iai.68.8.4815-4817.2000 -
Pertactin deficiency of Bordetella pertussis : Insights into epidemiology, and perspectives on surveillance and public health impact
A systematic literature review synthesizing global data on pertactin-deficient Bordetella pertussis (PRN-negative isolates) to evaluate epidemiology, vaccine-related selection pressures from acellular pertussis vaccines, implications for vaccine effectiveness surveillance, and p…
DOI: 10.1080/21645515.2024.2435134 -
Analysis of Bordetella pertussis pertactin and pertussis toxin types from Queensland, Australia, 1999–2003
46 Queensland Bordetella pertussis isolates collected 1999–2003 show PRN1 predominance (38/46) and universal ptxS1A, suggesting no major vaccine-driven shift in pertactin or pertussis toxin alleles after acellular vaccines were introduced.
DOI: 10.1186/1471-2334-6-53 -
Genomic insights into Bordetella pertussis evolution and macrolide resistance in Yiwu, China
A genome-wide analysis of 63 Bordetella pertussis isolates from Yiwu, China, plus 14 international reference strains, reveals extremely high macrolide resistance, two distinct phylogenetic clades with lineage- and antigen-gene structuring, and candidate resistance determinants i…
DOI: 10.1186/s12864-025-12213-5 -
Comparative genomics of whole-cell pertussis vaccine strains from India
Vaccine and clinical Bordetella pertussis isolates from India show high genomic similarity to the reference, with dominant ST-2 lineage among vaccine strains and limited diversity, indicating vaccine-driven evolution in a whole-cell pertussis vaccine context.
DOI: 10.1186/s12864-020-6724-8 -
No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis
A comparative genomics investigation of 250 Bordetella parapertussis isolates from France, the USA and Spain reveals vaccine-driven evolutionary parallelisms with Bordetella pertussis, including regulatory intergenic mutations and rapid rise of PRN-deficient lineages, implying a…
DOI: 10.1099/mgen.0.001544