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Objectives: Changes in circulating Bordetella pertussis genotypes, including a novel pertussis toxin promoter ptxP3 allele and absence of pertactin (Prn) antigen, have been reported from several countries but limited data on relative severity are available. We compared markers of disease severity in children with B. pertussis infection due to strains of differing genotype. Methods: Culture confirmed cases presenting to tertiary paediatric hospitals in three Australian states between 2008 and 2012 were classified as severe if they required a hospital stay greater than seven days, were admitted to intensive care, or if death occurred. Associations between age, vaccination, genotype and severity were assessed. Results: Of 199 pertussis cases, 81 (41%) were <3 months, including 32/39 (82%) of severe cases. The proportion of isolates from these cases that were Prn deficient increased markedly between 2008 and 2012. Of B. pertussis isolates, the proportion considered severe was similar for Prn positive (27/128, 21%) and Prn deficient (12/71, 17%) cases but only 1/22 (4.5%) of non ptxP3 cases were severe versus 38/177 (21.4%) ptxP3 positive. Adjusting for ptxP type, vaccination status and age, disease severity was not significantly associated with Prn status (RRA: 0.95, [0.57-1.56]; p= 0.83). Conclusions: In children, we found no relationship between Prn status and markers of severe pertussis. An increased proportion of severe disease in isolates with the ptxP3allele was observed.© 2015 The British Infection Association.