Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic

Summary Objectives Despite high pertussis vaccination coverage, Australia experienced a prolonged epidemic in 2008–2012. The predominant Bordetella pertussis genotype harboured pertussis toxin promoter allele, ptxP3 , and pertactin gene allele, prn2 . The emergence and expansion of prn non-expressing isolates (Prn negative), were also observed. We aimed to investigate the microevolution and genomic diversity of epidemic B. pertussis isolates. Methods We sequenced 22 B . pertussis isolates collected in 2008–2012 from two states of Australia which are geographically widely separated. Ten of the 22 were Prn negative isolates with three different modes of silencing of prn ( prn ::IS 481 F, prn ::IS 481 R and prn ::IS 1002 ). Five pre-epidemic isolates were also sequenced for comparison. Results Five single nucleotide polymorphisms were common in the epidemic isolates and differentiated them from pre-epidemic isolates. The Australian epidemic isolates can be divided into five lineages (EL1–EL5) with EL1 containing only Prn negative isolates. Comparison with global isolates showed that three lineages remained geographically and temporally distinct whereas two lineages mixed with isolates from 2012 UK outbreak. Conclusion Our results suggest significant diversification and the microevolution of B. pertussis within the 2008–2012 Australian epidemic.