Background: Pertussis (whooping cough) is a vaccine preventable disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, pertussis has re-emerged to cause epidemic level disease. Our prior studies have shown a rapid increase in the proportion of B. pertussis isolates not expressing PRN (PRN-negative) during the 2008-2012 epidemic. As a new pertussis epidemic occurred in 2015 and to further our understanding of pertussis epidemiology, we characterised Australian B. pertussis isolates from 2013-2017, and compared their molecular characteristics with isolates from the 2008-2012 epidemic.
Methods: Whole-genome sequencing was performed on 78 clinical isolates collected from 2013-2017 to detect single-nucleotide polymorphisms (SNPs) in virulence genes and to determine their SNP profiles (SP). Together with previous 27 previously sequenced Australian B. pertussis isolates, a total of 105 isolates were analysed to determine their phylogenetic relationships. Western immunoblotting was performed to detect the expression of pertussis toxin (PTX), PRN and Filamentous haemagglutinin (FHA) proteins.
Results: The 78 isolates were typed into two SPs: SP13 (SNP cluster I, ptxP3, 96.15% [75/78]) and SP18 (non-cluster I, ptxP1, 3.85% [3/78]). The majority (75/78, 96.15%) of the SP13 isolates had the prn2 and fim3A allele. Three non-cluster I SP18 isolates genotyped as ptxP1-fim3A*-prn1. The frequency of ptxP and fim3 alleles were higher than those observed during the last epidemic. For PRN, 89.74% (70/78) of the isolates were found to be PRN-negative. By contrast, the percentage of PRN-negative isolates increased from 5.13% in 2008 to 77.78% in 2012. One novel PRN inactivation mechanism and a novel fim2-3 allele were also found in this study. Importantly, we detected the first FHA-negative B. pertussis isolate in Australia.
Conclusion: The Australian 2013-2017 pertussis epidemic was predominantly caused by PRN-negative isolates, with local and interstate expansion. Our results suggest that B. pertussis continues to evolve under vaccine-induced selective pressure.