Genomic epidemiology of Iranian <i>Bordetella pertussis</i>: 50 years after the implementation of whole cell vaccine

Pertussis caused by <i>Bordetella pertussis,</i> remains a public health problem worldwide, despite high vaccine coverage in infants and children in many countries. Iran has been using whole cell vaccine for the last 50 years with more than 95% vaccination rate since 1988 and has experienced pertussis resurgence in recent years. Here, we sequenced 55 <i>B. pertussis</i> isolates mostly collected from three provinces with the highest number of pertussis cases in Iran, including Tehran, Mazandaran, and Eastern-Azarbayjan from the period of 2008-2016. Most isolates carried <i>ptxP3</i>/<i>prn2</i> alleles (42/55, 76%), the same genotype as isolates circulating in acellular vaccine-administrating countries. The second most frequent genotype was <i>ptxP3</i>/<i>prn9</i> (8/55, 14%). Only three isolates (5%) were <i>ptxP1</i>. Phylogenetic analysis showed that Iranian <i>ptxP3</i> isolates can be divided into eight clades (Clades 1-8) with no temporal association. Most of the isolates from Tehran grouped together as one distinctive clade (Clade 8) with six unique single nucleotide polymorphisms (SNPs). In addition, the <i>prn9</i> isolates were grouped together as Clade 5 with 12 clade-supporting SNPs. No pertactin deficient isolates were found among the 55 Iranian isolates. Our findings suggest that there is an ongoing adaptation and evolution of <i>B. pertussis</i> regardless of the types of vaccine used.