Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 02 1 10 Samaneh Saedi Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran Azadeh Safarchi Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran Mojtaba Noofeli Department of Human Bacterial Vaccine, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran Keyvan Tadayon Department of Aerobic Bacterial Research and Vaccine Production, Razi Vaccine & Serum Research Institute, Karaj, Iran Alfred Chin Yen Tay The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia; Shenzhen Dapeng New District Kuichong People Hospital, Shenzhen, Guangdong, China Binit Lamichhane The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia Hamzeh Rahimi Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran Fereshteh Shahcheraghi Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran 2020 01 13 2020 01 15 Background and Objectives: The re-emergence of pertussis still is being reported all over the world. Pathogen adaptation and antigenic divergence of circulating isolates from vaccine strains are the main reasons of infection resurgence. Waning immunity is also an important factor contributing to resurgence of pertussis. Materials and Methods: The genetic diversity and evolutionary characteristics of circulating Iranian isolates of Bordetella pertussis during February 2015 to October 2018 was investigated by pulsed-field gel electrophoresis (PFGE) and subsequently ptxA, ptxP and fim3 alleles were characterized. The next generation genome sequencing was then used to compare the genomics of ptxP1 and ptxP3 of selected isolates from PFGE dendrogram. Results: PFGE differentiated 62 clinical isolates and vaccine and reference strains into 19 PFGE profiles, indicating the higher level of heterogeneity in the population during 2015-2018. The predominant B. pertussis genotype harbored pertussis toxin promoter allele, ptxP3 and the expansion of ptxA1 isolates, were also observed in our population. Conclusion: No changes in allelic profile of predominant clone in recent years was observed but antigenic divergence between recently circulating isolates and the vaccine strain has been progressed and significantly was higher than previous studies. The comparative genomic analysis of the ptxP3 and ptxP1 isolates indicate that changes in ptxP3 genome structure including 32 unique SNPs and three unique indels may have contributed to the expansion of the ptxP3 clone. We compared ptxP3 and ptxP1 isolates in pathogenicity-associated genes and found five of them were specific for the ptxP3 isolates. The polymorphisms in pathogenicity-associated genes suggest structural adaptations for these virulence factors. https://ijm.tums.ac.ir/index.php/ijm/article/view/2450 https://ijm.tums.ac.ir/index.php/ijm/article/download/2450/1215