Genome diversity and evolutionary characteristics of clinical isolates of Bordetella pertussis circulating in Iran

Abstract


 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 subse- quently 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.

Isolation and Genomics of multidrug-resistant Brevundimonas diminuta collected from patients with pertussis-like symptoms

“…The nasal swabs were collected and sent to the Reference Pertussis Laboratory of Pasture Institute of Iran for laboratory confirmation based on the National Pertussis guideline [25]. Bacterial isolation from nasal swabs was carried out as previously described [23, 26]. Isolates were initially confirmed as B. pertussis due to their growth on Bordet Gengou agar and some biochemical analysis such as catalase, oxidase and urease test.…”

“…Isolates were initially confirmed as B. pertussis due to their growth on Bordet Gengou agar and some biochemical analysis such as catalase, oxidase and urease test. However, the molecular determination by real-time PCR targeting IS 1002 , IS 481 and the ptx promoter as a gold molecular standard for B. pertussis confirmation [26] for these three isolates was negative. Therefore, additional biochemical tests such as oxidase production and antibody neutralizing teste as well as 16s rRNA sequencing were performed.…”

“…This may lead to false pertussis reports if there are respiratory tract infections especially when there are respiratory symptoms in infants. In this case, it is suggested to perform some additional molecular tests including real-time PCR targeting ptxP , the promoter of pertussis toxin, IS 481 and IS 1002 which are two insertion sequence in B. pertussis [26]. According to new pertussis guidelines and policies implemented in 2009 by Iran Centre for Communicable Disease Control [25] all nationwide suspected samples from patients with pertussis symptoms must be notified.…”

Genome characteristic of Bordetella parapertussis isolated from Iran

“…B. parapertussis isolates were confirmed by a combination of colony morphology, Gram stain and conventional biochemical tests such as oxidase and real-time PCR. DNA extraction was performed using High Pure PCR Template Preparation Kit (Roche Diagnostics GmbH, Mannheim, Germany) and real-time PCR was performed by targeting IS481, IS1001 and IS1002 with designed primers [9] to confirm the presence of IS1001 for B. parapertussis as recommended by WHO [5].…”

“…There are few reports of widespread infection of B. parapertussis [6]. In Iran, we reported increase in the number of B. pertussis isolates in recent years and investigated their genomics [7][8][9][10].…”