Genomic epidemiology of Iranian Bordetella pertussis: 50 years after the implementation of whole cell vaccine

References

• Burns DL, Meade BD, Messionnier NE. Pertussis resurgence: perspectives from the Working group Meeting on pertussis on the causes, possible paths forward, and gaps in our knowledge. J Infect Dis. 2014 Apr 1;209(Suppl 1):S32–S35. PubMed PMID: 24626870. doi: 10.1093/infdis/jit491
   PubMed Web of Science ®Google Scholar
• Bouchez V, Guiso N. Bordetella pertussis, B. parapertussis, vaccines and cycles of whooping cough. Pathog Dis. 2015 Oct;73(7). PubMed PMID: 26242280. doi: 10.1093/femspd/ftv055
   PubMed Web of Science ®Google Scholar
• Mooi FR, Van Der Maas NA, De Melker HE. Pertussis resurgence: waning immunity and pathogen adaptation – two sides of the same coin. Epidemiol Infect. 2014 Apr;142(4):685–694. PubMed PMID: 23406868. doi: 10.1017/S0950268813000071
   PubMed Web of Science ®Google Scholar
• Belcher T, Preston A. Bordetella pertussis evolution in the (functional) genomics era. Pathog Dis. 2015 Nov;73(8), ftv064. PubMed PMID: 26297914; PubMed Central PMCID: PMCPMC4626590. doi: 10.1093/femspd/ftv064
   PubMed Web of Science ®Google Scholar
• King AJ, van der Lee S, Mohangoo A, et al. Genome-wide gene expression analysis of Bordetella pertussis isolates associated with a resurgence in pertussis: elucidation of factors involved in the increased fitness of epidemic strains. PLoS One. 2013;8(6):e66150. PubMed PMID: 23776625; PubMed Central PMCID: PMCPMC3679012. doi: 10.1371/journal.pone.0066150
   PubMed Web of Science ®Google Scholar
• Xu Y, Liu B, Grondahl-Yli-Hannuksila K, et al. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis. Sci Rep. 2015 Aug 18;5:12888. PubMed PMID: 26283022; PubMed Central PMCID: PMCPMC4539551. doi: 10.1038/srep12888
   PubMed Web of Science ®Google Scholar
• Bart MJ, Harris SR, Advani A, et al. Global population structure and evolution of Bordetella pertussis and their relationship with vaccination. MBio. 2014 Apr 22;5(2):e01074. PubMed PMID: 24757216; PubMed Central PMCID: PMCPMC3994516. doi: 10.1128/mBio.01074-14
   PubMed Web of Science ®Google Scholar
• Safarchi A, Octavia S, Luu LD, et al. Better colonisation of newly emerged Bordetella pertussis in the co-infection mouse model study. Vaccine. 2016 Jul 25;34(34):3967–3971. PubMed PMID: 27346304. doi: 10.1016/j.vaccine.2016.06.052
   PubMed Web of Science ®Google Scholar
• Moradi-Lakeh M, Esteghamati A. National immunization Program in Iran: whys and why nots. Hum Vaccin Immunother. 2013 Jan;9(1):112–114. PubMed PMID: 23442584; PubMed Central PMCID: PMCPMC3667923. doi: 10.4161/hv.22521
   PubMed Web of Science ®Google Scholar
• Shahcheraghi F, Lotfi M N, Parzadeh M, et al. Isolation of Bordetella pertussis and Bordetella Parapertussis from clinical specimens at different provinces. J Mazandaran Univ Med Sci. 2012;22(88):2–8. eng.
   Google Scholar
• Saffar MJ, Ghorbani G, Hashemi A, et al. Pertussis resurgence in a highly vaccinated population, Mazandaran, north of Iran 2008-2011: an epidemiological analysis. Indian J Pediatr. 2014 Dec;81(12):1332–1336. PubMed PMID: 24788914. doi: 10.1007/s12098-014-1445-0
   PubMed Web of Science ®Google Scholar
• Centre for Diseases Control and Prevention MoH, Islamic Republic of Iran. A comprehensive guidefor family physicians (2012): The contagious disease surveillance system Ministry of Health, Islamic Republic of Iran. Standard No.: ISBN:978-964-519-138-0.
   Google Scholar
• Shojaei J, Saffar M, Hashemi A, et al. Clinical and laboratory features of pertussis in hospitalized infants with confirmed versus probable pertussis cases. Ann Med Health Sci Res. 2014 Nov;4(6):910–914. PubMed PMID: 25506485; PubMed Central PMCID: PMCPMC4250990. doi: 10.4103/2141-9248.144911
   PubMedGoogle Scholar
• Khazaei S, Ayubi E, Mansori K, et al. Pertussis incidence by time, province and age group in Iran, 2006-2011. Iran J Public Health. 2016 Nov;45(11):1525–1527. PubMed PMID: 28028509; PubMed Central PMCID: PMCPMC5182268.
   PubMed Web of Science ®Google Scholar
• The World Health Organization (WHO). World Health Statistics 2015. 2015.
   Google Scholar
• Centre for Diseases Control and Prevention MoH, Islamic Republic of Iran. A comprehensive guide for family physicians (2009): the contagious disease surveillance system Iran: Standard No.: ISBN:978-964-519-138-0.
   Google Scholar
• Safarchi A, Octavia S, Wu SZ, et al. Genomic dissection of Australian Bordetella pertussis isolates from the 2008–2012 epidemic. J Infect. 2016 Apr;72(4):468–477. PubMed PMID: 26826518. doi: 10.1016/j.jinf.2016.01.005
   PubMed Web of Science ®Google Scholar
• Darling AE, Mau B, Perna NT. Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010 Jun 25;5(6):e11147. PubMed PMID: 20593022; PubMed Central PMCID: PMCPMC2892488. doi: 10.1371/journal.pone.0011147
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754–1760. PubMed PMID: 19451168; PubMed Central PMCID: PMCPMC2705234. doi: 10.1093/bioinformatics/btp324
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078–2079. PubMed PMID: 19505943; PubMed Central PMCID: PMCPMC2723002. doi: 10.1093/bioinformatics/btp352
   PubMed Web of Science ®Google Scholar
• Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068–2069. PubMed PMID: 24642063. doi: 10.1093/bioinformatics/btu153
   PubMed Web of Science ®Google Scholar
• Page AJ, Cummins CA, Hunt M, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015 Nov 15;31(22):3691–3693. PubMed PMID: 26198102; PubMed Central PMCID: PMCPMC4817141. doi: 10.1093/bioinformatics/btv421
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012 May;19(5):455–477. PubMed PMID: 22506599; PubMed Central PMCID: PMCPMC3342519. doi: 10.1089/cmb.2012.0021
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011 Oct;28(10):2731–2739. PubMed PMID: 21546353; PubMed Central PMCID: PMCPMC3203626. doi: 10.1093/molbev/msr121
   PubMed Web of Science ®Google Scholar
• Barkoff AM, Mertsola J, Pierard D, et al. Surveillance of circulating Bordetella pertussis strains in Europe during 1998 to 2015. J Clin Microbiol. 2018 May;56(5). doi:10.1128/JCM.01998-17. PubMed PMID: 29491017; PubMed Central PMCID: PMCPMC5925733.
   PubMed Web of Science ®Google Scholar
• Weigand MR, Williams MM, Peng Y, et al. Genomic Survey of Bordetella pertussis Diversity, United States, 2000-2013. Emerg Infect Dis. 2019 Apr;25(4):780–783. PubMed PMID: 30882317; PubMed Central PMCID: PMCPMC6433035. doi: 10.3201/eid2504.180812
   PubMed Web of Science ®Google Scholar
• Locht C, Geoffroy MC, Renauld G. Common accessory genes for the Bordetella pertussis filamentous hemagglutinin and fimbriae share sequence similarities with the papC and papD gene families. EMBO J. 1992 Sep;11(9):3175–3183. PubMed PMID: 1354611; PubMed Central PMCID: PMCPMC556850. doi: 10.1002/j.1460-2075.1992.tb05394.x
   PubMed Web of Science ®Google Scholar
• Bouchez V, Hegerle N, Strati F, et al. New data on vaccine antigen deficient Bordetella pertussis isolates. Vaccines (Basel). 2015 Sep 14;3(3):751–770. doi:10.3390/vaccines3030751. PubMed PMID: 26389958; PubMed Central PMCID: PMCPMC4586476.
   PubMed Web of Science ®Google Scholar
• Sealey KL, Harris SR, Fry NK, et al. Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving. J Infect Dis. 2015 Jul 15;212(2):294–301. PubMed PMID: 25489002. doi: 10.1093/infdis/jiu665
   PubMed Web of Science ®Google Scholar
• Octavia S, Wu SZ, Kaur S, et al. Whole-genome sequencing and comparative genomic analysis of Bordetella pertussis isolates from the 2007-2008 epidemic in Israel. J Infect. 2017 Feb;74(2):204–207. PubMed PMID: 27914992. doi: 10.1016/j.jinf.2016.11.012
   PubMed Web of Science ®Google Scholar
• Bowden KE, Weigand MR, Peng Y, et al. Genome structural diversity among 31 Bordetella pertussis isolates from two recent U.S. whooping cough Statewide Epidemics. mSphere. 2016 May-Jun;1(3). PubMed PMID: 27303739; PubMed Central PMCID: PMCPMC4888882. doi: 10.1128/mSphere.00036-16
   PubMed Web of Science ®Google Scholar
• Park J, Zhang Y, Buboltz AM, et al. Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens. BMC Genomics. 2012 Oct 10;13:545. PubMed PMID: 23051057; PubMed Central PMCID: PMCPMC3533505. doi: 10.1186/1471-2164-13-545
   PubMed Web of Science ®Google Scholar
• Kallonen T, Grondahl-Yli-Hannuksela K, Elomaa A, et al. Differences in the genomic content of isolates before and after introduction of pertussis vaccines in four European countries. Infect Genet Evol. 2011 Dec;11(8):2034–2042. PubMed PMID: 21964035. doi: 10.1016/j.meegid.2011.09.012
   PubMed Web of Science ®Google Scholar
• Heikkinen E, Kallonen T, Saarinen L, et al. Comparative genomics of Bordetella pertussis reveals progressive gene loss in Finnish strains. PLoS One. 2007 Sep 19;2(9):e904. PubMed PMID: 17878939; PubMed Central PMCID: PMCPMC1975675. doi: 10.1371/journal.pone.0000904
   PubMed Web of Science ®Google Scholar
• Cummings CA, Brinig MM, Lepp PW, et al. Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J Bacteriol. 2004 Mar;186(5):1484–1492. PubMed PMID: 14973121; PubMed Central PMCID: PMCPMC344407. doi: 10.1128/JB.186.5.1484-1492.2004
   PubMed Web of Science ®Google Scholar
• Zhang S, Xu Y, Zhou Z, et al. Complete genome sequence of Bordetella pertussis CS, a Chinese pertussis vaccine strain. J Bacteriol. 2011 Aug;193(15):4017–4018. PubMed PMID: 21622744; PubMed Central PMCID: PMCPMC3147532. doi: 10.1128/JB.05184-11
   PubMed Web of Science ®Google Scholar
• Caro V, Bouchez V, Guiso N. Is the sequenced Bordetella pertussis strain Tohama I representative of the species? J Clin Microbiol. 2008 Jun;46(6):2125–2128. PubMed PMID: 18385436; PubMed Central PMCID: PMCPMC2446832. doi: 10.1128/JCM.02484-07
   PubMed Web of Science ®Google Scholar
• Weigand MR, Peng Y, Loparev V, et al. Complete genome sequences of four Bordetella pertussis vaccine reference strains from Serum Institute of India. Genome Announc. 2016 Dec 22;4(6). PubMed PMID: 28007855; PubMed Central PMCID: PMCPMC5180383. doi: 10.1128/genomeA.01404-16
   Google Scholar
• Zarei S, Jeddi-Tehrani M, Akhondi MM, et al. Primary immunization with a triple diphtheria-tetanus-whole cell pertussis vaccine in Iranian infants: an analysis of antibody response. Iran J Allergy Asthma Immunol. 2009 Jun;8(2):85–93. PubMed PMID: 19671937.
   PubMed Web of Science ®Google Scholar
• Sadeghpour Heravi F, Nikbin VS, Nakhost Lotfi M, et al. Strain variation and antigenic divergence among Bordetella pertussis circulating strains isolated from patients in Iran. Eur J Clin Microbiol Infect Dis. 2018 Oct;37(10):1893-1900. PubMed PMID: 30094521. doi: 10.1007/s10096-018-3323-6
   PubMed Web of Science ®Google Scholar
• Sadeghpour Heravi F, Nikbin V, Shahcheraghi F. Allelic variations between vaccine strains and circulating strains in pxtP of Bordetella pertussis in Iran. Vaccine Res. 2015;2(3):19-23. eng. doi: 10.18869/acadpub.vacres.2.3.19
   Google Scholar
• Lan R, Octavia S. Vaccine-driven selection and the changing molecular epidemiology of Bordetella pertussis. In: Rohani P, Scarpino SV, editors. Pertussis: epidemiology, immunology, & evolution. Oxford: Oxford University Press; 2019. p. 166–181.
   Google Scholar
• Mosiej E, Zawadka M, Krysztopa-Grzybowska K, et al. Sequence variation in virulence-related genes of Bordetella pertussis isolates from Poland in the period 1959–2013. Eur J Clin Microbiol Infect Dis. 2015 Jan;34(1):147–152. doi:10.1007/s10096-014-2216-6. PubMed PMID: 25090968.
   PubMed Web of Science ®Google Scholar
• Mosiej E, Krysztopa-Grzybowska K, Polak M, et al. Multi-locus variable-number tandem repeat analysis of Bordetella pertussis isolates circulating in Poland in the period 1959-2013. J Med Microbiol. 2017 Jun;66(6):753–761. PubMed PMID: 28598302. doi: 10.1099/jmm.0.000408
   PubMed Web of Science ®Google Scholar
• Polak M, Zasada AA, Mosiej E, et al. Pertactin-deficient Bordetella pertussis isolates in Poland-a country with whole-cell pertussis primary vaccination. Microbes Infect. 2018 Dec 21. PubMed PMID: 30580013.
   PubMed Web of Science ®Google Scholar
• Xu Z, Wang Z, Luan Y, et al. Genomic epidemiology of erythromycin-resistant Bordetella pertussis in China. Emerg Microbes Infect. 2019;8(1):461–470. PubMed PMID: 30898080; PubMed Central PMCID: PMCPMC6455148. doi: 10.1080/22221751.2019.1587315
   PubMed Web of Science ®Google Scholar
• Luu LDW, Octavia S, Zhong L, et al. Comparison of the whole cell proteome and secretome of epidemic Bordetella pertussis strains from the 2008-2012 Australian epidemic under Sulfate-Modulating Conditions. Front Microbiol. 2018;9:2851. PubMed PMID: 30538686; PubMed Central PMCID: PMCPMC6277516. doi: 10.3389/fmicb.2018.02851
   PubMed Web of Science ®Google Scholar
• Luu LDW, Octavia S, Zhong L, et al. Proteomic adaptation of Australian epidemic Bordetella pertussis. Proteomics. 2018 Apr;18(8):e1700237. PubMed PMID: 29464899. doi: 10.1002/pmic.201700237
   PubMed Web of Science ®Google Scholar
• Han HJ, Kuwae A, Abe A, et al. Differential expression of type III effector BteA protein due to IS481 insertion in Bordetella pertussis. PLoS One. 2011 Mar 10;6(3):e17797. PubMed PMID: 21423776; PubMed Central PMCID: PMCPMC3053399. doi: 10.1371/journal.pone.0017797
   PubMed Web of Science ®Google Scholar
• de Gouw D, Hermans PW, Bootsma HJ, et al. Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally. PLoS One. 2014;9(1):e84523. PubMed PMID: 24416242; PubMed Central PMCID: PMCPMC3885589. doi: 10.1371/journal.pone.0084523
   PubMed Web of Science ®Google Scholar
• Bouchez V, Brun D, Dore G, et al. Bordetella parapertussis isolates not expressing pertactin circulating in France. Clin Microbiol Infect. 2011 May;17(5):675–682. doi:10.1111/j.1469-0691.2010.03303.x. PubMed PMID: 20636430.
   PubMed Web of Science ®Google Scholar
• Otsuka N, Han HJ, Toyoizumi-Ajisaka H, et al. Prevalence and genetic characterization of pertactin-deficient Bordetella pertussis in Japan. PLoS One. 2012;7(2):e31985. PubMed PMID: 22348138; PubMed Central PMCID: PMCPMC3279416. doi: 10.1371/journal.pone.0031985
   PubMed Web of Science ®Google Scholar
• Lam C, Octavia S, Ricafort L, et al. Rapid increase in pertactin-deficient Bordetella pertussis isolates, Australia. Emerg Infect Dis. 2014 Apr;20(4):626–633. PubMed PMID: 24655754; PubMed Central PMCID: PMCPMC3966384. doi: 10.3201/eid2004.131478
   PubMed Web of Science ®Google Scholar
• Xu Z, Octavia S, Luu LDW, et al. Pertactin-negative and filamentous hemagglutinin-negative Bordetella pertussis, Australia, 2013-2017. Emerg Infect Dis. 2019 Jun;25(6):1196–1199. PubMed PMID: 31107218. doi: 10.3201/eid2506.180240
   PubMed Web of Science ®Google Scholar
• Miyaji Y, Otsuka N, Toyoizumi-Ajisaka H, et al. Genetic analysis of Bordetella pertussis isolates from the 2008-2010 pertussis epidemic in Japan. PLoS One. 2013;8(10):e77165. PubMed PMID: 24124606; PubMed Central PMCID: PMCPMC3790747. doi: 10.1371/journal.pone.0077165
   PubMed Web of Science ®Google Scholar
• Shuel M, Jamieson FB, Tang P, et al. Genetic analysis of Bordetella pertussis in Ontario, Canada reveals one predominant clone. Int J Infect Dis. 2013 Jun;17(6):e413–e417. PubMed PMID: 23352492. doi: 10.1016/j.ijid.2012.12.015
   PubMed Web of Science ®Google Scholar
• Advani A, Donnelly D, Hallander H. Reference system for characterization of Bordetella pertussis pulsed-field gel electrophoresis profiles. J Clin Microbiol. 2004 Jul;42(7):2890–2897. PubMed PMID: 15243034; PubMed Central PMCID: PMCPMC446263. doi: 10.1128/JCM.42.7.2890-2897.2004
   PubMed Web of Science ®Google Scholar
• He Q, Makinen J, Berbers G, et al. Bordetella pertussis protein pertactin induces type-specific antibodies: one possible explanation for the emergence of antigenic variants? J Infect Dis. 2003 Apr 15;187(8):1200–1205. PubMed PMID: 12695998. doi: 10.1086/368412
   PubMed Web of Science ®Google Scholar
• Zarei S, Jeddi-Tehrani M, Akhondi MM, et al. Immunogenicity of a triple diphtheria-tetanus-whole cell pertussis vaccine in Iranian preschool children. Iran J Immunol. 2007 Jun;4(2):101–109. PubMed PMID: 17652850.
   PubMedGoogle Scholar
• Zarei S, Jeddi-Tehrani M, Mehdi Akhondi M, et al. Immunogenicity and reactogenicity of two diphtheria-tetanus-whole cell pertussis vaccines in Iranian pre-school children, a randomized controlled trial. Hum Vaccin Immunother. 2013 Jun;9(6):1316–1322. PubMed PMID: 23442608; PubMed Central PMCID: PMCPMC3901823. doi: 10.4161/hv.24093
   PubMed Web of Science ®Google Scholar