Comparative genomics of whole-cell pertussis vaccine strains from India.
Antigenic variation
Bordetella pertussis
Genome organization
Resurgence
Vaccine-mediated selection
Virulence genes
Whooping cough
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
07 May 2020
07 May 2020
Historique:
received:
11
01
2020
accepted:
06
04
2020
entrez:
9
5
2020
pubmed:
10
5
2020
medline:
12
1
2021
Statut:
epublish
Résumé
Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of Bordetella pertussis has been reported as one of the contributing factors for the resurgence of the disease. Our current knowledge of B. pertussis genetic evolution in circulating strains is mostly based on studies conducted in countries using ACVs targeting only a few antigens used in the production of ACVs. To better understand the adaptation to vaccine-induced selection pressure, it will be essential to study B. pertussis populations in developing countries which are using WCVs. India is a significant user and global supplier of WCVs. We report here comparative genome analyses of vaccine and clinical isolates reported from India. Whole-genome sequences obtained from vaccine strains: WCV (J445, J446, J447 and J448), ACV (BP165) were compared with Tohama-I reference strain and recently reported clinical isolates from India (BPD1, BPD2). Core genome-based phylogenetic analysis was also performed using 166 isolates reported from countries using ACV. Whole-genome analysis of vaccine and clinical isolates reported from India revealed high genetic similarity and conserved genome among strains. Phylogenetic analysis showed that clinical and vaccine strains share genetic closeness with reference strain Tohama-I. The allelic profile of vaccine strains (J445:ptxP1/ptxA2/prn1/fim2-1/fim3-1; J446: ptxP2/ptxA4/prn7/fim2-2/fim3-1; J447 and J448: ptxP1/ptxA1/ prn1/fim2-1/fim3-1), which matched entirely with clinical isolates (BPD1:ptxP1/ptxA1/prn1/fim2-1 and BPD2: ptxP1/ptxA1/prn1/fim2-1) reported from India. Multi-locus sequence typing (MLST) demonstrated the presence of dominant sequence types ST2 and primitive ST1 in vaccine strains which will allow better coverage against circulating strains of B. pertussis. The study provides a detailed characterization of vaccine and clinical strains reported from India, which will further facilitate epidemiological studies on genetic shifts in countries which are using WCVs in their immunization programs.
Sections du résumé
BACKGROUND
BACKGROUND
Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of Bordetella pertussis has been reported as one of the contributing factors for the resurgence of the disease. Our current knowledge of B. pertussis genetic evolution in circulating strains is mostly based on studies conducted in countries using ACVs targeting only a few antigens used in the production of ACVs. To better understand the adaptation to vaccine-induced selection pressure, it will be essential to study B. pertussis populations in developing countries which are using WCVs. India is a significant user and global supplier of WCVs. We report here comparative genome analyses of vaccine and clinical isolates reported from India. Whole-genome sequences obtained from vaccine strains: WCV (J445, J446, J447 and J448), ACV (BP165) were compared with Tohama-I reference strain and recently reported clinical isolates from India (BPD1, BPD2). Core genome-based phylogenetic analysis was also performed using 166 isolates reported from countries using ACV.
RESULTS
RESULTS
Whole-genome analysis of vaccine and clinical isolates reported from India revealed high genetic similarity and conserved genome among strains. Phylogenetic analysis showed that clinical and vaccine strains share genetic closeness with reference strain Tohama-I. The allelic profile of vaccine strains (J445:ptxP1/ptxA2/prn1/fim2-1/fim3-1; J446: ptxP2/ptxA4/prn7/fim2-2/fim3-1; J447 and J448: ptxP1/ptxA1/ prn1/fim2-1/fim3-1), which matched entirely with clinical isolates (BPD1:ptxP1/ptxA1/prn1/fim2-1 and BPD2: ptxP1/ptxA1/prn1/fim2-1) reported from India. Multi-locus sequence typing (MLST) demonstrated the presence of dominant sequence types ST2 and primitive ST1 in vaccine strains which will allow better coverage against circulating strains of B. pertussis.
CONCLUSIONS
CONCLUSIONS
The study provides a detailed characterization of vaccine and clinical strains reported from India, which will further facilitate epidemiological studies on genetic shifts in countries which are using WCVs in their immunization programs.
Identifiants
pubmed: 32381023
doi: 10.1186/s12864-020-6724-8
pii: 10.1186/s12864-020-6724-8
pmc: PMC7204287
doi:
Substances chimiques
Pertussis Vaccine
0
Types de publication
Comparative Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
345Références
Infect Dis Clin North Am. 2015 Dec;29(4):699-713
pubmed: 26337739
mBio. 2014 Apr 22;5(2):e01074
pubmed: 24757216
Nucleic Acids Res. 2017 Jul 3;45(W1):W30-W35
pubmed: 28472413
Microbiol Resour Announc. 2019 Apr 18;8(16):
pubmed: 31000545
MMWR Recomm Rep. 2005 Dec 9;54(RR-14):1-16
pubmed: 16340941
PLoS Pathog. 2005 Dec;1(4):e45
pubmed: 16389302
Pediatr Infect Dis J. 2015 Sep;34(9):e222-32
pubmed: 26376316
PLoS One. 2007 Sep 19;2(9):e904
pubmed: 17878939
Expert Rev Vaccines. 2009 Jul;8(7):863-75
pubmed: 19538113
Clin Microbiol Infect. 2014 Nov;20(11):O825-30
pubmed: 24816168
Res Microbiol. 2010 Dec;161(10):810-5
pubmed: 20870020
Clin Vaccine Immunol. 2014 Feb;21(2):119-25
pubmed: 24256623
Epidemics. 2011 Sep;3(3-4):183-8
pubmed: 22094341
J Bacteriol. 2017 Mar 28;199(8):
pubmed: 28167525
J Appl Microbiol. 2012 Jun;112(6):1266-76
pubmed: 22471652
Genome Announc. 2016 Dec 22;4(6):
pubmed: 28007855
Clin Vaccine Immunol. 2007 Mar;14(3):234-8
pubmed: 17202309
Nucleic Acids Res. 2016 Aug 19;44(14):6614-24
pubmed: 27342282
BMC Genomics. 2018 May 2;19(1):310
pubmed: 29716534
Commun Dis Intell. 1998 May 14;22(5):76-80
pubmed: 9621495
PLoS One. 2008 Jun 18;3(6):e2437
pubmed: 18560590
Proc Biol Sci. 2016 Jan 13;283(1822):
pubmed: 26763701
N Engl J Med. 2013 Feb 7;368(6):583-4
pubmed: 23388024
Euro Surveill. 2014 Aug 21;19(33):
pubmed: 25166348
Indian Pediatr. 2013 Nov 8;50(11):1001-9
pubmed: 24382899
mSphere. 2016 May 11;1(3):
pubmed: 27303739
Bioinformatics. 2010 Dec 15;26(24):3125-6
pubmed: 20956244
Infect Genet Evol. 2010 Jan;10(1):36-49
pubmed: 19879977
Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91
pubmed: 24225323
Emerg Infect Dis. 2012 Jun;18(6):966-8
pubmed: 22608348
J Bacteriol. 2004 Mar;186(5):1484-92
pubmed: 14973121
FEMS Immunol Med Microbiol. 2007 Oct;51(1):149-54
pubmed: 17854476
Future Microbiol. 2008 Jun;3(3):329-39
pubmed: 18505398
Comp Immunol Microbiol Infect Dis. 2019 Jun;64:168-175
pubmed: 31174694
Isr Med Assoc J. 2006 May;8(5):308-11
pubmed: 16805226
J Antimicrob Chemother. 2012 Nov;67(11):2640-4
pubmed: 22782487
Emerg Infect Dis. 2018 Jun;24(6):988-994
pubmed: 29774847
Vaccines (Basel). 2015 Sep 14;3(3):751-70
pubmed: 26389958
Res Microbiol. 2008 Nov-Dec;159(9-10):602-8
pubmed: 18790049
Eur J Clin Microbiol Infect Dis. 2000 Mar;19(3):174-81
pubmed: 10795589
J Clin Microbiol. 2005 Nov;43(11):5457-61
pubmed: 16272470
Indian J Med Res. 2014 Apr;139(4):491-511
pubmed: 24927336
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7
pubmed: 17537822
Emerg Microbes Infect. 2019;8(1):1416-1427
pubmed: 31543006
BMC Genomics. 2012 Oct 10;13:545
pubmed: 23051057
Epidemiol Infect. 2014 Apr;142(4):672-84
pubmed: 23324361
Sci Rep. 2016 Apr 13;6:24373
pubmed: 27071527
J Clin Microbiol. 2011 Apr;49(4):1452-7
pubmed: 21307213
Bioinformatics. 2007 Jan 1;23(1):127-8
pubmed: 17050570
BMC Genomics. 2008 Feb 08;9:75
pubmed: 18261238
J Clin Microbiol. 2017 May;55(5):1446-1453
pubmed: 28228490
Curr Opin Microbiol. 2008 Oct;11(5):472-7
pubmed: 19086349
Clin Microbiol Infect. 2014 May;20 Suppl 5:37-44
pubmed: 24476201
RNA Biol. 2018;15(7):967-975
pubmed: 29683387
Nucleic Acids Res. 2016 Jul 8;44(W1):W16-21
pubmed: 27141966
Genome Res. 2003 Sep;13(9):2178-89
pubmed: 12952885
Nat Rev Microbiol. 2004 May;2(5):379-90
pubmed: 15100691
Emerg Infect Dis. 2019 Apr;25(4):780-783
pubmed: 30882317
Sci Rep. 2015 Aug 18;5:12888
pubmed: 26283022
BMC Microbiol. 2016 Jan 27;16 Suppl 1:10
pubmed: 26823184
Epidemiol Infect. 2014 Apr;142(4):685-94
pubmed: 23406868
J Infect Dis. 2014 Apr 1;209 Suppl 1:S4-9
pubmed: 24626871
N Engl J Med. 2012 Aug 30;367(9):785-7
pubmed: 22894554
J Med Microbiol. 2004 May;53(Pt 5):355-365
pubmed: 15096543
Bull World Health Organ. 2011 Sep 1;89(9):666-74
pubmed: 21897487
Mol Biol Evol. 2011 Jan;28(1):707-15
pubmed: 20833694
J Korean Med Sci. 2014 Mar;29(3):328-33
pubmed: 24616579
Genome Res. 2004 Jul;14(7):1394-403
pubmed: 15231754
Med Microbiol Immunol. 2018 Feb;207(1):3-26
pubmed: 29164393
Emerg Microbes Infect. 2019;8(1):461-470
pubmed: 30898080
Int J Infect Dis. 2017 Sep;62:56-58
pubmed: 28751008
BMC Genomics. 2010 Jan 26;11:64
pubmed: 20102608
Vaccine. 1985 Mar;3(1):11-22
pubmed: 2860757
Brief Bioinform. 2019 Jul 19;20(4):1160-1166
pubmed: 28968734
Curr Opin Genet Dev. 2004 Dec;14(6):627-33
pubmed: 15531157
Hum Vaccin Immunother. 2016 May 3;12(5):1274-6
pubmed: 26889694
Nat Genet. 2003 Sep;35(1):32-40
pubmed: 12910271
J Infect Dis. 2015 Jul 15;212(2):294-301
pubmed: 25489002
Philos Trans R Soc Lond B Biol Sci. 2012 Mar 19;367(1590):860-7
pubmed: 22312053
PLoS One. 2015 Jul 16;10(7):e0132623
pubmed: 26182210
Vaccine. 2009 Oct 9;27(43):6034-41
pubmed: 19666155
J Pediatr (Rio J). 2015 Jul-Aug;91(4):315-7
pubmed: 25704450
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D32-6
pubmed: 16381877
Infect Immun. 2001 Sep;69(9):5520-8
pubmed: 11500425