Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent, Treponema pallidum.
genome analysis
phylogenetic congruence
recombination
selection
treponematoses
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
07 01 2022
07 01 2022
Historique:
pubmed:
19
11
2021
medline:
1
4
2022
entrez:
18
11
2021
Statut:
ppublish
Résumé
The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
Identifiants
pubmed: 34791386
pii: 6427636
doi: 10.1093/molbev/msab318
pmc: PMC8789261
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIAID NIH HHS
ID : U19 AI144133
Pays : United States
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Curr Biol. 2020 Oct 5;30(19):R1092-R1095
pubmed: 33022244
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Curr Opin Microbiol. 2016 Jun;31:116-123
pubmed: 27057964
Syst Biol. 2006 Feb;55(1):21-30
pubmed: 16507521
Syst Biol. 2009 Feb;58(1):35-54
pubmed: 20525567
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
Theor Popul Biol. 2001 Feb;59(1):27-40
pubmed: 11243926
PLoS One. 2018 Jul 19;13(7):e0201068
pubmed: 30024965
Curr Biol. 2020 Oct 5;30(19):3788-3803.e10
pubmed: 32795443
J Med Microbiol. 2013 Feb;62(Pt 2):196-207
pubmed: 23082031
Biol Direct. 2011 May 26;6:28
pubmed: 21615910
PLoS One. 2017 Aug 7;12(8):e0182768
pubmed: 28787460
PLoS One. 2014 Jul 17;9(7):e101717
pubmed: 25032825
PLoS Negl Trop Dis. 2012 Jan;6(1):e1471
pubmed: 22292095
Nat Microbiol. 2016 Dec 19;2:16240
pubmed: 27991885
Genome Biol. 2016 Mar 31;17:60
pubmed: 27036623
J Bacteriol. 2012 Aug;194(16):4208-25
pubmed: 22661689
Clin Infect Dis. 2018 Mar 5;66(6):818-824
pubmed: 29045605
Oncotarget. 2016 Jul 12;7(28):42904-42918
pubmed: 27344187
Genome Biol. 2007;8(5):R71
pubmed: 17475002
Annu Rev Microbiol. 2008;62:53-70
pubmed: 18785837
PLoS Negl Trop Dis. 2008 Jan 15;2(1):e148
pubmed: 18235852
PLoS One. 2018 Jul 30;13(7):e0200773
pubmed: 30059541
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6815-9
pubmed: 9192648
Genetics. 2003 Jul;164(3):1229-36
pubmed: 12871927
Bioinformatics. 2016 Jan 15;32(2):292-4
pubmed: 26428292
Mol Biol Evol. 2006 Nov;23(11):2220-33
pubmed: 16926243
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
PLoS Negl Trop Dis. 2018 Oct 10;12(10):e0006867
pubmed: 30303967
PLoS One. 2020 Apr 1;15(4):e0230926
pubmed: 32236138
Infect Immun. 2008 May;76(5):1848-57
pubmed: 18332212
Nat Genet. 2014 Nov;46(11):1205-11
pubmed: 25282102
Mol Biol Evol. 2015 May;32(5):1365-71
pubmed: 25701167
Trends Microbiol. 2010 Jul;18(7):315-22
pubmed: 20452218
PLoS Pathog. 2021 Jul 6;17(7):e1009612
pubmed: 34228757
Front Microbiol. 2019 Jul 31;10:1691
pubmed: 31417509
Nat Microbiol. 2016 Oct 17;2:16190
pubmed: 27748767
Sci Adv. 2019 Jun 12;5(6):eaaw3307
pubmed: 31448322
Mol Biol Evol. 2015 Mar;32(3):820-32
pubmed: 25540451
PLoS Negl Trop Dis. 2012;6(9):e1832
pubmed: 23029591
Nat Rev Microbiol. 2018 Apr;16(4):202-213
pubmed: 29456241
PLoS Negl Trop Dis. 2012;6(6):e1698
pubmed: 22720110
mBio. 2018 Jun 12;9(3):
pubmed: 29895642
Infect Genet Evol. 2012 Mar;12(2):191-202
pubmed: 22198325
PLoS Negl Trop Dis. 2017 Mar 6;11(3):e0005434
pubmed: 28263990
J Hosp Infect. 2021 Feb;108:7-14
pubmed: 33181279
PLoS Negl Trop Dis. 2014 Nov 06;8(11):e3261
pubmed: 25375929
Microbiol Mol Biol Rev. 2010 Sep;74(3):417-33
pubmed: 20805405
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
PLoS Negl Trop Dis. 2019 Jun 19;13(6):e0007463
pubmed: 31216284
Nat Commun. 2019 Jul 22;10(1):3255
pubmed: 31332179
PLoS Negl Trop Dis. 2018 Jun 21;12(6):e0006447
pubmed: 29927932
Proc Biol Sci. 2002 Jan 22;269(1487):137-42
pubmed: 11798428
Nat Rev Genet. 2003 Jan;4(1):50-60
pubmed: 12509753
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041
pubmed: 25675341
PLoS Comput Biol. 2021 Jan 27;17(1):e1008678
pubmed: 33503026
Nat Microbiol. 2016 Dec 05;2:16245
pubmed: 27918528
Clin Microbiol Rev. 1999 Apr;12(2):187-209
pubmed: 10194456
Bioinformatics. 2005 Mar 1;21(5):676-9
pubmed: 15509596
Philos Trans R Soc Lond B Biol Sci. 2012 Mar 19;367(1590):860-7
pubmed: 22312053
Front Microbiol. 2019 May 22;10:1006
pubmed: 31191463
Mol Microbiol. 2004 Jun;52(6):1579-96
pubmed: 15186410
J Bacteriol. 2006 Dec;188(23):8169-77
pubmed: 16997954
Nucleic Acids Res. 2015 Feb 18;43(3):e15
pubmed: 25414349
PLoS Negl Trop Dis. 2017 Dec 27;11(12):e0006113
pubmed: 29281641