Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.
Journal
PLoS biology
ISSN: 1545-7885
Titre abrégé: PLoS Biol
Pays: United States
ID NLM: 101183755
Informations de publication
Date de publication:
10 2020
10 2020
Historique:
received:
06
03
2020
accepted:
18
09
2020
entrez:
22
10
2020
pubmed:
23
10
2020
medline:
15
12
2020
Statut:
epublish
Résumé
Predicting how pathogen populations will change over time is challenging. Such has been the case with Streptococcus pneumoniae, an important human pathogen, and the pneumococcal conjugate vaccines (PCVs), which target only a fraction of the strains in the population. Here, we use the frequencies of accessory genes to predict changes in the pneumococcal population after vaccination, hypothesizing that these frequencies reflect negative frequency-dependent selection (NFDS) on the gene products. We find that the standardized predicted fitness of a strain, estimated by an NFDS-based model at the time the vaccine is introduced, enables us to predict whether the strain increases or decreases in prevalence following vaccination. Further, we are able to forecast the equilibrium post-vaccine population composition and assess the invasion capacity of emerging lineages. Overall, we provide a method for predicting the impact of an intervention on pneumococcal populations with potential application to other bacterial pathogens in which NFDS is a driving force.
Identifiants
pubmed: 33091022
doi: 10.1371/journal.pbio.3000878
pii: PBIOLOGY-D-20-00582
pmc: PMC7580979
doi:
Substances chimiques
Pneumococcal Vaccines
0
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
Pagination
e3000878Subventions
Organisme : NIAID NIH HHS
ID : R01 AI106786
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI048935
Pays : United States
Organisme : NIGMS NIH HHS
ID : U54 GM088558
Pays : United States
Organisme : World Health Organization
ID : 001
Pays : International
Organisme : Wellcome Trust
ID : 104169/Z/14/A
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Déclaration de conflit d'intérêts
I have read the journal’s policy and the authors of this manuscript have the following competing interests. ML has consulted for Pfizer, Affinivax, and Merck and has received grant support not related to this paper from Pfizer and PATH Vaccine Solutions. WPH, ML, and NJC have consulted for Antigen Discovery Inc. The authors have declared that no competing interests exist. KLOB has received grant support for pneumococcal work not related to this paper from Pfizer, GSK, and Gavi. KLOB has consulted for Merck and Sanofi Pasteur. LRG, LLH, and RCW have received grant support not related to this paper from Pfizer, Merck, and GSK.
Références
Microb Genom. 2019 Feb;5(2):
pubmed: 30777813
Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1075-1080
pubmed: 28096340
Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3102-3107
pubmed: 29511100
Science. 1999 Feb 5;283(5403):806-9
pubmed: 9933155
Philos Trans R Soc Lond B Biol Sci. 1988 Jul 6;319(1196):459-72
pubmed: 2905487
PLoS Genet. 2006 Mar;2(3):e31
pubmed: 16532061
EBioMedicine. 2019 May;43:338-346
pubmed: 31003929
Nat Rev Microbiol. 2014 Apr;12(4):263-73
pubmed: 24590245
Hum Vaccin Immunother. 2016;12(2):358-74
pubmed: 26905681
Pediatr Infect Dis J. 2016 Aug;35(8):901-6
pubmed: 27420806
Science. 2012 Mar 16;335(6074):1376-80
pubmed: 22383809
Genetics. 2018 Mar;208(3):1247-1260
pubmed: 29330348
Genome Biol. 2010;11(10):R107
pubmed: 21034474
Epidemics. 2010 Jun;2(2):80-4
pubmed: 21031138
Antimicrob Agents Chemother. 2014 Nov;58(11):6484-9
pubmed: 25136018
Trends Microbiol. 2018 Feb;26(2):102-118
pubmed: 29097090
Int J Circumpolar Health. 2013 Aug 05;72:
pubmed: 23984279
Infect Immun. 2013 Dec;81(12):4519-24
pubmed: 24082068
Microb Genom. 2015 Nov 5;1(5):e000038
pubmed: 28348822
Vaccine. 2010 Dec 16;29(2):283-8
pubmed: 21029807
Emerg Infect Dis. 2018 Mar;24(3):453-461
pubmed: 29460732
Lancet. 2003 Aug 2;362(9381):355-61
pubmed: 12907008
Mol Biol Evol. 2013 May;30(5):1224-8
pubmed: 23408797
PLoS Med. 2011 Apr;8(4):e1001017
pubmed: 21483718
Clin Infect Dis. 2010 May 1;50(9):1238-46
pubmed: 20367225
PLoS Pathog. 2018 Apr 4;14(4):e1006966
pubmed: 29617440
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
PLoS Pathog. 2015 Jul 16;11(7):e1005034
pubmed: 26181911
PLoS One. 2011;6(10):e24581
pubmed: 22022358
Int J Cancer. 2018 Jun 15;142(12):2491-2500
pubmed: 29377141
J Infect Dis. 2017 Mar 1;215(5):713-722
pubmed: 28035010
Hum Vaccin Immunother. 2016;12(2):451-66
pubmed: 26308796
Diagn Microbiol Infect Dis. 2015 Feb;81(2):145-8
pubmed: 25483278
Am Nat. 2013 Jan;181(1):12-24
pubmed: 23234842
Trends Genet. 2013 Mar;29(3):170-5
pubmed: 23332119
J Clin Microbiol. 2016 Apr;54(4):967-71
pubmed: 26818670
Pediatr Infect Dis J. 2011 Apr;30(4):302-8
pubmed: 21085049
Lancet Glob Health. 2018 Jul;6(7):e744-e757
pubmed: 29903376
Curr Opin Pediatr. 2011 Feb;23(1):98-104
pubmed: 21191300
Curr Opin Microbiol. 2008 Oct;11(5):472-7
pubmed: 19086349
mBio. 2019 Apr 23;10(2):
pubmed: 31015329
Vaccine. 2010 Jul 5;28(30):4842-6
pubmed: 20434550
Pediatr Infect Dis J. 2007 Jun;26(6):468-72
pubmed: 17529860
Nat Ecol Evol. 2017 Dec;1(12):1950-1960
pubmed: 29038424
Lancet. 2011 Dec 3;378(9807):1962-73
pubmed: 21492929
Sci Rep. 2017 Aug 22;7(1):9023
pubmed: 28831154
PLoS One. 2013 Sep 23;8(9):e74906
pubmed: 24086394
Pediatr Infect Dis J. 2016 Aug;35(8):907-14
pubmed: 27171679
Nat Ecol Evol. 2017 Feb 21;1(3):77
pubmed: 28812721
Bioinformatics. 2004 Jan 22;20(2):289-90
pubmed: 14734327
Nat Commun. 2014 Nov 19;5:5471
pubmed: 25407023
Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1701-9
pubmed: 26951657
Nat Genet. 2013 Jun;45(6):656-63
pubmed: 23644493
Science. 2011 Jan 28;331(6016):430-4
pubmed: 21273480
Pediatr Infect Dis J. 2009 Aug;28(8):711-6
pubmed: 19593248
Curr Opin Genet Dev. 2005 Dec;15(6):589-94
pubmed: 16185861