14th century Yersinia pestis genomes support emergence of pestis secunda within Europe.
Journal
PLoS pathogens
ISSN: 1553-7374
Titre abrégé: PLoS Pathog
Pays: United States
ID NLM: 101238921
Informations de publication
Date de publication:
07 2023
07 2023
Historique:
received:
30
11
2022
accepted:
04
05
2023
revised:
10
08
2023
medline:
14
8
2023
pubmed:
18
7
2023
entrez:
18
7
2023
Statut:
epublish
Résumé
Pestis secunda (1356-1366 CE) is the first of a series of plague outbreaks in Europe that followed the Black Death (1346-1353 CE). Collectively this period is called the Second Pandemic. From a genomic perspective, the majority of post-Black Death strains of Yersinia pestis thus far identified in Europe display diversity accumulated over a period of centuries that form a terminal sub-branch of the Y. pestis phylogeny. It has been debated if these strains arose from local evolution of Y. pestis or if the disease was repeatedly reintroduced from an external source. Plague lineages descended from the pestis secunda, however, are thought to have persisted in non-human reservoirs outside Europe, where they eventually gave rise to the Third Pandemic (19th and 20th centuries). Resolution of competing hypotheses on the origins of the many post-Black Death outbreaks has been hindered in part by the low representation of Y. pestis genomes in archaeological specimens, especially for the pestis secunda. Here we report on five individuals from Germany that were infected with lineages of plague associated with the pestis secunda. For the two genomes of high coverage, one groups within the known diversity of genotypes associated with the pestis secunda, while the second carries an ancestral genotype that places it earlier. Through consideration of historical sources that explore first documentation of the pandemic in today's Central Germany, we argue that these data provide robust evidence to support a post-Black Death evolution of the pathogen within Europe rather than a re-introduction from outside. Additionally, we demonstrate retrievability of Y. pestis DNA in post-cranial remains and highlight the importance of hypothesis-free pathogen screening approaches in evaluations of archaeological samples.
Identifiants
pubmed: 37463152
doi: 10.1371/journal.ppat.1011404
pii: PPATHOGENS-D-22-02071
pmc: PMC10414589
doi:
Substances chimiques
DNA, Bacterial
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1011404Informations de copyright
Copyright: © 2023 Parker et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have no conflicts of interest to report.
Références
Sci Rep. 2020 Jun 11;10(1):9499
pubmed: 32528126
Cell Host Microbe. 2014 May 14;15(5):578-86
pubmed: 24832452
Genome Biol. 2016 Mar 31;17:60
pubmed: 27036623
Nature. 2014 Oct 23;514(7523):494-7
pubmed: 25141181
Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448
pubmed: 20516186
Sci Rep. 2020 Oct 26;10(1):18225
pubmed: 33106554
Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13110-5
pubmed: 16924109
Methods Mol Biol. 2019;1963:25-29
pubmed: 30875041
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nat Commun. 2019 Oct 2;10(1):4470
pubmed: 31578321
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Nucleic Acids Res. 2010 Apr;38(6):e87
pubmed: 20028723
Methods Mol Biol. 2019;1963:75-83
pubmed: 30875046
Science. 2021 Oct 08;374(6564):182-188
pubmed: 34618559
Proc Natl Acad Sci U S A. 2022 Apr 26;119(17):e2116722119
pubmed: 35412864
Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14527-32
pubmed: 21856946
Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):577-82
pubmed: 23271803
Nature. 2022 Jun;606(7915):718-724
pubmed: 35705810
Nat Genet. 2011 May;43(5):491-8
pubmed: 21478889
Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190569
pubmed: 33012225
Ecol Evol. 2018 Feb 26;8(6):3534-3542
pubmed: 29607044
Elife. 2016 Jan 21;5:e12994
pubmed: 26795402
Bioinformatics. 2013 Jul 01;29(13):1682-4
pubmed: 23613487
Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11790-E11797
pubmed: 30478041
Cell. 2019 Jan 10;176(1-2):295-305.e10
pubmed: 30528431
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12363-12372
pubmed: 31164419
Cell. 2015 Oct 22;163(3):571-82
pubmed: 26496604
Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):E746-52
pubmed: 21876176
Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2223-7
pubmed: 23341637
Infect Immun. 2009 Jun;77(6):2242-50
pubmed: 19289506
Nature. 2001 Oct 4;413(6855):523-7
pubmed: 11586360
PLoS Pathog. 2010 Feb 26;6(2):e1000783
pubmed: 20195507
Clin Microbiol Rev. 1997 Jan;10(1):35-66
pubmed: 8993858
Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28328-28335
pubmed: 33106412
Genome Biol. 2019 Dec 16;20(1):280
pubmed: 31842945
PLoS Pathog. 2010 Oct 07;6(10):e1001134
pubmed: 20949072
Bioinformatics. 2006 Nov 1;22(21):2688-90
pubmed: 16928733
Lancet Infect Dis. 2014 Apr;14(4):319-26
pubmed: 24480148
Nature. 2011 Oct 12;478(7370):506-10
pubmed: 21993626
Mol Biol Evol. 2016 Nov;33(11):2911-2923
pubmed: 27578768
Proc Biol Sci. 2019 Apr 24;286(1901):20182429
pubmed: 30991930
PLoS One. 2014 May 07;9(5):e96513
pubmed: 24806459
Proc Biol Sci. 2007 Aug 22;274(1621):1963-9
pubmed: 17550884
Cell Host Microbe. 2016 Jun 8;19(6):874-81
pubmed: 27281573
Sci Rep. 2017 Oct 11;7(1):12973
pubmed: 29021541
Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12637-40
pubmed: 9770538
Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3020-5
pubmed: 25713390
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427