CoChat
Sign Up
Cited by 498

The DOI matches its Crossref record.

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

Morelli, Giovanna, Song, Yajun, Mazzoni, Camila J, Eppinger, Mark, Roumagnac, Philippe, Wagner, David M, Feldkamp, Mirjam, Kusecek, Barica, Vogler, Amy J, Li, Yanjun, Cui, Yujun, Thomson, Nicholas R, Jombart, Thibaut, Leblois, Raphael, Lichtner, Peter, Rahalison, Lila, Petersen, Jeannine M, Balloux, Francois, Keim, Paul, Wirth, Thierry, Ravel, Jacques, Yang, Ruifu, Carniel, Elisabeth, Achtman, Mark·2010·Nature Genetics
DOI 10.1038/ng.705PMC PMC2999892
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/ng.705

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 44

  1. Linz, B. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445, 915–918 (2007). · DOI
  2. Stenseth, N.C. et al. Plague: past, present, and future. PLoS Med. 5, e3 (2008). · DOI
  3. Keeling, M.J. & Gilligan, C.A. Metapopulation dynamics of bubonic plague. Nature 407, 903–906 (2000). · DOI
  4. Pollitzer, R. Plague studies. 1. A summary of the history and survey of the present distribution of the disease. Bull. World Health Organ. 4, 475–533 (1951).
  5. Devignat, R. Variétés de l′espèce Pasteurella pestis. Nouvelle hypothèse. Bull. World Health Organ. 4, 247–263 (1951).
  6. Wu, L.T. Chapter I: historical aspects. in Plague: A Manual for Medical and Public Health Workers 1–55 (Weishengshu, National Quarantine Service, Shanghai, China, 1936).
  7. Anisimov, A.P., Lindler, L.E. & Pier, G.B. Intraspecific diversity of Yersinia pestis. Clin. Microbiol. Rev. 17, 434–464 (2004). · DOI
  8. Achtman, M. Evolution, population structure and phylogeography of genetically monomorphic bacterial pathogens. Annu. Rev. Microbiol. 62, 53–70 (2008). · DOI
  9. Achtman, M. et al. Microevolution and history of the plague bacillus, Yersinia pestis. Proc. Natl. Acad. Sci. USA 101, 17837–17842 (2004). · DOI · Paper page
  10. Brygoo, E.R. Epidemiologie de la peste à Madagascar. Archive de l′lnstitut Pasteur de Madagascar 35, 7–147 (1966).
  11. Girard, G. Immunity in plague. Acquisitions supplied by 30 years of work on the “Pasteurella pestis EV” (Girard and Robic) strain. Biol. Med. (Paris) 52, 631–731 (1963).
  12. Li, Y. et al. Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: insights into the worldwide expansion of Central Asia plague foci. PLoS ONE 4, e6000 (2009). · DOI
  13. Haensch, S. et al. Distinct clones of Yersinia pestis caused the Black Death. PLoS Pathog 6, e1001134 (2010). · DOI
  14. Levathes, L. When China Ruled the Seas: The Treasure Fleet of the Dragon Throne, 1405–1433 1–252 (Oxford University Press, New York, 1996).
  15. Link, V.B. A history of plague in United States of America. Public Health Monogr. 26, 1–120 (1955).
  16. Yu, H.L. & Christakos, G. Spatiotemporal modelling and mapping of the bubonic plague epidemic in India. Int. J. Health Geogr. 5, 12 (2006). · DOI
  17. Del Rio, A., Zegers, R., Boza, R.D. & Montero, L. Informe sobre la epidemia de peste bubonica. La Chilena di Hijiene IX, 1–7 (1904).
  18. Lauzeral, P. & Millischer, P. A propos de la filiation de deux cas. Bull. Soc. Pathol. Exot. 25, 935–941 (1932).
  19. Drummond, A.J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007). · DOI
  20. Adjemian, J.Z., Foley, P., Gage, K.L. & Foley, J.E. Initiation and spread of traveling waves of plague, Yersinia pestis, in the western United States. Am. J. Trop. Med. Hyg. 76, 365–375 (2007). · DOI
  21. Guiyoule, A. et al. Recent emergence of new variants of Yersinia pestis in Madagascar. J. Clin. Microbiol. 35, 2826–2833 (1997). · DOI
  22. Zhou, D. et al. DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation. J. Bacteriol. 186, 5138–5146 (2004). · DOI
  23. Eppinger, M. et al. Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. J. Bacteriol. 191, 7628–7629 (2009). · DOI
  24. Eppinger, M. et al. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J. Bacteriol. 192, 1685–1699 (2010). · DOI
  25. Auerbach, R.K. et al. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS ONE 2, e770 (2007). · DOI
  26. Touchman, J.W. et al. A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS ONE 2, e220 (2007). · DOI
  27. Garcia, E. et al. Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union. Adv. Exp. Med. Biol. 603, 17–22 (2007). · DOI
  28. Song, Y. et al. Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res. 11, 179–197 (2004). · DOI
  29. Chain, P.S. et al. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J. Bacteriol. 188, 4453–4463 (2006). · DOI
  30. Parkhill, J. et al. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523–527 (2001). · DOI
  31. Deng, W. et al. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184, 4601–4611 (2002). · DOI
  32. Chain, P.S.G. et al. Insights into the genome evolution of Yersinia pestis through whole genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 101, 13826–13831 (2004). · DOI
  33. Welch, T.J. et al. Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS ONE 2, e309 (2007). · DOI
  34. Galimand, M. et al. Multidrug resistance in Yersinia pestis mediated by a transferable plasmid. N. Engl. J. Med. 337, 677–680 (1997). · DOI
  35. Pearson, T., Okinaka, R.T., Foster, J.T. & Keim, P. Phylogenetic understanding of clonal populations in an era of whole genome sequencing. Infect. Genet. Evol. 9, 1010–1019 (2009). · DOI
  36. Roumagnac, P. et al. Evolutionary history of Salmonella Typhi. Science 314, 1301–1304 (2006). · DOI
  37. Nelson, K.E. et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–329 (1999). · DOI
  38. Eppinger, M. et al. The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative Agent of Far East scarlet-like fever. PLoS Genet. 3, e142 (2007). · DOI
  39. Huson, D.H. et al. Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics 17 (Suppl 1), S132–S139 (2001). · DOI
  40. Holt, K.E. et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 40, 987–993 (2008). · DOI
  41. Lowder, B.V. et al. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc. Natl. Acad. Sci. USA 106, 19545–19550 (2009). · DOI
  42. Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004). · DOI · Paper page
  43. Vogler, A.J. et al. Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92. Biotechniques 44, 201 203–204, 207 (2008). · DOI
  44. Vogler, A.J. et al. Phylogeography of Francisella tularensis: global expansion of a highly fit clone. J. Bacteriol. 191, 2474–2484 (2009). · DOI

Cited by

See all 498

Metadata

Authors
Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., Feldkamp, M., Kusecek, B., Vogler, A. J., Li, Y., Cui, Y., Thomson, N. R., Jombart, T., Leblois, R., Lichtner, P., Rahalison, L., Petersen, J. M., Balloux, F., Keim, P., Wirth, T., Ravel, J., Yang, R., Carniel, E., & Achtman, M.
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2010-10-31
Volume
42
Issue
12
Pages
1140-1143
ISSN
  • 1061-4036
  • 1546-1718
DOI
10.1038/ng.705
PMC
PMC2999892
Cited by
498
References
0
Language
en
Licence
www.springer.com/tdm (tdm)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. https://app.cochat.ai/papers/10.1038/ng.705
The paper
Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., Feldkamp, M., Kusecek, B., Vogler, A. J., Li, Y., Cui, Y., Thomson, N. R., Jombart, T., Leblois, R., Lichtner, P., Rahalison, L., Petersen, J. M., Balloux, F., Keim, P., . . . Achtman, M. (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics. https://doi.org/10.1038/ng.705