Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico

@article{Vgene2017SalmonellaEG,
  title={Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico},
  author={{\AA}shild J. V{\aa}gene and Alexander Herbig and Michael G. Campana and Nelly M Robles Garc{\'i}a and Christina G Warinner and Susanna Sabin and Maria A. Spyrou and Aida Andrades Valtue{\~n}a and Daniel H. Huson and Noreen Tuross and Kirsten I. Bos and Johannes Krause},
  journal={Nature Ecology \& Evolution},
  year={2017},
  volume={2},
  pages={520-528}
}
Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery… 
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References

SHOWING 1-10 OF 141 REFERENCES
Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica
TLDR
The results indicate that Paratyphi C has been a pathogen of humans for at least 1,000 years, and may have evolved after zoonotic transfer from swine during the Neolithic period.
A draft genome of Yersinia pestis from victims of the Black Death
TLDR
A reconstructed ancient genome of Yersinia pestis is reported at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348–1350, suggesting that contemporary Y. pestis epidemics have their origins in the medieval era.
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis
TLDR
Three 1,000-year-old mycobacterial genomes from Peruvian human skeletons are presented, revealing that a member of the M. tuberculosis complex caused human disease before contact and implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.
Salmonella paratyphi C: Genetic Divergence from Salmonella choleraesuis and Pathogenic Convergence with Salmonella typhi
TLDR
S. paratyphi C does not share a common ancestor with other human-adapted typhoid agents, supporting the convergent evolution model of the Typhoid agents.
What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B
TLDR
Genomics provides the first high-resolution view of this serotype, placing strains carrying serotype Paratyphi B into the wider genomic context of the Salmonella enterica species, and reveals a history of disease dating back to the middle ages caused by a group of distinct lineages with various abilities to cause invasive disease.
Typhoid fever.
  • A. B. CiusnE
  • Medicine
    The Journal of the Arkansas Medical Society
  • 1967
TLDR
This Review will focus on recent developments in the understanding of Typhoid fever, a disease caused by Salmonella enterica serovar typhi which is one of the most common causes of bowel perforation in the developing world.
The 5300-year-old Helicobacter pylori genome of the Iceman
TLDR
The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.
False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing
TLDR
8 16th-century Mixtec individuals from the site of Teposcolula Yucundaa (Oaxaca, Mexico) who are reported to have died from the huey cocoliztli (‘Great Pestilence’ in Nahautl), an unknown disease that decimated native Mexican populations during the Spanish colonial period are shotgun-sequenced in order to identify the pathogen.
Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ
TLDR
The differences in epidemiology, clinical manifestations, and the human immune response to typhoidal and NTS infections are outlined and the current thinking on why these differences might exist is summarized.
Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae
TLDR
The origins of leprosy bacilli are probed by using a genomic capture-based approach on DNA obtained from skeletal remains from the 10th to 14th centuries, suggesting a link between the middle-eastern and medieval European strains, and remarkable genomic conservation during the past 1000 years.
...
1
2
3
4
5
...