Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

Wagner, David M.; Klunk, Jennifer; Harbeck, Michaela; Devault, Alison; Waglechner, Nicholas; Sahl, Jason W.; Enk, Jacob; Birdsell, Dawn N.; Kuch, Melanie; Lumibao, Candice Y.; Poinar, Debi; Pearson, Talima; Fourment, Mathieu; Golding, Brian; Riehm, Julia M.; Earn, David J. D.; DeWitte, Sharon N.; Rouillard, Jean Marie; Grupe, Gisela; Wiechmann, Ingrid; Bliska, James B.; Keim, Paul; Scholz, Holger C.; Holmes, Edward C.; Poinar, Hendrik N.

doi:10.1016/s1473-3099(13)70323-2

Cited by 390 publications

(352 citation statements)

References 35 publications

Supporting

Mentioning

311

Contrasting

Unclassified

Order By: Relevance

“…Branch 0 begins with ancient genomes from the teeth of Bronze-age individuals who died up to 5000 years ago [31] (populations 0.PRE1, 0.PRE2). These are followed by a variety of extant populations found today in eastern and central Asia (0.PE7, 0.PE1-4, 0.ANT1) [16,30] and then by a genome from the Justinianic pandemic in Germany (0.ANT4) [32]. Branch 0 continues with extant populations from eastern and central Asia (0.ANT2-3), and culminates in a 'big bang' of explosive radiation [16], as witnessed by a polytomy that yielded extant branches 1, 2, 3 and 4.…”

Section: (A) Populations and Phylogenymentioning

confidence: 99%

How old are bacterial pathogens?

Achtman¹

2016

Proc. R. Soc. B.

View full text Add to dashboard Cite

Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori , which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis , the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis . Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.

show abstract

Section: (A) Populations and Phylogenymentioning

confidence: 99%

How old are bacterial pathogens?

Achtman¹

2016

Proc. R. Soc. B.

View full text Add to dashboard Cite

show abstract

“…pestis gene was done to find out about the pandemic and it was found that Y pestis emerged from rodents. 2 Even for different common diseases like Malaria, DNA isolation is used as tool to study the plasmodium. PCR assay targeting the 18S RNA gene, which was considered for finding the affected plasmodium.…”

Section: Introductionmentioning

confidence: 99%

Optimized genomic DNA extraction by a modified organic phenol- chloroform method without using PCR for best results

Ali¹,

Jafar²,

Quratulain³

2016

Int J Res Med Sci

View full text Add to dashboard Cite

INTRODUCTIONDNA studies are widely used now-a-days, for this purpose DNA isolation is done, which is the bases for all the genomic studies. In order to find the best results in shortest time, keeping in view cost effectiveness lot of strategies has been used. Different DNA extraction kits are available in market. A genomic DNA from permafrost was isolated. The fast DNA ® SPIN (FDS) kit results were best as compared to Meta-G-Nome TM (MGN) isolation kit. 1 DNA was isolated from teeth using a modified phenolchloroform method. Screening and analysis of Yesinia ABSTRACT Background: The objective of the study was to design a cost effective, efficient and better protocol for genomic deoxyribonucleic acid (DNA) extraction. Methods: This was an experimental study, which is carried out ARID Research laboratory. The duration of study was four months from March 2015 to June 2015. White blood cells were used for extraction of DNA. Two procedures RBC lysis and extraction of DNA from the pellet was done. The goal was to obtain high quality and quantity DNA yield. Even the amount of blood less than 1 ml can be used for extraction. The extraction of DNA comprise of disruption of nuclear membrane and removal of protein from the pellet. After extraction DNA was purified. DNA was confirmed with the help of Nanodrop technology. Genomic DNA was also confirmed by using horizontal agrose gel electrophoresis and visualized using Gel Doc System. Whole blood approximately 10ml µg, yields 250 µg of DNA, using latest organic phenol chloroform method. Results: Successful extraction of DNA from the WBCs without compromising quality and quantity was the end result. Shelf life of DNA was increased. Current modified protocol of DNA isolation, extraction and purification of DNA is not only cost-effective and highly yielding but also reproducible. Conclusions: The DNA extracted with modified organic phenol-chloroform method was of high quality and quantity. The bands of DNA were confirmed with horizontal electrophoresis. Clear DNA band were visualized indicating the precision of latest protocol. Another important advantage was that very small amount of blood sample is required for DNA extraction and the protocol was cost effective and efficient. Present protocol will be very beneficial for genomic studies, requiring DNA extraction. It will enable researchers to work with fewer budgets and less sample size, obtaining best results.

show abstract

“…Next generation sequencing as applied to ancient DNA has improved our understanding of the evolutionary history of pathogenic bacteria and the phylogeographic distribution of their associated diseases [1][2][3][4][5][6]. Thus far, most genomic analyses have relied on molecular capture techniques designed to target DNA from individual organisms suspected to have left molecular traces in preserved tissues.…”

Section: Introductionmentioning

confidence: 99%

“…Thus far, most genomic analyses have relied on molecular capture techniques designed to target DNA from individual organisms suspected to have left molecular traces in preserved tissues. Candidate biological specimens have been selected based on either historical documentation [1,4,6], a burial context that links them to a past pandemic [5], or diagnostic pathological changes that occur in bone as a result of prolonged infection [2,3]. Such exclusive evidence that links an individual to a specific disease, however, is rare in the archaeological record.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Parallel detection of ancient pathogens via array-based DNA capture

Bos

Jaeger

Schuenemann

et al. 2015

Phil. Trans. R. Soc. B

View full text Add to dashboard Cite

DNA capture coupled with next generation sequencing is highly suitable for the study of ancient pathogens. Screening for pathogens can, however, be meticulous when assays are restricted to the enrichment of single organisms, which is common practice. Here, we report on an array-based DNA capture screening technique for the parallel detection of nearly 100 pathogens that could have potentially left behind molecular signatures in preserved ancient tissues. We demonstrate the sensitivity of our method through evaluation of its performance with a library known to harbour ancient Mycobacterium leprae DNA. This rapid and economical technique will be highly useful for the identification of historical diseases that are difficult to characterize based on archaeological information alone.

show abstract

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

Cited by 390 publications

References 35 publications

How old are bacterial pathogens?

How old are bacterial pathogens?

Optimized genomic DNA extraction by a modified organic phenol- chloroform method without using PCR for best results

Parallel detection of ancient pathogens via array-based DNA capture

Contact Info

Product

Resources

About