Ancient pathogen genomics

Their genome, referred to as ancient DNA (aDNA), is isolated from the burial's remains (bones and teeth) of victims of the pandemics caused by these pathogens.

[1] Therefore, for that infections that have caused the death of the host in the acute phase, the preferred sampling material is the inner chamber of the teeth[1][3] since this is a tissue that is highly vascularized during life.

[4] To exploit this characteristic feature of ancient DNA, improved silica-based extraction protocols with modified volume and composition of the DNA-binding buffer were introduced.

In this method, aDNA is end-repaired and then an adenine residue is added to the 3' ends of the strands, which can facilitate the ligation of the template with adaptors that contain a tailor of thymine.

These approaches can mainly be divided into three types: those used during library construction, by preferentially incorporating aDNA fragments characterised by the high level of damage, those applied after library construction, by separating exogenous and endogenous fractions through annealing to pre-defined sets of probes (in solution or on microarrays), or those based on targeted digestion of environmental microbial DNA using restriction enzymes and primer extension capture (PEC).

This technique is based on the use of a genome-wide biotinylated RNA probe library generated through in vitro transcription of fresh modern DNA extracts from species closely related to the target aDNA sample.

To improve stringency and reduce enrichment for highly repetitive regions, low-complexity DNA and adaptor-blocking RNA oligonucleotides are added.

A widely used tool to align reads from aDNA against reference genomes is the PALEOMIX package, which can quantify DNA damage levels through mapDamage2 and perform phylogenomic and metagenomic analyses.

It is important to consider that the alignment will always exhibit substantial fractions of nucleotides mismatched that do not result from sequencing errors or polymorphisms but from the presence of damaged bases.

All references, complete bacterial genomes, are contained in a database called National Center for Biotechnology Information (NCBI) RefSeq.

To authenticate the candidate taxonomic assignments complete alignments are needed, but the target DNA is often present in a low amount so a small number of a marked region may not be sufficient for identification.

This method is useful for studies dealing with the identification of pathogens responsible for ancient and modern disease, especially in cases for which candidate organisms are not known a priori.

[10] One interesting application of the different sequencing techniques available nowadays is the investigation of historical disease outbreaks to provide an answer to important and long-standing questions in epidemiology, pathogen evolution and also human history.

Today Y.pestis and S. enterica seem to be harmless to humans, but scientists are still interested in the long-term tracing of genetic adaptation of these bacteria and accurate quantification of rates of their evolutionary change.

[2] Being perfectly aware of the fact that bacteria and viruses are one of the most variable elements in nature, prone to unlimited mutational events, and taking for granted that it is impossible to manage all the external factors that can influence the development of a pathogenic virus, nobody is talking about defeating a new possible outbreak of plague or any other infective agent of the past: here the aim is to define a strategy, a "guideline", to be more prepared when a new dangerous pathogen will come.

While they continue to develop strategies to defeat emerging threats using diagnostic, molecular and advanced tools, they are still looking back at how ancient pathogens have evolved and adapted through historical events.

[11] In this continuous challenge through the years, next to infective diseases and other illnesses afflicting modern human society, cancer recently represents one of the most enigmatical ailments.

Scientists are investigating if neoplastic diseases are restricted to postindustrial human society or if their origins can be found further back in time, maybe into prehistory.

For this reason, molecular analytical techniques are applied to archaeological remains to study hominin evolution, but also to improve the research in understanding the epidemiology and aetiology of tumours.

After all, archaeologists, geneticists, and medical scientists are concerned in exploring the influences of pathogens that can contribute, threatening or improving, human health and longevity.

This gene is present on the pMT1 plasmid and allowed the survival of the bacterium in the flea vector and facilitated colonization of the midgut in arthropod, giving rise to the past millennium large-scale pandemics.

These differences are given by two plasmids: pPCP1, that confer to the bacterium its invasive properties in humans and pMT1, which is involved in flea colonisation (along with some loss of function on bacterial chromosomal genes).

[citation needed] Samples dated on the Late Neolithic and Bronze Age allowed identifying a first genetic divergence between Y. pseudotuberculosis and Y. pestis ancestors.

[1] The comparison of a draft of the genome and the two plasmids (pCD1 and pMT1) with samples of Black Death victims (1348–1349) in the East Smithfield burial ground underlined a very high genetic conservation of the sequence: only 97 single-nucleotide differences over 660 years.

However, the Ellwangen strain genome sequenced in this study may be considered a proof of the second hypothesis due to the geographical position of the city that tends to exclude the possibility of an introduction of plague from eastward.

[15] Sequencing of Y. pestis genomes allowed to discover a variation event preceding Black Death that gave rise to many strains that circulate today.

[15] A series of 16th epidemics in Mexico, called the "huey cocoliztli" in the native Nahuatl language, caused high mortality in indigenous Aztec population, leading to demographic collapse.

[citation needed] A group of scientists from Harvard and Max-Planck Institute published a study in the journal of Nature ecology and Evolution, and they suggest Salmonella enterica as a good candidate for the strong epidemic in Mexico during the 16th century.

[citation needed] A further analysis was carried out to identify the classical pattern of damage of aDNA in the three positive tooth samples and this was conducted by mapping the data sets to the S. Paratyphy C genome reference.

They performed a whole-genome target array and in-solution hybridization capture using probes that include the modern S. enterica genome differences and using S. Paratyphi C as reference.