Palaeopathology and genes: Investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations

Anastasiou, Evilena; Mitchell, Piers D.

doi:10.1016/j.gene.2013.06.017

Cited by 70 publications

(26 citation statements)

References 110 publications

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“…For example, similar lesions occur in tuberculosis and brucellosis, even though the causative organisms are quite different taxonomically and in cell structure. Amplification of pathogen DNA from human remains via PCR has provided an alternative source of information about a range of past infections (5). However, only a single study has reported success in using PCR amplification to confirm historical brucellosis (6).…”

Section: Introductionmentioning

confidence: 99%

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

Kay

Sergeant

Giuffra

et al. 2014

mBio

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Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens.

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Section: Introductionmentioning

confidence: 99%

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

Kay

Sergeant

Giuffra

et al. 2014

mBio

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“…Ectoparasites can be detected by fine sieving of soil, and also looking for them on hair combs, mummies or ancient textiles (Mumcuoglu, 2008;Arriaza et al 2013;Forbes et al 2013). Mummies also have the potential to preserve the ancient DNA of endoparasites, the proteins secreted by these parasites when alive, and possibly the host antibodies made to fight the infection (Anastasiou and Mitchell, 2013b).…”

Section: How To Study Ancient Parasites (Palaeoparasitology)mentioning

confidence: 99%

Human parasites in the Roman World: health consequences of conquering an empire

Mitchell

2016

Parasitology

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Roman era is presented in order to demonstrate the species present at that time, and highlight the health consequences for people living under Roman rule. Despite their large multi-seat public latrines with washing facilities, sewer systems, sanitation legislation, fountains and piped drinking water from aqueducts, we see the widespread presence of whipworm (Trichuris trichiura), roundworm (Ascaris lumbricoides) and Entamoeba histolytica that causes dysentery. This would suggest that the public sanitation measures were insufficient to protect the population from parasites spread by fecal contamination. Ectoparasites such as fleas, head lice, body lice, pubic lice and bed bugs were also present, and delousing combs have been found. The evidence fails to demonstrate that the Roman culture of regular bathing in the public baths reduced the prevalence of these parasites. Fish tapeworm was noted to be widely present, and was more common than in Bronze and Iron Age Europe. It is possible that the Roman enthusiasm for fermented, uncooked fish sauce (garum) may have facilitated the spread of this helminth. Roman medical practitioners such as Galen were aware of intestinal worms, explaining their existence and planning treatment using the humoural theory of the period.

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“…The study described above is typical of those undertaking molecular examination of ancient-pathogen DNA until recently (9). Since the emergence of the use of genetics in paleomicrobiology some 20 years ago, studies have relied largely on PCR amplification of small fragments of DNA from historical material.…”

Section: Commentarymentioning

confidence: 99%

“…Compared against modern genomes, no unique derived positions were detected in the medieval genomes, indicating that the perceived increase in virulence associated with the Black Death may not reflect bacterial genotype but other factors, such as environmental or social changes, the impact of concurrent infectious disease, vector dynamics, or changes in host susceptibility. However, an alternative explanation that cannot be excluded is that the virulence of the organisms may be affected by areas of the genome other than those currently recognized (9). This reflects the fact that this study, as well as a further recent study confirming that the Y. pestis associated with the plague of Justinian in AD 541 to 543 is an independent emergence into humans from rodents that may now be extinct (11), utilizes capture techniques in which modern sequences are used to drive hybridization and “enrich” for DNA of interest.…”

Section: Commentarymentioning

confidence: 99%

Ancient-Pathogen Genomics: Coming of Age?

Whatmore

2014

mBio

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The potentially debilitating zoonotic disease brucellosis is thought to have been a scourge of mankind throughout history. New work by Kay et al. [mBio 5(4):e01337-14, 2014] adds to evidence for this by exploiting the huge advances in next-generation sequencing technology and applying shotgun metagenomics to a calcified nodule obtained from a 14th-century skeleton from Sardinia. While not the first DNA-based confirmation of Brucella in medieval DNA samples, Kay et al.’s study goes much further than previous reports based on single gene fragments in that it allows a full-genome reconstruction and thus facilitates meaningful comparative analysis of relationships with extant Brucella strains. These analyses confirm the close relationship of the genome to contemporary isolates from the western Mediterranean, illustrating the continuity of this lineage in the region over centuries. The study, along with recent studies characterizing other ancient-pathogen genomes, confirms that shotgun metagenomics offers us a powerful tool to fully characterize pathogens from ancient samples. Such studies promise to revolutionize our understanding of the nature of infectious disease in these materials and of the wider picture of the emergence, evolution, and spread of bacterial pathogens over history.

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Palaeopathology and genes: Investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations

Cited by 70 publications

References 110 publications

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

Human parasites in the Roman World: health consequences of conquering an empire

Ancient-Pathogen Genomics: Coming of Age?

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