Ancient DNA analysis – An established technique in charting the evolution of tuberculosis and leprosy

Abstract

Many tuberculosis and leprosy infections are latent or paucibacillary, suggesting a long time-scale for host and pathogen co-existence. Palaeopathology enables recognition of archaeological cases and PCR detects pathogen ancient DNA (aDNA). Mycobacterium tuberculosis and Mycobacterium leprae cell wall lipids are more stable than aDNA and restrict permeability, thereby possibly aiding long-term persistence of pathogen aDNA. Amplification of aDNA, using specific PCR primers designed for short fragments and linked to fluorescent probes, gives good results, especially when designed to target multi-copy loci. Such studies have confirmed tuberculosis and leprosy, including co-infections. Many tuberculosis cases have non-specific or no visible skeletal pathology, consistent with the natural history of this disease. M. tuberculosis and M. leprae are obligate parasites, closely associated with their human host following recent clonal distribution. Therefore genotyping based on single nucleotide polymorphisms (SNPs) can indicate their origins, spread and phylogeny. Knowledge of extant genetic lineages at particular times in past human populations can be obtained from well-preserved specimens where molecular typing is possible, using deletion analysis, microsatellite analysis and whole genome sequencing. Such studies have identified non-bovine tuberculosis from a Pleistocene bison from 17,500 years BP, human tuberculosis from 9000 years ago and leprosy from over 2000 years ago.

Paleoproteomics of the Dental Pulp: The plague paradigm

“…New insights into bacteria and archaea constituting past microbiota have been gained notably by analyzing ancient dental calculus microbiota [2–4] and digestive tract microbiota [5]. Furthermore, an expanding knowledge of the evolution of pathogens such as Yersinia pestis [6, 7], Mycobacterium tuberculosis and Mycobacterium leprae [8] and variola [9] helped reconstitute the dynamics of past devastating epidemics caused by these pathogens.…”

“…Later studies culminated in the reconstitution of the complete genome of ancient strains of Y . pestis in Bronze Age individuals [6] and historical plague pandemic victims [7, 14, 15], Vibrio cholerae [16], Mycobacterium tuberculosis [8], Borrelia burgdorferi [17] and Treponema denticola [18]; and host-associated viruses [19] including smallpox virus from human specimens buried for 300 years [9]. …”

A Case Study: Was Private William Braine of the 1845 Franklin Expedition a Victim of Tuberculosis? + Supplementary Appendix 1 (See Article Tools)

“…In recent years, the possibility of diagnosing tuberculosis in archaeological skeletons by detection of preserved "ancient" DNA (aDNA) of M. tuberculosis has been explored (Donoghue et al, 2015), and unambiguous identifications have been reported with material dating back several hundred years, especially when the latest "nextgeneration" sequencing (NGS) methods are used (Bouwman et al, 2012;Chan et al, 2013;Kay et al, 2015). In this paper, we report on testing a portion of a rib bone from William Braine for the presence of M. tuberculosis aDNA.…”

A Mycobacterium tuberculosis komplex archaikus DNS kimutatása emberi csontvázmaradványokból

“…Nerlich 1997-ben kevéssé specifikus primereket alkalmazott, ahol 133 bp-os terméket kapott a hsp65 génből, de később bizonyítást nyert, hogy az IS6110 sokkal specifikusabb (Donoghue, 2008;Rault és Drancourt, 2008;Nerlich et al, 1997Nerlich et al, , 2009). Helen Donoghue és munkatársai a 2000-es évek elejétől párhuzamosan kétféle inszerciós szekvenciát vizsgáltak (IS6110 és IS1081) a nagyobb diagnosztikus biztonság érdekében (Donoghue 2008(Donoghue , 2011Donoghue et al, 2005Donoghue et al, , 2015.…”

“…A tuberkulózis (tbc) az egyik legrégebbi fertőző betegség, a megbetegedések száma napjainkban is nagy méreteket ölt (Ortner, 2003;Gutierrez et al, 2005;Hershkovitz et al, 2008;Donoghue, 2009;Baker et al, 2015;Donoghue et al, 2015;Pálfi et al, 2015). A tuberkulózis pandémiás megjelenésű, a WHO becslései szerint jelenleg a Föld népességének mintegy 30%-a látens Mycobacterium tuberculosis hordozó lehet.…”