RESUMO
The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.
Assuntos
Doenças Transmissíveis/história , DNA Antigo/análise , Fósseis/microbiologia , Paleopatologia/métodos , Evolução Biológica , DNA Bacteriano , Fósseis/parasitologia , Genoma Bacteriano , Genômica/métodos , Helicobacter pylori/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , História Antiga , Humanos , Mycobacterium leprae/genética , Mycobacterium tuberculosis/genética , Paleontologia/métodos , Filogenia , Yersinia pestis/genéticaRESUMO
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.
Assuntos
Bactérias/genética , Bactérias/patogenicidade , DNA Bacteriano/genética , Fósseis , Técnicas Genéticas , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Osso e Ossos/química , DNA Bacteriano/isolamento & purificação , Biblioteca Gênica , Testes Genéticos , Mycobacterium leprae/genéticaRESUMO
Leprosy was endemic in Europe until the Middle Ages. Using DNA array capture, we have obtained genome sequences of Mycobacterium leprae from skeletons of five medieval leprosy cases from the United Kingdom, Sweden, and Denmark. In one case, the DNA was so well preserved that full de novo assembly of the ancient bacterial genome could be achieved through shotgun sequencing alone. The ancient M. leprae sequences were compared with those of 11 modern strains, representing diverse genotypes and geographic origins. The comparisons revealed remarkable genomic conservation during the past 1000 years, a European origin for leprosy in the Americas, and the presence of an M. leprae genotype in medieval Europe now commonly associated with the Middle East. The exceptional preservation of M. leprae biomarkers, both DNA and mycolic acids, in ancient skeletons has major implications for palaeomicrobiology and human pathogen evolution.