False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing

被引：30
作者：
Campana M.G. [1 ,2 ]
Robles García N. [3 ]
Rühli F.J. [1 ,2 ]
Tuross N. [1 ]
机构：
[1] Department of Human Evolutionary Biology, Harvard University, Peabody Museum, Cambridge, MA 02138
[2] Centre for Evolutionary Medicine, Anatomy Institute, University of Zurich, Zurich 8057
[3] Instituto Nacional de Antropología e Historia, Mexico City
来源：
BMC Research Notes | / 7卷 / 1期
关键词：
Ancient DNA; False positive; High-throughput sequencing; Pathogen; True single molecule sequencing;
D O I：
10.1186/1756-0500-7-111
中图分类号：
学科分类号：
摘要：
Background: Identification of historic pathogens is challenging since false positives and negatives are a serious risk. Environmental non-pathogenic contaminants are ubiquitous. Furthermore, public genetic databases contain limited information regarding these species. High-throughput sequencing may help reliably detect and identify historic pathogens. Results: We shotgun-sequenced 8 16th-century Mixtec individuals from the site of Teposcolula Yucundaa (Oaxaca, Mexico) who are reported to have died from the huey cocoliztli ('Great Pestilence' in Nahautl), an unknown disease that decimated native Mexican populations during the Spanish colonial period, in order to identify the pathogen. Comparison of these sequences with those deriving from the surrounding soil and from 4 precontact individuals from the site found a wide variety of contaminant organisms that confounded analyses. Without the comparative sequence data from the precontact individuals and soil, false positives for Yersinia pestis and rickettsiosis could have been reported. Conclusions: False positives and negatives remain problematic in ancient DNA analyses despite the application of high-throughput sequencing. Our results suggest that several studies claiming the discovery of ancient pathogens may need further verification. Additionally, true single molecule sequencing's short read lengths, inability to sequence through DNA lesions, and limited ancient-DNA-specific technical development hinder its application to palaeopathology. © 2014 Campana et al.; licensee BioMed Central Ltd.
引用
收藏
相关论文
共 57 条
[1]  
Papagrigorakis M.J., Yapijakis C., Synodinos P.N., Baziotopoulou-Valavani E., DNA examination of ancient dental pulp incriminates typhoid fever as a probable cause of the Plague of Athens, Int J Infect Dis, 10, pp. 206-214, (2006)
[2]  
Shapiro B., Rambaut A., Gilbert M.T.P., No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.), Int J Infect Dis, 10, pp. 334-335, (2006)
[3]  
Drancourt M., Aboudharam G., Signoli M., Dutour O., Raoult D., Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia, Proc Natl Acad Sci USA, 95, pp. 12637-12640, (1998)
[4]  
Zink A.R., Sola C., Reischl U., Grabner W., Rastogi N., Wolf H., Nerlich A.G., Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping, J Clin Microbiol, 41, pp. 359-367, (2003)
[5]  
Nguyen-Hieu T., Aboudharam G., Signoli M., Rigeade C., Drancourt M., Raoult D., Evidence of a louse-born outbreak involving typhus in Douai, 1710-1712 during the War of Spanish Succession, PLoS One, 5, (2010)
[6]  
Gernaey A.M., Minnikin D.E., Copley M.S., Dixon R.A., Middleton J.C., Roberts C.A., Mycolic acids and ancient DNA confirm an osteological diagnosis of tuberculosis, Tuberculosis, 81, pp. 259-265, (2001)
[7]  
Kolman C.J., Centurion-Lara A., Lukehart S.A., Owsley D.A., Tuross N., Identification of Treponema pallidum subspecies pallidum in a 200-year-old skeletal specimen, J Infect Dis, 1999, (2060)
[8]  
Bianucci R., Rahalison L., Ferroglio E., Massa E.R., Signoli M., Détection de l'antigène F1 de Yersinia pestis dans les restes humains anciens à l'aide d'un test de diagnostic rapide, C R Biol, 330, pp. 747-754, (2007)
[9]  
Bianucci R., Rahalison L., Massa E.R., Peluso A., Ferroglio E., Signoli M., Technical note: A rapid diagnostic test detects plague in ancient human remains: An example of the interaction between archaeological and biological approaches (Southeastern France, 16th18th centuries), Am J Phys Anthropol, 136, pp. 361-367, (2008)
[10]  
Bianucci R., Rahalison L., Peluso A., Massa E.R., Ferroglio E., Signoli M., Langlois J.-Y., Gallien V., Plague immunodetection in remains of religious exhumed from burial sites in central France, J Arch Sci, 36, pp. 616-621, (2009)
123456