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

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.

Scenes from the past: MR imaging versus CT of ancient Peruvian and Egyptian mummified tissues.

Ancient Egyptian and Peruvian mummies are extremely valuable historical remains, and noninvasive methods for their examination are desirable. The current standard of reference for radiologic imaging of mummies is computed tomography (CT), with tissue having a homogeneous appearance on all CT images. It was long believed that ancient mummified tissue could not be studied with magnetic resonance (MR) imaging because of the low water content in mummies. Recently, however, the usefulness of MR imaging in the evaluation of mummified tissue was demonstrated for the first time, with use of a special ultrashort echo time technique. The authors of the present study acquired and analyzed MR imaging and CT data from the left hands of two ancient Egyptian mummies and the head of a third Egyptian mummy (ca 1500-1100 bce), as well as data from an ancient Peruvian mummy (ca 1100 ce). CT was found to provide superior detail of the anatomic structures, mainly because of its higher spatial resolution. The signal intensity of mummified tissue varied greatly on MR images; thus, the quality of these images is not yet comparable to that of clinical MR images, and further research will be needed to determine the full capacity of MR imaging in this setting. Nevertheless, additional information may theoretically be obtained with MR imaging, which should be viewed as complementary to, rather than a replacement for, CT.