ArticleBMC research notes2014
False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing.
Article in BMC research notes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed.
- Towards predicting the geographical origin of ancient samples with metagenomic data.Scientific reports · 2024Article
- Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen.iScience · 2024Article
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- aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.Genome biology · 2023Article
- Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.Environmental microbiology reports · 2023Article
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- The past, present and future of ancient bacterial DNA.Microbial genomics · 2020Review
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- Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples.GigaScience · 2019Article
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- Article
- Environmental Microbial Forensics and Archaeology of Past Pandemics.Microbiology spectrum · 2017Review
- Screening ancient tuberculosis with qPCR: challenges and opportunities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Article
- Ancient-pathogen genomics: coming of age?mBio · 2014Article
- Editors' Pick: Contamination has always been the issue!Investigative genetics · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentification 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.
resultsWe 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.
conclusionsFalse 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.
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