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Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
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False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing.

Michael G Campana1, Nelly Robles García, Frank J Rühli

  • 1Department of Human Evolutionary Biology, Harvard University, Peabody Museum, 11 Divinity Avenue, Cambridge, MA 02138, USA. mcampana63@gmail.com.

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|February 27, 2014
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Summary

Ancient DNA analysis faces challenges with contamination. This study highlights the risk of false positives in identifying historic pathogens like huey cocoliztli, emphasizing the need for rigorous verification in paleopathology research.

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Area of Science:

  • Paleopathology
  • Ancient Genomics
  • Microbial Forensics

Background:

  • Identifying historical pathogens is difficult due to ubiquitous environmental contaminants and limited genetic databases.
  • High-throughput sequencing (HTS) offers potential for reliable detection and identification of ancient pathogens.
  • Distinguishing true pathogens from contaminants is crucial for accurate paleopathological studies.

Observation:

  • Shotgun sequencing of 16th-century Mixtec individuals linked to huey cocoliztli ('Great Pestilence') was performed.
  • Comparative analysis included sequences from surrounding soil and precontact individuals to control for contamination.
  • A wide array of contaminant organisms complicated the identification of causative agents.

Findings:

  • Without comparative data from soil and precontact samples, false positive identifications of *Yersinia pestis* and rickettsiosis were possible.
  • The study underscores the persistent challenge of false positives and negatives in ancient DNA (aDNA) analyses.
  • Several purported discoveries of ancient pathogens may require re-evaluation due to potential contamination.

Implications:

  • Rigorous controls and comparative sequencing are essential for validating findings in ancient pathogen identification.
  • Current limitations in true single molecule sequencing (e.g., short read lengths, DNA lesion issues) impact palaeopathology.
  • Further technical development is needed for reliable application of sequencing technologies in ancient DNA research.