Screening ancient tuberculosis with qPCR: Challenges and opportunities

Kelly M. Harkins, Jane Buikstra, Tessa Campbell, Kirsten I. Bos, Eric D. Johnson, Johannes Krause, Anne Stone

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.

Original languageEnglish (US)
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Volume370
Issue number1660
DOIs
StatePublished - Jan 19 2015

Fingerprint

tuberculosis
Mycobacterium tuberculosis complex
Screening
quantitative polymerase chain reaction
Tuberculosis
screening
Mycobacterium tuberculosis
Polymerase Chain Reaction
DNA
Pathogens
Assays
Bacteria
DNA libraries
Mycobacterium
Tissue
lesion
sampling
lesions (animal)
probes (equipment)
Libraries

Keywords

  • Ancient DNA
  • Bioarchaeology
  • qPCR
  • Tuberculosis

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Screening ancient tuberculosis with qPCR : Challenges and opportunities. / Harkins, Kelly M.; Buikstra, Jane; Campbell, Tessa; Bos, Kirsten I.; Johnson, Eric D.; Krause, Johannes; Stone, Anne.

In: Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 370, No. 1660, 19.01.2015.

Research output: Contribution to journalArticle

Harkins, Kelly M. ; Buikstra, Jane ; Campbell, Tessa ; Bos, Kirsten I. ; Johnson, Eric D. ; Krause, Johannes ; Stone, Anne. / Screening ancient tuberculosis with qPCR : Challenges and opportunities. In: Philosophical Transactions of the Royal Society B: Biological Sciences. 2015 ; Vol. 370, No. 1660.
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