Parallel Detection of Ancient Pathogens Via Array-based DNA Capture

Overview

Journal Philos Trans R Soc Lond B Biol Sci

Specialty Biology

Date 2014 Dec 10

PMID 25487327

Citations 17

Authors

Kirsten I Bos

Gunter Jager

Verena J Schuenemann

Ashild J Vagene

Maria A Spyrou

Alexander Herbig

Kay Nieselt

Johannes Krause

Affiliations

Soon will be listed here.

Abstract

DNA capture coupled with next generation sequencing is highly suitable for the study of ancient pathogens. Screening for pathogens can, however, be meticulous when assays are restricted to the enrichment of single organisms, which is common practice. Here, we report on an array-based DNA capture screening technique for the parallel detection of nearly 100 pathogens that could have potentially left behind molecular signatures in preserved ancient tissues. We demonstrate the sensitivity of our method through evaluation of its performance with a library known to harbour ancient Mycobacterium leprae DNA. This rapid and economical technique will be highly useful for the identification of historical diseases that are difficult to characterize based on archaeological information alone.

Citing Articles

An Adagio for Viruses, Played Out on Ancient DNA.

de-Dios T, Scheib C, Houldcroft C Genome Biol Evol. 2023; 15(3).

PMID: 36930529 PMC: 10063219. DOI: 10.1093/gbe/evad047.

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.

Sarhan M, Wurst C, Tzankov A, Bircher A, Wittig H, Briellmann T BMC Biol. 2023; 21(1):9.

PMID: 36747166 PMC: 9903526. DOI: 10.1186/s12915-022-01509-7.

The Recovery, Interpretation and Use of Ancient Pathogen Genomes.

Duchene S, Ho S, Carmichael A, Holmes E, Poinar H Curr Biol. 2020; 30(19):R1215-R1231.

PMID: 33022266 PMC: 7534838. DOI: 10.1016/j.cub.2020.08.081.

Insights into health and disease from ancient biomolecules.

Stone A, Lewis Jr C, Schuenemann V Philos Trans R Soc Lond B Biol Sci. 2020; 375(1812):20190568.

PMID: 33012226 PMC: 7702800. DOI: 10.1098/rstb.2019.0568.

Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples.

Borowka P, Pulaski L, Marciniak B, Borowska-Struginska B, Dziadek J, Zadzinska E Gigascience. 2019; 8(6).

PMID: 31220249 PMC: 6586198. DOI: 10.1093/gigascience/giz065.

References

Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Gordon D, Brizuela L . Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc. 2009; 4(6):960-74. PMC: 2990409. DOI: 10.1038/nprot.2009.68. View

Brook M, Currie B, Desmarchelier P . Isolation and identification of Burkholderia pseudomallei from soil using selective culture techniques and the polymerase chain reaction. J Appl Microbiol. 1997; 82(5):589-96. View

Monot M, Honore N, Garnier T, Zidane N, Sherafi D, Paniz-Mondolfi A . Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet. 2009; 41(12):1282-9. DOI: 10.1038/ng.477. View

Krause J, Briggs A, Kircher M, Maricic T, Zwyns N, Derevianko A . A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol. 2010; 20(3):231-6. DOI: 10.1016/j.cub.2009.11.068. View

Meyer M, Kircher M . Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010; 2010(6):pdb.prot5448. DOI: 10.1101/pdb.prot5448. View

Okello J, Rodriguez L, Poinar D, Bos K, Okwi A, Bimenya G . Quantitative assessment of the sensitivity of various commercial reverse transcriptases based on armored HIV RNA. PLoS One. 2010; 5(11):e13931. PMC: 2978101. DOI: 10.1371/journal.pone.0013931. View

Singer M . Pathogen-pathogen interaction: a syndemic model of complex biosocial processes in disease. Virulence. 2010; 1(1):10-8. PMC: 3080196. DOI: 10.4161/viru.1.1.9933. View

Falup-Pecurariu O, Bleotu L, Zavarache C, Peled N, Anton O, Robu M . Streptococcus pneumoniae nasopharyngeal colonization in children in Brasov, Central Romania: high antibiotic resistance and coverage by conjugate vaccines. Pediatr Infect Dis J. 2010; 30(1):76-8. DOI: 10.1097/INF.0b013e3181f42bb6. View

Schuenemann V, Bos K, DeWitte S, Schmedes S, Jamieson J, Mittnik A . Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proc Natl Acad Sci U S A. 2011; 108(38):E746-52. PMC: 3179067. DOI: 10.1073/pnas.1105107108. View

10.

Bos K, Schuenemann V, Golding G, Burbano H, Waglechner N, Coombes B . A draft genome of Yersinia pestis from victims of the Black Death. Nature. 2011; 478(7370):506-10. PMC: 3690193. DOI: 10.1038/nature10549. View

11.

Federhen S . The NCBI Taxonomy database. Nucleic Acids Res. 2011; 40(Database issue):D136-43. PMC: 3245000. DOI: 10.1093/nar/gkr1178. View

12.

Kircher M, Sawyer S, Meyer M . Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 2011; 40(1):e3. PMC: 3245947. DOI: 10.1093/nar/gkr771. View

13.

Jonsson H, Ginolhac A, Schubert M, Johnson P, Orlando L . mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013; 29(13):1682-4. PMC: 3694634. DOI: 10.1093/bioinformatics/btt193. View

14.

Schuenemann V, Singh P, Mendum T, Krause-Kyora B, Jager G, Bos K . Genome-wide comparison of medieval and modern Mycobacterium leprae. Science. 2013; 341(6142):179-83. DOI: 10.1126/science.1238286. View

15.

Devault A, Golding G, Waglechner N, Enk J, Kuch M, Tien J . Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. N Engl J Med. 2014; 370(4):334-40. DOI: 10.1056/NEJMoa1308663. View

16.

Devault A, McLoughlin K, Jaing C, Gardner S, Porter T, Enk J . Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array. Sci Rep. 2014; 4:4245. PMC: 3945050. DOI: 10.1038/srep04245. View

17.

Wagner D, Klunk J, Harbeck M, Devault A, Waglechner N, Sahl J . Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis. Lancet Infect Dis. 2014; 14(4):319-26. DOI: 10.1016/S1473-3099(13)70323-2. View

18.

Bos K, Harkins K, Herbig A, Coscolla M, Weber N, Comas I . Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature. 2014; 514(7523):494-7. PMC: 4550673. DOI: 10.1038/nature13591. View

19.

Zuker M . Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31(13):3406-15. PMC: 169194. DOI: 10.1093/nar/gkg595. View

20.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View