Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Devault, Alison M ^a   McLoughlin, Kevin ^b   Jaing, Crystal ^b   Gardner, Shea ^b   Porter, Teresita M ^c   Enk, Jacob M ^a,c   Thissen, James ^b   Allen, Jonathan ^b   Borucki, Monica ^b   Dewitte, Sharon N ^d   Dhody, Anna N ^e   Poinar, Hendrik N ^a,c,f  

^a MCMASTER UNIVERSITY   (Canada)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^c MCMASTER UNIVERSITY   (Canada)

^d UNIVERSITY OF SOUTH CAROLINA   (United States)

^e Mütter Museum   (United States)

^f MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARCHEOLOGY; BIOLOGY; CLASSIFICATION; DNA MICROARRAY; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; PHYLOGENY; VIBRIO CHOLERAE; YERSINIA PESTIS;

ARCHAEOLOGY; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; VIBRIO CHOLERAE; YERSINIA PESTIS;

EID: 84896763149     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep04245     Document Type: Article

References (24)

1. Ortner, D. J. Human skeletal paleopathology. Int. J. Paleopathol. 1, 4-11, doi:10.1016/j.ijpp.2011.01.002 (2011).
2. Rizzi, E., Lari, M., Gigli, E., De Bellis, G. & Caramelli, D. Ancient DNA studies: new perspectives on old samples. Genet. Sel. Evol. 44, 21, doi:10.1186/1297-9686- 44-21 (2012).
3. Devault, A. M. et al. Second-Pandemic Strain of Vibrio cholerae from the Philadelphia Cholera Outbreak of 1849. N. Engl. J. Med. 370, 334-340, doi:10.1056/NEJMoa1308663 (2014).
4. Bos, K. I. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506-510, doi:10.1038/nature10549 (2011).
5. Schuenemann, V. J. et al. Genome-wide comparison of Medieval and modern Mycobacterium leprae. Science 341, 179-183, doi:10.1126/science.1238286 (2013).
6. Brogden, K. A., Guthmiller, J. M. & Taylor, C. E. Human polymicrobial infections. Lancet 365, 253-255, doi:10.1016/s0140-6736(05)70155-0 (2005).
7. Gonzalez, J. M., Portillo, M. C., Belda-Ferre, P. & Mira, A. Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities. PLoS ONE 7, e29973, doi:10.1371/journal.pone.0029973 (2012).
8. Dabney, J. & Meyer, M. Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52, 87-1, doi:10.2144/ 000113809 (2012).
9. Khairat, R. et al. First insights into the metagenome of Egyptian mummies using next-generation sequencing. J. Appl. Genetics 54, 309-325, doi:10.1007/s13353- 013-0145-1 (2013).
10. Keller, A. et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3, 698, doi:10.1038/ ncomms1701 (2012).
11. Hoheisel, J. D. Microarray technology: beyond transcript profiling and genotype analysis. Nat. Rev. Genet. 7, 200-210, doi:10.1038/nrg1809 (2006).
12. Gardner, S., Jaing, C., McLoughlin, K. & Slezak, T. A microbial detection array (MDA) for viral and bacterial detection. BMC Genomics 11, 668, doi:10.1186/ 1471-2164-11-668 (2010).
13. Erlandsson, L., Rosenstierne, M. W., McLoughlin, K., Jaing, C. & Fomsgaard, A. The Microbial Detection Array combined with random Phi29-amplification used as a diagnostic tool for virus detection in clinical samples. PLoS ONE 6, e22631, doi:10.1371/journal.pone.0022631 (2011).
14. McLoughlin, K. S. Microarrays for pathogen detection and analysis. Brief. Funct. Genom. 10, 342-353, doi:10.1093/bfgp/elr027 (2011).
15. Wang, D. et al. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. U. S. A. 99, 15687-15692, doi:10.1073/pnas. 242579699 (2002).
16. Palacios, G. et al. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg. Infect. Dis 13, 73-81, doi:10.3201/eid1301.060837 (2007).
17. Victoria, J. G. et al. Viral nucleic acids in live-attenuated vaccines: Detection of minority variants and an adventitious virus. J. Virol. 84, 6033-6040, doi:10.1128/ jvi.02690-09 (2010).
18. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25, doi:10.1186/gb-2009-10-3-r25 (2009).
19. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic Local Alignment Search Tool. J. Mol. Biol. 215, 403-410, doi:10.1006/jmbi.1990.9999 (1990).
20. Huson, D. H.,Mitra, S., Ruscheweyh,H.-J., Weber, N.& Schuster, S. C. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 21, 1552-1560, doi:10.1101/gr.120618.111 (2011).
21. Pruitt, K. D., Tatusova, T., Brown, G. R. & Maglott, D. R. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130-D135, doi:10.1093/nar/gkr1079 (2012).
22. Reen, F. J., Almagro-Moreno, S., Ussery, D. & Boyd, E. F. The genomic code: inferring Vibrionaceae niche specialization. Nat. Rev. Microbiol. 4, 697-704, doi:10.1038/nrmicro1476 (2006).
23. Brenner, D. J. & Farmer, J. J., III. in Bergey's Manual of Systematic Bacteriology - Volume 2: The Proteobacteria, Part B: The Gammaproteobacteria (eds Don J. Brenner., Noel R. Krieg. & James R. Staley) 587-850 (Springer, 2005).
24. Parkhill, J. et al.Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523-527, doi:10.1038/35097083 (2001).