High-throughput bacterial genome sequencing: An embarrassment of choice, a world of opportunity

Nature Reviews Microbiology

Volumn 10, Issue 9, 2012, Pages 599-606

  Loman, Nicholas J ^a   Constantinidou, Chrystala ^a   Chan, Jacqueline Z M ^a   Halachev, Mihail ^a   Sergeant, Martin ^a   Penn, Charles W ^a   Robinson, Esther R ^b   Pallen, Mark J ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; DNA POLYMERASE; DOUBLE STRANDED DNA;

ALGORITHM; ARTICLE; BACTERIAL GENOME; DNA CLEAVAGE; DNA HYBRIDIZATION; DNA SYNTHESIS; FLUOROMETRY; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; IMMOBILIZED CELL; METAGENOMICS; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PYROSEQUENCING; QUALITY CONTROL; RNA SEQUENCE; SEQUENCE ALIGNMENT;

DNA, BACTERIAL; GENETICS, MICROBIAL; GENOME, BACTERIAL; HIGH-THROUGHPUT SCREENING ASSAYS; MOLECULAR BIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 84865179264     PISSN: 17401526     EISSN: 17401534     Source Type: Journal    
DOI: 10.1038/nrmicro2850     Document Type: Article

References (58)

1. Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512 (1995).
2. Metzker, M. L. Emerging technologies in DNA sequencing. Genome Res. 15, 1767-1776 (2005). (Pubitemid 41780407)
3. Venter, J. C. Multiple personal genomes await. Nature 464, 676-677 (2010).
4. Caruccio, N. in High-Throughput Next Generation Sequencing: Methods and Applications. Methods in Molecular Biology Vol. 733 (eds Kwon, Y. M. & Ricke, S. C.) 241-255 (Humana Press, 2011).
5. Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
6. Ronaghi, M., Uhlen, M. & Nyren, P. A sequencing method based on real-time pyrophosphate. Science 281 363-365 (1998). (Pubitemid 28340773)
7. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005). (Pubitemid 41613494)
8. Rothberg, J. M. et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-352 (2011).
9. Valouev, A. et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18, 1051-1063 (2008). (Pubitemid 351931156)
10. Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78-81 (2010).
11. Bowers, J. et al. Virtual terminator nucleotides for next-generation DNA sequencing. Nature Methods 6, 593-595 (2009).
12. Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
13. Levene, M. J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682-686 (2003).
14. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
15. Hess, M. et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463-467 (2011).
16. Mutreja, A. et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462-465 (2011).
17. Harris, S. R. et al. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nature Genet. 44, 413-419 (2012).
18. Loman, N. J. et al. Performance comparison of bench-top high-throughput sequencing platforms. Nature Biotech. 30, 434-439 (2012).
19. Rohde, H. et al. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N. Engl. J. Med. 365, 718-724 (2011).
20. Mellmann, A. et al. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS ONE 6, e22751 (2011).
21. Bashir, A. et al. A hybrid approach for the automated finishing of bacterial genomes. Nature Biotech. 1 Jul 2012 (doi:10.1038/nbt.2288).
22. Koren, S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotech. 1 Jul 2012 (doi:10.1038/nbt.2280).
23. Chevreux, B. et al. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147-1159 (2004). (Pubitemid 38811551)
24. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008). (Pubitemid 351645072)
25. Darling, A. C., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403 (2004). (Pubitemid 39029237)
26. Angiuoli, S. V. & Salzberg, S. L. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27, 334-342 (2011).
27. Milne, I. et al. Tablet-next generation sequence assembly visualization. Bioinformatics 26, 401-402 (2010).
28. Delcher, A. L., Harmon, D., Kasif, S., White, O. & Salzberg, S. L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27, 4636-4641 (1999).
29. Schattner, P., Brooks, A. N. & Lowe, T. M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, W686-W689 (2005). (Pubitemid 44530010)
30. Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108 (2007). (Pubitemid 47073647)
31. Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).
32. Markowitz, V. M. et al. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25, 2271-2278 (2009).
33. Richardson, E. J. & Watson, M. The automatic annotation of bacterial genomes. Brief. Bioinform. 9 Mar 2012 (doi:10.1093/bib/bbs007).
34. Chaudhuri, R. R. et al. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res. 36, D543-D546 (2008). (Pubitemid 351149782)
35. Marttinen, P. et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40, e6 (2012).
36. Didelot, X. & Falush, D. Inference of bacterial microevolution using multilocus sequence data. Genetics 175, 1251-1266 (2007). (Pubitemid 46798228)
37. Didelot, X., Lawson, D., Darling, A. & Falush, D. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics 186, 1435-1449 (2010).
38. Domazet-Lošo, M. & Haubold, B. Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics 27, 1466-1472 (2011).
39. Köser, C. U. et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N. Engl. J. Med. 366, 2267-2275 (2012).
40. Lewis, T. et al. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J. Hosp. Infect. 75, 37-41 (2010).
41. Gardy, J. L. et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N. Engl. J. Med. 364, 730-739 (2011).
42. Harris, S. R. et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469-474 (2011).
43. Beres, S. B. et al. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc. Natl Acad. Sci. USA 107, 4371-4376 (2010).
44. Cramer, N. et al. Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs. Environ. Microbiol. 13, 1690-1704 (2011).
45. Dunham, E. J. et al. Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses. J. Virol. 83, 5485-5494 (2009).
46. Bos, K. I. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506-510 (2011).
47. Woyke, T. et al. Assembling the marine metagenome, one cell at a time. PLoS ONE 4, e5299 (2009).
48. Lipkin, W. I. Microbe hunting. Microbiol. Mol. Biol. Rev. 74, 363-377 (2010).
49. Sorek, R. & Cossart, P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nature Rev. Genet. 11, 9-16 (2010).
50. Passalacqua, K. D. et al. Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191, 3203-3211 (2009).
51. Sharma, C. M. et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464, 250-255 (2010).
52. van Opijnen, T., Bodi, K. L. & Camilli, A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nature Methods 6, 767-772 (2009).
53. Langridge, G. C. et al. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res. 19, 2308-2316 (2009).
54. Grainger, D. et al. Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria. Curr. Opin. Microbiol. 12, 531-535 (2009).
55. Branton, D. et al. The potential and challenges of nanopore sequencing. Nature Biotech. 26, 1146-1153 (2008).
56. Pallen, M. J. & Loman, N. J. Are diagnostic and public health bacteriology ready to become branches of genomic medicine? Genome Med. 3, 53 (2011).
57. Adey, A. et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Res. 11, R119 (2010).
58. Glenn, T. C. A field guide to next generation DNA sequencers. Mol. Ecol. Res. 11, 759-769 (2011).