Rapid bacterial genome sequencing: Methods and applications in clinical microbiology

Clinical Microbiology and Infection

Volumn 19, Issue 9, 2013, Pages 803-813

  Bertelli, C ^a,b   Greub, G ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

Antibiotic resistance; Bacterial genome; Diagnostic; High throughput sequencing; Virulence factor

Indexed keywords

ANTIGEN; CIPROFLOXACIN; GENOMIC DNA; PENICILLIN DERIVATIVE; PETHIDINE; SHIGA TOXIN;

ACINETOBACTER BAUMANNII; ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; BACTERIAL GENETICS; BACTERIAL VIRULENCE; BURKHOLDERIA; COST EFFECTIVENESS ANALYSIS; DISEASE TRANSMISSION; DNA SEQUENCE; EPIDEMIC; EPIDEMIOLOGY; ESCHERICHIA COLI; GENE SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; HOST PATHOGEN INTERACTION; HUMAN; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOLOGY; PATIENT CARE; PENICILLIN RESISTANCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; REVIEW; RISK MANAGEMENT; RNA SEQUENCE; STAPHYLOCOCCUS AUREUS;

BACTERIA (MICROORGANISMS);

EID: 84882712754     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1111/1469-0691.12217     Document Type: Review

References (84)

1. Croxatto A, Prod'hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012; 36: 380-407.
2. Lasken RS. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 2012; 10: 631-640.
3. Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS. Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 2008; 11: 198-204.
4. Greub G, Kebbi-Beghdadi C, Bertelli C et al. High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach. PLoS ONE 2009; 4: e8423.
5. La Scola B, Elkarkouri K, Li W et al. Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensis paradigm. Genome Res 2008; 18: 742-750.
6. Chen Y, Johnson JA, Pusch GD, Morris JG Jr, Stine OC. The genome of non-O1 vibrio cholerae nrt36s demonstrates the presence of pathogenic mechanisms that are distinct from those of O1 Vibrio cholerae. Infect Immun 2007; 75: 2645-2647.
7. Chen PE, Willner KM, Butani A et al. Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing. PLoS ONE 2010; 5: e12397.
8. Qin J, Cui Y, Zhao X et al. Identification of the shiga toxin-producing Escherichia coli O104:H4 strain responsible for a food poisoning outbreak in Germany by PCR. J Clin Microbiol 2011; 49: 3439-3440.
9. Mardis ER. A decade's perspective on DNA sequencing technology. Nature 2011; 470: 198-203.
10. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010; 11: 31-46.
11. Margulies M, Egholm M, Altman WE et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437: 376-380.
12. Bennett S. Solexa ltd. Pharmacogenomics 2004; 5: 433-438.
13. Pandey V, Nutter RC, Prediger E. Applied biosystems solid™ system: ligation-based sequencing. In: Janitz M, ed. Next-generation genome sequencing: towards personalized medicine. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2008; 29-41.
14. Steinmann KE, Hart CE, Thompson JF, Milos PM. Helicos single-molecule sequencing of bacterial genomes. Methods Mol Biol 2011; 733: 3-24.
15. Rothberg JM, Hinz W, Rearick TM et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011; 475: 348-352.
16. Eid J, Fehr A, Gray J et al. Real-time DNA sequencing from single polymerase molecules. Science 2009; 323: 133-138.
17. Stoddart D, Heron AJ, Mikhailova E, Maglia G, Bayley H. Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc Natl Acad Sci USA 2009; 106: 7702-7707.
18. Auburn S, Campino S, Clark TG et al. An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. PLoS ONE 2011; 6: e22213.
19. Kuroda M, Sekizuka T, Shinya F et al. Detection of a possible bioterrorism agent, Francisella sp., in a clinical specimen by use of next-generation direct DNA sequencing. J Clin Microbiol 2012; 50: 1810-1812.
20. Bizzini A, Jaton K, Romo D, Bille J, Prod'hom G, Greub G. Matrix-assisted laser desorption ionization-time of flight mass spectrometry as an alternative to 16s rRNA gene sequencing for identification of difficult-to-identify bacterial strains. J Clin Microbiol 2011; 49: 693-696.
21. Balasingham SV, Davidsen T, Szpinda I, Frye SA, Tonjum T. Molecular diagnostics in tuberculosis: basis and implications for therapy. Mol Diagn Ther 2009; 13: 137-151.
22. Millar BC, Xu J, Moore JE. Molecular diagnostics of medically important bacterial infections. Curr Issues Mol Biol 2007; 9: 21-39.
23. Fenollar F, Puechal X, Raoult D. Whipple's disease. N Engl J Med 2007; 356: 55-66.
24. Ripa T, Nilsson PA. A Chlamydia trachomatis strain with a 377-bp deletion in the cryptic plasmid causing false-negative nucleic acid amplification tests. Sex Transm Dis 2007; 34: 255-256.
25. Ho CC, Wu AK, Tse CW, Yuen KY, Lau SK, Woo PC. Automated pangenomic analysis in target selection for PCR detection and identification of bacteria by use of ssgenefinder webserver and its application to Salmonella enterica serovar typhi. J Clin Microbiol 2012; 50: 1905-1911.
26. Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 2012; 13: 601-612.
27. Jolley KA, Bliss CM, Bennett JS et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012; 158: 1005-1015.
28. Larsen MV, Cosentino S, Rasmussen S et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 2012; 50: 1355-1361.
29. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57: 81-91.
30. Fox GE, Stackebrandt E, Hespell RB et al. The phylogeny of prokaryotes. Science 1980; 209: 457-463.
31. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102: 2567-2572.
32. Priest FG, Barker M, Baillie LW, Holmes EC, Maiden MC. Population structure and evolution of the Bacillus cereus group. J Bacteriol 2004; 186: 7959-7970.
33. Bennett JS, Jolley KA, Earle SG et al. A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria. Microbiology 2012; 158: 1570-1580.
34. Fournier PE, Drancourt M, Raoult D. Bacterial genome sequencing and its use in infectious diseases. Lancet Infect Dis 2007; 7: 711-723.
35. Grad YH, Lipsitch M, Feldgarden M et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci USA 2012; 109: 3065-3070.
36. Harris SR, Clarke IN, Seth-Smith HM et al. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet 2012; 44: 413-419.
37. Rasko DA, Worsham PL, Abshire TG et al. Bacillus anthracis comparative genome analysis in support of the amerithrax investigation. Proc Natl Acad Sci USA 2011; 108: 5027-5032.
38. Monot M, Honore N, Garnier T et al. Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet 2009; 41: 1282-1289.
39. Harris SR, Feil EJ, Holden MT et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010; 327: 469-474.
40. McAdam PR, Templeton KE, Edwards GF et al. Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci USA 2012; 109: 9107-9112.
41. Lewis T, Loman NJ, Bingle L et al. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J Hosp Infect 2010; 75: 37-41.
42. Koser CU, Holden MT, Ellington MJ et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 2012; 366: 2267-2275.
43. Eyre DW, Golubchik T, Gordon NC et al. A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open 2012; 2: e001124.
44. Walker AS, Eyre DW, Wyllie DH et al. Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing. PLoS Med 2012; 9: e1001172.
45. Mellmann A, Harmsen D, Cummings CA et al. Prospective genomic characterization of the german enterohemorrhagic E. coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS ONE 2011; 6: e22751.
46. Rasko DA, Webster DR, Sahl JW et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011; 365: 709-717.
47. Rohde H, Qin J, Cui Y et al. Open-source genomic analysis of shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011; 365: 718-724.
48. Wolk DM, Struelens MJ, Pancholi P et al. Rapid detection of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in wound specimens and blood cultures: multicenter preclinical evaluation of the cepheid xpert mrsa/sa skin and soft tissue and blood culture assays. J Clin Microbiol 2009; 47: 823-826.
49. Hillemann D, Weizenegger M, Kubica T, Richter E, Niemann S. Use of the genotype MTBDR assay for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J Clin Microbiol 2005; 43: 3699-3703.
50. Telenti A, Imboden P, Marchesi F et al. Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis. Lancet 1993; 341: 647-650.
51. Iacono M, Villa L, Fortini D et al. Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob Agents Chemother 2008; 52: 2616-2625.
52. Lieberman TD, Michel JB, Aingaran M et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat Genet 2011; 43: 1275-1280.
53. Serizawa M, Sekizuka T, Okutani A et al. Genomewide screening for novel genetic variations associated with ciprofloxacin resistance in Bacillus anthracis. Antimicrob Agents Chemother 2010; 54: 2787-2792.
54. Kaper JB, Nataro JP, Mobley HL. Pathogenic Escherichia coli. Nat Rev Microbiol 2004; 2: 123-140.
55. Lappin E, Ferguson AJ. Gram-positive toxic shock syndromes. Lancet Infect Dis 2009; 9: 281-290.
56. Holmes RK. Biology and molecular epidemiology of diphtheria toxin and the tox gene. J Infect Dis 2000; 181(suppl 1): S156-S167.
57. Chin CS, Sorenson J, Harris JB et al. The origin of the Haitian cholera outbreak strain. N Engl J Med 2011; 364: 33-42.
58. Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 1998; 180: 4765-4774.
59. Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 2008; 4: e1000255.
60. Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 2008; 11: 442-446.
61. Quince C, Lanzen A, Curtis TP et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 2009; 6: 639-641.
62. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008; 6: e280.
63. Armougom F, Raoult D. Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans. BMC Genomics 2008; 9: 576.
64. Armougom F, Bittar F, Stremler N et al. Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing. Eur J Clin Microbiol Infect Dis 2009; 28: 1151-1154.
65. Lazarevic V, Whiteson K, Huse S et al. Metagenomic study of the oral microbiota by illumina high-throughput sequencing. J Microbiol Methods 2009; 79: 266-271.
66. Qin J, Li R, Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
67. Group NHW, Peterson J, Garges S et al. The NIH human microbiome project. Genome Res 2009; 19: 2317-2323.
68. Gevers D, Knight R, Petrosino JF et al. The human microbiome project: a community resource for the healthy human microbiome. PLoS Biol 2012; 10: e1001377.
69. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486: 207-214.
70. Abubucker S, Segata N, Goll J et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 2012; 8: e1002358.
71. Greub G. Culturomics: a new approach to study the human microbiome. Clin Microbiol Infect 2012; 18: 1157-1159.
72. Lagier JC, Armougom F, Million M et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18: 1185-1193.
73. Dean FB, Hosono S, Fang L et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 2002; 99: 5261-5266.
74. Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 2001; 11: 1095-1099.
75. Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 2005; 71: 3342-3347.
76. Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 2009; 4: e6864.
77. Mussmann M, Hu FZ, Richter M et al. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 2007; 5: e230.
78. Siegl A, Kamke J, Hochmuth T et al. Single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 2011; 5: 61-70.
79. Grindberg RV, Ishoey T, Brinza D et al. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS ONE 2011; 6: e18565.
80. Frerichs RR, Keim PS, Barrais R, Piarroux R. Nepalese origin of cholera epidemic in Haiti. Clin Microbiol Infect 2012; 18: E158-E163.
81. Schneider T, Stallmach A, von Herbay A, Marth T, Strober W, Zeitz M. Treatment of refractory Whipple disease with interferon-gamma. Ann Intern Med 1998; 129: 875-877.
82. Qu HQ, Fisher-Hoch SP, McCormick JB. Molecular immunity to mycobacteria: knowledge from the mutation and phenotype spectrum analysis of mendelian susceptibility to mycobacterial diseases. Int J Infect Dis 2011; 15: e305-e313.
83. Morre SA, Karimi O, Ouburg S. Chlamydia trachomatis: identification of susceptibility markers for ocular and sexually transmitted infection by immunogenetics. FEMS Immunol Med Microbiol 2009; 55: 140-153.
84. Westermann AJ, Gorski SA, Vogel J. Dual RNA-seq of pathogen and host. Nat Rev Microbiol 2012; 10: 618-630.