Chapter 3 : Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819071/9781555819088.ch3-1.gif /docserver/preview/fulltext/10.1128/9781555819071/9781555819088.ch3-2.gif


The genomic era of bacteriology began in 1995 when the first bacterial genome () was sequenced using the Sanger sequencing method (1). A decade later, the introduction of high-throughput or next-generation sequencing (NGS) technologies allowed sequencing of bacterial genomes to be performed in days rather than months or years (2). These newer technologies use different processes but rely on a combination of template preparation, sequencing and imaging, and genome alignment and assembly methods (3). The major advantages of NGS over Sanger sequencing are speed of sequencing combined with lower costs (4). The ability to readily sequence the whole genome of microorganisms has enabled the performance of large-scale comparative and evolutionary studies that were unimaginable even a few years ago (5–9). Furthermore, the development of rapid benchtop sequencing platforms (10) that are able to sequence a microbial genome in a day makes them increasingly appropriate for introduction into the diagnostic microbiology laboratory environment (11). This chapter will briefly review the currently available NGS technologies and platforms, followed by an in-depth review of the potential clinical applications of whole-genome sequencing (WGS) in the microbiology laboratory. We will also present the challenges for implementation of WGS in the clinical setting and consider some future directions.

Citation: Török M, Peacock S. 2016. Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health, p 32-48. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch3
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

The current diagnostic microbiology processes for bacterial pathogens. A schematic representation of the current workflow for processing samples for bacterial pathogens is presented, showing high complexity and a typical timescale of a few weeks to a few months. The schematic is an approximation that highlights the principal steps in the workflow; it is not intended to be a comprehensive or precise description. Samples that are likely to be normally sterile are often cultured on a rich medium that will support the growth of any culturable organism. Samples that are contaminated with colonizing flora present a challenge for growing the infecting pathogen. Many types of culture media (referred to as selective media) are used to favor the growth of the suspected pathogen; this approach is particularly important for culturing pathogens from feces. Boxes A to H arbitrarily represent the many different media for culture. Medium H represents a medium designed for growing mycobacteria that have specific growth requirements. When an organism is growing, the morphological appearance and density of growth are properties that need specialist knowledge for deciding whether it is likely to be pathogenic. The likely pathogens are then processed through a complex pathway that has many contingencies to determine species and antimicrobial susceptibility. Broadly, there are two approaches. One approach uses matrix-assisted laser desorption ionization–time of flight mass spectrometry for species identification before setting up susceptibility testing. The other uses Gram staining followed by biochemical testing to determine species; susceptibility testing is often set up simultaneously with biochemical tests. Categorization of pathogens into groups of species is needed to choose the appropriate susceptibility-testing panel. Finally, depending on the species and perceived likelihood of an outbreak, a small subset of isolates may be chosen for further investigation using a wide range of typing tests that are often only provided by reference laboratories. The dashed lines and question marks are positioned arbitrarily to indicate that the further investigation is varied and happens in only a small number of cases. (Reprinted from reference with permission.)

Citation: Török M, Peacock S. 2016. Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health, p 32-48. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

NGS platforms. The schematic shows the main high-throughput sequencing platforms available to microbiologists today and the associated sample preparation and template amplification procedures. PGM, personal genome machine. (Reprinted from reference with permission.)

Citation: Török M, Peacock S. 2016. Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health, p 32-48. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Global spread of the seventh cholera pandemic. Transmission events inferred for the seventh-pandemic phylogenetic tree, drawn on a global map. The date ranges shown for transmission events are taken from the BEAST analysis and represent the median values for the most recent common ancestor of the transmitted strains (later bound) and the most recent common ancestor of the transmitted strains and their closest relative from the source location (earlier bound). (Reprinted from reference with permission.)

Citation: Török M, Peacock S. 2016. Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health, p 32-48. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Epidemiology and phylogeny of a neonatal MRSA ST2371 outbreak. (a) Epidemiological map of 14 infants (patients 1 to 14) on the special care baby unit (SCBU). Boxes shown for infants in the SCBU in panel a represent duration of hospital stay (black boxes show infants included by the infection-control investigation and white boxes show infants excluded by the infection-control team). Gray vertical blocks in panels a, c, and e show the time periods on the SCBU when there were no known carriers of MRSA. (b) Phylogenetic tree based on WGS of MRSA isolates from patients 1 to 14. (c) Epidemiological map of patients 1 to 14 and 10 other patients (patients 16, 17, and 19 to 26) with linked MRSA infection detected in the community. The colored lines link members of the same family. (d) Phylogenetic tree based on WGS of MRSA isolates from patients 1 to14 and patients 16, 17, and 19 to 26. (e) Epidemiological map of all cases of MRSA identified by WGS and one patient (patient 18) suspected of being linked to the outbreak but for whom no MRSA colonization was detected. (f) Phylogenetic tree of all cases of MRSA in the outbreak. Twenty individual MRSA colonies from a staff member are shown in red boxes, with multiple colonies from the staff member shown in parentheses. MRSA, methicillin-resistant ; SCBU, special care baby unit; SNP, single-nucleotide polymorphism; P, patient. Note: Out-group was the sequence type 22 reference genome. (Reprinted from reference with permission.)

Citation: Török M, Peacock S. 2016. Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health, p 32-48. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM . 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269 : 496 512.[CrossRef][PubMed]
2. Metzker ML . 2005. Emerging technologies in DNA sequencing. Genome Res 15 : 1767 1776.[CrossRef][PubMed]
3. Metzker ML . 2010. Sequencing technologies: the next generation. Nat Rev Genet 11 : 31 46.[CrossRef][PubMed]
4. Wetterstrand KA . 2014. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP). http://www.genome.gov/sequencingcosts.
5. Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SH, Bentley SD . 2010. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327 : 469 474.[CrossRef][PubMed]
6. Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH, Kariuki S, Croucher NJ, Choi SY, Harris SR, Lebens M, Niyogi SK, Kim EJ, Ramamurthy T, Chun J, Wood JL, Clemens JD, Czerkinsky C, Nair GB, Holmgren J, Parkhill J, Dougan G . 2011. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477 : 462 465.[CrossRef][PubMed]
7. Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A, Yu J, Sangal V, Brown DJ, Coia JE, Kim DW, Choi SY, Kim SH, da Silveira WD, Pickard DJ, Farrar JJ, Parkhill J, Dougan G, Thomson NR . 2012. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet 44 : 1056 1059.[CrossRef][PubMed]
8. He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB, D'Arc S, Brazier J, Brown D, Coia JE, Douce G, Gerding G, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J, Lawley TD . 2013. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet 45 : 109 113.[CrossRef][PubMed]
9. Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S . 2013. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 45 : 1176 1182.[CrossRef][PubMed]
10. Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ . 2012 High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10 : 599 606.[CrossRef][PubMed]
11. Torok ME, Peacock SJ . 2012. Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory: pipe dream or reality? J Antimicrob Chemother 67 : 2307 2308.[CrossRef][PubMed]
12. Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW . 2012. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13 : 601 612.[CrossRef][PubMed]
13. Koser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ . 2012. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8( 8) : e1002824.[CrossRef][PubMed]
14. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D . 2009. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49 : 543 551.[CrossRef][PubMed]
15. Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B . 2003. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci USA 100 : 8817 8822.[CrossRef][PubMed]
16. Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G . 2006. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 34 : e22.[CrossRef][PubMed]
17. Landegren U, Kaiser R, Sanders J, Hood L . 1988. A ligase-mediated gene detection technique. Science 241 : 1077 1080.[CrossRef][PubMed]
18. Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T . 2006. DNA ligases: structure, reaction mechanism, and function. Chem Rev 106 : 687 699.[CrossRef][PubMed]
19. Ronaghi M, Uhlen M, Nyren P . 1998. A sequencing method based on real-time pyrophosphate. Science 281 : 363, 365.[CrossRef][PubMed]
20. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P . 1996. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242 : 84 89.[CrossRef][PubMed]
21. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J . 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475 : 348 352.[CrossRef][PubMed]
22. Metzker ML . 2009. Sequencing in real time. Nat Biotechnol 27 : 150 151.[CrossRef][PubMed]
23. Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW . 2003. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299 : 682 686.[CrossRef][PubMed]
24. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, Meller A, Oliver JS, Pershin YV, Ramsey JM, Riehn R, Soni GV, Tabard-Cossa V, Wanunu M, Wiggin M, Schloss JA . 2008. The potential and challenges of nanopore sequencing. Nat Biotechnol 26 : 1146 1153.[CrossRef][PubMed]
25. Wanunu M . 2012. Nanopores: a journey towards DNA sequencing. Phys Life Rev 9 : 125 158.[CrossRef][PubMed]
26. Kasianowicz JJ, Brandin E, Branton D, Deamer DW . 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93 : 13770 13773.[CrossRef][PubMed]
27. Li J, Gershow M, Stein D, Brandin E, Golovchenko JA . 2003. DNA molecules and configurations in a solid-state nanopore microscope. Nat Mater 2 : 611 615.[CrossRef][PubMed]
28. Eisenstein M . 2012. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30 : 295 296.[CrossRef][PubMed]
29. Steinbock LJ, Radenovic A . 2015. The emergence of nanopores in next-generation sequencing. Nanotechnology 26 : 074003.[CrossRef][PubMed]
30. Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR, Sanders M, Enright MC, Dougan G, Bentley SD, Parkhill J, Fraser LJ, Betley JR, Schulz-Trieglaff OB, Smith GP, Peacock SJ . 2012. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 366 : 2267 2275.[CrossRef][PubMed]
31. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, NISC Comparative Sequencing Program Group Henderson DK, Palmore TN, Segre JA . 2012. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4 : 148ra116.[CrossRef][PubMed]
32. Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, Reacher M, Haworth CS, Curran MD, Harris SR, Peacock SJ, Parkhill J, Floto RA . 2013. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet 381 : 1551 1560.[CrossRef][PubMed]
33. Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O'Connor L, Ip CL, Golubchik T, Batty EM, Finney JM, Wyllie DH, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH, Peto TE, Walker AS . 2013. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Engl J Med 369 : 1195 1205.[CrossRef][PubMed]
34. Harris SR, Cartwright EJ, Torok ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ . 2013. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 13 : 130 136.[CrossRef][PubMed]
35. Reuter S, Ellington MJ, Cartwright EJ, Koser CU, Torok ME, Gouliouris T, Harris SR, Brown NM, Holden MT, Quail M, Parkhill J, Smith GP, Bentley SD, Peacock SJ . 2013. Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med 173 : 1397 1404.[CrossRef][PubMed]
36. Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D . 2010. High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster. J Clin Microbiol 48 : 3403 3406.[CrossRef][PubMed]
37. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P . 2011. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364 : 730 739.[CrossRef][PubMed]
38. Torok ME, Reuter S, Bryant J, Koser CU, Stinchcombe SV, Nazareth B, Ellington MJ, Bentley SD, Smith GP, Parkhill J, Peacock SJ . 2013. Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak. J Clin Microbiol 51 : 611 614.[CrossRef][PubMed]
39. Reuter S, Harrison TG, Koser CU, Ellington MJ, Smith GP, Parkhill J, Peacock SJ, Bentley SD, Torok ME . 2013. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ Open 3( 1) : e002175.[CrossRef][PubMed]
40. Uhlemann AC, Dordel J, Knox JR, Raven KE, Parkhill J, Holden MT, Peacock SJ, Lowy FD . 2014. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci USA, 111 : 6738 6743.[CrossRef][PubMed]
41. Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium . 2011. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365 : 718 724.[CrossRef][PubMed]
42. Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P . 2008. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9 : 603.[CrossRef][PubMed]
44. National Institutes of Health . 2014. The Cancer Genome Atlas. http://cancergenome.nih.gov/.
45. The 1000 Genomes Project Consortium . 2014. 1000 Genomes. A Deep Catalogue of Human Genetic Variation. http://www.1000genomes.org/home.
46. UC Davis School of Veterinary Medicine . 2014. 100K Foodborne Pathogen Genome Project. http://100kgenome.vetmed.ucdavis.edu/
47. McAdam PR, Templeton KE, Edwards GF, Holden MT, Feil EJ, Aanensen DM, Bargawi HJ, Spratt BG, Bentley SD, Parkhill J, Enright MC, Holmes A, Girvan EK, Godfrey PA, Feldgarden M, Kearns AM, Rambaut A, Robinson DA, Fitzgerald JR . 2012. Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci USA 109 : 9107 9112.[CrossRef][PubMed]
48. Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlickova H, Coombs G, Kearns AM, Hill RL, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramirez S, Feil EJ, Hudson LO, Enright MC, Balloux F, Aanensen DM, Spratt BG, Fitzgerald JR, Parkhill J, Achtman M, Bentley SD, Nubel U . 2013. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res 23 : 653 664.[CrossRef][PubMed]
49. Colquhoun J, Weetch RS . 1950. Resistance to chloramphenicol developing during treatment of typhoid fever. Lancet 2 : 621 623.[CrossRef][PubMed]
50. Anderson ES . 1975. The problem and implications of chloramphenicol resistance in the typhoid bacillus. J Hyg (Lond) 74 : 289 299.[CrossRef][PubMed]
51. Holt KE, Phan MD, Baker S, Duy PT, Nga TV, Nair S, Turner AK, Walsh C, Fanning S, Farrell-Ward S, Dutta S, Kariuki S, Weill FX, Parkhill J, Dougan G, Wain J . 2011. Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid. PLoS Negl Trop Dis 5( 7) : e1245.[CrossRef][PubMed]
52. Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G . 2008. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 40 : 987 993.[CrossRef][PubMed]
53. Bartlett JG . 2010. Clostridium difficile: progress and challenges. Ann NY Acad Sci 1213 : 62 69.[CrossRef][PubMed]
54. Warny M, Pepin J, Fang A, Killgore G, Thompson A, Brazier J, Frost E, McDonald LC . 2005. Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe. Lancet 366 : 1079 1084.[CrossRef][PubMed]
55. World Health Organization . 2013. Global tuberculosis report 2013. WHO, Geneva, Switzerland.
56. Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina , Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M . 2013. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet 45 : 1183 1189.[CrossRef][PubMed]
57. Torok ME, Harris SR, Cartwright EJ, Raven KE, Brown NM, Allison ME, Greaves D, Quail MA, Limmathurotsakul D, Holden MT, Parkhill J, Peacock SJ . 2014. Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic? J Antimicrob Chemother 69 : 2238 2245.[CrossRef][PubMed]
58. Lewis T, Loman NJ, Bingle L, Jumaa P, Weinstock GM, Mortiboy D, Pallen MJ . 2010. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J Hosp Infect 75 : 37 41.[CrossRef][PubMed]
59. Snyder LA, Loman NJ, Faraj LA, Levi K, Weinstock G, Boswell TC, Pallen MJ, Ala'Aldeen DA . 2013. Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing. Euro Surveill 18( 42).[CrossRef][PubMed]
60. Eyre DW, Griffiths D, Vaughan A, Golubchik T, Acharya M, O'Connor L, Crook DW, Walker AS, Peto TE . 2013. Asymptomatic Clostridium difficile colonisation and onward transmission. PLoS One 8( 11) : e78445.[CrossRef][PubMed]
61. Walker TM, Ip CL, Harrell RL, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TE . 2013. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 13 : 137 146.[CrossRef][PubMed]
62. Kundu S, Lockwood J, Depledge DP, Chaudhry Y, Aston A, Rao K, Hartley JC, Goodfellow I, Breuer J . 2013. Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Clin Infect Dis. 57 : 407 414.[CrossRef][PubMed]
63. Vaughan G, Forbi JC, Xia GL, Fonseca-Ford M, Vazquez R, Khudyakov YE, Montiel S, Waterman S, Alpuche C, Goncalves Rossi LM, Luna N . 2014. Full-length genome characterization and genetic relatedness analysis of hepatitis A virus outbreak strains associated with acute liver failure among children. J Med Virol. 86 : 202 208.[CrossRef][PubMed]
64. Barzon L, Pacenti M, Franchin E, Lavezzo E, Masi G, Squarzon L, Pagni S, Toppo S, Russo F, Cattai M, Cusinato R, Palu G . 2013. Whole genome sequencing and phylogenetic analysis of West Nile virus lineage 1 and lineage 2 from human cases of infection, Italy, August 2013. Euro Surveill 18( 38).[CrossRef][PubMed]
65. Litvintseva AP, Hurst S, Gade L, Frace MA, Hilsabeck R, Schupp JM, Gillece JD, Roe C, Smith D, Keim P, Lockhart SR, Changayil S, Weil MR, MacCannell DR, Brandt ME, Engelthaler DM . 2014. Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections. J Clin Microbiol 52 : 3216 3222.[CrossRef][PubMed]
66. Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Moller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK . 2011. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365 : 709 717.[CrossRef][PubMed]
67. Howden BP, Holt KE, Lam MM, Seemann T, Ballard S, Coombs GW, Tong SW, Grayson ML, Johnson PD, Stinear TP . 2013. Genomic insights to control the emergence of vancomycin-resistant enterococci. MBio. 4( 4) : e00412 13.[CrossRef][PubMed]
68. Graham RM, Doyle CJ, Jennison AV . 2014. Real-time investigation of a Legionella pneumophila outbreak using whole genome sequencing. Epidemiol Infect 142 : 2347 2351.[CrossRef][PubMed]
69. Revez J, Zhang J, Schott T, Kivisto R, Rossi M, Hanninen ML . 2014. Genomic variation between Campylobacter jejuni isolates associated with milk-borne-disease outbreaks. J Clin Microbiol 52 : 2782 2786.[CrossRef][PubMed]
70. Schmid D, Allerberger F, Huhulescu S, Pietzka A, Amar C, Kleta S, Prager R, Preussel K, Aichinger E, Mellmann A . 2014. Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013. Clin Microbiol Infect 20 : 431 436.[CrossRef][PubMed]
71. Roetzer A, Diel R, Kohl TA, Ruckert C, Nubel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rusch-Gerdes S, Supply P, Kalinowski J, Niemann S . 2013. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 10( 2) : e1001387.[CrossRef][PubMed]
72. Kato-Maeda M, Ho C, Passarelli B, Banaei N, Grinsdale J, Flores L, Anderson J, Murray M, Rose G, Kawamura LM, Pourmand N, Tariq MA, Gagneux S, Hopewell PC . 2013. Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. PLoS One 8( 3) : e58235.[CrossRef][PubMed]
73. Nelson MI, Tan Y, Ghedin E, Wentworth DE, St George K, Edelman L, Beck ET, Fan J, Lam TT, Kumar S, Spiro DJ, Simonsen L, Viboud C, Holmes EC, Henrickson KJ, Musser JM . 2011. Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. J Virol 85 : 828 834.[CrossRef][PubMed]
74. Baillie GJ, Galiano M, Agapow PM, Myers R, Chiam R, Gall A, Palser AL, Watson SJ, Hedge J, Underwood A, Platt S, McLean E, Pebody RG, Rambaut A, Green J, Daniels R, Pybus OG, Kellam P, Zambon M . 2012. Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis. J Virol 86 : 11 18.[CrossRef][PubMed]
75. World Health Organization . 2012. New coronavirus identified in two patients in the Eastern Mediterranean Region. Weekly Epidemiol Monitor 5.
76. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA . 2012. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 367 : 1814 1820.[CrossRef][PubMed]
77. Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA, Cummings DA, Alabdullatif ZN, Assad M, Almulhim A, Makhdoom H, Madani H, Alhakeem R, Al-Tawfiq JA, cotton M, Watson SJ, Kellam P, Zumla AI, Memish ZA , KSA MERS-CoV Investigation Team . 2013. Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med 369 : 407 416.[CrossRef][PubMed]
78. World Health Organization . 2014. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Summary and Literature Update as of 11 June 2014. http://www.who.int/emergencies/mers-cov/en/
79. Neblett Fanfair R, Benedict K, Bos J, Bennett SD, Lo YC, Adebanjo T, Etienne K, Deak E, Derado G, Shieh WJ, Drew C, Zaki S, Sugerman D, Gade L, Thompson EH, Sutton DA, Engelthaler DM, Schupp JM, Brandt ME, Harris JR, Lockhart SR, Turabelidze G, Park BJ . 2012. Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011. N Engl J Med 367 : 2214 2225.[CrossRef][PubMed]
80. Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo Elias C, Johnson JR, Walker AS, Peto TE, Crook DW . Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 68 : 2234 2244.[PubMed]
81. Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agerso Y, Lund O, Larsen MV, Aarestrup FM . 2013. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 68 : 771 777.[CrossRef][PubMed]
82. Gordon NC, Price JR, Cole K, Everitt R, Morgan M, Finney J, Kearns AM, Pichon B, Young B, Wilson DJ, Llewelyn MJ, Paul J, Peto TE, Crook DW, Walker AS, Golubchik T . 2014. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol 52 : 1182 1191.[CrossRef][PubMed]
83. Köser CU, Bryant JM, Becq J, Torok ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ . 2013. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med 369 : 290 292.[CrossRef][PubMed]
84. Health Protection Agency . 2012. Potentially transferable linezolid resistance in Enterococcus faecium in the United Kingdom. http://www.hpa.org.uk/webc/HPAwebFile/HPAweb_C/1317135991530.
85. Public Health England . 2013. Acute trust toolkit for the early detection, management and control of carbapenemase-producing Enterobacteriaceae. https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/329227/Acute_trust_toolkit_for_the_early_detection.pdf
86. Palmer AC, Kishony R . 2013. Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nat Rev Genet 14 : 243 248.[CrossRef][PubMed]
87. Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R . 2012. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 44 : 101 105.[CrossRef][PubMed]
88. Safi H, Lingaraju S, Amin A, Kim S, Jones M, Holmes M, McNeil M, Peterson SN, Chatterjee D, Fleischmann R, Alland D . 2013. Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-beta -D-arabinose biosynthetic and utilization pathway genes. Nat Genet 45 : 1190 1197.[CrossRef][PubMed]
89. Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM . 2013. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet 45 : 784 790.[CrossRef][PubMed]
90. Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S . 2012. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet 44 : 106 110.[CrossRef][PubMed]
91. de Vos M, Muller B, Borrell S, Black PA, van Helden PD, Warren RM, Gagneux S, Victor TC . 2013. Putative compensatory mutations in the rpoC gene of rifampin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrob Agents Chemother 57 : 827 832.[CrossRef][PubMed]
92. Andries K, Verhasselt P, Guillemont J, Gohlmann HW, Neefs JM, Winkler H, Van Gestel J, Timmerman P, Zhu M, Lee E, Williams P, de Chaffoy D, Huitric E, Hoffner S, Cambau E, Truffot-Pernot C, Lounis N, Jarlier V . 2005. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307 : 223 227.[CrossRef][PubMed]
93. Diacon AH, Pym A, Grobusch M, Patientia R, Rustomjee R, Page-Shipp L, Pistorius C, Krause R, Bogoshi M, Churchyard G, Venter A, Allen J, Palomino JC, De Marez T, van Heeswijk RP, Lounis N, Meyvisch P, Verbeeck J, Parys W, de Beule K, Andries K, McNeeley DF . 2009. The diarylquinoline TMC207 for multidrug-resistant tuberculosis. N Engl J Med 360 : 2397 2405.[CrossRef][PubMed]
94. Feuerriegel S, Koser CU, Niemann S . 2014. Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex. J Antimicrob Chemother 69 : 1205 1210.[CrossRef][PubMed]
95. Hartkoorn RC, Uplekar S, Cole ST . 2014. Cross-resistance between clofazimine and bedaquiline through upregulation of MmpL5 in Mycobacterium tuberculosis. Antimicrob Agents Chemother 58 : 2979 2981.[CrossRef][PubMed]
96. Dunne WM Jr, Westblade LF, Ford B . 2012. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31 : 1719 1726.[CrossRef][PubMed]
97. Pflughoeft KJ, Versalovic J . 2012. Human microbiome in health and disease. Annu Rev Pathol 7 : 99 122.[CrossRef][PubMed]
98. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J . 2006. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55 : 205 211[CrossRef].[PubMed]
99. Ubeda C, Taur Y, Jenq RR, Equinda MJ, Son T, Samstein M, Viale A, Socci ND, van den Brink MR, Kamboj M, Pamer EG . 2010. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest 120 : 4332 4341.[CrossRef][PubMed]
100. Boyd MA . 2009. Improvements in antiretroviral therapy outcomes over calendar time. Curr Opin HIV AIDS 4 : 194 199.[CrossRef][PubMed]
101. Nakagawa F, May M, Phillips A . 2013. Life expectancy living with HIV: recent estimates and future implications. Curr Opin Infect Dis 26 : 17 25.[CrossRef][PubMed]
102. Williams I, Churchill D, Anderson J, Boffito M, Bower M, Cairns G, Cwynarski K, Edwards S, Fidler S, Fisher M, Freedman A, Geretti AM, Gilleece Y, Horne R, Johnson M, Khoo S, Leen C, Marshall N, Nelson M, Orkin C, Paton N, Phillips A, Post F, Pozniak A, Sabin C, Trevelion R, Ustianowski A, Walsh J, Waters L, Wilkins E, Winston A, Youle M . 2012. British HIV Association guidelines for the treatment of HIV-1-positive adults with antiretroviral therapy 2012. HIV Med 13( Suppl 2) : 1 85.[CrossRef][PubMed]
103. Writing Group , Williams I, Churchill D, Anderson J, Boffito M, Bower M, Cairns G, Cwynarski K, Edwards S, Fidler S, Fisher M, Freedman A, Geretti AM, Gilleece Y, Horne R, Johnson M, Khoo S, Leen C, Marshall N, Nelson M, Orkin C, Paton N, Phillips A, Post F, Pozniak A, Sabin C, Trevelion R, Ustianowski A, Walsh J, Waters L, Wilkins E, Winston A, Youle M . 2014. British HIV Association guidelines for the treatment of HIV-1-positive adults with antiretroviral therapy 2012 (Updated November 2013. All changed text is cast in yellow highlight.). HIV Med 15( Suppl 1) : 1 85.[CrossRef][PubMed]
104. Harris SR, Torok ME, Cartwright EJ, Quail MA, Peacock SJ, Parkhill J . 2013. Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks. Nat Biotechnol 31 : 592 594.[CrossRef][PubMed]
105. Long SW, Williams D, Valson C, Cantu CC, Cernoch P, Musser JM, Olsen RJ . 2013. A genomic day in the life of a clinical microbiology laboratory. J Clin Microbiol 51 : 1272 1277.[CrossRef][PubMed]
106. Lasken RS, McLean JS . 2014. Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet 15 : 577 584.[CrossRef][PubMed]
107. Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS . 2005. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71 : 3342 3347.[CrossRef][PubMed]
108. Grindberg RV, Ishoey T, Brinza D, Esquenazi E, Coates RC, Liu WT, Gerwick L, Dorrestein PC, Pevzner P, Lasken R, Gerwick WH . 2011. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One 6( 4) : e18565.[CrossRef][PubMed]


Generic image for table

Comparison of NGS platforms

Citation: Török M, Peacock S. 2016. Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health, p 32-48. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch3

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error