title: Whole-genome sequencing to control antimicrobial resistance.
abstract: Following recent improvements in sequencing technologies, whole-genome sequencing (WGS) is positioned to become an essential tool in the control of antibiotic resistance, a major threat in modern healthcare. WGS has already found numerous applications in this area, ranging from the development of novel antibiotics and diagnostic tests through to antibiotic stewardship of currently available drugs via surveillance and the elucidation of the factors that allow the emergence and persistence of resistance. Numerous proof-of-principle studies have also highlighted the value of WGS as a tool for day-to-day infection control and, for some pathogens, as a primary diagnostic tool to detect antibiotic resistance. However, appropriate data analysis platforms will need to be developed before routine WGS can be introduced on a large scale.
authors.affiliation: Department of Medicine, University of Cambridge, Cambridge, UK. Electronic address: cuk21@cam.ac.uk.
authors.forename: Claudio U
authors.initials: CU
authors.lastname: Köser
authors.affiliation: Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Ellington
authors.affiliation: Department of Medicine, University of Cambridge, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Peacock
mesh_terms: D000890:Anti-Infective Agents / Q000627:therapeutic use*; D001424:Bacterial Infections / Q000517:prevention & control*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D006801:Humans
chemical_list: D000890:Anti-Infective Agents
keywords: antibiotic resistance; diagnostics; surveillance; whole-genome sequencing
references.citation: Science. 2013 Sep 27;341(6153):1514-7
references.pmid: 24030491
references.citation: PLoS One. 2009 Oct 12;4(10):e7407
references.pmid: 19823582
references.citation: J Antimicrob Chemother. 2013 Oct;68(10):2234-44
references.pmid: 23722448
references.citation: Nat Biotechnol. 2012 May;30(5):434-9
references.pmid: 22522955
references.citation: PLoS One. 2010 Jul 12;5(7):e11518
references.pmid: 20634954
references.citation: PLoS Pathog. 2012;8(8):e1002824
references.pmid: 22876174
references.citation: Clin Microbiol Infect. 2013 Sep;19(9):784-9
references.pmid: 23331482
references.citation: Expert Rev Anti Infect Ther. 2013 Nov;11(11):1193-205
references.pmid: 24151834
references.citation: BMJ. 2014 May 27;348:g3535
references.pmid: 24868091
references.citation: J Clin Microbiol. 2013 May;51(5):1596-9
references.pmid: 23447641
references.citation: J Clin Microbiol. 2012 Dec;50(12):3838-44
references.pmid: 22993180
references.citation: J Clin Microbiol. 2014 Jan;52(1):139-46
references.pmid: 24172157
references.citation: Pharmacotherapy. 2009 Nov;29(11):1326-43
references.pmid: 19857149
references.citation: Nat Genet. 2013 Jul;45(7):784-90
references.pmid: 23749189
references.citation: Lancet. 2013 May 4;381(9877):1551-60
references.pmid: 23541540
references.citation: Trends Genet. 2013 Mar;29(3):160-9
references.pmid: 23245857
references.citation: Genome Res. 2013 Apr;23(4):653-64
references.pmid: 23299977
references.citation: Curr Opin Crit Care. 2013 Oct;19(5):432-9
references.pmid: 23856896
references.citation: Trends Microbiol. 2014 Jan;22(1):42-7
references.pmid: 24331435
references.citation: Clin Microbiol Infect. 2013 Sep;19(9):796-802
references.pmid: 23432709
references.citation: Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):E1768-76
references.pmid: 24733896
references.citation: Nat Genet. 2013 Oct;45(10):1190-7
references.pmid: 23995136
references.citation: Nat Genet. 2011 Dec 18;44(1):106-10
references.pmid: 22179134
references.citation: Nat Genet. 2013 Oct;45(10):1107-8
references.pmid: 24071843
references.citation: Nat Rev Genet. 2012 Sep;13(9):601-612
references.pmid: 22868263
references.citation: Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):21065-70
references.pmid: 24324153
references.citation: Nat Biotechnol. 2013 Jul;31(7):592-4
references.pmid: 23839141
references.citation: J Clin Microbiol. 2012 Nov;50(11):3726-8
references.pmid: 22895038
references.citation: PLoS Comput Biol. 2013;9(5):e1003059
references.pmid: 23658511
references.citation: Antimicrob Agents Chemother. 2012 Dec;56(12):6080-7
references.pmid: 23006760
references.citation: Antimicrob Agents Chemother. 2013 Jul;57(7):3461
references.pmid: 23761426
references.citation: J Antimicrob Chemother. 2013 Apr;68(4):771-7
references.pmid: 23233485
references.citation: Genome Biol. 2012 Dec 21;13(12):R118
references.pmid: 23259504
references.citation: mBio. 2012 Feb 21;3(1):
references.pmid: 22354957
references.citation: Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2013;30(8):1422-36
references.pmid: 23199033
references.citation: Lancet Infect Dis. 2014 Mar;14(3):220-6
references.pmid: 24462211
references.citation: Antimicrob Agents Chemother. 2011 Dec;55(12):5718-22
references.pmid: 21930879
references.citation: Science. 2005 Jan 14;307(5707):223-7
references.pmid: 15591164
references.citation: Lancet Infect Dis. 2013 Feb;13(2):130-6
references.pmid: 23158674
references.citation: N Engl J Med. 2013 Jan 24;368(4):299-302
references.pmid: 23343059
references.citation: Bull World Health Organ. 2013 Mar 1;91(3):163-4
references.pmid: 23476087
references.citation: BMJ Open. 2012 Jun 06;2(3):
references.pmid: 22674929
references.citation: Nat Genet. 2011 Dec 18;44(1):101-5
references.pmid: 22179135
references.citation: Nat Rev Drug Discov. 2013 May;12(5):388-404
references.pmid: 23629506
references.citation: Lancet Infect Dis. 2007 May;7(5):328-37
references.pmid: 17448936
references.citation: Nat Rev Genet. 2013 Apr;14(4):243-8
references.pmid: 23419278
references.citation: Antimicrob Agents Chemother. 2014 May;58(5):2979-81
references.pmid: 24590481
references.citation: Ups J Med Sci. 2014 May;119(2):87-95
references.pmid: 24694024
references.citation: Emerg Infect Dis. 2014 Mar;20(3):364-71
references.pmid: 24565502
references.citation: Genome Med. 2013 Apr 29;5(4):36
references.pmid: 23673226
references.citation: J Infect Dis. 2014 May 1;209(9):1446-51
references.pmid: 24218500
references.citation: Bull World Health Organ. 2012 Sep 1;90(9):693-8
references.pmid: 22984314
references.citation: Emerg Infect Dis. 2012 Nov;18(11):e1
references.pmid: 23092707
references.citation: N Engl J Med. 2012 Jun 14;366(24):2267-75
references.pmid: 22693998
references.citation: Antimicrob Agents Chemother. 2014 Jun;58(6):3270-5
references.pmid: 24687490
references.citation: J Antimicrob Chemother. 2014 May;69(5):1275-81
references.pmid: 24370932
references.citation: Nat Chem Biol. 2013 Apr;9(4):222-31
references.pmid: 23508188
references.citation: Expert Rev Anti Infect Ther. 2013 Mar;11(3):277-96
references.pmid: 23458768
references.citation: Nat Genet. 2013 Jan;45(1):109-13
references.pmid: 23222960
references.citation: Nat Rev Microbiol. 2012 Sep;10(9):599-606
references.pmid: 22864262
references.citation: J Med Microbiol. 2001 Dec;50(12):1018-1020
references.pmid: 11761184
references.citation: Lancet Respir Med. 2013 Dec;1(10):759-61
references.pmid: 24461746
references.citation: Curr Opin Microbiol. 2010 Oct;13(5):640-5
references.pmid: 20846899
references.citation: JAMA. 2013 Apr 10;309(14):1502-10
references.pmid: 23571589
references.citation: PLoS Med. 2013;10(2):e1001387
references.pmid: 23424287
references.citation: Tuberculosis (Edinb). 2014 Jul;94(4):451-3
references.pmid: 24870943
references.citation: Antimicrob Agents Chemother. 2013 Feb;57(2):827-32
references.pmid: 23208709
references.citation: Pathogens. 2014 Jun 11;3(2):437-58
references.pmid: 25437808
references.citation: N Engl J Med. 2014 Jun 19;370(25):2408-17
references.pmid: 24896819
references.citation: Mol Microbiol. 2014 Feb;91(3):538-47
references.pmid: 24354762
references.citation: J Infect Dis. 2012 Dec 1;206(11):1724-33
references.pmid: 22984115
references.citation: J Clin Microbiol. 2013 Dec;51(12):4141-9
references.pmid: 24108611
references.citation: Tuberculosis (Edinb). 2011 Nov;91(6):510-23
references.pmid: 21835699
references.citation: J Antimicrob Chemother. 2014 Aug;69(8):2298-9
references.pmid: 24752956
references.citation: Lancet Respir Med. 2013 Dec;1(10):786-92
references.pmid: 24461758
references.citation: J Clin Microbiol. 2014 Apr;52(4):1182-91
references.pmid: 24501024
references.citation: N Engl J Med. 2013 Jul 18;369(3):290-2
references.pmid: 23863072
references.citation: J Clin Microbiol. 2014 May;52(5):1501-10
references.pmid: 24574290
references.citation: Sci Transl Med. 2012 Aug 22;4(148):148ra116
references.pmid: 22914622
references.citation: JAMA Intern Med. 2013 Aug 12;173(15):1397-404
references.pmid: 23857503
references.citation: PLoS One. 2013 Apr 29;8(4):e62774
references.pmid: 23658651
references.citation: Nat Genet. 2014 Mar;46(3):305-309
references.pmid: 24509479
references.citation: Clin Infect Dis. 2014 Mar;58(5):609-18
references.pmid: 24336829
references.citation: N Engl J Med. 2013 Sep 26;369(13):1195-205
references.pmid: 24066741
references.citation: Nat Rev Genet. 2014 Jan;15(1):49-55
references.pmid: 24281148
references.citation: J Antimicrob Chemother. 2014 May;69(5):1205-10
references.pmid: 24458512
references.citation: Science. 2010 Jan 22;327(5964):469-74
references.pmid: 20093474
references.citation: Lancet Respir Med. 2014 Apr;2(4):285-292
references.pmid: 24717625
references.citation: Infect Chemother. 2013 Mar;45(1):1-10
references.pmid: 24265945
references.citation: J Antimicrob Chemother. 2014 Mar;69(3):632-6
references.pmid: 24155060