title: Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.
abstract: Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average≤0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.
authors: Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA stevesal@uw.edu.
authors: Stephen J
authors: SJ
authors: Salipante
authors: Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
authors: Dhruba J
authors: DJ
authors: SenGupta
authors: Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
authors: Lisa A
authors: LA
authors: Cummings
authors: Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
authors: Tyler A
authors: TA
authors: Land
authors: Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
authors: Daniel R
authors: DR
authors: Hoogestraat
authors: Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors: Brad T
authors: BT
authors: Cookson
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D001424:Bacterial Infections / Q000382:microbiology; D003428:Cross Infection / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004196:Disease Outbreaks; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods*; D058889:Molecular Typing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial
references: Science. 2010 Jan 22;327(5964):469-74
references: 20093474
references: New Microbiol. 2014 Jan;37(1):1-15
references: 24531166
references: PLoS One. 2010;5(3):e9490
references: 20224823
references: Infect Genet Evol. 2010 Oct;10(7):866-75
references: 20692376
references: Infect Genet Evol. 2011 Jan;11(1):92-102
references: 20959148
references: Genome Biol. 2010;11(10):R99
references: 20932289
references: J Genet Genomics. 2011 Mar 20;38(3):95-109
references: 21477781
references: N Engl J Med. 2011 Aug 25;365(8):709-17
references: 21793740
references: Nat Biotechnol. 2012 Jan;30(1):78-82
references: 22178993
references: PLoS Med. 2012 Feb;9(2):e1001172
references: 22346738
references: Nat Rev Genet. 2012 Sep;13(9):601-12
references: 22868263
references: Sci Transl Med. 2012 Aug 22;4(148):148ra116
references: 22914622
references: Poult Sci. 2013 Feb;92(2):573-80
references: 23300325
references: Lancet Infect Dis. 2013 Feb;13(2):137-46
references: 23158499
references: J Clin Microbiol. 2000 Mar;38(3):1008-15
references: 10698988
references: Microb Drug Resist. 2000 Fall;6(3):189-98
references: 11144419
references: Emerg Infect Dis. 2001 May-Jun;7(3):382-9
references: 11384513
references: J Clin Microbiol. 2002 Jul;40(7):2498-503
references: 12089269
references: J Clin Microbiol. 2003 May;41(5):1843-9
references: 12734215
references: Infect Genet Evol. 2002 Dec;2(2):145-8
references: 12797991
references: J Clin Microbiol. 2003 Jul;41(7):3181-6
references: 12843061
references: J Clin Microbiol. 2003 Dec;41(12):5442-8
references: 14662923
references: Methods Mol Biol. 2004;266:323-52
references: 15148426
references: Infect Genet Evol. 2004 Sep;4(3):193-7
references: 15450198
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: J Clin Microbiol. 1992 Mar;30(3):577-80
references: 1313045
references: J Clin Microbiol. 1995 Sep;33(9):2233-9
references: 7494007
references: J Med Microbiol. 1996 Mar;44(3):179-84
references: 8636934
references: Lancet Infect Dis. 2014 Apr;14(4):341-52
references: 24631223
references: J Clin Microbiol. 2014 Aug;52(8):2787-96
references: 24850346
references: MBio. 2014;5(5):e01692-14
references: 25293757
references: Genome Res. 2015 Jan;25(1):119-28
references: 25373147
references: J Clin Microbiol. 2005 Jul;43(7):3346-55
references: 16000459
references: J Clin Microbiol. 2005 Apr;43(4):1776-81
references: 15814998
references: Eur J Clin Microbiol Infect Dis. 2010 Mar;29(3):295-300
references: 20082105
references: Nat Rev Genet. 2005 Aug;6(8):654-62
references: 16136655
references: Clin Microbiol Rev. 2006 Jul;19(3):512-30
references: 16847083
references: J Clin Microbiol. 2007 Feb;45(2):453-60
references: 17108068
references: J Clin Microbiol. 2007 Nov;45(11):3707-12
references: 17881548
references: Nat Methods. 2009 Apr;6(4):291-5
references: 19287394
references: Infect Genet Evol. 2009 Jul;9(4):430-40
references: 19460308
references: Genome Res. 2009 Jun;19(6):1117-23
references: 19251739
references: Bioinformatics. 2009 Jul 15;25(14):1754-60
references: 19451168
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: J Antimicrob Chemother. 2009 Sep;64(3):441-6
references: 19608582
references: Nature. 2009 Oct 29;461(7268):1243-7
references: 19838166
references: J Clin Microbiol. 1996 May;34(5):1096-9
references: 8727883
references: Genetics. 1998 Apr;148(4):1667-86
references: 9560386
references: Lancet Infect Dis. 2013 Feb;13(2):130-6
references: 23158674
references: Genome Res. 2013 Apr;23(4):653-64
references: 23299977
references: Genome Res. 2013 May;23(5):843-54
references: 23382536
references: J Hosp Infect. 2013 Jul;84(3):200-5
references: 23688708
references: Ann Ig. 2013 Nov-Dec;25(6):485-92
references: 24284534
references: JAMA Intern Med. 2013 Dec 9-23;173(22):2039-46
references: 23999949
references: Nat Rev Genet. 2014 Jan;15(1):49-55
references: 24281148
references: PLoS One. 2014;9(2):e87991
references: 24505344
references: Clin Infect Dis. 2014 Mar;58(5):609-18
references: 24336829
references: Infect Genet Evol. 2014 Jan;21:548-53
references: 23665384