title: Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study.
abstract: BACKGROUND
  Increasing numbers of individuals with cystic fibrosis are becoming infected with the multidrug-resistant non-tuberculous mycobacterium (NTM) Mycobacterium abscessus, which causes progressive lung damage and is extremely challenging to treat. How this organism is acquired is not currently known, but there is growing concern that person-to-person transmission could occur. We aimed to define the mechanisms of acquisition of M abscessus in individuals with cystic fibrosis.
  
  
  METHODS
  Whole genome sequencing and antimicrobial susceptibility testing were done on 168 consecutive isolates of M abscessus from 31 patients attending an adult cystic fibrosis centre in the UK between 2007 and 2011. In parallel, we undertook detailed environmental testing for NTM and defined potential opportunities for transmission between patients both in and out of hospital using epidemiological data and social network analysis.
  
  
  RESULTS
  Phylogenetic analysis revealed two clustered outbreaks of near-identical isolates of the M abscessus subspecies massiliense (from 11 patients), differing by less than ten base pairs. This variation represents less diversity than that seen within isolates from a single individual, strongly indicating between-patient transmission. All patients within these clusters had numerous opportunities for within-hospital transmission from other individuals, while comprehensive environmental sampling, initiated during the outbreak, failed to detect any potential point source of NTM infection. The clusters of M abscessus subspecies massiliense showed evidence of transmission of mutations acquired during infection of an individual to other patients. Thus, isolates with constitutive resistance to amikacin and clarithromycin were isolated from several individuals never previously exposed to long-term macrolides or aminoglycosides, further indicating cross-infection.
  
  
  CONCLUSIONS
  Whole genome sequencing has revealed frequent transmission of multidrug resistant NTM between patients with cystic fibrosis despite conventional cross-infection measures. Although the exact transmission route is yet to be established, our epidemiological analysis suggests that it could be indirect.
  
  
  BACKGROUND
  The Wellcome Trust, Papworth Hospital, NIHR Cambridge Biomedical Research Centre, UK Health Protection Agency, Medical Research Council, and the UKCRC Translational Infection Research Initiative.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Josephine M
authors.initials: JM
authors.lastname: Bryant
authors.forename: Dorothy M
authors.initials: DM
authors.lastname: Grogono
authors.forename: Daniel
authors.initials: D
authors.lastname: Greaves
authors.forename: Juliet
authors.initials: J
authors.lastname: Foweraker
authors.forename: Iain
authors.initials: I
authors.lastname: Roddick
authors.forename: Thomas
authors.initials: T
authors.lastname: Inns
authors.forename: Mark
authors.initials: M
authors.lastname: Reacher
authors.forename: Charles S
authors.initials: CS
authors.lastname: Haworth
authors.forename: Martin D
authors.initials: MD
authors.lastname: Curran
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Peacock
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: R Andres
authors.initials: RA
authors.lastname: Floto
mesh_terms: D015331:Cohort Studies; D003550:Cystic Fibrosis / Q000150:complications / Q000382:microbiology*; D055106:Genome-Wide Association Study; D006801:Humans; D009165:Mycobacterium Infections, Nontuberculous / Q000235:genetics* / Q000382:microbiology / Q000635:transmission*; D009170:Nontuberculous Mycobacteria / Q000235:genetics* / Q000302:isolation & purification; D012189:Retrospective Studies
references.citation: Am J Respir Crit Care Med. 2007 Feb 15;175(4):367-416
references.pmid: 17277290
references.citation: Emerg Infect Dis. 2003 Dec;9(12):1587-91
references.pmid: 14720400
references.citation: Emerg Infect Dis. 2010 Feb;16(2):294-6
references.pmid: 20113563
references.citation: Int J Syst Evol Microbiol. 2011 Sep;61(Pt 9):2311-2313
references.pmid: 21037035
references.citation: J Cyst Fibros. 2010 Mar;9(2):117-23
references.pmid: 20071249
references.citation: Am J Respir Crit Care Med. 2012 Nov 1;186(9):822-3
references.pmid: 23118083
references.citation: Am J Respir Crit Care Med. 2008 Nov 15;178(10):999-1000
references.pmid: 18987345
references.citation: PLoS One. 2009 Jun 19;4(6):e5660
references.pmid: 19543527
references.citation: Microbiol Immunol. 2010 Jun;54(6):347-53
references.pmid: 20536733
references.citation: Am J Respir Crit Care Med. 2009 Nov 1;180(9):896-902
references.pmid: 19661243
references.citation: Emerg Infect Dis. 2011 Mar;17(3):419-24
references.pmid: 21392432
references.citation: J Clin Microbiol. 2012 May;50(5):1758-61
references.pmid: 22403419
references.citation: Am J Respir Crit Care Med. 2011 Feb 1;183(3):405-10
references.pmid: 20833823
references.citation: Am J Respir Crit Care Med. 2003 Mar 15;167(6):828-34
references.pmid: 12433668
references.citation: J Clin Microbiol. 2009 Dec;47(12):4124-8
references.pmid: 19846643
references.citation: Clin Microbiol Rev. 2004 Jan;17(1):57-71
references.pmid: 14726455
references.citation: Am Rev Respir Dis. 1980 Aug;122(2):259-63
references.pmid: 7416602
references.citation: J Heart Lung Transplant. 2006 Jul;25(7):745-55
references.pmid: 16818116
references.citation: Int J Syst Evol Microbiol. 2006 Jan;56(Pt 1):133-43
references.pmid: 16403878
references.citation: Antimicrob Agents Chemother. 2009 Apr;53(4):1367-76
references.pmid: 19171799
references.citation: Emerg Infect Dis. 2010 Oct;16(10):1576-83
references.pmid: 20875283
references.citation: Annu Rev Microbiol. 1998;52:453-90
references.pmid: 9891805
references.citation: Am J Respir Crit Care Med. 2010 Oct 1;182(7):970-6
references.pmid: 20538958
references.citation: BMC Evol Biol. 2007 Nov 08;7:214
references.pmid: 17996036
references.citation: Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16393-9
references.pmid: 19805310
references.citation: Proc Natl Acad Sci U S A. 2007 May 8;104(19):8101-6
references.pmid: 17468398
references.citation: J Clin Microbiol. 2011 Feb;49(2):491-9
references.pmid: 21106786
references.citation: J Clin Invest. 2011 Sep;121(9):3554-63
references.pmid: 21804191
references.citation: Am J Respir Cell Mol Biol. 2010 Oct;43(4):387-93
references.pmid: 20081053
references.citation: Antimicrob Agents Chemother. 1996 Jul;40(7):1676-81
references.pmid: 8807061
references.citation: Clin Infect Dis. 2011 Mar 1;52(5):565-71
references.pmid: 21292659
references.citation: J Clin Microbiol. 2004 Dec;42(12):5493-501
references.pmid: 15583272
references.citation: Am J Respir Crit Care Med. 2012 Jan 15;185(2):231-2
references.pmid: 22246710
references.citation: J Med Microbiol. 2010 Oct;59(Pt 10):1203-1211
references.pmid: 20616186