title: In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?
abstract: OBJECTIVE
  To obtain an expanded understanding of antibiotic resistance evolution in vivo, particularly in the context of vancomycin exposure.
  
  
  METHODS
  The whole genomes of six consecutive methicillin-resistant Staphylococcus aureus blood culture isolates (ST239-MRSA-III) from a single patient exposed to various antimicrobials (over a 77 day period) were sequenced and analysed.
  
  
  RESULTS
  Variant analysis revealed the existence of non-susceptible sub-populations derived from a common susceptible ancestor, with the predominant circulating clone(s) selected for by type and duration of antimicrobial exposure.
  
  
  CONCLUSIONS
  This study highlights the dynamic nature of bacterial evolution and that non-susceptible sub-populations can emerge from clouds of variation upon antimicrobial exposure. Diagnostically, this has direct implications for sample selection when using whole-genome sequencing as a tool to guide clinical therapy. In the context of bacteraemia, deep sequencing of bacterial DNA directly from patient blood samples would avoid culture 'bias' and identify mutations associated with circulating non-susceptible sub-populations, some of which may confer cross-resistance to alternate therapies.
authors.affiliation: Antibiotic Resistance & Mobile Elements Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia.
authors.forename: Sebastiaan J
authors.initials: SJ
authors.lastname: van Hal
authors.forename: Jason A
authors.initials: JA
authors.lastname: Steen
authors.forename: Björn A
authors.initials: BA
authors.lastname: Espedido
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Cooper
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.forename: Iain B
authors.initials: IB
authors.lastname: Gosbell
authors.forename: Slade O
authors.initials: SO
authors.lastname: Jensen
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000235:genetics* / Q000302:isolation & purification*; D013211:Staphylococcus aureus / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification
chemical_list: D000900:Anti-Bacterial Agents
keywords: MRSA; diagnostics; genomics; sub-populations
references.citation: Eur J Clin Microbiol Infect Dis. 2011 May;30(5):603-10
references.pmid: 21191627
references.citation: Antimicrob Agents Chemother. 2007 Jun;51(6):2048-52
references.pmid: 17404009
references.citation: PLoS Pathog. 2012 Feb;8(2):e1002505
references.pmid: 22319446
references.citation: Antimicrob Agents Chemother. 2011 Jun;55(6):2989-91
references.pmid: 21444696
references.citation: PLoS One. 2012;7(1):e28316
references.pmid: 22238576
references.citation: Clin Microbiol Rev. 2012 Apr;25(2):362-86
references.pmid: 22491776
references.citation: Mol Microbiol. 1995 Jun;16(5):825-34
references.pmid: 7476181
references.citation: Proc Natl Acad Sci U S A. 2007 May 29;104(22):9451-6
references.pmid: 17517606
references.citation: Antimicrob Agents Chemother. 2009 Dec;53(12):5265-74
references.pmid: 19752277
references.citation: Antimicrob Agents Chemother. 2010 Dec;54(12):5222-33
references.pmid: 20837752
references.citation: Clin Infect Dis. 2011 Feb 1;52(3):e18-55
references.pmid: 21208910
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4550-5
references.pmid: 22393007
references.citation: PLoS One. 2013 May 01;8(5):e61319
references.pmid: 23658690
references.citation: PLoS Pathog. 2011 Nov;7(11):e1002359
references.pmid: 22102812
references.citation: Lancet Infect Dis. 2013 Feb;13(2):130-6
references.pmid: 23158674
references.citation: J Infect Dis. 2012 Jun;205(11):1677-87
references.pmid: 22492855