title: Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy.
abstract: OBJECTIVE
  The whole genomes of two Acinetobacter baumannii isolates recovered from a single patient were sequenced to gain insight into the nature and extent of genomic plasticity in this important nosocomial pathogen over the course of a short infection. The first, AB210, was recovered before tigecycline therapy and was susceptible to this agent; the second, AB211, was recovered after therapy and was resistant.
  
  
  METHODS
  DNA from AB210 was sequenced by 454 GS FLX pyrosequencing according to the standard protocol for whole-genome shotgun sequencing, producing ∼250 bp fragment reads. AB211 was shotgun sequenced using the Illumina Genetic Analyzer to produce fragment reads of exactly 36 bp. Single nucleotide polymorphisms (SNPs) and large deletions detected in AB211 in relation to AB210 were confirmed by PCR and DNA sequencing.
  
  
  RESULTS
  Automated gene prediction detected 3850 putative coding sequences (CDSs). Sequence analysis demonstrated the presence of plasmids pAB0057 and pACICU2 in both isolates. Eighteen putative SNPs were detected between the pre- and post-therapy isolates, AB210 and AB211. Three contigs in AB210 were not covered by reads in AB211, representing three deletions of ∼15, 44 and 17 kb.
  
  
  CONCLUSIONS
  This study demonstrates that significant differences were detectable between two bacterial isolates recovered 1 week apart from the same patient, and reveals the potential of whole-genome sequencing as a tool for elucidating the processes responsible for changes in antibiotic susceptibility profiles.
authors.affiliation: Antimicrobial Research Group, Centre for Immunology & Infectious Disease, Blizard Institute, Barts and The London, Queen Mary's School of Medicine and Dentistry, 4 Newark Street, London, E1 2AT, UK. m.hornsey@qmul.ac.uk
authors.forename: Michael
authors.initials: M
authors.lastname: Hornsey
authors.forename: Nick
authors.initials: N
authors.lastname: Loman
authors.forename: David W
authors.initials: DW
authors.lastname: Wareham
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Ellington
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
authors.forename: Jane F
authors.initials: JF
authors.lastname: Turton
authors.forename: Anthony
authors.initials: A
authors.lastname: Underwood
authors.forename: Tom
authors.initials: T
authors.lastname: Gaulton
authors.forename: Claire P
authors.initials: CP
authors.lastname: Thomas
authors.forename: Michel
authors.initials: M
authors.lastname: Doumith
authors.forename: David M
authors.initials: DM
authors.lastname: Livermore
authors.forename: Neil
authors.initials: N
authors.lastname: Woodford
mesh_terms: D000151:Acinetobacter Infections / Q000188:drug therapy* / Q000382:microbiology*; D040981:Acinetobacter baumannii / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D024881:Drug Resistance, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D008911:Minocycline / Q000031:analogs & derivatives* / Q000494:pharmacology / Q000627:therapeutic use; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D000078304:Tigecycline
chemical_list: D004269:DNA, Bacterial; D000078304:Tigecycline; D008911:Minocycline