title: Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance.
abstract: OBJECTIVE
  To characterize at the genomic level the evolution of multiresistance during an outbreak of Klebsiella pneumoniae in a burns intensive care unit. The outbreak involved a DHA-1 β-lactamase-producing strain that later acquired carbapenem and fosfomycin resistance, and in one case colistin resistance.
  
  
  METHODS
  The genomes of two isolates were sequenced and compared with a previously sequenced genome. The role of hypermutability was investigated by measuring the mutation frequencies of the isolates and comparison with a collection of control strains.
  
  
  RESULTS
  Sequence comparison identified four single-nucleotide variants and two transposon insertions. Analysis of the variants in the whole collection related carbapenem and fosfomycin resistance to a nonsense mutation in the ompK36 porin gene and colistin resistance to an IS1 insertion in the mgrB gene. The plasmid carrying the blaDHA-1 gene was unstable in the absence of antibiotics, and analysis of isolates that had lost the plasmid showed that the porin mutation alone was not sufficient to generate carbapenem resistance. The mutation frequencies were similar among all the strains analysed.
  
  
  CONCLUSIONS
  Carbapenem resistance required production of the DHA-1 β-lactamase and decreased permeability, but fosfomycin resistance depended only on permeability. Resistance to colistin might be related to an alteration in the regulation of the phoPQ system. Hypermutation is not related to the selection of porin mutants. Plasmid instability might be due to the high number of mobile elements and suggests a major role for antibiotic selection pressure in the emergence and evolution of this outbreak.
authors.affiliation: Servicio de Microbiología, Hospital Universitario La Paz, IdiPaz, Paseo de La Castellana 261, 28046 Madrid, Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: López-Camacho
authors.forename: Rosa
authors.initials: R
authors.lastname: Gómez-Gil
authors.forename: Raquel
authors.initials: R
authors.lastname: Tobes
authors.forename: Marina
authors.initials: M
authors.lastname: Manrique
authors.forename: María
authors.initials: M
authors.lastname: Lorenzo
authors.forename: Beatriz
authors.initials: B
authors.lastname: Galván
authors.forename: Estefanía
authors.initials: E
authors.lastname: Salvarelli
authors.forename: Youssef
authors.initials: Y
authors.lastname: Moatassim
authors.forename: Iñigo J
authors.initials: IJ
authors.lastname: Salanueva
authors.forename: Eduardo
authors.initials: E
authors.lastname: Pareja
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Codoñer
authors.forename: Miguel
authors.initials: M
authors.lastname: Alvarez-Tejado
authors.forename: María Pilar
authors.initials: MP
authors.lastname: Garcillán-Barcia
authors.forename: Fernando
authors.initials: F
authors.lastname: De la Cruz
authors.forename: Jesús
authors.initials: J
authors.lastname: Mingorance
mesh_terms: D000328:Adult; D000368:Aged; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D015780:Carbapenems / Q000494:pharmacology*; D003091:Colistin / Q000494:pharmacology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004196:Disease Outbreaks; D018432:Drug Resistance, Multiple; D019143:Evolution, Molecular; D005260:Female; D016680:Genome, Bacterial; D006801:Humans; D007710:Klebsiella Infections / Q000453:epidemiology / Q000382:microbiology*; D007711:Klebsiella pneumoniae / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D059645:Mutation Rate; D017422:Sequence Analysis, DNA
chemical_list: D000900:Anti-Bacterial Agents; D015780:Carbapenems; D004269:DNA, Bacterial; D003091:Colistin
keywords: Klebsiella pneumoniae genome; antibiotic resistance; hypermutation; outbreak genomics