title: Genomic analysis of an emerging multiresistant Staphylococcus aureus strain rapidly spreading in cystic fibrosis patients revealed the presence of an antibiotic inducible bacteriophage.
abstract: BACKGROUND
  Staphylococcus aureus is a major human pathogen responsible for a variety of nosocomial and community-acquired infections. Recent reports show that the prevalence of Methicillin-Resistant S. aureus (MRSA) infections in cystic fibrosis (CF) patients is increasing. In 2006 in Marseille, France, we have detected an atypical MRSA strain with a specific antibiotic susceptibility profile and a unique growth phenotype. Because of the clinical importance of the spread of such strain among CF patients we decided to sequence the genome of one representative isolate (strain CF-Marseille) to compare this to the published genome sequences. We also conducted a retrospective epidemiological analysis on all S. aureus isolated from 2002 to 2007 in CF patients from our institution.
  
  
  RESULTS
  CF-Marseille is multidrug resistant, has a hetero-Glycopeptide-Intermediate resistance S. aureus phenotype, grows on Cepacia agar with intense orange pigmentation and has a thickened cell wall. Phylogenetic analyses using Complete Genome Hybridization and Multi Locus VNTR Assay showed that CF-Marseille was closely related to strain Mu50, representing vancomycin-resistant S. aureus. Analysis of CF-Marseille shows a similar core genome to that of previously sequenced MRSA strains but with a different genomic organization due to the presence of specific mobile genetic elements i.e. a new SCCmec type IV mosaic cassette that has integrated the pUB110 plasmid, and a new phage closely related to phiETA3. Moreover this phage could be seen by electron microscopy when mobilized with several antibiotics commonly used in CF patients including, tobramycin, ciprofloxacin, cotrimoxazole, or imipenem. Phylogenetic analysis of phenotypically similar h-GISA in our study also suggests that CF patients are colonized by polyclonal populations of MRSA that represents an incredible reservoir for lateral gene transfer.
  
  
  CONCLUSIONS
  In conclusion, we demonstrated the emergence and spreading of a new isolate of MRSA in CF patients in Marseille, France, that has probably been selected in the airways by antibiotic pressure. Antibiotic-mediated phage induction may result in high-frequency transfer and the unintended consequence of promoting the spread of virulence and/or antibiotic resistance determinants. The emergence of well-adapted MRSA is worrying in such population chronically colonized and receiving many antibiotics and represents a model for emergence of uncontrollable super bugs in a specific niche.
  
  
  METHODS
  This article was reviewed by Eric Bapteste, Pierre Pontarotti, and Igor Zhulin. For the full reviews, please go to the Reviewers' comments section.
authors.affiliation: URMITE CNRS-IRD UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France. jean-marc.rolain@univmed.fr
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Rolain
authors.forename: Patrice
authors.initials: P
authors.lastname: François
authors.forename: David
authors.initials: D
authors.lastname: Hernandez
authors.forename: Fadi
authors.initials: F
authors.lastname: Bittar
authors.forename: Hervé
authors.initials: H
authors.lastname: Richet
authors.forename: Ghislain
authors.initials: G
authors.lastname: Fournous
authors.forename: Yves
authors.initials: Y
authors.lastname: Mattenberger
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Bosdure
authors.forename: Nathalie
authors.initials: N
authors.lastname: Stremler
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Dubus
authors.forename: Jacques
authors.initials: J
authors.lastname: Sarles
authors.forename: Martine
authors.initials: M
authors.lastname: Reynaud-Gaubert
authors.forename: Stephanie
authors.initials: S
authors.lastname: Boniface
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001435:Bacteriophages / Q000187:drug effects*; D001483:Base Sequence; D049109:Cell Proliferation / Q000187:drug effects; D002473:Cell Wall / Q000648:ultrastructure; D003550:Cystic Fibrosis / Q000453:epidemiology / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D005602:France / Q000453:epidemiology; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D016106:Methicillin Resistance / Q000187:drug effects / Q000235:genetics; D018598:Minisatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D013211:Staphylococcus aureus / Q000166:cytology* / Q000235:genetics* / Q000648:ultrastructure; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial