title: Within-host diversity of MRSA antimicrobial resistances.
abstract: OBJECTIVE
  MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and potential mechanisms of resistance gene transfer in vivo.
  
  
  METHODS
  Nasal swabs from 38 MRSA carriers admitted to hospital were plated and 20 individual colonies from each patient tested for phenotypic antibiotic susceptibility and genetically for lineage, carriage of four prophages and three plasmid families. Free bacteriophages were detected in swabs as well as their capacity for transducing resistance genes.
  
  
  RESULTS
  Nine (24%) patients carried phenotypic AMR variants and 24 (63%) carried prophage and plasmid variants. If a single colony was selected for testing, the probability of detecting all AMR in that patient was 87%. Sixty-four different AMR and mobile genetic element (MGE) profiles were detected, mostly in the MRSA CC22 background (where CC stands for clonal complex), with up to 8 profiles per patient. Nearly half of the patients carried detectable free bacteriophages and phages successfully transduced resistance genes between laboratory and patient isolates in vitro. WGS showed MRSA core genomes were stable, while AMR and MGEs varied.
  
  
  CONCLUSIONS
  'Clouds' of MRSA variants that have acquired or lost AMR and MGEs are common in nasal colonizing populations and bacteriophages may play an important role in gene transfer. Accurate estimation of AMR and genetic variability has implications for diagnostics, epidemiology, antimicrobial stewardship and understanding the evolutionary selection of AMR in colonizing populations.
authors.affiliation: Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK.
authors.forename: Kinga I
authors.initials: KI
authors.lastname: Stanczak-Mrozek
authors.affiliation: Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK.
authors.forename: Anusha
authors.initials: A
authors.lastname: Manne
authors.affiliation: Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
authors.forename: Gwenan M
authors.initials: GM
authors.lastname: Knight
authors.affiliation: Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK.
authors.forename: Katherine
authors.initials: K
authors.lastname: Gould
authors.affiliation: Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK.
authors.forename: Adam A
authors.initials: AA
authors.lastname: Witney
authors.affiliation: Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK jlindsay@sgul.ac.uk.
authors.forename: Jodi A
authors.initials: JA
authors.lastname: Lindsay
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001435:Bacteriophages / Q000302:isolation & purification; D002353:Carrier State / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000187:drug effects* / Q000302:isolation & purification; D008826:Microbial Sensitivity Tests; D009297:Nasal Mucosa / Q000382:microbiology; D010641:Phenotype; D010957:Plasmids / Q000032:analysis; D013203:Staphylococcal Infections / Q000382:microbiology*; D014161:Transduction, Genetic
chemical_list: D000900:Anti-Bacterial Agents
keywords: horizontal gene transfer; mobile genetic elements; transduction; whole-genome sequencing