title: Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing.
abstract: BACKGROUND
  Staphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient's risk of postoperative infection. The impact of surgical prophylaxis on the nasal staphylococcal microbiome is largely unknown. Here, we report the species present in the nasal staphylococcal microbiome and the impact of surgical prophylaxis revealed by a novel culture independent technique. Daily nasal samples from 18 hospitalised patients, six of whom received no antibiotics and 12 of whom received antibiotic surgical prophylaxis (flucloxacillin and gentamicin or teicoplanin +/- gentamicin), were analysed by tuf gene fragment amplicon sequencing.
  
  
  RESULTS
  On admission to hospital, the species diversity of the nasal staphylococcal microbiome varied from patient to patient ranging from 4 to 10 species. Administration of surgical prophylaxis did not substantially alter the diversity of the staphylococcal species present in the nose; however, surgical prophylaxis did impact on the relative abundance of the staphylococcal species present. The dominant staphylococcal species present in all patients on admission was Staphylococcus epidermidis, and antibiotic administration resulted in an increase in species relative abundance. Following surgical prophylaxis, a reduction in the abundance of Staphylococcus aureus was observed in carriers, but not a complete eradication.
  
  
  CONCLUSIONS
  Utilising the tuf gene fragment has enabled a detailed study of the staphylococcal microbiome in the nose and highlights that although there is no change in the heterogeneity of species present, there are changes in abundance. The sensitivity of the methodology has revealed that the abundance of S. aureus is reduced to a low level by surgical prophylaxis and therefore reduces the potential risk of infection following surgery but also highlights that S. aureus does persist.
authors.affiliation: Heart of England NHS Foundation Trust, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, B9 5SS, UK. clairelmcmurray@gmail.com.|Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK. clairelmcmurray@gmail.com.
authors.forename: Claire L
authors.initials: CL
authors.lastname: McMurray
authors.affiliation: Public Health England Birmingham Laboratory, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, B9 5SS, UK.|Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK.
authors.forename: Katherine J
authors.initials: KJ
authors.lastname: Hardy
authors.affiliation: Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK.|Present address: Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Szymon T
authors.initials: ST
authors.lastname: Calus
authors.affiliation: Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman
authors.affiliation: Public Health England Birmingham Laboratory, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, B9 5SS, UK.|Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Hawkey
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D019072:Antibiotic Prophylaxis; D001426:Bacterial Proteins / Q000032:analysis; D005260:Female; D005436:Floxacillin / Q000627:therapeutic use; D005839:Gentamicins / Q000627:therapeutic use; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D009666:Nose / Q000382:microbiology*; D010444:Peptide Elongation Factor Tu / Q000032:analysis*; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods; D013203:Staphylococcal Infections / Q000382:microbiology / Q000517:prevention & control*; D013210:Staphylococcus / Q000145:classification* / Q000187:drug effects; D017334:Teicoplanin / Q000627:therapeutic use
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D005839:Gentamicins; D005436:Floxacillin; D017334:Teicoplanin; D010444:Peptide Elongation Factor Tu
keywords: Antibiotics; Nose; S. aureus; S. epidermidis; Staphylococcus; Surgical prophylaxis; tuf gene