title: Genomic analysis of ST88 community-acquired methicillin resistantStaphylococcus aureusin Ghana.
abstract: BACKGROUND
  The emergence and evolution of community-acquired methicillin resistantStaphylococcus aureus(CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an "African" CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide.
  
  
  METHODS
  We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages.
  
  
  RESULTS
  We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the otherS. aureuslineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics includingβ-lactams, tetracycline and chloramphenicol.
  
  
  CONCLUSIONS
  This study reveals thatS. aureusST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.
authors.affiliation: Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana; Department of Molecular Parasitology and Immunology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
authors.forename: Grace
authors.initials: G
authors.lastname: Kpeli
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Buultjens
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia.
authors.forename: Stefano
authors.initials: S
authors.lastname: Giulieri
authors.affiliation: Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana , Accra , Ghana.
authors.forename: Evelyn
authors.initials: E
authors.lastname: Owusu-Mireku
authors.affiliation: Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana , Accra , Ghana.
authors.forename: Samuel Y
authors.initials: SY
authors.lastname: Aboagye
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Baines
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; University of Melbourne, Victorian Life Sciences Computation Initiative, Melbourne, VIC, Australia.
authors.forename: Torsten
authors.identifier: 0000-0001-6046-610X
authors.initials: T
authors.lastname: Seemann
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; University of Melbourne, Victorian Life Sciences Computation Initiative, Melbourne, VIC, Australia.
authors.forename: Dieter
authors.identifier: 0000-0001-9823-6078
authors.initials: D
authors.lastname: Bulach
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia.
authors.forename: Anders
authors.initials: A
authors.lastname: Gonçalves da Silva
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia.
authors.forename: Ian R
authors.identifier: 0000-0001-6982-8074
authors.initials: IR
authors.lastname: Monk
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology and Immunology, Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Howden
authors.affiliation: Department of Molecular Parasitology and Immunology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
authors.forename: Gerd
authors.initials: G
authors.lastname: Pluschke
authors.affiliation: Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana , Accra , Ghana.
authors.forename: Dorothy
authors.initials: D
authors.lastname: Yeboah-Manu
authors.affiliation: Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia.
authors.forename: Timothy
authors.identifier: 0000-0003-0150-123X
authors.initials: T
authors.lastname: Stinear
keywords: CA-MRSA; Comparative genomics; MRSA; Phylogeography; ST88; Staphylococcus aureus; Whole genome sequencing