title: A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistantStaphylococcus aureus.
abstract: Distinct clones of methicillin-resistantStaphylococcus aureus(MRSA) have emerged as important causes of infection in individuals who have exposure to livestock (livestock-associated MRSA; LA-MRSA). Clonal complex 398 (CC398) is the most prevalent LA-MRSA clone, and has been reported from several geographical settings, including Europe, the Americas and Asia. To understand the factors contributing to the global dissemination of this clone, we analysed CC398 MRSA isolates from New Zealand (NZ), a geographically isolated country with an economy strongly dependent on livestock farming. We supplemented the NZ CC398 MRSA collection with global datasets of CC398 MRSA and CC398 methicillin-susceptibleS. aureus.Here, we demonstrate multiple sporadic incursions of CC398 MRSA into NZ, as well as recent importation and spread of a swine-associated clade related to the European LA-MRSA lineage. Within a larger global phylogenomic framework, Bayesian modelling suggested that this NZ clade emerged in the late 2000s, with a probable origin in swine from Western Europe. Elucidating the factors responsible for the incursion and spread of LA-MRSA in geographically distant regions, such as NZ, provides important insights into global pathways ofS. aureustransmission, and will inform strategies to control importation and spread.
authors.affiliation: 1​Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.|2​Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
authors.forename: Anders
authors.initials: A
authors.lastname: Gonçalves da Silva
authors.affiliation: 1​Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Baines
authors.affiliation: 1​Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
authors.forename: Glen P
authors.initials: GP
authors.lastname: Carter
authors.affiliation: 3​Institute of Environmental Science and Research, Wellington, New Zealand.
authors.forename: Helen
authors.initials: H
authors.lastname: Heffernan
authors.affiliation: 4​Infectious Disease Research Centre, Massey University, Palmerston North, New Zealand.
authors.forename: Nigel P
authors.initials: NP
authors.lastname: French
authors.affiliation: 3​Institute of Environmental Science and Research, Wellington, New Zealand.
authors.forename: Xiaoyun
authors.initials: X
authors.lastname: Ren
authors.affiliation: 2​Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.|5​Victorian Life Sciences Computation Initiative, Melbourne, Australia.
authors.forename: Torsten
authors.initials: T
authors.lastname: Seemann
authors.affiliation: 2​Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.|5​Victorian Life Sciences Computation Initiative, Melbourne, Australia.
authors.forename: Dieter
authors.initials: D
authors.lastname: Bulach
authors.affiliation: 1​Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
authors.forename: Jason
authors.initials: J
authors.lastname: Kwong
authors.affiliation: 1​Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Stinear
authors.affiliation: 1​Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.|2​Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Howden
authors.affiliation: 1​Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.|2​Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Williamson
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D021821:Communicable Diseases, Emerging / Q000453:epidemiology* / Q000382:microbiology*; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D009520:New Zealand / Q000453:epidemiology; D010802:Phylogeny; D015995:Prevalence; D013203:Staphylococcal Infections / Q000453:epidemiology* / Q000382:microbiology*; D013552:Swine / Q000382:microbiology*
keywords: Livestock-MRSA; Staphylococcus aureus; epidemiology; swine; zoonosis