title: Architecture of a Species: Phylogenomics of Staphylococcus aureus.
abstract: A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia & University of Pennsylvania, Philadelphia, PA, USA. Electronic address: planetp@email.chop.edu.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Planet
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
authors.forename: Apurva
authors.initials: A
authors.lastname: Narechania
authors.affiliation: Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA.
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.affiliation: Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
authors.forename: Barun
authors.initials: B
authors.lastname: Mathema
authors.affiliation: Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
authors.forename: Sam
authors.initials: S
authors.lastname: Boundy
authors.affiliation: Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
authors.forename: Gordon
authors.initials: G
authors.lastname: Archer
authors.affiliation: Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA.
authors.forename: Barry
authors.initials: B
authors.lastname: Kreiswirth
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001483:Base Sequence; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000502:physiology*; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D008826:Microbial Sensitivity Tests; D017422:Sequence Analysis, DNA; D013203:Staphylococcal Infections / Q000382:microbiology; D037521:Virulence Factors / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D037521:Virulence Factors
keywords: Staphylococcus aureus; clonal complex; phylogenomics; recombination