title: Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.
abstract: Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.
  
  
  
  The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia University of Warwick, Coventry, United Kingdom.
authors.forename: Madikay
authors.initials: M
authors.lastname: Senghore
authors.affiliation: University of Bath, Bath, United Kingdom.
authors.forename: Sion C
authors.initials: SC
authors.lastname: Bayliss
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Brenda A
authors.initials: BA
authors.lastname: Kwambana-Adams
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Ebenezer
authors.initials: E
authors.lastname: Foster-Nyarko
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Jainaba
authors.initials: J
authors.lastname: Manneh
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Michel
authors.initials: M
authors.lastname: Dione
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Henry
authors.initials: H
authors.lastname: Badji
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Chinelo
authors.initials: C
authors.lastname: Ebruke
authors.affiliation: University of Warwick, Coventry, United Kingdom.
authors.forename: Emma L
authors.initials: EL
authors.lastname: Doughty
authors.affiliation: University of Bath, Bath, United Kingdom.
authors.forename: Harry A
authors.initials: HA
authors.lastname: Thorpe
authors.affiliation: University of California Los Angeles, Los Angeles, California, USA.
authors.forename: Anna J
authors.initials: AJ
authors.lastname: Jasinska
authors.affiliation: University of California Los Angeles, Los Angeles, California, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Schmitt
authors.affiliation: American Military University and American Public University, Charles Town, West Virginia, USA.
authors.forename: Jennifer D
authors.initials: JD
authors.lastname: Cramer
authors.affiliation: University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA University of the Free State, Bloemfontein, South Africa.
authors.forename: Trudy R
authors.initials: TR
authors.lastname: Turner
authors.affiliation: Washington University, St. Louis, Missouri, USA.
authors.forename: George
authors.initials: G
authors.lastname: Weinstock
authors.affiliation: University of California Los Angeles, Los Angeles, California, USA.
authors.forename: Nelson B
authors.initials: NB
authors.lastname: Freimer
authors.affiliation: University of Warwick, Coventry, United Kingdom m.pallen@warwick.ac.uk.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
authors.affiliation: University of Bath, Bath, United Kingdom.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
authors.affiliation: Medical Research Council Unit, Fajara, The Gambia University of Warwick, Coventry, United Kingdom London School of Hygiene and Tropical Medicine, London, United Kingdom.
authors.forename: Martin
authors.initials: M
authors.lastname: Antonio
mesh_terms: D000818:Animals; D002353:Carrier State; D002522:Chlorocebus aethiops; D005714:Gambia; D016680:Genome, Bacterial; D006801:Humans; D008992:Monkey Diseases / Q000382:microbiology / Q000635:transmission*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013203:Staphylococcal Infections / Q000382:microbiology / Q000635:transmission*; D013211:Staphylococcus aureus / Q000145:classification / Q000235:genetics / Q000502:physiology*