Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

Guillaume Méric, Leonardos Mageiros, Johan Pensar, Maisem Laabei, Koji Yahara, Ben Pascoe, Nattinee Kittiwan, Phacharaporn Tadee, Virginia Post, Sarah Lamble, Rory Bowden, James E. Bray, Mario Morgenstern, Keith A. Jolley, Martin C. J. Maiden, Edward J. Feil, Xavier Didelot, Maria Miragaia, Herminia Lencastre, T. Fintan Moriarty, Holger Rohde, Ruth Massey, Dietrich Mack, Jukka Corander and Samuel K. Sheppard ()
Additional contact information
Guillaume Méric: University of Bath
Leonardos Mageiros: University of Bath
Johan Pensar: University of Helsinki
Maisem Laabei: University of Bath
Koji Yahara: National Institute of Infectious Diseases
Ben Pascoe: University of Bath
Nattinee Kittiwan: Faculty of Veterinary Medicine, Chiang Mai University
Phacharaporn Tadee: Maejo University
Virginia Post: AO Research Institute Davos
Sarah Lamble: University of Oxford
Rory Bowden: University of Oxford
James E. Bray: University of Oxford
Mario Morgenstern: University Hospital Basel
Keith A. Jolley: University of Oxford
Martin C. J. Maiden: University of Oxford
Edward J. Feil: University of Bath
Xavier Didelot: Imperial College
Maria Miragaia: Universidade Nova de Lisboa
Herminia Lencastre: Universidade Nova de Lisboa
T. Fintan Moriarty: AO Research Institute Davos
Holger Rohde: Universität Hamburg
Ruth Massey: University of Bath
Dietrich Mack: Institut für Medizinische Diagnostik GmbH
Jukka Corander: University of Helsinki
Samuel K. Sheppard: University of Bath

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.

Date: 2018
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DOI: 10.1038/s41467-018-07368-7

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