Title: Severe infections emerge from the microbiome by adaptive evolution
Authors: orcid: http://orcid.org/0000-0001-6071-6770
last_name: Young
first_name: Bernadette C
name: Bernadette C Young
corresponding: yes
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: b
institution: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital
country: UK
name: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital , Oxford OX3 9DU, UK
last_name: Wu
first_name: Chieh-Hsi
name: Chieh-Hsi Wu
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
last_name: Gordon
first_name: N Claire
name: N Claire Gordon
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
last_name: Cole
first_name: Kevin
name: Kevin Cole
affiliations: label: c
institution: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital
country: UK
name: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital , Brighton BN2 5BE, UK
orcid: http://orcid.org/0000-0003-2541-8545
last_name: Price
first_name: James R
name: James R Price
affiliations: label: c
institution: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital
country: UK
name: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital , Brighton BN2 5BE, UK
label: d
institution: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex
country: UK
name: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex , Falmer BN1 9PS, UK
last_name: Liu
first_name: Elian
name: Elian Liu
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: b
institution: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital
country: UK
name: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital , Oxford OX3 9DU, UK
orcid: http://orcid.org/0000-0002-2913-0920
last_name: Sheppard
first_name: Anna E
name: Anna E Sheppard
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: e
institution: NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England
name: NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England , Oxford, United Kingdom
last_name: Perera
first_name: Sanuki
name: Sanuki Perera
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: b
institution: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital
country: UK
name: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital , Oxford OX3 9DU, UK
last_name: Charlesworth
first_name: Jane
name: Jane Charlesworth
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
last_name: Golubchik
first_name: Tanya
name: Tanya Golubchik
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
last_name: Iqbal
first_name: Zamin
name: Zamin Iqbal
affiliations: label: f
institution: Wellcome Trust Centre for Human Genetics, University of Oxford
name: Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford OX3 7BN, United Kingdom
orcid: http://orcid.org/0000-0001-8596-0366
last_name: Bowden
first_name: Rory
name: Rory Bowden
affiliations: label: f
institution: Wellcome Trust Centre for Human Genetics, University of Oxford
name: Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford OX3 7BN, United Kingdom
orcid: http://orcid.org/0000-0002-8154-4039
last_name: Massey
first_name: Ruth C.
name: Ruth C. Massey
affiliations: label: g
institution: Department of Biology and Biochemistry and The Milner Centre for Evolution, University of Bath
name: Department of Biology and Biochemistry and The Milner Centre for Evolution, University of Bath , Bath BA2 7AY, United Kingdom
last_name: Paul
first_name: John
name: John Paul
affiliations: label: h
institution: National Infection Service, Public Health England
country: UK
name: National Infection Service, Public Health England , London, UK
label: i
institution: National Institute for Health Research, Oxford Biomedical Research Centre
country: UK
name: National Institute for Health Research, Oxford Biomedical Research Centre , Oxford, UK
last_name: Crook
first_name: Derrick W
name: Derrick W Crook
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: h
institution: National Infection Service, Public Health England
country: UK
name: National Infection Service, Public Health England , London, UK
label: i
institution: National Institute for Health Research, Oxford Biomedical Research Centre
country: UK
name: National Institute for Health Research, Oxford Biomedical Research Centre , Oxford, UK
last_name: Peto
first_name: Timothy E A
name: Timothy E A Peto
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: i
institution: National Institute for Health Research, Oxford Biomedical Research Centre
country: UK
name: National Institute for Health Research, Oxford Biomedical Research Centre , Oxford, UK
last_name: Walker
first_name: A Sarah
name: A Sarah Walker
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: i
institution: National Institute for Health Research, Oxford Biomedical Research Centre
country: UK
name: National Institute for Health Research, Oxford Biomedical Research Centre , Oxford, UK
orcid: http://orcid.org/0000-0002-6811-1124
last_name: Llewelyn
first_name: Martin J
name: Martin J Llewelyn
affiliations: label: c
institution: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital
country: UK
name: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital , Brighton BN2 5BE, UK
label: d
institution: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex
country: UK
name: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex , Falmer BN1 9PS, UK
last_name: Wyllie
first_name: David H
name: David H Wyllie
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: j
institution: Jenner Institute, Centre for Molecular and Cellular Physiology
country: UK
name: Jenner Institute, Centre for Molecular and Cellular Physiology , Oxford OX3 7BN, UK
orcid: http://orcid.org/0000-0002-0940-3311
last_name: Wilson
first_name: Daniel J
name: Daniel J Wilson
corresponding: yes
affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: f
institution: Wellcome Trust Centre for Human Genetics, University of Oxford
name: Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford OX3 7BN, United Kingdom
label: k
institution: Institute for Emerging Infections, Oxford Martin School, University of Oxford
country: UK
name: Institute for Emerging Infections, Oxford Martin School, University of Oxford , Oxford, OX1 3BD, UK
Affiliations: label: a
institution: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital
country: UK
name: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: b
institution: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital
country: UK
name: Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Trust, John Radcliffe Hospital , Oxford OX3 9DU, UK
label: c
institution: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital
country: UK
name: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital , Brighton BN2 5BE, UK
label: d
institution: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex
country: UK
name: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex , Falmer BN1 9PS, UK
label: e
institution: NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England
name: NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England , Oxford, United Kingdom
label: f
institution: Wellcome Trust Centre for Human Genetics, University of Oxford
name: Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford OX3 7BN, United Kingdom
label: g
institution: Department of Biology and Biochemistry and The Milner Centre for Evolution, University of Bath
name: Department of Biology and Biochemistry and The Milner Centre for Evolution, University of Bath , Bath BA2 7AY, United Kingdom
label: h
institution: National Infection Service, Public Health England
country: UK
name: National Infection Service, Public Health England , London, UK
label: i
institution: National Institute for Health Research, Oxford Biomedical Research Centre
country: UK
name: National Institute for Health Research, Oxford Biomedical Research Centre , Oxford, UK
label: j
institution: Jenner Institute, Centre for Molecular and Cellular Physiology
country: UK
name: Jenner Institute, Centre for Molecular and Cellular Physiology , Oxford OX3 7BN, UK
label: k
institution: Institute for Emerging Infections, Oxford Martin School, University of Oxford
country: UK
name: Institute for Emerging Infections, Oxford Martin School, University of Oxford , Oxford, OX1 3BD, UK
Field: Biochemistry, Genetics and Molecular Biology
Document type: preprint
Year: 2017