Imperial College London


Faculty of Natural SciencesDepartment of Mathematics

Visiting Professor



+44 (0)20 7594 2647c.colijn Website




626Huxley BuildingSouth Kensington Campus






BibTex format

author = {Aanensen, DM and Feil, EJ and Holden, MT and Dordel, J and Yeats, CA and Fedosejev, A and Goater, R and Castillo-Ramírez, S and Corander, J and Colijn, C and Chlebowicz, MA and Schouls, L and Heck, M and Pluister, G and Ruimy, R and Kahlmeter, G and Åhman, J and Matuschek, E and Friedrich, AW and Parkhill, J and Bentley, SD and Spratt, BG and Grundmann, H and European, SRL Working Group},
doi = {10.1128/mBio.00444-16},
journal = {mBio},
title = {Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive staphylococcus aureus in Europe.},
url = {},
volume = {7},
year = {2016}

RIS format (EndNote, RefMan)

AB - UNLABELLED: The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL ( Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that in silico predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools. IMPORTANCE: The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context
AU - Aanensen,DM
AU - Feil,EJ
AU - Holden,MT
AU - Dordel,J
AU - Yeats,CA
AU - Fedosejev,A
AU - Goater,R
AU - Castillo-Ramírez,S
AU - Corander,J
AU - Colijn,C
AU - Chlebowicz,MA
AU - Schouls,L
AU - Heck,M
AU - Pluister,G
AU - Ruimy,R
AU - Kahlmeter,G
AU - Åhman,J
AU - Matuschek,E
AU - Friedrich,AW
AU - Parkhill,J
AU - Bentley,SD
AU - Spratt,BG
AU - Grundmann,H
AU - European,SRL Working Group
DO - 10.1128/mBio.00444-16
PY - 2016///
SN - 2161-2129
TI - Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive staphylococcus aureus in Europe.
T2 - mBio
UR -
UR -
UR -
VL - 7
ER -