Dr Francesc Coll


Research Fellow

Keppel Street
United Kingdom

Francesc is a computational biologist with expertise in bacterial genomics and clinical microbiology. He joined the London School in July 2016 as a Postdoctoral Fellow in Prof. Sharon Peacock's lab funded by a Sir Henry Wellcome Postdoctoral Fellowship. He is currently working in the application of genome-wide association studies (GWAS) in bacteria to identify the genes that make bacteria resistant to antibiotics and able to cause infections. Since he joined Sharon’s group in 2014 at the University of Cambridge, he has worked in the genomic epidemiology of Methicillin-Resistant Staphylococcus aureus and Vancomycin-resistance Enterococcus faecium, two major nosocomial pathogens. In October 2014, he completed his Ph.D. at the School under the supervision of Prof. Taane Clark, which focused on strain genotyping and drug resistance in Mycobacterium tuberculosis using whole genome sequencing. He obtained his degree in Biotechnology from the Polytechnic University of Valencia in 2010, Spain, followed by an MSc in Bioinformatics in Cranfield University, UK.


Department of Pathogen Molecular Biology
Faculty of Infectious and Tropical Diseases


Antimicrobial Resistance Centre


Francesc has taught in multiple short courses on bioinformatics and microbial genomics including:

- Genomic Epidemiology of Infectious Diseases (GEID 2017) in Manila, Philippines (July 2017)

- Kenya-United Kingdom Staphylococcus aureus training collaboration (KUK-SATC) workshop in Nairobi, Kenya (February 2017)

- Genomic Epidemiology of Infectious Diseases (GEID 2016) in Bangkok, Thailand (March 2016)

- Pathogen genomics and genomic epidemiology of infectious diseases in London, UK (September 2012, 2013 and 2014)

- High throughput sequencing in disease studies in London, UK (September 2012, 2013 and 2014)


The introduction of genome-wide association studies (GWAS) in microbial genetics has recently become possible as a result of falling DNA sequencing costs. GWAS in pathogenic bacteria have the potential to shed light on the genes that make bacterial strains resistant to antibiotics, able to cause infection and colonise and transmit within and beyond their host population. Despite the potential of GWAS to characterise the genetic determinants of bacterial phenotypes, its wider adoption is hindered by limited expertise and lack of methodologies suitable to bacterial genomes.

Francesc wants to develop robust GWAS designs suitable for bacterial genomes and provide practical guidelines for future studies. He will evaluate the performance of different GWAS designs using large bacterial collections with available whole-genome sequences (WGS) and antimicrobial resistance phenotypes. He will also develop and release software tools implementing the GWAS methods.

In broad terms, his research interests focus on integrating whole-genome sequences from bacterial strains with other types of data - epidemiological, clinical and phenotypic - to glean biological insights in the area of clinical bacteriology.

Research Area
Drug resistance
Molecular epidemiology
Molecular biology
Disease and Health Conditions
Infectious disease
Hospital acquired infection
European Union
Sub-Saharan Africa (all income levels)

Selected Publications

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.
Coll, F. ; Phelan, J. ; Hill-Cawthorne, G.A. ; Nair, M.B. ; Mallard, K. ; Ali, S. ; Abdallah, A.M. ; Alghamdi, S. ; Alsomali, M. ; Ahmed, A.O. ; Portelli, S. ; Oppong, Y. ; Alves, A. ; Bessa, T.B. ; Campino, S. ; Caws, M. ; Chatterjee, A. ; Crampin, A.C. ; Dheda, K. ; Furnham, N. ; Glynn, J.R. ; Grandjean, L. ; Minh Ha, D. ; Hasan, R. ; Hasan, Z. ; Hibberd, M.L. ; Joloba, M. ; Jones-López, E.C. ; Matsumoto, T. ; Miranda, A. ; Moore, D.J. ; Mocillo, N. ; Panaiotov, S. ; Parkhill, J. ; Penha, C. ; Perdigão, J. ; Portugal, I. ; Rchiad, Z. ; Robledo, J. ; Sheen, P. ; Shesha, N.T. ; Sirgel, F.A. ; Sola, C. ; Oliveira Sousa, E. ; Streicher, E.M. ; Helden, P.V. ; Viveiros, M. ; Warren, R.M. ; McNerney, R. ; Pain, A. ; Clark, T.G. ;
Nat Genet
Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England.
Harrison, E.M. ; Coll, F. ; Toleman, M.S. ; Blane, B. ; Brown, N.M. ; Török, M.E. ; Parkhill, J. ; Peacock, S.J. ;
Sci Rep
Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.
Jamrozy, D. ; Coll, F. ; Mather, A.E. ; Harris, S.R. ; Harrison, E.M. ; MacGowan, A. ; Karas, A. ; Elston, T. ; Estée Török, M. ; Parkhill, J. ; Peacock, S.J. ;
BMC Genomics
Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.
Coll, F. ; Harrison, E.M. ; Toleman, M.S. ; Reuter, S. ; Raven, K.E. ; Blane, B. ; Palmer, B. ; Kappeler, A.R.M. ; Brown, N.M. ; Török, M.E. ; Parkhill, J. ; Peacock, S.J. ;
Sci Transl Med
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences.
Coll, F. ; McNerney, R. ; Preston, M.D. ; Guerra-Assunção, J.A. ; Warry, A. ; Hill-Cawthorne, G. ; Mallard, K. ; Nair, M. ; Miranda, A. ; Alves, A. ; Perdigão, J. ; Viveiros, M. ; Portugal, I. ; Hasan, Z. ; Hasan, R. ; Glynn, J.R. ; Martin, N. ; Pain, A. ; Clark, T.G. ;
Genome Med
PolyTB: A genomic variation map for Mycobacterium tuberculosis.
Coll, F.; Preston, M.; Guerra-Assunção, J.A.; Hill-Cawthorn, G.; Harris, D.; Perdigão, J.; Viveiros, M.; Portugal, I.; Drobniewski, F.; Gagneux, S.; Glynn, J.R.; Pain, A.; Parkhill, J.; McNerney, R.; Martin, N.; Clark, T.G.;
Tuberculosis (Edinb)
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.
Coll, F. ; McNerney, R. ; Guerra-Assunção, J.A. ; Glynn, J.R. ; Perdigão, J. ; Viveiros, M. ; Portugal, I. ; Pain, A. ; Martin, N. ; Clark, T.G. ;
Nat Commun
SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
Coll, F.; Mallard, K.; Preston, M.D.; Bentley, S.; Parkhill, J.; McNerney, R.; Martin, N.; Clark, T.G.;
See all Dr Francesc Coll's Publications