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Dr Francesc Coll

BSc MSc PhD

Research Fellow

LSHTM
Keppel Street
London
WC1E 7HT
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.

Affiliations

Faculty of Infectious and Tropical Diseases
Department of Infection Biology

Centres

Antimicrobial Resistance Centre

Teaching

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

- Antimicrobial Resistance in Bacterial Pathogens in Nairobi, Kenya. (September 2018). link

- Antimicrobial Resistance (AMR): a Multidisciplinary Approach, LSHTM, UK (July 2018). link

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

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

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

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

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

Research

Francesc’s research is focused on the following areas:

- The genetics of antibiotic resistance. Sequencing the genomes of bacterial strains that differ in their susceptibility to antibiotics can be used to characterise the genes and mutations that cause antibiotic resistance. These markers can improve our biological understanding of how bacteria are equipped and evolve to resist killing by antibiotics. These can also be used as genetic markers for the diagnosis and surveillance of antibiotic resistance infections.

- Epidemiology of bacterial pathogens. Sequencing the genomes of bacterial strains from colonised or infected individuals, combined with patients’ data extracted from electronic health-care records, can be used to track the spread of bacteria. In a clinical setting, this can inform infection control practices to, ultimately, contribute to the reduction of hospital-acquired infections.

- Genome-wide association studies (GWAS) in bacteria. GWAS are a group of statistical and comparative genomics techniques that can be used to identify the genes that make bacterial strains resistant to antibiotics, able to cause infection and colonise and transmit within and beyond their host population. Francesc wants to develop robust GWAS designs suitable for bacterial genomes and provide practical guidelines for future studies.

 

Francesc Coll is interested in collaborating in the research areas described above.

Francesc Coll is available for consultancy in the area of translational bacterial genomics and bioinformatics.

For a list of selected publications see below. For the full list of publications see link

Research Area
Bacteria
Diagnostics
Drug resistance
Outbreaks
Discipline
Genomics
Molecular epidemiology
Bacteriology
Genetics
Microbiology
Bioinformatics
Disease and Health Conditions
Infectious disease
Tuberculosis
Hospital acquired infection
Region
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. ;
2018
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. ;
2017
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. ;
2017
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. ;
2017
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. ;
2015
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.;
2014
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. ;
2014
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.;
2012
Bioinformatics
See all Dr Francesc Coll's Publications