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 Infection Biology
Faculty of Infectious and Tropical Diseases


Antimicrobial Resistance Centre (AMR)


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, 2019). 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)


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

Selected Publications

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.
Volz E; Hill V; McCrone JT; Price A; Jorgensen D; O'Toole Á; Southgate J; Johnson R; Jackson B; Nascimento FF
Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis.
Coll F; Raven KE; Knight GM; Blane B; Harrison EM; Leek D; Enoch DA; Brown NM; Parkhill J; Peacock SJ
The Lancet. Microbe
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance.
Gouliouris T; Coll F; Ludden C; Blane B; Raven KE; Naydenova P; Crawley C; Török ME; Enoch DA; Brown NM
Nature microbiology
Defining metrics for whole-genome sequence analysis of MRSA in clinical practice.
Raven KE; Blane B; Kumar N; Leek D; Bragin E; Coll F; Parkhill J; Peacock SJ
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data
Stirrup OT; Hughes J; Parker M; Partridge DG; Shepherd JG; Blackstone J; Coll F; Keeley AJ; Lindsey BB; Marek A
medRxiv preprint - BMJ Yale
Mathematical modelling for antibiotic resistance control policy: do we know enough?
Knight GM; Davies NG; Colijn C; Coll F; Donker T; Gifford DR; Glover RE; Jit M; Klemm E; Lehtinen S
BMC infectious diseases
See more Publications