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


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)


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

Genomic surveillance of methicillin-resistant Staphylococcus aureus: a mathematical early modelling study of cost effectiveness.
Dymond A; Davies H; Mealing S; Pollit V; Coll F; Brown NM; Peacock SJ
Clinical infectious diseases
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade.
Conceição EC; Refregier G; Gomes HM; Olessa-Daragon X; Coll F; Ratovonirina NH; Rasolofo-Razanamparany V; Lopes ML; van Soolingen D; Rutaihwa L
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
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
Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus.
Harrison EM; Ba X; Coll F; Blane B; Restif O; Carvell H; Köser CU; Jamrozy D; Reuter S; Lovering A
Nature microbiology
rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.
Wailan AM; Coll F; Heinz E; Tonkin-Hill G; Corander J; Feasey NA; Thomson NR
Microbial genomics
Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure.
Kime L; Randall CP; Banda FI; Coll F; Wright J; Richardson J; Empel J; Parkhill J; O'Neill AJ
Revised interpretation of the Hain Lifescience GenoType MTBC to differentiate Mycobacterium canettii and members of the M. tuberculosis complex
Loiseau C; Brites D; Moser I; Coll F; Pourcel C; Robbe-Austerman S; Escuyer V; Musser KA; Peacock SJ; Feuerriegel S
Antimicrobial Agents and Chemotherapy
See more Publications