Dr Francesc Coll


Assistant Professor

Keppel Street
United Kingdom

Francesc is a computational biologist with expertise in bacterial genomics, antibiotic resistance and clinical microbiology. He is currently an Assistant Professor in the Department of Infection Biology supported by an Institutional Strategic Support Fund Fellowship (ISSF), funded by Wellcome & LSHTM. His research projects focus on the applications of whole-genome sequencing as a research, surveillance and diagnostic tool for bacterial infections.

Francesc has worked in the development of bioinformatics analysis pipelines, easy-to-use genome interpretation tools, standards for genome analyses and interpretation, and the development of genetic markers needed to extract actionable information from bacterial genomic data. He has conducted large genomic epidemiology studies to map the spread of bacterial clones, particularly applied to the epidemiology of nosocomial pathogens. He has also worked in the application of Genome-Wide Association Studies (GWAS) to bacteria, which can be used to identify the genetic mechanisms mediating antibiotic susceptibility, host adaptation and disease presentation in pathogenic bacteria.

Francesc 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. 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.


Faculty of Infectious and Tropical Diseases
Department of Infection Biology


Antimicrobial Resistance Centre (AMR)


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

- Antimicrobial Resistance in Bacterial Pathogens, Wellcome Genome Campus Advanced Courses. Kenya (virtual) September 2021, Vietnam September 2019, Kenya September 2018.

- Antimicrobial Resistance (AMR): a Multidisciplinary Approach. LSHTM short course. July 2021, July 2019 and July 2018.

- Kenya-UK Staphylococcus aureus training collaboration workshop. Kenya February 2017

- Genomic Epidemiology of Infectious Diseases. Philippines July 2017, Thailand March 2016.


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

Selected Publications

Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study.
Ludden C; Coll F; Gouliouris T; Restif O; Blane B; Blackwell GA; Kumar N; Naydenova P; Crawley C; Brown NM
The Lancet Microbe
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
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
Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.
Coll F; Phelan J; Hill-Cawthorne GA; Nair MB; Mallard K; Ali S; Abdallah AM; Alghamdi S; Alsomali M; Ahmed AO
Nature genetics
Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.
Coll F; Harrison EM; Toleman MS; Reuter S; Raven KE; Blane B; Palmer B; Kappeler ARM; Brown NM; Török ME
Science translational medicine
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences.
Coll F; McNerney R; Preston MD; Guerra-Assunção JA; Warry A; Hill-Cawthorne G; Mallard K; Nair M; Miranda A; Alves A
Genome medicine
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.
Coll F; McNerney R; Guerra-Assunção JA; Glynn JR; Perdigão J; Viveiros M; Portugal I; Pain A; Martin N; Clark TG
Nature communications
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
Coll F; Mallard K; Preston MD; Bentley S; Parkhill J; McNerney R; Martin N; Clark TG
Bioinformatics (Oxford, England)
See more Publications