Francesc Coll I Cerezo
Biography
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I am a principal investigator (Científico titular) at the Institute of Biomedicine of Valencia (IBV, Spanish National Research Council) where I lead the Applied Microbial Genomics Unit. Before that I was a senior Staff Scientist at the Wellcome Sanger Institute (UK), and an Assistant Professor at the London School of Hygiene & Tropical Medicine (LSHTM), supported by an Institutional Strategic Support Fund Fellowship (ISSF), funded by Wellcome & LSHTM. I joined LSHTM in July 2016 as an Research Fellow (post-doc) funded by a Sir Henry Wellcome Postdoctoral Fellowship, after joining the research group led by Prof. Sharon Peacock at the University of Cambridge, UK. In October 2014, I completed my Ph.D. at LSHTM under the supervision of Prof. Taane Clark, which focused on strain genotyping and drug resistance in Mycobacterium tuberculosis using whole genome sequencing. I obtained my degree in Biotechnology from the Polytechnic University of Valencia in 2010, Spain, followed by an MSc in Bioinformatics in Cranfield University, UK. |
Profile
| Institution | IBV |
| Position | Group leader, científico titular |
| Home page | https://www.ibv.csic.es/en/project/applied-microbial-genomics/ |
| Contact email | fcoll@ibv.csic.es |
| ORCID | 0000-0002-7882-2325 |
BCB Hub
| BCB Committee | Talent attraction and training |
| BCB Tools | |
| BCB Services | Bioinformatics Unit at IBV |
Research
Research topics
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Research lines
Publications 74 entries
- Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data Article · Feb 2024
- Impact of a new hospital with close to 100% single-occupancy rooms on environmental contamination and incidence of vancomycin-resistant Enterococcus faecium colonization or infection: a genomic surveillance study Article · Sep 2023
- Improved Accuracy of Antibiotic Resistance Determination from Enterococcus faecium Whole-Genome Sequences Preprint · 2023
- Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya Article · 9 Dec 2022
- Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya Article · 1 Dec 2022
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- Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study Article · 13 Sep 2022
- The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis Article · Apr 2022
- PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies Article · 25 Mar 2022
- Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission Article · 23 Feb 2022
- Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission Article · 8 Feb 2022
- Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study Article · Jan 2022
- Key variables affecting genetic distance calculations in genomic epidemiology Article · Oct 2021
- Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study Article · Sep 2021
- Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data Article · 29 Jun 2021
- Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7 Article · Jun 2021
- Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study Article · May 2021
- Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England Article · 25 Mar 2021
- Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies Article · 11 Mar 2021
- SARS-CoV-2 evolution during treatment of chronic infection Article · 5 Feb 2021
- SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies Preprint · 20 Jan 2021
- Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein Preprint · 15 Jan 2021
- Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread Preprint · 6 Jan 2021
- Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data Preprint · 4 Jan 2021
- Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity Article · Jan 2021
- Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis Article · Dec 2020
- The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity Preprint · 5 Nov 2020
- Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance Article · 26 Oct 2020
- MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance Preprint · 7 Oct 2020
- Feasibility of informing syndrome-level empiric antibiotic recommendations using publicly available antibiotic resistance datasets [version 2; peer review: 2 approved, 1 approved with reservations] Article · 24 Jun 2020
- Ferric Citrate Regulator FecR Is Translocated across the Bacterial Inner Membrane via a Unique Twin-Arginine Transport-Dependent Mechanism Article · 9 Apr 2020
- Defining metrics for whole-genome sequence analysis of MRSA in clinical practice Article · 1 Apr 2020
- Mathematical modelling for antibiotic resistance control policy: do we know enough? Article · 29 Nov 2019
- Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure Article · 29 Oct 2019
- Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade Article · Sep 2019
- Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus Article · 24 Jun 2019
- Genomic Surveillance of Methicillin-resistant Staphylococcus aureus: A Mathematical Early Modeling Study of Cost-effectiveness Article · 18 Jun 2019
- Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex Article · Jun 2019
- rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree Article · 1 Apr 2019
- Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment Article · 21 Mar 2019
- One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock Article · 26 Feb 2019
- Prospective genomic surveillance of meticillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013 Article · 24 Jan 2019
- Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity Article · 26 Feb 2018
- Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis Article · 22 Jan 2018
- Role of Alanine Racemase Mutations in Mycobacterium tuberculosis D-Cycloserine Resistance Article · Dec 2017
- Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community Article · 25 Oct 2017
- Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting Article · 25 Oct 2017
- Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events Article · 4 Sep 2017
- Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England Article · 7 Aug 2017
- Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing Article · 1 Aug 2017
- Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays Article · Apr 2017
- Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing` Article · 23 Feb 2017
- Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor Article · Nov 2016
- Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks Article · 3 Oct 2016
- Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011-2013 Article · Sep 2016
- Erratum: Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites (PLoS Genet (2015) 11: 4 (e1005131) doi: 10.1371/journal.pgen.1005131) Article · 31 Aug 2016
- Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England Article · 27 Apr 2016
- Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance Article · 23 Mar 2016
- Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages Article · 29 Feb 2016
- Ocular chlamydial genomic variants and disease severity in trachoma: a cross-sectional population-based genome-wide association study Article · Feb 2016
- Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations Article · 21 Oct 2015
- The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae Article · Jul 2015
- Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences Article · 27 May 2015
- PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis Article · 13 May 2015
- Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites Article · 30 Apr 2015
- Large-scale whole genome sequencing of M-tuberculosis provides insights into transmission in a high prevalence area Article · 3 Mar 2015
- Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan Article · 26 Feb 2015
- Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan Article · Jan 2015
- A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture Article · 4 Dec 2014
- Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting Article · 18 Nov 2014
- Recurrence due to Relapse or Reinfection With Mycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up Article · 21 Oct 2014
- A robust SNP barcode for typing Mycobacterium tuberculosis complex strains Article · 1 Sep 2014
- PolyTB: A genomic variation map for Mycobacterium tuberculosis Article · May 2014
- Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing Article · 11 Dec 2013
- SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences Article · 26 Sep 2012
