Dr. Sophia David

Postdoctoral Fellow - Bacterial Genomics


Uses genomic approaches to understand the evolution and transmission of antibiotic-resistant bacteria.

Learn more about my work

Using bioinformatic analysis of large genomic data sets, Sophia's research aims to understand the emergence and spread of carbapenemase-producing Enterobacteriaceae (CPE). This group of bacteria causes a broad range of infections in humans and has become a major public health concern due to its ability to resist the last-line class of antibiotics, carbapenems.


1. David S, Cohen V, Reuter S, Sheppard AE, Giani T, Parkhill J, the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) Working Group, the ESCMID Study Group for Epidemiological Markers, Rossolini GM, Feil EJ, et al. Genomic analysis of carbapenemase-encoding plasmids from Klebsiella pneumoniae across Europe highlights three major patterns of dissemination. bioRxiv. 2019.

2. David S, Reuter S, Harris SR, Glasner C, Feltwell T, Argimon S, Abudahab K, Goater R, Giani T, Errico G, et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nature Microbiology. 2019;4:1919-1929.

3. David S, Mentasti M, Lai S, Vaghji L, Ready D, Chalker VJ, Parkhill J. Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building. Microbial Genomics. 2018;4(10).

4. David S, Mentasti M, Parkhill J, Chalker VJ. Low genomic diversity of Legionella pneumophila within clinical specimens. Clinical Microbiology and Infection. 2018;24(9):1020.e1-1020.e4.

5. David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG, Parkhill J. Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLoS Genetics. 2017;13(6):e1006855.

6. David S, Afshar B, Mentasti M, Ginevra C, Podglajen I, Harris SR, Chalker VJ, Jarraud S, Harrison TG, Parkhill J. Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease. Clinical Infectious Diseases. 2017;64(9):1251-9.

7. David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, et al. Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently. Genome Research. 2016;26(11):1555-1564.

8. David S, Mentasti M, Tewolde R, Aslett M, Harris SR, Afshar B, Underwood A, Fry NK, Parkhill J, Harrison TG. Evaluation of an optimal epidemiologic typing scheme for Legionella pneumophila with whole genome sequence data using validation guidelines. Journal of Clinical Microbiology. 2016;54(8):2135-48.

Our Research Alliances and Funders


Centers for Disease
Control and Prevention


European Centre for Disease Prevention and Control


Food and Agriculture Organisation
of the United Nations


National Institutes
for Health


National Institute for
Health Research


World Health Organisation

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Ⓒ 2019 Centre for Genomic Pathogen Surveillance