New Insights into High Priority Pathogens

WHO has identified high priority pathogens to guide research, drug discovery, and development. Through the widespread use of genome sequencing, researchers are tracking the spread of bacteria around the globe to underpin public health interventions. CGPS works closely with partners around the world to generate new insights into high priority pathogens.

Real-Time Epidemiology: COVID-19

Pathogen surveillance is a crucial part of early-stage and ongoing responses to COVID-19. CGPS is pleased to be a partner in the UK consortium on COVID-19 genomics (COG), that aims to link local sequencing centres with large scale facilities from across the UK to apply real-time genomic epidemiology to our understanding and ability to respond to the pandemic.

Tackling Anti-Microbial Resistance: Country Innovation

Policymakers are exploring the use of big data for precision public health which combines traditional data with technologies from fields including genomics. Low- and middle-income countries can innovate to improve real-time surveillance using data science and genomic technologies to improve real-time surveillance consistent with the International Health Regulation (2005). With the UK NIHR, CGPS has supported four countries - Colombia, India, Nigeria and the Philippines - to enhance their use of genomic methods, using tools and innovation to provide real-time surveillance and epidemiology within their national policies and health systems.


Integrating Whole-Genome Sequencing Within the National Antimicrobial Resistance Surveillance Program in the Philippines.

Argimón S., Masim M.A.L., Gayeta J.M., Lagrada M.L., Macaranas P.K.V., Cohen V., et al.

Nature Communications 2020; 11:2719.

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.

David S, Reuter S, Harris SR, Glasner C, Feltwell T et al.

Nature microbiology 2019; 4; 11;1919-1929

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

A McNally, T Kallonen, C Connor, K Abudahab, DM Aanensen, C Horner, SJ Peacock, J Parkhill, J Croucher, J Corander.

mBio 2019; 10 (2), e00644-19

Genomic sequence investigation Streptococcus pyogenes clusters in England (2010-2015).

Coelho JM, Kapatai G, Jironkin A, Al-Shahib A, Daniel R, Dhami C, Laranjeira AM, Chambers T, Phillips S, Tewolde R, Underwood A, Chalker VJ.

Clin Microbiol Infect. 2019; 25(1):96‐101. doi:10.1016/j.cmi.2018.04.011

PANINI: Pangenome Neighbour Identification for Bacterial Populations

K Abudahab, JM Prada, Z Yang, SD Bentley, NJ Croucher, J Corander, DM Aanensen.

Microb Genom. 2019; 5(4):e000220. doi:10.1099/mgen.0.000220

Phandango: an interactive viewer for bacterial population genomics.

J Hadfield, NJ Croucher, RJ Goater, K Abudahab, DM Aanensen, SR Harris.

Bioinformatics 2018; 34 (2), 292-293.

Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey

SR Harris, MJ Cole, G Spiteri, L Sánchez-Busó, D Golparian, et al.

The Lancet Infectious Diseases 2018; 18(7): 758-768

Sustained transmission of high-level azithromycin-resistant Neisseria gonorrhoeae in England: an observational study.

Fifer H, Cole M, Hughes G, Padfield S, Smolarchuk C, Woodford N, Wensley A, Mustafa N, Schaefer U, Myers R, Templeton K, Shepherd J, Underwood A.

Lancet Infect Dis. 2018;18(5):573‐581. doi:10.1016/S1473-3099

Gene exchange drives the ecological success of a multi-host bacterial pathogen.

Richardson EJ, Bacigalupe R, Harrison EM, …..Aanensen DM et al.

Nat Ecol Evol. 2018; 2(9):1468‐1478. doi:10.1038/s41559-018-0617-0

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Park SE, Pham DT, Boinett C, …. Aanensen DM et al.

Nat Commun. 2018; 9(1):5094. Published 2018 Nov 30. doi:10.1038/s41467-018-07370-z

Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective multinational study.

Grundmann H, Glasner C, Albiger B, Aanensen DM et al.

Lancet Ifect Dis. 2017; 17(2):153‐163. doi:10.1016/S1473-3099(16)30257-2

Scarlet Fever Incident Management Team. Genome analysis following a national increase in Scarlet Fever in England 2014

Chalker V, Jironkin A, Coelho J, Al-Shahib A, Platt S, Kapatai G, Daniel R, Dhami C, Laranjeira M, Chambers T, Guy R, Lamagni T, Harrison T, Chand M, Johnson AP, Underwood A.

BMC Genomics. 2017; 18(1):224. doi:10.1186/s12864-017-3603-z

The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.

Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM et al.

Front Microbiol. 2017; 8:121. doi:10.3389/fmicb.2017.00121

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

Aanensen DM, Feil EJ, Holden MT, … Yeats CA, et al.

mBio. 2016;7(3):e00444-16. doi:10.1128/mBio.00444-16

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.

Argimón S., Abudahab K., Goater R.J.E., Fedosejev A., Bhai J., Glasner C., Feil E.J., Holden M.T.G., Yeats C.A., Grundmann H., Spratt B.G., Aanensen D.M.

Microbial Genomics 2016; 2(11):000093.

Genomic Analysis and Comparison of Two Gonorrhea Outbreaks.

Didelot X, Dordel J, Whittles LK, … Aanensen DM et al.

mBio. 2016;7(3):e00525-16. doi:10.1128/mBio.00525-16

Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently.

David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, Bouchier C, Underwood A, Jarraud S, Harrison TG, Parkhill J, Buchrieser C.

Genome Res. 2016; 26(11):1555‐1564. doi:10.1101/gr.209536.116

Species Mash-up.

Argimón S, Aanensen DM.

Nat Rev Microbiol. 2016; 14(12):730. doi:10.1038/nrmicro.2016.175

Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline.

Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, Fry NK. PeerJ.

2016;4:e2477. Published 2016 Sep 14. doi:10.7717/peerj.2477

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

Sun Z., Harris H.M.B., McCann A., Yang X., Argimón S., et al.

Nature Biotechnology 2015; 6:8322.

Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries.

Argimón S., Konganti K., Chen H., Alekseyenko A.V., Brown S., and Caufield P.W.

Infection Genetics and Evolution 2014; 21:269-278.

Phylogenetic Analysis of Glucosyltransferases and Implications for the Coevolution of Mutans Streptococci with their Mammalian Hosts.

Argimón S., Alekseyenko A.V., DeSalle R., and Caufield P.W.

PLoS One. 2013; 8(2):e56305.