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An Interdisciplinary Research Centre at the University of Cambridge


2015-present, PI, University of Cambridge
2008-2015, PDRA, University of Edinburgh, Université Montpellier II, Imperial College London, University College London, University of Cambridge
2008, PhD, Institute of Evolutionary Biology, University of Edinburgh
2004, BSc, Biology, University of Bristol


The ecology and genomics of bacterial pathogens

I am an evolutionary biologist whose major research goal is to understand why and how bacteria become pathogens. Identifying common features of pathogen emergence - whether they be repeated genomic changes or shared epidemiological contexts - would give us predictive power. This might allow us to forecast pathogen emergence, to develop preventative strategies, or improve treatments.

Genome reduction and pathogenicity

We are currently studying the link between reductive genome evolution and pathogenicity. Bacterial pathogens very often have smaller genomes and fewer genes than their nearest non-pathogenic relatives. However, despite much speculation, it remains unclear why this pattern holds. We are addressing this phenomenon using Streptococcus suis, a bacterium that is common in non-pathogenic forms, but which also causes serious diseases in pigs and humans (Weinert et al. 2015a). We sample whole genomes of global S. suis populations and use bioinformatic and laboratory approaches to test hypotheses about gene loss and pathogenicity.

Host switches

Some of our most serious pandemics are caused by pathogens switching and establishing in a new host species. We use bacterial genomes, molecular dating and information about host species to examine how bacteria adapt to the new host and the ecological context for switching. For example, we showed that farming practices (Weinert et al. 2012; Weinert et al. 2015a), host relatedness (Waxman et al. 2014) and host immunity (Weinert et al. 2015b) are predictors of host switch and/or establishment success.

Antimicrobial resistance and vaccine development

Antimicrobial resistance threatens the effective treatment of bacterial infections and makes routine medical procedures less safe. We investigate the genetic basis of antimicrobial resistance and look how these alleles evolve in a range of different bacteria. We also use bacterial genomics to create new vaccines with the goal of reducing antimicrobial usage.


Key publications: 

Matuszewska M, Murray GG, Harrison EM, Holmes MA, Weinert LA (2020) The Evolutionary Genomics of Host Specificity in Staphylococcus aureus. Trends in Microbiology 28(6), 465-477 (doi: 10.1016/j.tim.2019.12.007)

Richardson EJ*, Bacigalupe R*, Harrison EM*, Weinert LA*, Lycett SJ, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR (2018) Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nature ecology & evolution 2(9): 1468 (doi: 10.1038/s41559-018-0617-0)

Weinert LA, Welch JJ (2017) Why Might Bacterial Pathogens Have Small Genomes? Trends in Ecology and Evolution 32(12): 936-947 (doi: 10.1016/j.tree.2017.09.006)

Weinert LA, Chaudhuri RR, Wang J, Peters SE, Jukka Corander J, Jombart T, Baig A, Howell KJ, Harris D, Chieu TTB, Chau NVV, Campbell J, Schultsz C, Julian Parkhill J, Bentley SD, Langford PR, Rycroft AN, Wren BW, Farrar J, Baker S, Hoa NT, Holden MTG, Tucker AW, Maskell DJ (2015) Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Commuications 6: 7640 (doi: 10.1038/ncomms7740)

Weinert LA*, Viera Araujo E*, Ahmed MZ, Welch JJ (2015) The incidence of bacterial endosymbionts in terrestrial arthropods. Proceedings of the Royal Society, Series B 282: 20150249 (doi: 10.1098/rspb.2015.0249)

Weinert LA, Depledge DP, Kundu S, Gershon AA, Balloux F, Nichols RA, Welch JJ, Breuer J (2015) Rates of vaccine evolution show strong effects of latency, but argue against an Out-of-Africa spread of Varicella Zoster virus. Molecular Biology and Evolution 32: 1020-1028 (doi: 10.1093/molbev/msu406)

Weinert LA. (2015) The diversity and phylogeny of Rickettsia bacteria. In: Morand S, Krasnov BR, Littlewood, DTJ (eds.) Parasite diversity and diversification: evolutionary ecology meets phylogenetics pp. 150-183. Cambridge: Cambridge University Press

Waxman D*, Weinert LA*, Welch JJ (2014) Inferring host range dynamics from comparative data: the protozoan parasites of New World monkeys. The American Naturalist 184: 65-74 (doi: 10.1086/676589)

Cui Y*,Yu C*, Yan Y*, Li D*,Li Y*, Jombart T*, Weinert LA*, Wang Z, Guo Z, Xu L, Zhang Y, Zheng H, Qin N, Xiao X, Wu M, Wang X, Zhou D, Qi Z, Du Z, Wu H, Yang X, Cao H, Wang H, Wang J, Yao S, Rakin A, Li Y, Falush D, Balloux F, Achtman M, Song Y, Wang J, Yang R (2013) Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proceedings of the National Academy of Sciences, USA 110: 577-582 (doi: 10.1073/pnas.1205750110)

Weinert LA, Welch JJ, Suchard M, Lemey P, Rambaut A, Fitzgerald JR. (2012) Molecular dating of human-to-bovid host jumps in Staphylococcus aureus reveals an association with the spread of domestication. Biology Letters 8: 829-832 (doi: 10.1098/rsbl.2012.0290)

Richardson MF, Weinert LA, Welch JJ, Linheiro RS, Magwire MM, Jiggins FM, Bergman, CM (2012) Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLoS Genetics 8: e1003129 (doi: 10.1371/journal.pgen.1003129)

Farrer RA, Weinert LA, Bielby J, Garner TW, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, Anderson L, Pond SL, Shahar-Golan R, Henk DA, Fisher MC (2011) Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proceedings of the National Academy of Sciences, USA 108: 18732-18736 (doi: 10.1073/pnas.1111915108)

Weinert LA, Werren JH, Aebi A, Stone GN, Jiggins FM. (2009) Evolution and diversity of Rickettsia bacteria. BMC Biology 7: 6 (doi: 10.1186/1741-7007-7-6)

*= joint lead authorship

Other publications: 

see my Google Scholar page

Wellcome Trust and Royal Society Henry Dale Fellow
Principal Investigator
Dr Lucy  Weinert

Contact Details

Department of Veterinary Medicine
Madingley Road
01223 766247
Not available for consultancy


Departments and institutes: 
Person keywords: 
Host-Pathogen Interaction
Pathogen Evolution