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Department of Veterinary Medicine

Cambridge Veterinary School

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.

My main areas of focus are:

  • Genome reduction and pathogenicity
  • Host switches
  • Antimicrobial resistance and vaccine development



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


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 genetic variants 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: 

Google Scholar - list of all publications

Murray GG, Hossain AM, Miller E, Bruchmann S, Balmer AJ, Matuszewska M, Herbert J, Hadjirin NF, Mugabi R, Li G, Ferrando ML, Fernandes de Oliveira IM, Nguyen T, Yen PLK, Moe AZ, Wai TS, Gottschalk M, Aragon V, Valentin-Weigand P, Heegaard PMH, Vrieling M, Maw MT, Myint HT, Win YT, Hoa NT, Bentley SD, Clavijo MJ, Wells JM, Tucker AW, Weinert LA (2023) The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs Proceedings of the National Academy of Sciences 120(47): e2307773120

Matuszewska M, Murray GGR, Ba X, Wood R, Holmes MA, Weinert LA (2022) Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA eLife 11: e74819

Hadjirin NF, Miller EL, Murray GG, Yen PL, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW, Hoa NT, Welch JJ, Weinert LA (2021) Large scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis BMC Biology 19(191)

Murray GGR, Balmer AJ, Herbert J, Hadijirn NF, Kemp CL, Matuszewska M, Bruchmann S, Hossain AM, Gottschalk M, Tucker AW, Miller EL, Weinert LA (2021) Mutation rate dynamics reflect ecological changes in an emerging zoonotic pathogen PLoS Genetics 17(11): e1009864

Murray GG*, Charlesworth J*, Miller EL, Casey MJ, Lloyd CT, Gottschalk M, Tucker AW, Welch, JJ, Weinert, LA (2021) Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence Molecular biology and evolution, 38(4): 1570-1579

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

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

Weinert LA, Welch JJ (2017) Why Might Bacterial Pathogens Have Small Genomes? Trends in Ecology and Evolution 32: 936-947

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 (2015a) Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications 6: 7640 

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

Weinert LA, Depledge DP, Kundu S, Gershon AA, Balloux F, Nichols RA, Welch JJ, Breuer J (2015c) 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 

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

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)

*= joint lead authorship

Teaching and Supervisions


Part II Genetics, Evolutionary Genetics and Adaptation, Module 4 (ZL5)

Part II Pathology, Dynamics of Infectious Disease

Associate Professor
Takes PhD students
Available for consultancy


Local Affiliations: 
Person keywords: 
Host-Pathogen Interaction
Molecular epidemiology
Bacterial evolution
Infectious Diseases
Royal Society
Medical Research Council
The Newton Fund
Wellcome Trust
Global Challenges Research Fund (GCRF)