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Cambridge Infectious Diseases

An Interdisciplinary Research Centre at the University of Cambridge

Studying at Cambridge


Dr Lucy Weinert

Dr Lucy Weinert

Wellcome Trust and Royal Society Henry Dale Fellow

Principal Investigator

Department of Veterinary Medicine
Madingley Road

Office Phone: 01223 766247


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

Departments and Institutes

Veterinary Medicine:

Research Interests

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.


  • Genomics
  • Evolution
  • Ecology
  • Genetics
  • Host-Pathogen Interaction
  • Virology
  • Pathogen Evolution
  • Epidemiology
  • Bioinformatics
  • Bacteriology
  • Dynamics


  • Genomics
  • HIV
  • MRSA
  • Staphylococcus aureus
  • Herpesvirus
  • Streptococcus
  • Zoonoses
  • Pneumonic plague


  • Statistical Methods

Key Publications

Murray GG, Weinert LA, Rhule EL, Welch JJ. (2016) The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution? Systematic biology 65:2, 265-279 (doi: 10.1093/sysbio/syv084)

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, LinheiroRS, Magwire MM, JigginsFM, 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

Willemse N, Howell KJ, Weinert LA, Heuvelink A, Pannekoek Y, Wagenaar JA, Smith HE, van der Ende A, Schultsz C. (2016) An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis. Scientific Reports, (doi: 10.1038/srep28984)

Bossé JT, Li Y, Walker S, AthertonT,Fernandez CR, WilliamsonSM, Rogers J, Chaudhuri RR, Weinert LA, OshotaO, HoldenMT, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR (2015) Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae. Journal of Antimicrobial Chemotherapy 70: 2217–2222 (doi: 10.1093/jac/dkv121)

Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MT, Parkhill J, Langford PR, Rycroft AN, Wren BW (2015) Whole genome investigation of a divergent clade of the pathogen Streptococcus suis. Frontiers in microbiology 6 (doi: 10.3389/fmicb.2015.01191)

Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco JM, Nabholz B, Roux C, Tsagkogeorga G, Weber AA, Weinert LA, Belkhir K, Bierne N, Glémin S, Galtier N (2014) Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515: 261-263 (doi: 10.1038/nature13685)

Howell KJ, Weinert LA, Chaudhuri RR, Luan SL, Peters SE, Corander J, Harris D, Angen Ø, Aragon V, Bensaid A, Williamson SM, Parkhill J, Langford PR, Rycroft AN, Wren BW, Holden MTG, Tucker AW, Maskell DJ (2014) The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis. BMC Genomics 15:1179 (doi:10.1186/1471-2164-15-1179)

Harrison EM, Weinert LA, Holden MTG, Welch JJ,  Wilson K,  Morgan FJE, Harris SR,  Loeffler A,  Boag AK, Peacock SJ,  Paterson GK, Waller AS, Parkhill J, Holmes MA (2014) A shared population of epidemic methicillin-resistant Staphylococcus aureus 15 circulates in humans and companion animals. mBio 5:e00985-13 (doi: 10.1128/mBio.00985-13)

Rieux A, Eriksson A, Li M, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares  A, Manica A, Balloux F (2014) Improved calibration of the human mitochondrial clock using ancient genomes. Molecular Biology and Evolution 31: 2780-2792 (doi: 10.1093/molbev/msu222)

Bossé JT, Li Y, Angen Ø, Weinert LA, Chaudhuri  RR, Holden MT, Williamson SM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR (2014) A multiplex PCR to unequivocally differentiate Actinobacillus pleuropneumoniae Serovars 1-3, 5-8, 10 and 12. Journal of Clinical Microbiology 52: 2380-2385 (doi: 10.1128/JCM.00685-14)

Brisse S, Brehony C, Conceição T, Cubero Gonzales M, Glasner C, Le Gouil M, Renvoisé A, Sheppard S, Weinert LA (2014) Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference. Research in Microbiology 165: 140-153 (doi: 10.1016/j.resmic.2014)

Romiguier J, Lourenco J, Gayral P, Faivre N, Weinert LA, Ravel S, Ballenghien M, Cahais V, Bernard A, Loire E, Keller L, Galtier N (2014) Population genomics of eusocial insects: the cost of a vertebrate-like effective population size. Journal of Evolutionary Biology 27: 593-603 (doi: 10.1111/jeb.12331)

Howell KJ, Weinert LA, Luan S, Peters SE, Chaudhuri RR, Harris D, Angen O, Aragon V, Parkhill J, Langford P, Rycroft A, Wren BW, Tucker AW, Maskell D (2013) Gene content and diversity of the loci encoding biosynthesis of capsular polysaccharides of the fifteen serovar reference strains of Haemophilus parasuis. Journal of Bacteriology 195: 4264-4273 (doi: 10.1128/JB.00471-13)

Chrostek E, Marialva M, Esteves S, Weinert LA, Martinez J, Bergman CM, Jiggins FM, Teixeira L (2013) Wolbachia variants induce differential protection to viruses in Drosophila melanogaster: a phenotypic and phylogenomic analysis. PLoS Genetics 8: e1003129 (doi: 10.1371/journal.pgen.1003896)

Luan S, Chaudhuri RR, Peters SE, Mayho M, Weinert LA, Crowther SA, Wang J, Langford P, Rycroft A, Wren BW, Tucker AW, Maskell DJ (2013) Generation of a Tn5 transposon library in Haemophilus parasuis  and analysis by Transposon-Directed Insertion-Site Sequencing (TraDIS). Veterinary Microbiology 166, 558-566 (doi: 10.1016/j.vetmic.2013.07.008)

Spoor LE, McAdam P, Weinert LA, Hasman H, Aarestrup FM, Kearns AM, Larsen AR, Skov R, Fitzgerald JR (2013) Livestock origin for emergent human pandemic MRSA. mBio 4: e00356-13 (doi: 10.1128/mBio.00356-13)

Holden MTG, Hsu L, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlicková H, Coombs G, Kearns AM, Hill RL, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramírez S, Feil EJ, Hudson LO, Enright MC, Balloux F, Aanensen DM, Spratt BG, Fitzgerald JR, Parkhill J, Achtman M, Bentley SD, Nübel U (2013) A genomic portrait of the emergence, evolution, and global spread of a methiciliin-resistant Staphylococcus aureus pandemic. Genome Research 23: 653-664 (doi: 10.1101/gr.147710.112)

Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert LA, Chiari Y, Belkhir K, Ranwez V, Galtier N (2012) Reference-free transcriptome assembly in non-model animals from next generation sequencing data. Molecular Ecology Resources 5: 834-845 (doi: 10.1111/j.1755-0998.2012.03148.x.)

Rasmussen M, Guo X, Wang Y, Lohmueller KE,  Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega F, Tridico A, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E (2011) An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334: 94-98 (doi: 10.1126/science.1211177)

Leigh Brown AJ, Lycett SJ, Weinert LA, Hughes GJ, Fearnhill E, Dunn DT on behalf of the UK HIV Drug Resistance Collaboration (2011) Transmission network parameters estimated from HIV sequences from a nationwide epidemic. Journal of Infectious Diseases 204: 1463-1469 (doi: 10.1093/infdis/jir550)

Gayral P, Weinert LA, Chiari Y, Tsagkogeorga G, Ballenghien M, Galtier N (2011) Next-generation sequencing of transcriptomes: a guide to RNA isolation in non-model animals. Molecular Ecology Resources 11: 650-661 (doi: 10.1111/j.1755-0998.2011.03010.x)

Guinane CM, Ben Zakour NL, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay J, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penades J,  Fitzgerald JR (2010) Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution 2: 454-466 (doi: 10.1093/gbe/evq031)

Weinert LA, Welch JJ, Jiggins FM. (2009) Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally. Proceedings of the Royal Society, Series B 276: 3619-3627 (doi: 10.1098/rspb.2009.0875)

Lowder BV, Guinane CM, Ben Zakour NL, Weinert LA, Conway-Morris A, Cartwright RA, Simpson AJ, Rambaut A, Nübel U, Fitzgerald JR (2009) Recent human to poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proceedings of the National Academy of Sciences USA 106: 19545-19550 (doi: 10.1073/pnas.0909285106)

Weinert LA, Tinsley MC, Temperley M, Jiggins FM (2007) Are we underestimating the incidence and diversity of insect symbionts? A case study in ladybird beetles. Biology Letters 3: 678-681 (doi: 10.1098/rsbl.2007.0373)