Publications

(Selected publications arising from our work are listed here. Please see individual members' pages for more detail.)

2022

Dishon M. Muloi, Bryan A. Wee, Deirdre M. H. McClean, Melissa J. Ward, Louise Pankhurst, Hang Phan, Alasdair C. Ivens, Velma Kivali, Alice Kiyong’a, Christine Ndinda, Nduhiu Gitahi, Tom Ouko, James M. Hassell, Titus Imboma, James Akoko, Maurice K. Murungi, Samuel M. Njoroge, Patrick Muinde, Yukiko Nakamura, Lorren Alumasa, Erin Furmaga, Titus Kaitho, Elin M. Öhgren, Fredrick Amanya, Allan Ogendo, Daniel J. Wilson, Judy M. Bettridge, John Kiiru, Catherine Kyobutungi, Cecila Tacoli, Erastus K. Kang’ethe, Julio D. Davila, Samuel Kariuki, Timothy P. Robinson, Jonathan Rushton, Mark E. J. Woolhouse & Eric M. Fèvre. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape. Nat. Microbiol. doi: 10.1038/s41564-022-01079-y

2021

Utkarsh Agrawal, Amaya Azcoaga-Lorenzo, Adeniyi Francis Fagbamigbe, Eleftheria Vasileiou, Paul Henery, Colin R Simpson, Sarah J Stock, Syed Ahmar Shah, Chris Robertson, Mark Woolhouse, Lewis D Ritchie, Aziz Shiekh, Ewen M Harrison, Annemarie B Docherty, Colin McCowan. Association between multimorbidity and mortality in a cohort of patients admitted to hospital with COVID-19 in Scotland. J. Roy. Soc. Med. doi: 10.1177/01410768211051715

 

Yvan Butera, Enatha Mukantwari, Maria Artesi, Jeanne d’arc Umuringa, Áine Niamh O’Toole, Verity Hill, Stefan Rooke, Samuel Leandro Hong, Simon Dellicour, Onesphore Majyambere, Sebastien Bontems, Bouchra Boujemla, Josh Quick, Paola Cristina Resende, Nick Loman, Esperance Umumararungu, Alice Kabanda, Marylin Milumbu Murindahabi, Patrick Tuyisenge, Misbah Gashegu, Jean Paul Rwabihama, Reuben Sindayiheba, Djordje Gikic, Jacob Souopgui, Wilfred Ndifon, Robert Rutayisire, Swaibu Gatare, Tharcisse Mpunga, Daniel Ngamije, Vincent Bours, Andrew Rambaut, Sabin Nsanzimana, Guy Baele, Keith Durkin, Leon Mutesa & Nadine Rujeni. Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nat. Commun. doi: 10.1038/s41467-021-25985-7

 

Meghan R. Perry, Hannah C. Lepper, Luke McNally, Bryan A. Wee, Patrick Munk, Amanda Warr, Barbara Moore, Pota Kalima, Carol Philip, Ana Maria de Roda Husman, Frank M. Aarestrup, Mark E. J. Woolhouse and Bram A. D. van Bunnik. Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family. Front. Microbiol. doi: 10.3389/fmicb.2021.703560

 

Feifei Zhang, Humphrey Karamagi, Ngoy Nsenga, Miriam Nanyunja, Miriam Karinja, Seth Amanfo, Margo Chase-Topping, Giles Calder-GerverMiles McGibbonAlexandra HuberTara Wagner-Gamble, Chuan-Guo Guo, Samuel HaynesAlistair MorrisonMiranda Ferguson, Gordon A. Awandare, Francisca Mutapi, Zabulon Yoti, Joseph Cabore, Matshidiso R. Moeti & Mark E. J. Woolhouse. Predictors of COVID-19 epidemics in countries of the World Health Organization African Region. Nat Med. doi: 10.1038/s41591-021-01491-7

 

Bram A.D. van BunnikAlex L.K. Morgan, Paul Bessell, Giles Calder-Gerver, Feifei Zhang, Samuel Haynes, Jordan AshworthShengyuan ZhaoNicola Rose CaveMeghan R. PerryHannah C. LepperLu Lu, Paul Kellam, Aziz Sheikh, Graham F. Medley, Mark E.J. Woolhouse. Segmentation and shielding of the most vulnerable members of the population as elements of an exit strategy from COVID-19 lockdown. Phil. Trans. R. Soc. 376:20200275.20200275 doi: 10.1098/rstb.2020.0275

 

Morgan ALK, Woolhouse MEJ, Medley GF, and van Bunnik BAD. Optimising time-limited non-pharmaceutical interventions for COVID-19 outbreak controlPhil Trans R Soc B376: 20200282.20200282. DOI: 10.1098/rstb.2020.0282

 

Vasileiou, E., Simpson, C.R., Ting, S., Kerr, S., Agrawal, U., Akbari, A., Bedston, S., Beggs, J., Bradley, D., Chuter, A., de Lusignan, S., Docherty, A.B., Ford, D., Hobbs, F.D.R., Joy, M., Katikireddi, S.V., Marple, J., McCowan, C., McGagh, D., McMenamin, J., Moore, E., Murray, J.L.K., Pan, J., Ritchie, L., Shah, S.A., Stock, S., Torabi, F., Tsang, R.S.M., Wood, R., Woolhouse, M., Robertson, C. and Sheikh, A. (2021). Interim findings from first does mass COVID-19 vaccination roll-out and COVID-19 hospitalisations in Scotland: a prospective cohort study of 5.4 million people. The Lancet 397(10285):1646-1657.

 

Flook, M., Jackson, C., Vasileiou, E., Simpson, C.R., Muckian, M.D., Agrawal, U., McCowan, C., Jia, Y., Murray, J.L.K., Ritchie, L.D., Robertson, C., Stock, S.J., Wang, X., Woolhouse, M.E.J., Sheikh, A. and Stagg, H.R. (2021) (in press). Informing the public health response to COVID-19: a systematic review of risk factors for disease severity and mortality. BMC Infectious Diseases 21:342.

 

Mulholland, R.H., Vasileiou, E., Simpson, C.R., Robertson, C., Ritchie, L.D., Agrawal, U., Woolhouse, M., Murray, J.L.K., Stagg, H.R., Docherty, A.B., McCowan, C., Wood, R., Stock, S.J. and Sheikh, A. (in press). Cohort profile: early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II) database. International Journal of Epidemiology. Available at: https://www.researchgate.net/publication/348931386_Cohort_Profile_Early_...

 

Zhao, S., Kennedy, S., Perry, M.R., Wilson, J., Chase-Topping, M., Anderson, E., Woolhouse, M.E.J. and Lockhart, M. (2021). Epidemiology of and risk factors for mortality due to carbapenemase-producing organisms (CPO) in healthcare facilities. Journal of Hospital Infection 110: 184-193.

 

Everett, H., van Diemen, P., Aramouni, M., Ramsay, A., Coward, V., Pavot, V., Canini, L., Holzer, B., Morgan, S., The Dynamics sLoLa Consortium, Woolhouse, M., Tchilian, E., Brookes, S., Brown, I., Charleston, B. and Gilbert, S. (2021). Vaccines that reduce viral shedding do not prevent transmission of H1N1 pandemic 2009 swine influenza A virus infection to unvaccinated pigs. Journal of Virology 95: e01787-20.

 

Fukushige M, Chase-Topping M, Woolhouse MEJ, Mutapi F. Efficacy of praziquantel has been maintained over four decades (from 1977 to 2018): A systematic review and meta-analysis of factors influence its efficacy. PLoS Negl Trop Dis 15(3): e0009189. DOI: 10.1371/journal.pntd.0009189

 

 

Lu L, Lycett S, Ashworth J, Mutapi F, Woolhouse M. What are SARS-CoV-2 genomes from the WHO Africa region member states telling us? BMJ Global Health 2021; 6(1): e004408. PMID: 33419930.

 

du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O’Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 2021: eabf2946. PMID: 33419936 doi: 10.1126/science.abf2946

 

Earlier papers (selected)

 

Zhang F, Chase-Topping M, Guo C-G, van Bunnik BAD, Brierley L, Woolhouse MEJ. Global discovery of human-infective RNA viruses: A modelling analysis. PLoS Pathog. 2020,16(11): e1009079. doi: 10.1371/journal.ppat.1009079.

 

Lycett, S. J., Pohlmann, A., Staubach, C., Caliendo, V., Woolhouse, M., Beer, M., & Kuiken, T. Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia. Proceedings of the National Academy of Sciences 2020; 117(34): 20814-25. doi:10.1073/pnas.2001813117

 

Aarestrup FM, Woolhouse MEJ. Using sewage for surveillance of antimicrobial resistance. Science 2020;367(6478):630. doi: 10.1126/science.aba3432

 

Liam Brierley, Amy B. Pedersen, Mark E. J. Woolhouse. Tissue tropism and transmission ecology predict virulence of human RNA viruses. PLoS Biol. November 26, 2019. doi: 10.1371/journal.pbio.3000206

 

Mutapi F, Maizels R, Fenwick A, Woolhouse M. Human schistosomiasis in the post mass drug administration era. Lancet Infect Dis. 2017 Feb;17(2):e42-e48.doi: 10.1016/S1473-3099(16)30475-3. Epub 2016 Dec 15. Review. PubMed PMID:27988094.

 

Laxminarayan R, Sridhar D, Blaser M, Wang M, Woolhouse M. Achieving global targets for antimicrobial resistance. Science. 2016 Aug 26;353(6302):874-5. doi: 10.1126/science.aaf9286. Epub 2016 Aug 18. PubMed PMID: 27540009.

 

Woolhouse ME, Thumbi SM, Jennings A, Chase-Topping M, Callaby R, Kiara H,Oosthuizen MC, Mbole-Kariuki MN, Conradie I, Handel IG, Poole EJ, Njiiri E,Collins NE, Murray G, Tapio M, Auguet OT, Weir W, Morrison WI, Kruuk LE,Bronsvoort BM, Hanotte O, Coetzer K, Toye PG. Co-infections determine patterns ofmortality in a population exposed to parasite infection. Sci Adv. 2015 Mar20;1(2):e1400026. doi: 10.1126/sciadv.1400026. eCollection 2015 Mar. PubMed PMID:26601143; PubMed Central PMCID: PMC4643819.

 

Woolhouse ME, Rambaut A, Kellam P. Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management. Sci Transl Med. 2015 Sep30;7(307):307rv5. doi: 10.1126/scitranslmed.aab0191. Review. PubMed PMID:26424572; PubMed Central PMCID: PMC5819730.

 

Woolhouse M, Drury P, Dye C. Zero infection. Science. 2014 Dec12;346(6215):1271. doi: 10.1126/science.aaa4117. PubMed PMID: 25504691.

 

Woolhouse M, Farrar J. Policy: An intergovernmental panel on antimicrobialresistance. Nature. 2014 May 29;509(7502):555-7. PubMed PMID: 24877180.

 

Ciccolini M, Donker T, Grundmann H, Bonten MJ, Woolhouse ME. Efficientsurveillance for healthcare-associated infections spreading between hospitals.Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2271-6. doi:10.1073/pnas.1308062111. Epub 2014 Jan 27. PubMed PMID: 24469791; PubMed Central PMCID: PMC3926017.

 

Morse SS, Mazet JA, Woolhouse M, Parrish CR, Carroll D, Karesh WB, Zambrana-Torrelio C, Lipkin WI, Daszak P. Prediction and prevention of the next pandemic zoonosis. Lancet. 2012 Dec 1;380(9857):1956-65. doi: 10.1016/S0140-6736(12)61684-5. Review. PubMed PMID: 23200504; PubMed Central PMCID: PMC3712877.

 

Charleston B, Bankowski BM, Gubbins S, Chase-Topping ME, Schley D, Howey R, Barnett PV, Gibson D, Juleff ND, Woolhouse ME. Relationship between clinical signs and transmission of an infectious disease and the implications for control. Science. 2011 May 6;332(6030):726-9. doi: 10.1126/science.1199884.

 

Chase-Topping M, Gally D, Low C, Matthews L, Woolhouse M. Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157. Nat Rev Microbiol. 2008 Dec;6(12):904-12. doi: 10.1038/nrmicro2029. Review. PubMed PMID: 19008890; PubMed Central PMCID: PMC5844465.

 

King DA, Peckham C, Waage JK, Brownlie J, Woolhouse ME. Epidemiology. Infectious diseases: preparing for the future. Science. 2006 Sep 8;313(5792):1392-3. PubMed PMID: 16959992.

 

Savill NJ, St Rose SG, Keeling MJ, Woolhouse ME. Silent spread of H5N1 in vaccinated poultry. Nature. 2006 Aug 17;442(7104):757. PubMed PMID: 16915278.

 

Tildesley MJ, Savill NJ, Shaw DJ, Deardon R, Brooks SP, Woolhouse ME, Grenfell BT, Keeling MJ. Optimal reactive vaccination strategies for a foot-and-mouth outbreak in the UK. Nature. 2006 Mar 2;440(7080):83-6. PubMed PMID: 16511494.

 

Keeling MJ, Woolhouse ME, May RM, Davies G, Grenfell BT. Modelling vaccination strategies against foot-and-mouth disease. Nature. 2003 Jan 9;421(6919):136-42. Epub 2002 Dec 22. PubMed PMID: 12508120.

 

Keeling MJ, Woolhouse ME, Shaw DJ, Matthews L, Chase-Topping M, Haydon DT, Cornell SJ, Kappey J, Wilesmith J, Grenfell BT. Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape. Science. 2001 Oct 26;294(5543):813-7. Epub 2001 Oct 3. PubMed PMID: 11679661.

 

Fèvre EM, Coleman PG, Odiit M, Magona JW, Welburn SC, Woolhouse ME. The origins of a new Trypanosoma brucei rhodesiense sleeping sickness outbreak in eastern Uganda. Lancet. 2001 Aug 25;358(9282):625-8. PubMed PMID: 11530149.

 

Coleman PG, Perry BD, Woolhouse ME. Endemic stability--a veterinary idea applied to human public health. Lancet. 2001 Apr 21;357(9264):1284-6. PubMed PMID: 11418173.

 

Woolhouse M, Chase-Topping M, Haydon D, Friar J, Matthews L, Hughes G, Shaw D, Wilesmith J, Donaldson A, Cornell S, Keeling M, Grenfell B. Epidemiology. Foot-and-mouth disease under control in the UK. Nature. 2001 May 17;411(6835):258-9. PubMed PMID: 11357118.

 

Woolhouse ME, Taylor LH, Haydon DT. Population biology of multihost pathogens. Science. 2001 May 11;292(5519):1109-12. Review. PubMed PMID: 11352066.