Professor Roger PickupProfessor
My research interests lie in 'Environment and human health' with expertise in molecular microbial ecology/environmental microbiology. I am particularly interested in non-tuberculous mycobacteria and their environmental routes for human exposure. Of main interest is Mycobacterium avium subspecies paratuberculosis (Map) which causes inflammatory bowel disease (Johne’s disease) in the majority of animals. With collaborators, we are examining Map’s role in Crohn’s disease, a similar human inflammatory condition. Map is significantly associated with this crippling disease and we seek to ascertain whether it is the cause. Other interests include: antibiotic resistance in the natural and hospital environments, gene transfer in the environment and diversity of bacteria in bird guts and in those involved in bee nutrition.
Examples of my research include:
The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria
Glenn Rhodes, Hester Bosma, David Studholme, Dawn L. Arnold, Robert W. Jackson and Roger W. Pickup
Environmental Microbiology (2014) 16(8), 2374–2388
The rulAB operon of Pseudomonas spp. confers fitness traits on the host and has been suggested to be a hotspot for insertion of mobile elements that carry avirulence genes. Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site-specific integration of related integron-like elements (ILEs) found in six environmental pseudomonads (strains FH1–FH6). Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat. ILEs from FH1 and FH5 were 9403 bp in length and contained eight open reading frames (ORFs), while the ILE from FH4 was 16 233 bp in length and contained 16 ORFs. In all three ILEs, the first 5.1 kb (containing ORFs 1–4) were structurally conserved and contained three predicted site-specific recombinases/integrases and a tetR homologue. Downstream of these resided ORFs of the ‘variable side’ with structural and sequence similarity to those encoding survival traits on the fitness enhancing plasmid pGRT1 (ILEFH1 and ILEFH5) and the NR-II virulence region of genomic island PAGI-5 (ILEFH4). Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.
Mycobacterium avium subspecies paratuberculosis and Crohn's disease (with Dr Glenn Rhodes, CEH Lancaster)
Mycobacterium avium subspecies paratuberculosis (MAP) is a member of the Mycobacterium avium complex. Ithas the specific ability to cause chronic inflammation of the intestine, or Johne’s disease (JD), which can affect many animal species, including primates. This chronic enteric pathogen is significantly associated with chronic inflammation of the intestine of the Crohn’s disease (CD) type in humans
Subclinical infection is widespread in domestic livestock, especially cattle, sheep, and goats. Infection and disease are now spreading worldwide with Europe and North America being particularly affected. It is estimated that the herd prevalence for JD in cattle in the USA is 68% and 32% in UK. Both clinically and sub-clinically infected animals can shed MAP in variable numbers on to pasture in their faeces, depending on the animal, the pathogen strain and the disease characteristics). The organismcan survive for many months in agricultural slurry and in the wider environment
As with other potentially zoonotic pathogens rain falling onto pastures contaminated with M. avium subsp. paratuberculosis washes it into surface waters and into rivers. Previously, we showed that MAP was present in 39% of samples taken from the river Taff (Cardiff, South Wales, UK) and its presence was predictable from rain fall patterns and river flow. Furthermore deposition and transport from the catchment was extensive in that MAP was maintained in the river for several weeks at a time and was a consequence of the endemic presence of MAP in cattle in the Taff catchment. Pickup and co-workers (2006) modelled the main human exposure routes of MAP and suggested that although driven by shedding from clinically and sub-clinically infected animals, the presence and distribution of MAP in the environment may also be influenced by other factors such as slurrying, soil redistribution from water treatment that recycle MAP back from the catchment to the river.
Furthermore, Cardiff has one of the highest incidence of CD in the UK with a corrected incidence for the decade (1996-2005) of 6.6 per 105 population per year (with a 95% confidence interval of 58-76) with the concomitant increase in incidence in children under 16. This compares with 5.5 per 105 population per year (with a 95% confidence interval of 44-68) for the period 1991-1995, 5.9/105/year for 1986-1990 and 5.0/105/year over the period from 1976 to 1980 (Rose et al 1988). The epidemiological study carried out by Mayberry and Hitchens in the late 1970s examined the incidence and geographical distribution of Crohn's disease and ulcerative colitis in 25 electoral wards in the city of Cardiff. They found a statistically highly significant (P < 0.001) increase in the incidence of Crohn's disease, but not of ulcerative colitis, in 11 of the city wards. Although eight of these high-incidence wards bordered the river Taff, their apparent geographical relationship with the river was not statistically significant. The topography of the approaches to the southwest aspect of the river is characterized by hills to the north and south. The valley in between, open to the prevailing winds, is directly opposite the gap in the center of the high-incidence wards on the windward bank of the river. On the leeward side, three additional high-incidence wards lie immediately adjacent to those bordering the river to the northeast. Pickup et al (2005) suggested that this is the direction in which aerosols containing M. avium subsp. paratuberculosis would be carried on the prevailing southwesterly winds and proposed that aerosolisation of Map this exposure route as an explanation for the observed disease clusters around the river Taff. We continue to examine the environment factors that influence the epidemiology of Crohn’s Disease.
Mycobacterium avium subspecies paratuberculosis is a very slow growing mycobactin-dependent member of the Mycobacterium avium complex. Unlike other M. avium species, M. avium subspecies paratuberculosis has the specific ability to cause chronic inflammation of the intestine, Johne's disease which can affect many species including primates. Despite its broad pathogenicity M. avium subspecies paratuberculosis can live in animals for years without causing clinical disease. Subclinical infection is widespread in domestic livestock especially cattle, sheep, and goats. Europe and North America have been particularly affected, but infection and disease are now spreading worldwide. Clinically and subclinically infected animals shed M. avium subspecies paratuberculosis in their milk. These pathogens are more robust than M. bovis. Research so far carried out in the UK, USA and Czech Republic shows that M. avium subspecies paratuberculosis is from time to time transmitted to human populations in retail milk supplies. Recent research from several centres using appropriate laboratory methods shows that most people with chronic inflammation of the intestine of the Crohn's disease type are infected with these chronic enteric pathogens. Like Johne's disease, the incidence of Crohn's disease is increasing particularly in children.
Ultimately we wish to progress towards a multidisciplinary program of research designed to inform future policy decisions with quantitative data on the level of environmental contamination by MAP and provide the essential quantitative basis for future testing of the efficacy of potential remedial measures such as the use of new generation veterinary vaccines to minimise environmental contamination and cycling. However, in order to achieve this we have to understand the fate and behaviour of MAP in a number of environmental compartments as specified by our model (see reference; for instance, rivers, sediments, aerosols) through quantification and source identification in order to test the hypothesis that Mycobacterium avium subspecies paratuberculosis contaminating environmental compartments constitutes a significant and incremental threat to human health.
Pickup, R.W., Rhodes, G., Bull, T.J, Arnott, S., Sidi-Boumedine, K., Hurley, M.J. and Hermon-Taylor, J. (2006). Mycobacterium avium subspecies paratuberculosis in lake catchments, in river water sourced for domestic supply and in effluent from domestic sewage treatment works: diverse opportunities for environmental cycling and human exposure. Applied and Environmental Microbiology 72, 4067-4077.
Mycobacterium chelonae complex and respiratory disease (with Dr Glenn Rhodes, CEH Lancaster)
M. immunogenum, a known human pathogen is a recently described species and has as closest relatives M. chelonae, M. abscessus. Collectively these bacteria form the M. chelonae complex. In recent years M. immunogenum has been implicated in the causation of hypersensitivity pneumonitis (HP) in automobile workers and other occupational workers exposed to metal working fluids. The early detection of M. immunogenum and related bacteria may be important in the possible prevention of HP. Since developing a highly specific quantitative PCR detection method, our interests now focus on its source, diversity and role in hypersensitivity pneumonitis.
Current and developing projects in my laboratory include:-
- Mycobacterium avium subspecies paratuberculosis and Crohn's disease (NHS, King’s College London, Centre for Ecology and Hydrology)
- Mycobacterium avium subspecies paratuberculosis and Crohn's disease: Diverse opportunities for human exposure (NERC: with King’s College London, Centre for Ecology and Hydrology and Cardiff University )
- ‘Rapid quantum evolution of bacterial pathogens and biocontrol strains (with Reading University, Rothampstead and Centre for Ecology and Hydrology.
- Epidemiology of Crohn’s patients in the NW of England (with NHS)
- Role of Mycobacterium avium subspecies paratuberculosis in Type 1 Diabetes Mellitus (with NHS)
I am a Professor of Biomedicine and Life Sciences within the Division of Biomedical and Life Sciences of the Faculty of Health and Medicine. I am a member of the University Research Ethics Committee and the Faculty Promotion Board. I am a member of the core panel of Natural Environment Research Council’ss Peer Review College.
1979-1983 : PhD (Sir William Roberts Scholarship) ‘Physical and structural properties of TOL plasmids in Pseudomonas’
1983-1984 : Research Assistant, University of Wales, Bangor (SERC)
1984-1985 : Research Fellow at the University of Liverpool
1985-1988 : Higher Scientific Officer; Freshwater Biological Association
1988-1989 : Higher Scientific Officer; Institute of Freshwater Ecology
1989-1991 : Senior Scientific Officer; Institute of Freshwater Ecology
1991-2008 : Principal Scientific Officer (Band 4); Institute of Freshwater Ecology’ now Centre for Ecology and Hydrology’
2003-2008 : Head of ‘Ecological Processes in Freshwaters and Soils’ Section, CEH Lancaster
1992-1999 : Honorary Research Fellow, Department of Genetics and Microbiology, University of Liverpool
1992-1999 : Honorary Lecturer, Department of Biological Sciences, University of Lancaster
1999-2005 : Visiting Professor, Department of Genet. and Microbiol, University of Liverpool
1999- 2008 : Honorary Professor, School of Biological Sciences, University of Lancaster
2002-2011 : Visiting Professor, Department of Civil and Structural Engineering, University of Sheffield
2009- present : Professor; Chair, Division of Biomedical and Life Sciences, Lancaster University
PhD Supervisions Completed
33 awaiting examination (as of November 2015).
1979 : BSc (Joint Hons, IIi) in Biochemistry and Marine Biology (University of Wales, Bangor)
1984 : PhD (Sir William Roberts Scholarship) ‘Physical and structural properties of TOL plasmids inn Pseudomonas’
Erratum: Influenza C in Lancaster, UK, in the winter of 2014-2015
Atkinson, K.V., Bishop, L.A., Rhodes, G., Salez, N., McEwan, N.R., Hegarty, M.J., Robey, J., Harding, N., Wetherell, S., Lauder, R.M., Pickup, R.W., Wilkinson, M., Gatherer, D. 26/05/2017 In: Scientific Reports. 7, p. 46815.
Genome Sequence of Human Papillomavirus 23 Strain HPV-23/Lancaster/2015
Atkinson, K.V., Bishop, L.A., Rhodes, G., Salez, N., McEwan, N.R., Hegarty, M.J., Robey, J., Harding, N., Wetherell, S., Lauder, R.M., Pickup, R.W., Wilkinson, M., Gatherer, D. 18/05/2017 In: Genome Announcements. 5, 20, 2 p.
Influenza C in Lancaster, UK, in the winter of 2014-2015
Atkinson, K.V., Bishop, L.A., Rhodes, G., Salez, N., McEwan, N.R., Hegarty, M.J., Robey, J., Harding, N., Wetherell, S., Lauder, R.M., Pickup, R.W., Wilkinson, M., Gatherer, D. 13/04/2017 In: Scientific Reports. 7, 9 p.
Genome sequence of human rhinovirus A22, strain Lancaster/2015
Atkinson, K.V., Bishop, L.A., Rhodes, G., Salez, N., McEwan, N.R., Hegarty, M.J., Robey, J., Harding, N., Wetherell, S., Lauder, R.M., Pickup, R.W., Wilkinson, M., Gatherer, D. 23/03/2017 In: Genome Announcements. 5, 12
Contract Researcher Audit and Survey–Foundation Report
Brown, J.C., Shaw, E.J., Pickup, R.W., Morbey, H. 01/2017 Lancaster : Lancaster University.
Carbapenemase-producing Enterobacteriaceae in hospital wastewater: a reservoir that may be unrelated to clinical isolates [star]
White, L., Hopkins, K., Meunier, D., Perry, C.L., Pike, R., Wilkinson, P., Pickup, R.W., Cheesbrough, J., Woodford, N. 06/2016 In: Journal of Hospital Infection. 93, 2, p. 145-151. 7 p.
Immobilization of Shewanella oneidensis MR-1 in diffusive gradients in thin films for determining metal bioavailability
Baker, P., Hogstrand, C., Lead, J., Pickup, R., Zhang, H. 11/2015 In: Chemosphere. 138, p. 309-315. 7 p.
Life history correlates of faecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus
Benskin, C., Rhodes, G., Pickup, R., Mainwaring, M., Wilson, K., Hartley, I. 02/2015 In: Ecology and Evolution. 5, 4, p. 821-835. 15 p.
Honeybee nutrition is linked to landscape composition
Donkersley, P., Rhodes, G., Pickup, R., Jones, K., Wilson, K. 11/2014 In: Ecology and Evolution. 4, 21, p. 4195-4206 . 12 p.
The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria
Rhodes, G., Bosma, H., Studholme, D., Arnold, D., Robert, J., Pickup, R. 1/09/2014 In: Environmental Microbiology. 16, 8, p. 2374-2388 . 15 p.
Mycobacterium avium subspecies paratuberculosis: human exposure through environmental and domestic aerosols
Rhodes, G., Richardson, H., Hermon-Taylor, J., Weightman, A., Higham, A., Pickup, R. 14/07/2014 In: Pathogens. 3, 3, p. 577-595. 19 p.
Wrong, but useful: negotiating uncertainty in infectious disease modelling
Christley, R., Mort, M., Wynne, B., Wastling, J., Heathwaite, L., Pickup, R., Austin, Z., Latham, S. 16/10/2013 In: PLoS ONE. 8, 10, 13 p.
Mycobacterium avium subspecies paratuberculosis is widely distributed in British soils and waters: implications for animal and human health
Rhodes, G., Hentys, P., Thomson, B., Pickup, R. 10/2013 In: Environmental Microbiology. 15, 10, p. 2761-2774. 14 p.
Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer.
Rizoulis, A., Elliot, D.R., Rolfe, S.A., Thornton, S.F., Banwart, S.A., Pickup, R.W., Scholes, J.D. 1/07/2013 In: Microbial Ecology. 66, 1, p. 84-95. 12 p.
Policy, practice and decision making for zoonotic disease management: water and cryptosporidium
Austin, Z., Alcock, R., Christley, R., Haygarth, P., Heathwaite, L., Latham, S., Mort, M., Oliver, D., Pickup, R., Wastling, J.M., Wynne, B. 04/2012 In: Environment International. 40, n/a, p. 70-78. 9 p.
The bacteriology of Windermere and its catchments: insights from 70 years of study
Rhodes, G., Porter, J., Pickup, R. 02/2012 In: Freshwater Biology. 57, 2, p. 305-320. 16 p.
Uncertainties in the governance of animal disease: an interdisciplinary framework for analysis
Fish, R., Austin, Z., Christley, R., Haygarth, P.M., Heathwaite, A.L., Heathwaite, L.A., Latham, S., Medd, W., Mort, M., Oliver, D.M., Pickup, R., Wastling, J.M., Wynne, B. 27/09/2011 In: Philosophical Transactions B: Biological Sciences. 366, 1573, p. 2023-2034. 12 p.
Implementation of a quantitative real-time PCR assay for the detection of mycobacterium immunogenum in metalworking fluids
Rhodes, G., Fluri, A., Ruefenacht, A., Gerber, M., Pickup, R. 08/2011 In: Journal of Occupational and Environmental Hygiene. 8, 8, p. 478-483. 6 p.
Assessment of MTBE biodegradation in contaminated groundwater using 13C and 14C analysis: field and laboratory microcosm studies
Thornton, S., Bottrell, S., Spence, K., Pickup, R., Spence, M., Mallinson, H., Shah, N., Richnow, H. 05/2011 In: Applied Geochemistry. 26, 5, p. 828-837. 9 p.
Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch.
Benskin, C., Rhodes, G., Pickup, R.W., Wilson, K., Hartley, I.R. 12/2010 In: Molecular Ecology. 19, 24, p. 5531-5544. 14 p.
Engaging with the water sector for public health benefits: waterborne pathogens and diseases in developed countries
Bridge, J.W., Oliver, D.M., Chadwick, D., Godfray, H.C.J., Heathwaite, A.L., Kay, D., Maheswaran, R., McGonigle, D.F., Nichols, G., Pickup, R., Porter, J., Wastling, J., Banwart, S.A. 11/2010 In: Bulletin of the World Health Organization. 88, 11, 3 p.
The effect of bacterial prey species and their concentration on growth of the amoebae Acanthamoeba castellanii and Hartmannella vermiformis.
Pickup, Z.L., Pickup, R., Parry, J.D. 04/2007 In: Applied and Environmental Microbiology. 73, 8, p. 2631-2634. 4 p.
A comparison of the growth and starvation responses of Acanthamoeba castellanii and Hartmannella vermiformis in the presence of suspended and attached Escherichia coli K12
Pickup, Z.L., Pickup, R., Parry, J.D. 2007 In: FEMS Microbiology Ecology. 59, 3, p. 556-563. 8 p.
Growth of Acanthamoeba castellanii and Hartmannella vermiformis on live, heat-killed and DTAF-stained bacterial prey
Pickup, Z.L., Pickup, R., Parry, J.D. 2007 In: FEMS Microbiology Ecology. 61, 2, p. 264-272. 9 p.
Mechanisms for soil resistance.
Pickup, R., Rhodes, G. 28/04/2006 In: Science. 312, 5773, 1 p.
Review of the Predatory Bird Monitoring Scheme (PBMS).
Shore, R.F., Walker, L., Thomas, G.O., Barber, J.L., Martin, F.R., Jones, K.C., Beresford, N.A., Rowland, P., Pickup, R.W. 2006 Unknown Publisher.
The potential harbouring of coliform bacteria by protozoa in biofilms.
English, J., Pickup, R., Parry, J.D. 2001 In: Biofilm community interactions : chance or necessity?. Cardiff : Bioline p. 271-279. 9 p.
Internal Project – FHM RCAD Contract Researcher Audit and Survey
01/09/2016 → …
Pickup external collaboration
01/01/2016 → 30/06/2018