Dr John E. Pearl

Supervisor Details

Contact Details

Department of Respiratory Sciences, University of Leicester

Scientific Background

Research Interests

Our research group investigates the high rates of clinical treatment failure in pulmonary disease caused by non-tuberculous mycobacteria [NTM], commonly acquired through exposure to contaminated water in showerheads or in agricultural settings. In the UK, up to 34% of patients who have completed at least one year of multi-drug antibacterial treatment suffer from recurrence of disease. This recurrence is associated with the return of genotypically identical bacteria in the sputum and shows that the current standard of care cannot eradicate all NTM.

We are interested in how some bacteria are inherently resistant to front-line antimycobacterial drugs and hypothesize that their capacity to persist for years within the host is related to their unique energy metabolism. We are actively investigating the basis for this resistance to drugs and how non-permissive environments can drive the evolution of resistant, persistent and long-lived phenotypes in patients.

Scientific Inspiration

My scientific inspiration is Prof Rui Appelberg, University of Porto, Pt (d, 1960- 2020). Rui was my PhD supervisor who embodied what would become my aspirational model for student training. He was warm and personable, calm and reflective, and approached each student as a whole person equipped with their own unique set of experiences and goals. He was exceptionally supportive of his students and this support forms the aspirational cornerstone of my own approach to student training and scholarship.

Most importantly, Rui demonstrated how to inspire and how to lead. He was collaborative and willing to listen. He was open to challenging dogma because he understood the literature and was uniquely able to help the student see how their ideas fit into the larger scientific context. He was uniformly positive and always urged a thoughtful approach – often over dinner, in the lab or by email. Working with Rui was a transformative experience that I hope to share with students. He taught that science fun, that it was social and that the relationships built should last for decades.

Research Groups

NTM Network UK

AntiMicrobial Resistance in Agrifood Systems (AMAST) Network

Supervision Style

In three words or phrases:

1. Fun, low-stress, responsive.

2. Inclusive – high diversity leads to a broader approach to the science.

3. No backseat driving – you’ll become the trusted expert.

Provision of Training

Your training will be based on ‘see it, do it, demonstrate it.’ We’ll work together to develop basic and advanced lab skills and then jointly organize these into your independently performed workflows.

Progression Monitoring and Management

You will have required milestones and benchmarks associated with the program that you will need to track independently. We will plan your research to ensure it is feasible and achievable within the context of your program milestones and so that it helps you achieve your career goals.

Communication

Since we value teamwork, I am readily available through email, video chat, SMS and other means of communications as needed. You will always get a response to a question or request.

Meetings

PhD Students can expect scheduled meetings with me at least once per week. These meetings will be face-to-face. I am usually contactable for an instant response on every working day.

Work Patterns

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings) I expect students to manage their own time.

Notice Period for Feedback

I need at least 1 week's notice to provide feedback on written work of up to 5,000 words.

MIBTP Project Details

Primary supervisor for:

Non-tuberculous mycobacteria in agrifood and the environment at the human-animal-ecosystems interface: resistance, persistence and longevity

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Non-tuberculous mycobacteria in agrifood and the environment at the human-animal-ecosystems interface: resistance, persistence and longevity

Secondary Supervisor(s): Dr Marie Kirby, Dr Katharina Watson, Professor Ruben Sakrabani, Dr William Rickard, Dr Rodrigo Taketani, Dr Ian Clark

University of Registration: University of Leicester

BBSRC Research Themes:

Sustainable Agriculture and Food (Animal Health and Welfare, Microbial Food Safety, Plant and Crop Science)

Project Outline

Environmentally resident mycobacteria are important animal pathogens known to infect cattle, pigs, fowl, sheep and most other commercially valuable livestock. These mycobacteria also cause infection and disease in wildlife including birds, deer and other animals found near agricultural activities, the consequence of which is an increased risk of animal-ecosystem cross exposure, infection and establishment of disease-endemic locations. As animal pathogens, the genus Mycobacterium encompasses a range of species that cause distinct disease depending on the infected animal: gastrointestinal Johne's Disease in cattle, avian tuberculosis in chicken and pulmonary bovine tuberculosis in farmed pigs, wild boar, deer and other animals. In each of these species, there is a proven link between animal manure-contaminated soil and water with infection leading to subsequent disease. Since stored manure is often used to amend soils or as feedstock for anaerobic digestion, the risk of pathogenic amplification through these and other agricultural activities is unknown. This knowledge gap is important because these organisms exist at the intersection of animal-ecosystem-human activities, where the potential for cross-species agricultural and wild animal transmission is significant. Because of this, environmental mycobacteria constitute an emerging risk to agribusiness and to environmental security.

Based on work in my research group, we have developed a new insight into the metabolic and bioenergetic capacity of environmental mycobacteria from which we hypothesize that specific environmental conditions can lead to the development of bacterial phenotypes which may strengthen their association with soil, plants and crops leading to increased risk of infection for farmed and wild animals. We seek to test this hypothesis using a range of animal-origin materials with laboratory and field investigations, in collaboration with a transdisciplinary team of world-leading experts.