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MRC DiMeN Doctoral Training Partnership: How does the human innate immune system kill the Streptococcus pneumoniae bacterium during infection?

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  • Full or part time
    Dr A Fenton
    Dr L Prince
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The bacterium Streptococcus pneumoniae is a highly successful human pathogen and a leading cause of pneumonia, a disease responsible for millions of deaths every year. During these infections, the innate immune system has an important role clearing S.pneumoniae from the lung, restoring the usually sterile environments of the lower airways. However, bacterial clearance does not always work efficiently and the mechanisms by which S.pneumoniae resist this innate immune challenge are unclear.
Prolonged respiratory infections caused by S.pneumoniae trigger a rapid influx of neutrophils into the lung. Neutrophils phagocytose (eat) invading bacterial cells and subsequently kill them via antimicrobial peptides, oxidative molecules and destructive proteases. Efficient resolution of this host-pathogen interaction is important to prevent secondary bacterial infections and avoid lung injury through prolonged inflammation.

This project seeks to understand how S.pneumoniae cells resist clearance by the innate immune system during infection. Given the importance of S.pneumoniae–neutrophil interactions, this study will focus on the biological mechanisms deployed by the bacterial cells to resist neutrophil clearance.

Novelty and Timeliness
Set against the backdrop of increasing antimicrobial resistance in clinical S.pneumoniae isolates, there is an urgent need to seek out alternative treatment approaches, which includes ways of supporting immune function. This work will offer an objective measure of the contribution made by each gene to S.pneumoniae survival within phagosomes, building on the expertise of two labs to deliver the first use of S.pneumoniae Tn-seq applied to innate immune tissues. This work will be world leading and highly complementary to, but not overlapping with, mouse infection studies and RNA-seq datasets, all aimed at understanding S.pneumoniae survival in ‘host-like’ environments. Together these datasets are moving towards generating new therapeutic interventions that support the patients immune system over inhibiting essential processes within the bacterium.

Experimental Approach
To characterise S.pneumoniae-neutrophil survival strategies from the bacterial perspective, we will use whole genome fitness profiling (Tn-seq) to identify mechanisms of bacterial tolerance to phagocytosis. To achieve this, we will expose S.pneumoniae Tn-seq libraries to neutrophils, profiling bacterial killing over time.
S.pneumoniae cells are highly sensitive to acid-induced cell lysis when phagocytosed. To study this, we will apply our S.pneumoniae Tn-seq profiling to conditions where phagosome acidification is inhibited, identifying genes specifically required for bacterial tolerance to this stress. In a candidate-driven approach, linked to phagosome acidification, we will investigate the role S.pneumoniae ‘autolytic’ processes have on neutrophil survival.
The proposed experimental approach combines the primary supervisors’ experience with S.pneumoniae cell biology, genetics and analytical approaches to next-generation sequencing analysis (Tn-seq) with specialist clinical knowledge in the extraction and research of human neutrophil cell function from the second supervisor. This forms a truly interdisciplinary approach not possible without collaboration between groups. We are confident this project will offer the student an interesting and unique research approach, bridging two labs in a combined effort to understand this important host-pathogen interaction.

You can find the primary supervisor on twitter @AndrewKFenton,
email: [Email Address Removed] and website: Information on the secondary supervisor can be found on her website here:

Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:
Further information on the programme can be found on our website:

Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
Studentships commence: 1st October 2020.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here:

Good luck!


2016 - Fenton AK, El Mortaji L, Lau DTC, Rudner DZ, Bernhardt TG. CozE is a member of the MreCD complex that directs cell elongation in Streptococcus pneumoniae. Nature Microbiology. PMID: 27941863

2018 - Fenton AK, Manuse S, Flores-Kim J, Garcia PS, Mercy C, Grangeasse C, Bernhardt TG, Rudner, DZ. Phosphorylation-dependent activation of the cell wall synthase PBP2a in Streptococcus pneumoniae by MacP. PNAS. PMID: 29487215

2019 - Flores-Kim J, Dobihal GS, Fenton A, Rudner DZ, Bernhardt TG. A switch in surface polymer biogenesis triggers growth-phase-dependent and antibiotic-induced bacteriolysis. Elife. PMID: 30964003

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