This PhD opportunity is being offered as part of the LSTM and Lancaster University Doctoral Training Partnership. Find out more about the studentships and how to apply.
| Abstract | Non-tuberculous mycobacteria (NTM), including Mycobacterium abscessus and M. avium, are emerging pathogens causing significant morbidity, particularly in immunocompromised individuals such as those living with HIV or structural lung disease. While related to M. tuberculosis, the causative agent of TB, anti-TB drug regimens and vaccines do not work in NTM. Therapeutic regimens include multiple toxic, poorly effective antibiotics that must be taken for at least 12 months. Even if treatment is adhered to, ~50% of patients will fail to achieve a clinical cure. Progress in understanding their biology and pathogenesis is hindered by a lack of versatile and accessible molecular tools, particularly for M. avium. This project aims to develop a comprehensive molecular toolkit for NTM to enable functional genomics and high-resolution studies of gene function. Key components will include targeted genetic knockouts, CRISPR-based systems for tunable gene expression using inducible promoters, and fluorescent or luminescent reporter strains to facilitate visualisation and quantification in infection models. A key focus will be optimizing these tools for NTM, where molecular manipulation remains challenging, and ensuring protocols are robust and transferable for use in resource-limited settings. By generating accessible, high-utility molecular tools, this project will accelerate mechanistic studies of NTM biology, virulence, and antimicrobial resistance, and provide a platform for both fundamental research and translational applications in diverse laboratory settings. |
| Where does this project lie in the translational pathway? | T1 - Basic Research |
| Methodological Aspects | This project will develop and apply a suite of molecular tools for Mycobacterium abscessus and M. avium to enable functional genomics and quantitative analyses of gene function. Key methodologies include: Targeted Genetic Knockouts: Using homologous recombination and other mutagenesis strategies to disrupt specific genes, enabling assessment of their role in virulence, antimicrobial resistance, and physiology. Quantitative readouts of growth, survival, and phenotypic changes will be recorded. CRISPR-Based Tunable Expression: Inducible CRISPR systems will be used to modulate gene expression, allowing precise, quantitative assessment of gene dosage effects on bacterial phenotype. Gene expression levels will be measured using qPCR, reporter assays, or transcriptomic profiling. Fluorescent and Luminescent Reporter Strains: Construction of reporter strains will enable real-time monitoring of bacterial growth, survival, and host-pathogen interactions. Fluorescence and luminescence will provide quantitative, high-throughput data for infection assays and functional studies. Optimisation for Resource-Limited Settings: Protocols will be simplified and validated for reproducibility, ensuring these tools are accessible for laboratories in Malawi and similar settings. Together, these methodologies integrate molecular biology, quantitative analysis, and whole-organism experimentation to provide a versatile toolkit for NTM research. |
| Expected Outputs | Publications: At least two first-author peer-reviewed manuscripts in high-impact journals, covering (i) development and validation of genetic knockout and CRISPR-based expression systems for M. abscessus and M. avium, (ii) application of fluorescent and luminescent reporter strains in functional and infection studies, and (iii) demonstration of toolkit accessibility and utility in resource-limited settings. Funding and Grants: The toolkit and preliminary data will provide a foundation for future funding applications, including grants aimed at antimicrobial resistance, NTM pathogenesis, and capacity building in low-resource settings. There is potential for commercialisation of some of the tools that will be developed and so there could also be IP generated. Impact: This project will overcome key methodological bottlenecks in NTM research, enabling mechanistic studies of virulence, antimicrobial resistance, and host-pathogen interactions. The generation of accessible molecular tools will support research in diverse laboratories, including resource-limited environments, enhancing global research capacity. Additionally, the student will acquire interdisciplinary expertise in molecular biology, synthetic biology, functional genomics, and quantitative analysis, preparing them for academic or industry careers in infectious disease research. |
| Training Opportunities | Building on previous MRC DTP students’ experience, there will be a residential bioinformatics training course for one week offered, provided by the University of Birmingham. Full lab training will be provided covering wet lab and molecular biology, supported by both Fabrice and Giancarlo. |
| Skills Required | Student must possess experience of working in a lab in either microbiology or tissue culture. A life sciences degree such as biochemistry, microbiology or genetics would be preferred as would a relevant Masters but I would also be keen to consider students who have industry or research experience in lieu of a Masters. |
| Subject Areas | Lung health & tuberculosis; antimicrobial resistance |
| Key Publications associated with this project |
D Cantillon: Searching for new therapeutic options for the uncommon pathogen Mycobacterium chimaera: an open drug discovery approach: https://pubmed.ncbi.nlm.nih.gov/35544099/ D Cantillon: Characterization of the Mycobacterial MSMEG-3762/63 Efflux Pump in Mycobacterium smegmatis Drug Efflux: https://pubmed.ncbi.nlm.nih.gov/33343518/ D Cantillon: A non-canonical mismatch repair pathway in prokaryotes: https://pubmed.ncbi.nlm.nih.gov/28128207/ F Graf: Exploring photoinactivation of microbial biofilms using laser scanning microscopy and confined 2-photon excitation: https://pubmed.ncbi.nlm.nih.gov/29785840/ T Parish: The molecular biology of recombination in Mycobacteria: https://pubmed.ncbi.nlm.nih.gov/15119825/ |