Worms on a Chip: Automated C. elegans Biosensing for Rapid Antimicrobial Resistance Diagnostics

detection, and recent work shows that extended-spectrum β-lactamase (SBL) and metallo-β-lactamase (MBL) producing Pseudomonas aeruginosa alters C. elegans survival, chemotaxis and stress/immune gene expression relative to susceptible reference strains. Working closely with D-Tails’ scientists, the student will exploit these phenotypes in a disposable microfluidic assay imaged on the company’s proprietary iFLUOR platform, combining automated image analysis with machine-learning classification to assign resistance status. Diagnostic performance will be benchmarked against culture-based antimicrobial susceptibility testing across mechanistically distinct resistant/susceptible pairs, establishing a validated, commercially translatable route to AMR testing in hours rather than days.

Approaches and methods

The project is structured around three objectives that take the student from biological discovery to a validated proof-of-concept diagnostic device.

1. Phenotypic benchmarking. During a research visit to D-Tails’ laboratories in Italy, the student will learn the company’s established C. elegans infection and phenotyping protocols. They will then identify which short-format readouts (chemotaxis, survival) and which targeted stress/immune gene-expression panel best discriminate resistant from susceptible bacteria.

2. Microfluidic assay and machine-learning classification. At UCL, the student will design and fabricate a disposable microfluidic device that houses worms and exposes them to bacterial samples under controlled conditions, compatible with the iFLUOR imaging platform. They will build an automated image-analysis pipeline and train machine-learning classifiers that convert worm behaviour into a resistant/susceptible call.

3. Diagnostic validation. The platform will be benchmarked against culture-based AST in terms of sensitivity, specificity and time-to-result, using mechanistically distinct pairs and testing whether the strategy generalises across resistance mechanisms.

Impact and outlook

Rapid determination of resistance status would allow clinicians to move from empirical to targeted prescribing within the same day, directly supporting antimicrobial stewardship. Because the assay relies on a living sensor, low-cost disposable chips and automated readout rather than complex molecular workflows, it offers a route to affordable point-of-care testing.

Beyond this application, the project will establish whether whole-organism behavioural phenotyping can generalise across pathogens and resistance mechanisms, opening a new class of AMR diagnostics. Working in collaboration with a biotech company, the student will gain direct experience of how academic research is translated into a commercial diagnostic technology, enabling them to bridge engineering, data science and infection biology and preparing them to become a future leader in AMR research and innovation, in academia or industry

Training and student development

The student will receive interdisciplinary training spanning engineering, data science and biology, in both academic and industrial settings. They will gain hands-on expertise in C. elegans culture, behavioural phenotyping and operation of the iFLUOR platform within a commercial R&D environment. They will be trained also in microfluidic design and fabrication (soft/photolithography, 3D printing), Class 2 microbiology, quantitative imaging, and image analysis and machine learning. Funded attendance at national and international conferences will allow the student to present their work, develop communication skills and build an international network of academic and industrial scientists.

Research environment

PhD students in the Dr Bolognesi’s group and Prof Nguyen TK Thanh’s group labs benefit from a vibrant, interdisciplinary and supportive environment, with regular one-to-one supervision and group meetings. Students receive tailored support in scientific publishing, funded attendance and presentation at international conferences, and career planning towards both academic and industrial routes. Both supervisors serve on Royal Society of Chemistry and Institute of Physics special interest group committees and on the scientific boards of leading international journals and conferences, giving the student exceptional opportunities to build professional networks. This project extends an ongoing collaboration between UCL and D-Tails through the Ulysses EIC Pathfinder project. State-of-the-art facilities at UCL and D-Tails, including microfabrication, Class 2 containment laboratories and the iFLUOR platform, will support all stages of the project.

Desirable prior experience

Essential

• Strong interest in interdisciplinary research at the interface of engineering, data science and biology, and in translational AMR diagnostics
• Enthusiastic about oversea-research visits and conferences.

Desirable

• Background in chemical, biomedical or mechanical engineering, physics, chemistry, biology, microbiology, or related disciplines
• Experience with microfluidics, microfabrication or diagnostic assay development
• Experience in microbiology, cell culture or work with model organisms
• Programming skills (e.g. Python or MATLAB) for image analysis, data analysis or machine learning

Eligibility

UK Master’s degree with Merit or a minimum upper second-class UK Bachelor’s degree in a relevant discipline, or an overseas qualification of an equivalent standard. Relevant work experience may be considered.

Relevant disciplines include engineering, physics, chemistry, biology, biomedical sciences, computer science, mathematics, and related subjects.

How to apply

Interested candidates are encouraged to contact the primary supervisor (Guido Bolognesi email: g.bolognesi@ucl.ac.uk) with a CV, a degree transcript and a motivation letter expressing interest in the project.

References

• Lanza, E., Di Rocco, M., Schwartz, S., Caprini, D., Milanetti, E., Ferrarese, G., Lonardo, M.T., Pannone, L., Ruocco, G., Martinelli, S. and Folli, V., 2021. C. elegans-based chemosensation strategy for the early detection of cancer metabolites in urine samples. Scientific Reports, 11, 17133.
• Nandan, J., Janani, N., Heamchandsaravanan, A.R., Rajaram, H.A., Sharchil, C., Charles, S., Ramachandran, V., Vinu, R., Perumal, D., Damodharan, P. and Balakrishnan, A., 2025. Impact of ESBL and MBL-producing Pseudomonas aeruginosa on Caenorhabditis elegans: assessing survival, reproductive fitness, chemotaxis behaviour, and gene expression. Journal of microbiology, epidemiology and immunobiology, 102(6), pp.675-682.
• Chakra, A., Puijk, C., Vladisavljević, G.T., Cottin-Bizonne, C., Pirat, C. and Bolognesi, G., 2025. Surface chemistry-based continuous separation of colloidal particles via diffusiophoresis and diffusioosmosis. Journal of Colloid and Interface Science, 693, p.137577.
• Rossi, F., Huat, K. E., Thanh, N. T. K* and Su X. D. (2019) Study of the Effect of Anisotropic Gold Nanoparticles on Plasmonic Coupling with a Photosensitizer for Antimicrobial Film. ACS Applied Bio Materials. 3: 315-326.