Senior Microbiologist - Pathogen

Led by a world-class faculty of scientists, technologists, policy makers, economists and entrepreneurs, the Ellison Institute of Technology aims to develop and deploy commercially sustainable solutions to solve some of humanity’s most enduring challenges. Our work is guided by four Humane Endeavours: Health, Medical Science & Generative Biology, Food Security & Sustainable Agriculture, Climate Change & Managing Atmospheric CO2 and Artificial Intelligence & Robotics.

Set for completion in 2027, the EIT Campus in Littlemore will include more than 300,000 sq ft of research laboratories, educational and gathering spaces. Fuelled by growing ambition and the strength of Oxford’s science ecosystem, EIT is now expanding its footprint to a 2 million sq ft Campus across the western part of The Oxford Science Park. Designed by Foster + Partners led by Lord Norman Foster, this will become a transformative workplace for up to 7,000 people, with autonomous laboratories, purpose-built laboratories including a plant sciences building and dynamic spaces to spark interdisciplinary collaboration.

The Pathogen Mission highlights EIT’s transformative approach, using Whole Genome Sequencing (WGS) and Oracle’s cloud technology to create a global pathogen metagenomics system. This initiative aims to improve diagnostics, provide early epidemic warnings, and guide treatments by profiling antimicrobial resistance. The goal is to deliver certified diagnostic tools for widespread use in labs, hospitals, and public health.

EIT Oxford fosters a culture of collaboration, innovation, and resilience, valuing diverse expertise to drive sustainable solutions to humanity’s enduring challenges.

EIT is seeking a forward-thinking Senior Microbiologist to establish and lead pathogen phenotyping capabilities within its Pathogen Program. This is a primarily lab-based role, focused on building capacity for antimicrobial susceptibility testing (AST) of bacterial isolates, with future expansion into phenotyping of fungal and viral systems.

Working at the intersection of microbiology, automation, and global health innovation, the successful candidate will design and implement CLSI- and EUCAST-compliant assays, develop novel bacterial phenotyping methods, and collaborate with engineering and informatics teams to enable automated and data-integrated testing pipelines.

You will also play a key role in developing and standardising deployable workflows for use in EIT’s partner laboratories worldwide, contributing to a global network for pathogen surveillance and resistance monitoring.

Key Responsibilities:

Assay Design and Validation

• Design and implement AST protocols for bacterial pathogens that are compliant with EUCAST and CLSI standards.
• Develop and validate new or enhanced bacterial assays that increase the depth and quality of phenotypic data derived from each sample.
• Design phenotyping assays for fungal and viral pathogens as the program expands.
• Evaluate and recommend appropriate instrumentation platforms (e.g., Thermo Fisher Sensititre, BD Phoenix, bioMérieux VITEK, or equivalent systems).
• Establish and optimise MALDI-TOF MS workflows for pathogen identification and resistance mechanism profiling.
• Drive innovation in assay methodology, identifying opportunities to improve throughput, precision, or data richness.

Laboratory Operations

• Lead the build, commissioning, and operational readiness of a high-throughput reference testing facility, capable of processing 10,000+ isolates per year.
• Oversee day-to-day operations, ensuring high-quality, compliant, and safe laboratory practices.
• Supervise, train, and mentor a small team (1–2 scientists) to ensure consistent and reproducible assay performance.
• Participate in data generation and sample processing, contributing directly to the laboratory’s annual throughput.

Automation and Workflow Integration

• Collaborate closely with the Pathogen Automation Team to implement robotic and semi-automated workflows for sample processing, AST setup, plate reading, and data capture.
• Contribute to the development of integrated laboratory information management systems (LIMS) to streamline data collection, analysis, and reporting.
• Pilot and evaluate emerging technologies in automated liquid handling, optical detection, and AI-assisted interpretation of phenotypic data.

Global Standardisation and Collaboration

• Develop standardised and deployable SOPs and training materials to be shared with partner labs globally.
• Provide expert input into collaborative projects linking phenotypic, genomic, and clinical datasets for antimicrobial resistance research.
• Engage with external partners, regulatory agencies, and technology vendors to maintain alignment with global standards and innovation trends.

Essential Knowledge, Skills and Experience:

• MSc or PhD in Microbiology, Infectious Disease Biology, or a closely related field.
• Substantial experience in antimicrobial susceptibility testing (AST) and MIC determination following EUCAST or CLSI standards, ideally in an accredited clinical or industrial environment.
• Hands-on experience with phenotyping instruments such as Thermo Fisher Sensititre, BD Phoenix, bioMérieux VITEK, or comparable systems.
• Experience with MALDI-TOF MS for microbial identification.
• Demonstrated ability to establish, optimise, and troubleshoot complex microbiological workflows, including biosafety, QC, and data integrity.
• Experience in training and supervising scientists within a microbiology or clinical laboratory setting.
• Strong curiosity and ability to develop and implement novel approaches and creative scientific solutions.

Desirable Knowledge, Skills and Experience:

• HCPC registration, IBMS Specialist Diploma, or equivalent clinical microbiology accreditation.
• Experience in establishing or scaling laboratory operations.
• Knowledge of fungal and viral culture systems and associated phenotyping methods.
• Familiarity with Containment Level 2 and 3 (CL2/CL3) laboratory practices.
• Experience in technology transfer or deployment of laboratory workflows across multiple sites.
• Understanding of AI-assisted AST interpretation or data-driven microbiology pipelines.

Key Attributes:

• Innovative and solutions-oriented mindset.
• Strong leadership and mentoring capabilities.
• Excellent communication and collaboration skills.
• Commitment to global health impact and scientific excellence.

We offer the following benefits:

• Enhanced holiday pay
• Pension
• Life Assurance
• Income Protection
• Private Medical Insurance
• Hospital Cash Plan
• Therapy Services
• Perk Box
• Electrical Car Scheme

Why work for EIT:

At the Ellison Institute, we believe a collaborative, inclusive team is key to our success. We are building a supportive environment where creative risks are encouraged, and everyone feels heard. Valuing emotional intelligence, empathy, respect, and resilience, we encourage people to be curious and to have a shared commitment to excellence. Join us and make an impact!

Terms of Appointment:

• You must have the right to work permanently in the UK with a willingness to travel as necessary.
• You will live in, or within easy commuting distance of, Oxford.
• During peak periods, some longer hours may be required and some working across multiple time zones due to the global nature of the programme.