Senior Microbiologist - Pathogen

Senior Microbiologist - Pathogen

EIT - Ellison Institute of Technology

Oxford, United Kingdom

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.

Requirements

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.