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 Medical Microbiology/Virology 

 By combining clinical medicine and pathology, Medical Microbiology and Virology make for a challenging and rewarding specialty for trainees with an interest in infection.

The diagnosis and management of infection are constantly changing. New molecular methods of testing, combined with genetic sequencing, are changing the way we are able to detect pathogens, track outbreaks and uncover resistance to rapidly respond this shifting landscape. 

The field of Medical Microbiology and Virology is undergoing major changes with the ongoing developments in next generation sequencing.and reconfiguration of laboratory services. We are working more closely with our Infectious Diseases Physicians to provide the new Training in Infection curriculum. This means that the role of the microbiologist is rapidly changing and adapting to this new working environment with automation and rapid molecular testing. We continue to use traditional methods where molecular methods have not been developed. This is an exciting time to be training in these infection specialities.

We offer training in Medical Microbiology and Virology and work very closely with our Infectious Diseases colleagues to provide joint training in Microbiology or Virology and Infectious Diseases . In addition we have strong academic links with the universities in Cambridge and Norwich and offer academic training in our specialties.

Important information for trainees about The Royal College of Pathologists and the organisation of training can be found on the College website.

The East of England has two training programmes based on the two main teaching hospitals, Cambridge University Hospitals NHS Foundation Trust and Norfolk & Norwich University Hospitals Foundation Trust (NNUH).

Training in Medical Microbiology

Trainees in medical microbiology will have moved through Core Medical Training (CMT) or the Acute Care Common Stem (ACCS) into a 2 year Combined Infection Training rotation (CIT). After this phase trainee will enter Higher Specialist Training (HST) in either single speciality Medical Microbiology or dual training with Infectious Diseases.


The Cambridge Programme

The Clinical Microbiology and Public Health Laboratory (CMPHL) is located in purpose-built accommodation, including a Containment Level 3 laboratory in the of the John Bonnett Clinical Pathology Laboratories, located within Addenbrooke's Hospital. All Specialty trainees have their laboratory and office accommodation located within the Department.

The laboratory provides microbiology laboratory services for hospitals in the Cambridge Health District and for general practitioners in local PCGs and also supplies microbiological services for environmental health services. The laboratory performs variety of specialised tests (mainly in serology and virology) for other laboratories in the region.

CMPHL provides substantial services to the liver and heart transplant programmes administered by Addenbrooke's and Papworth Trusts. Regional specialties in Cambridge (including Neurosurgery and Neurology, Oncology, Haematological Medicine and Renal Transplantation and Dialysis) also make substantial use of the Department. Extensive clinical liaison to provide advice on the diagnosis and chemotherapy of microbial disease, and on control of infection is undertaken with regional and other clinical services. The infection control team collaborate closely with staff of the laboratory as do the Consultants in Communicable Disease Control for Cambridge and Huntingdon.

The Department provides epidemiological and clinical microbiology services within the local district and liases with clinical pharmacy, CSSD Services and environmental health service.

Departmental workload

The total laboratory workload is approximately 3 million specimens each year. Approximately one third of these specimens originate from General Practice and most of the rest from Addenbrooke's Hospital. 

Liaison with Major Clinical Units

There is a rotation of duties so that at any one time, two registrars are training by apprenticeship on clinical duties. These duties include liaison with specialty units on a daily basis. Currently these are; the adult, paediatric and neonatal ITU, neurosurgical ITU, renal transplant units and the haemato-oncology unit. A consultant medical microbiologist will closely supervise these duties.

Direct Clinical Responsibilities

A large amount of the clinical work undertaken by consultant and trainee Medical Microbiologists is in liaison with the hospital's specialty units and the admitting medical and surgical teams

Laboratory SOPs

The department has a comprehensive collection of Standard Operating Procedures for the laboratory organisation, and every laboratory procedure undertaken within Medical Microbiology. There is a separate SOP providing guidance on laboratory activities including authorisation of reports by medical staff.

Health and Safety

The Department of Microbiology has a Hazard Group 3 containment laboratory, and on-suite discard laboratory autoclaves.

It is mandatory for trainees to participate in Health and Safety training. This will start at induction but will also include specific H&S training sessions and tutorials with senior laboratory staff.

All trainees are required to comply with Trust and departmental Health and Safety policies and procedures.

Education and Training Programme

The Educational supervisor will assist the trainee in developing a personal training programme and annual training plan.


It is mandatory for trainees to attend the Trust and departmental induction courses. The trainee will be provided with the Trust and departmental induction packs. The educational supervisor (or deputy) will arrange the induction to commence immediately the trainee joins the department. The departmental safety supervisor will provide the majority of the Health and Safety induction and maintain the record of this.

Trainees' accommodation and equipment

The Specialty Registrar will be provided with office space, sole use of a desk; filing cabinet and shelf space.

The trainees will be provided with appropriate bench space and facilities to undertake approved laboratory projects and training. Appropriate secretarial support will be provided.

Training Agreement

An annual training agreement will be drawn up by the trainee for discussion and approval by the educational supervisor. This training agreement is an important part of the documentation for appraisals.


Individual appraisal for Specialty Registrars is provided to provide broader professional development of the trainee. These will be held in "protected time" at least every three months.

The appraisal will inform the educational supervisor's report for the annual ARCP.

Timetable of Educational Events

The Specialty Registrar will be encouraged to attend relevant courses of post-graduate training. Particular consideration will be given to attending the two year day-release MSc course in Clinical Microbiology held at the London Hospital. Attachments to units at the Central Public Health Laboratory, the Communicable Disease Surveillance Centre, London and the local Departments of Infectious Diseases and Genitourinary Medicine should also be considered.

There are weekly tutorials in term time with one of the Consultant staff. Please see timetable.

Trainees have free access to the departmental library with a comprehensive inventory of current texts and journals and access to the world wide web via the NHS net. The Addenbrooke's Postgraduate Medical Centre and Library is situated on-site at Addenbrooke's Hospital.

Study leave will be granted in accordance with paragraphs 250-254 of the Terms and Conditions of Service for Hospital Medical and Dental Staff.

Principal Service Responsibilities

The proportion of time spent on training by apprenticeship on clinical duties, including infection control,60-80%, in accord with the recommendation of the RCPath. Clinical Service Routine

The Registrar will participate in the work of the department in clinical liaison, laboratory and infection control, under supervision of the consultants. This includes authorization of laboratory reports, dealing with telephone enquiries from clinicians and participating in ward rounds.

He/she will liaise closely with clinical colleagues concerning the diagnosis and management of patients, and infection control.

Where appropriate, benchwork experience in all sections of the laboratory will be provided.

Norwich/Colchester Programme

The Norwich/Colchester Training Programme is based in the Microbiology Department at the Norfolk & Norwich University Hospital. Trainees rotate between Norwich and Colchester on a regular basis usually after years two and four (modified according to the individual trainee's needs and previous experience). There will usually be a trainee at each training site. The rotation between Norwich and Colchester offers specialist training opportunities in areas such as food and water and environmental microbiology, virology, molecular biology, medical mycology, health protection (epidemiology and outbreak investigation), management of infections in the immunocompromised patient and infection control. Trainees in their first year of training are expected to attend the MSc course at the London Hospital. In cases where the Specialty Registrar is not be able to join the MSc course during year one, both sites (Norwich and Colchester) are able to support training needs to gain competencies set out in the curriculum in order to sit MRCPath part 1. Under such circumstances, the trainee at Colchester is expected to spend some time at the Norwich site prior to the MRCPath part 1 exam to gain specific experience in "specialist" elements of the training such as: nucleic acid-based diagnostic techniques, microbiology/infections in the immunocompromised patient (including HIV, transplantation and neutropenia), Virology (one-month training pre part 1) and food and water microbiology.

The trainees will have regular, joint educational meetings at Norwich /Colchester. In order to help networking with other Specialty Registrars and to exchange experience and maximise training opportunities, the trainees will be encouraged to undertaking the MSc at the London Hospital and to attend joint tutorials at the Microbiology Department in Cambridge.

Research opportunities

Trainees need to develop R&D skills through participation in on-going research projects. It is expected that trainees will develop a well-defined research project, or a series of case reports in collaboration with other clinical teams. The research findings should be submitted for publication in the scientific literature. Presentations of research and case reports are encouraged. The department has particular research opportunities in the regional mycobacterium reference laboratory.

Trainees are encouraged to study for a higher degree, such as MD or to apply for research fellowships. This is usually undertaken as "Out of Programme Experience" and requires organisation with the educational supervisor and the Deanery.

Trainees are expected to contribute to journal and research meetings, and to attend relevant scientific meetings. Specific guidance should be sought from the educational supervisor.

The trainee should open discussions on career options with the Supervisor from an early stage in training. This should include the possibility of spending a period in full-time research (for example, MRC or Wellcome studentships) leading to an MD or PhD and a career in academic microbiology.

Management Training

Experience should be gained, under supervision, in planning departmental policies and developing leadership qualities to implement them. Tutorials will be provided by senior laboratory staff on specific topics. Attendance at appropriate management meetings and training courses is encouraged. The trainee should consider undertaking locum consultant duties in the later stages of training.

Senior trainees are expected to participate in the laboratory management meetings and in administration of the department such as organisation of on-call rotas.

The Specialty trainee will participate, on a rotational basis, in the following administrative duties: chair of the Specialty Registrars' committee, secretary to the CMPHL District Management Committee, membership of the laboratory technical committee, organising the intra-Departmental lecture series, organising the Medical Trainees clinical daytime duty, and on-call rota and bench attachment rota.

Contact for further details

Jumoke Sule ( Training Committee Chairman & Training Programme Director
Dr Celia Duff Associate Postgraduate Dean

Monday, 30 September, 2019
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Monday, 30 September, 2019