Medical Microbiology and Virology

Medical Microbiology and Virology

The Speciality

The challenge to combat clinical problems of healthcare acquired infection and worldwide pandemics of COVID, HIV, hepatitis and malaria,  to respond to emerging infection problems such as SARS or swine flu and to rationalise antibiotic use in the light of increasing microbial resistance, makes Infectious Diseases an exciting and contemporary specialty.

Although small in comparison to the system based specialties, ID provides the opportunity of having a career ranging from challenging and constantly varied clinical management, to intellectually stimulating frontier research into diseases of worldwide importance.

The Traditional Backgrounds of ID and Microbiology/Virology

Traditionally, infectious diseases was quite distinct from the laboratory based specialties: ID physicians had clinical responsibility for patients with mostly communicable diseases; microbiologists/virologists organised and supervised laboratory diagnostic services for infection, led on infection control services, and gave advice to other clinicians about management of various infections, often by telephone, with limited ward reviews. 

Changing Specialties

This separation of duties is becoming blurred over time. ID physicians deal with fewer communicable diseases, whilst with technological advances,laboratory supervision is slowing moving over to clinical scientists. The work of ID physicians and microbiologists and virologists has more overlap, particularly in areas of healthcare acquired infection, and antimicrobial resistance. 

Combined Infection Training


As a result of this change, and looking to the future, August 2015 saw the combined Royal Colleges introduce a new 2 year “combined infection training”(CIT) programme which all trainees in these infection specialties will undertake in their first 2 years of specialty training, before higher specialty training in later years. IMT/ACCS & MRCP will be essential for entry into this. ID/GIM trainees will see an extension by 6 months to accommodate GIM training during this time. All programmes are for a duration of 5 years overall. West Midlands is no longer appointing to mono-specialty microbiology or virology training programmes. Such training is still available in some regions.


Infection Training in West Midlands

Versions of Training offered

1             ID –GIM                                                              6 posts, plus 3 military

2             Tropical Medicine- GIM (see below)                  Post-CCT diploma

3             ID-Medical Microbiology                                   12-14 posts including 1-2 ACFs

4             ID-Virology:                                                       2 posts including 1 ACF

Typical rotations are shown in the last section



 Tropical medicine (TM) training is no longer a higher specialist training programme pathway. The ID and TM curricular are identical, however the following additional requirements are necessary for qualification, that can be achieved  post-CCT:

·         2 years of training to be at one of 4 UK approved tropical training centres, of which Birmingham Heartlands is one;

·         3mn full time DTM&H course must be completed

·         1yr of prospectively approved clinical training in a resource poor setting

Why Choose West Midlands for Infection Training?

The West Midlands programme, with approximately 24 infection trainees, is big enough to offer a broad, thorough training and friendly competition from a good number of fellow trainees, whilst being small enough to support individuals’ specific training aims.

The ID-Micro/Virology programmes are now well established in the region, and indeed the largest group of infection trainees are now the ID-Medical microbiology arm!  3 ID consultants, including the ID training Programme Director, are ID-micro trained and dually accredited. We are one of only 4 regions to be accredited for Tropical Medicine training in the UK, and we benefit from being the main centre for military infectious diseases medicine, including training of military personnel in infection specialties.

The largest ID unit in the West Midlands, and the major ID training centre, is at Birmingham Heartlands Hospital (BHH), which is part of the University Hospitals Birmingham Trust. The department is long established, vibrant, and expanding -reassuringly so in the current economic climate. There are now 7 ID consultants, and typically 4/5 registrars. All subspecialties are managed or co-managed by the ID consultants. This includes a large in- & out- patient TB service, HIV (900 patients), chronic Hepatitis B&C, bone infection and OPAT services etc.

There are 3 other training centres for ID in the region: trainees in ID-GIM generally spend their first year at either University Hospital of North Staffordshire, or Royal Worcester Hospital, and University Hospital of Coventry & Warwick is also accredited for training. Further years are largely based in BHH.

Microbiology and virology training takes place across region and trainees benefit from experiencing learning and working in a variety of settings. University Hospital Birmingham has one of the largest ITUs in Europe and is a supra-regional transplant centre

Is ID the Job for me?

What can I expect from the Infectious Diseases part of my rotation in West Midlands?

Infectious Diseases is very much a hands-on speciality where patient contact is imperative in helping to make the diagnosis. There is a huge variety in the cases that you will see as a Registrar, making your days highly varied, interesting and occasionally exciting. Given this variety, there are a large number of specific areas on which you will be able to focus for possible future research projects and also areas of interest as you progress through your training. As an Infectious Diseases Registrar, you will spend time on the wards, the consult service and in clinic. You don’t have to have travelled or worked abroad to consider a career in Infectious Diseases. You do, however, have to have an interest organisms as well as people, and develop knowledge of microbiology and how the lab and the processing of samples takes place.


The Infectious Diseases ward can have patients admitted with common infections such as cellulitis and pneumonia, to more unusual cases such as TB (including multi-drug resistant cases), HIV, tropical infections including malaria, leptospirosis, typhoid, and the acute and ongoing daily management of such patients is imperative for enhancing your knowledge of Infectious Diseases.


The Infectious Diseases consult service is an ever expanding service given the increasing numbers of complicated surgeries conducted, together with increasing foreign travel, an ageing population and increasing antibiotic resistance rates. The Infectious Diseases team work closely with Microbiology when managing such patients, which is essential when determining specimen collection, processing and interpretation of results. The range of problems seen by the consult service is vast, ranging from endocarditis, Staphylococcus aureus bacteraemia, bone and joint infection, to name just a few. Your role will involve interaction with various specialities when their patients have an infection issue, providing expertise on the management aiming to aid identification of the source of infection, optimal antibiotic choice and optimal duration of therapy. You will also provide a link to the Outpatient Antimicrobial Therapy (OPAT) nurses with whom you will work closely, ensuring prompt discharge of patients who are well enough to be managed in the community.

As part of the consult service, you will link with GPs in the community, providing travel advice, answers to general infection questions and accepting referrals when appropriate. A good example of an interesting case involved a patient being referred to me, having recently returned from the rainforest of Peru, with cellulitis on her scalp which was not improving following multiple courses of antibiotics. Her GP had reviewed her and thought he saw something moving underneath the skin, and wondered about an infestation. With gentle pressure, I was able to remove this from the patient’s scalp.


Dermatobiahominis (human botfly)

There are also a range of Infectious Diseases clinics, which you will be able to gain experience in throughout your years of training. These consist of general ID, TB, HIV (with ID and GUM Consultants), Hepatitis (with ID and Gastroenterology Consultants), bone infection and OPAT clinics.

Through the daily review of infection patients, understanding their long-term management and following them up in clinic, you will be provided with excellent first-hand Infectious Diseases experience and knowledge which will form the basis of your continued development in this speciality.


What can I expect from “microbiology” in West Midlands?

The workload is varied: in the morning you may be required to lead the laboratory ‘bench round’ during which new potentially significant isolates are shown to you that require your clinical input. You may then go on a ward round of the intensive care unit and then review ward patients with significant positive cultures. Due to time constraints, much clinical interaction in microbiology unfortunately takes place over the telephone. You will liaise with a variety of people during your time in microbiology: hospital based clinicians, general practitioners, the infection control team, the local public health team and reference laboratories to name but a few.

As a consultant, it is vital to have an understanding of the way results of investigations are derived, so that you can act on results that do not fit the clinical picture and communicate effectively with laboratory staff about what further work to do on patient isolates. Although you will not be expected to process specimens as a consultant, it is very important that, as a trainee, you spend time in the microbiology laboratory to gain an understanding of the way the laboratory works. You will do more of this in early part of your training than later on.

You will get involved in the management of outbreaks, perhaps dealing with an increased number of wound infections from the cardiac surgical unit or of diarrhoea and vomiting on an elderly care ward for example. As you get more senior, you may end up leading root cause analysis investigations to determine the cause of a patient’s hospital-acquired infection and make recommendations about how to reduce the risk of that event happening in future. All sorts of people will seek your advice about things that you have never had to deal with previously in your medical career: “are silver-impregnated urinary catheters better than non-silver impregnated ones?”, and “someone’s baby was given the wrong breast milk from the breast milk bank, what should we do?” are examples from the author’s recent experiences. You will become adept at searching literature and make pragmatic decisions based on your increasing knowledge and experience. You may get the opportunity to evaluate new diagnostic tests and laboratory equipment – perhaps presenting your findings regionally, nationally or internationally. Quality assurance and audit is an important part of being a microbiologist, as with all medical specialities.



1 This was submitted by a GP. It was found crawling in a patient's bed. What is it? (Answer below!). Photo: Hugh Morton, City Hospital, Birmingham

What personal qualities are desirable for the microbiology part of my job?

You must be able to interact effectively with everyone from hospital cleaners, junior medical staff and laboratory technical staff to senior surgeons, GPs and hospital management. Infection Prevention and Control is as much about understanding human behaviour and hospital politics as it is about the science of decontamination and organism biology. You will need persistence and patience if you want to bring about cultural change, perhaps in a unit that overuses antibiotics for example.

You should have an eye for detail and avoid jumping to conclusions; however obvious things may be at first glance, infectious diseases and patients do not read text books! Clarity of thought and expression are essential.

What else should I know about the training?

ID-microbiology has an extra examination (FRCPath) within it. Research during training is the norm, though this varies with training region to an extent. Diplomacy is an essential skill, because of the multiple interactions with other teams. The specialty is competitive, especially ID-GIM.  You need to be prepared to move region to get a training post (so too for consultant posts).

On call

All rotas across region are EWTD compliant.

On call rotas and corresponding pay supplements vary across the training years depending on the training programme (ID-GIM or ID-MM/MV). ID-GIM programmes have on call throughout. ID-MM/MV programmes may have up to 1 year without on call but this is variable. MM/MV rotas are normally an overnight on-call rota for phone advice, with weekend daytimes on-site


All infection trainees may undertake general acute medicine on call. Separate ID on-call is also done at Heartlands hospital (early evening and weekend daytime only), with a commensurate reduction in the GIM on-call frequency. We value some ongoing training in acute general medicine for all ID-micro trainees, particularly in the first year, given that most ID units do not have separate out of hours on-takes for emergencies, and also recognising the need for a good working knowledge of acute admissions units for all infection specialists.


What does a long term Career in ID Offer?
Huge variety! Thereis virtually no private medicine. Traditionally, many consultants’ posts have a strong academic component. The recent trend is for more full time clinical posts.ID-GIM trained consultants have also been sought after for jobs with a significant component of acute medicine. This variety of opportunities means there is very little concern about lack of consultant posts for infection specialists at the end of training.

How do I make myself competitive for training posts?

Commitment to the specialties needs to be demonstrated, particularly for ID-GIM,  for example by tropical electives, a self funded DTM&H, etc.


How can my Career be Further Developed?
Out of Programme Experience or Research is strongly encouraged and well supported for our trainees by the Deanery, and all recent trainees have spent or are embarking on extended periods of time in research or further studies, mostly in overseas, including resource-poor settings

Examples of OOP placements 2012-15:

  • Sierra Leone Ebola Treatment centres 
  • MRC funded studies in Guinea Bissau on trachoma
  • Wellcome Trust units in SE Asia studying severe malaria, and melioidosis as a model of sepsis
  • Wellcome Trust funded study of Cryptococcosis& immune reconstitution in HIV in South Africa 
  • Assessment of training needs for HIV care in Henan Province China
  • Epidemiology of Tuberculosis, Warwick
  • Rotavirus studies, Vaccine research group, Oxford

Other trainees have had time out of programme to do a Master’s in Public Health (in Sydney) and a Master in Medical Education

We regularly have Birmingham University Medical students from year 3-5 attached to the ID department at BHH. Trainees get involved with bedside teaching, as well as formal teaching sessions at both the University of Birmingham and the University of Warwick.




Please note, this is indicative only and programmes are necessarily changing with the overlapping rotations of current training programmes and the incoming combined infection programme from August 2015. We make every effort to avoid successive placements of any individual at hospitals at opposite poles of our geographical region and also to take personal circumstances into account when finalising rotations. Given the complexity of the ID-GIM-MM/MV training programmes, however, as well as the movement of many trainees in& out of programme,  we cannot guarantee specific rotation patterns more than 4 months before the main August rotation date.

A - Infectious Diseases with Microbiology or Virology

Note, Virology specialty training starts in year 3.

1st yr– single centre: 6mn Microbiology, 6mn ID.

2nd yr - single centre: 6mn ID, 6mn Microbiology . Within this, a 6-8 week placement in specialist virology service may be at another location.This year might be in the same centre as year 1, but is more likely to be different

3rd yr* - 6mn microbiology (Virology); 2mn ITU (usually at Heartlands) & 4mn ID at Birmingham Heartlands

4th yr* - 6mn ID Birmingham Heartlands, 6mn Microbiology (Virology) in region including 3mn at Birmingham children’s hospital

5th yr - 6mn microbiology (Virology), 6mn ID at Heartlands; this year to include 3mn acting consultant

B – Infectious Diseases with GIM

1st yr– single centre: 6mn Microbiology, 6mn ID. GIM on call throughout

2nd yr - single centre: 6mn ID, 6mn Microbiology . Within this, a 6-8 week placement in specialist virology service may be at another location. This year might be in the same centre as year 1, but is more likely to be different. GIM on call throughout

3rd yr* -3mn ITU (usually at Heartlands) &9mn ID at Birmingham Heartlands

4th yr* - 12mn ID Birmingham Heartlands

5th yr - 12mn ID at Heartlands; this year to include 3mn acting consultant

Trainees are likely to spend 40-50% of their time in ID at Heartlands overall

* OOP may be at any point after first and before final year. It often extends for 3yrs (occasionally more) Up to one year can theoretically count towards training though increasingly trainees are choosing not to request this accreditation because of overall shortened length of training.



Dr Peter Munthali, Training Programme Director for Medical Microbiology -


Dr Husam Osman, Training Programme Director for Medical Virology –


Dr Andrew Woodhouse, Training Programme Director for ID/GIM –


Dr Natasha Weston, Trainee Representative -


Dr Kiran Bhatt, Trainee Representative -