Learning microbiology through clinical consultation

319 Pages·2016·12.328 MB·English

by  Breathnach, Aodhan S., Langdon, Berenice C

Learning Microbiology through
Clinical Consultation

Learning Microbiology
through Clinical
Consultation
Berenice C. Langdon, MBBS BSc MRCGP
General Practitioner
Pavilion Practice, London, UK
Aodhán S. Breathnach, MBBChBAO MD FRCPath
Consultant Medical Microbiologist
St George’s University Hospitals NHS Foundation Trust, London, UK
1
3
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Preface
Overview
This book is intended for medical students and newly qualified doctors, and introduces microbi-
ology and infectious diseases using lifelike case stories linked to microbiology learning points for
each topic. The case stories make the subject matter immediate and instantly applicable, and the
microbiology discussion pulls out the important points on key microbes, differentials, specimen
processing, and antimicrobial therapy for each case.
Each case is a narrative and is a fly on the wall experience for the reader, who can listen to the
whole interaction (including any awkward moments), observe the examination and specimen
taking techniques, hear what advice should be given, and how the consultation can be drawn to a
close. The swabs sent in the story and the results obtained provide a clear link to the more techni-
cal information on microbiology, which is then discussed, and by this means each topic is embed-
ded in clinical practice with the relevant microbiological information being brought to the fore.
It is well known that learning information presented as a narrative is highly effective, but it is a
fact not yet used by most textbooks. That the information is presented as narrative does not mean
the information is trivial. The case stories bring to life both the presentation of the patient, the
consultation process and, embedded with it, the microbiology.
Microbiology is an essential part of medicine and is therefore a key part of the curriculum and
key knowledge for a working doctor. With modern systems-based and problem-based learning
it tends to be taught in an integrated fashion and is incorporated into the teaching of infectious
disease, general medicine and surgery. Learning Microbiology through Clinical Consultation also
presents the material in an integrated fashion and is therefore an ideal text to use on a systems-
based or problem-based course, or for a newly qualified doctor practising independently. The
structure of the book is laid out for easy navigation and has clear case story headings to enable
‘just in time learning’ as well as ‘just in case’ learning.
Learning Microbiology through Clinical Consultation encompasses not only what medical stu-
dents and newly qualified doctors need to know for their exams, but also what they need to know
to practise medicine.
The importance of consultation
The consultation features strongly in Learning Microbiology through Clinical Consultation, and,
as such, is worth a short discussion to try and explain what is going on, and what is meant to be
going on, in each interaction.
The consultation is the transaction between doctors and patients. It is central to the whole idea
of medicine as well as to the idea of this book. There is a lot going on in every real consultation
and, reflecting real life, a lot going on in each of these case stories.
The doctor’s introduction to the patient (if you have not met) is essential to every consultation,
and, in fact, the doctor’s introduction to each colleague is essential to every interaction with the
medical team. A description of every introduction has not been included in each case story as this
would become repetitive, but in real life it should be happening every single time. Unfortunately,
vi PREFACE
this element of basic, common courtesy is missed out in real life interactions more often than is
admissible.
The point of a consultation would seem obvious: to sort out the patient’s medical problem. But
the point of each individual consultation is, sometimes, not at all obvious. The patient’s agenda
and the doctor’s agenda are not necessarily at all the same thing.
As the knowledgeable party, the doctor has a duty to assess the patient appropriately, explain
things, and advise them as to tests and treatments. And patients want and expect the doctors to do
just that. But they will also have their own ideas: about what is happening, what should be done,
and what treatments are right. Patients are not usually able to judge if the doctor is clinically any
good or not, but they use the doctor’s manner and approach as a surrogate for this.
Added to the mix of patient’s and doctor’s agenda, there is the government’s agenda, insisting
on certain targets, safety measures, and cost issues, as well as, the public health agenda, a respon-
sibility of the doctor to consider public health measures, preventative treatments, and lifestyle
advice, and this is all to be achieved within a certain amount of time (10 minutes for GPs, longer
in hospitals) and with a certain (usually large) case load.
To start with, the doctor’s agenda is important. This is the basic requirement of each consulta-
tion: that the patient should be safely assessed and treated appropriately. This assessment starts
with the thorough history familiar to all doctors: the presenting complaint, the history of the
presenting complaint, the past medical history, the treatment history, the social history, family
history, and allergies. These elements of the consultation should be easily observed in the case
stories (although bear in mind that for the GP consultations, the GP has a lot of the background
information readily accessible on the computer notes and will therefore not ask it every time)
along with certain refinements; the sexual history in the genitourinary medicine (GUM) clinic,
the mini-mental test used for dementia assessment and the activities-of-daily-living history in
elderly or infirm patients, among others. The history taking can also be refined further, depend-
ing on the doctor’s differential, leading to noticeably more directive questioning.
The overall look of the patient is very important and is often noted in these case stories, and
should be seen as part of the examination. Part of the point of these case stories is to model and
describe in detail the physical examination of the patient and also how to take the correct samples
and transfer them to the laboratory for identification of microbes.
There are many different consultation models, and all consultation models attempt to address
not just the clinical agenda of the doctor but the other agendas mentioned, in particular the
patient’s. This is where the doctor’s additional consultation skills can be observed, and where a
patient has felt they have been properly listened to and their worries addressed there is a much
better outcome to quite measurable things, such as an improvement in health and mental issues.
This is sometimes known as the doctor being the medicine.
Various consultation models have developed over the past 60 years. Because there are lots of
models, doctors have to pick and choose techniques that work for them, for the patient, and the
time and place. Key consultation models include: Balint, ‘The doctor, the patient and his illness’,
Byrne and Long, ‘Doctors talking to patients’, Roger Neighbour, ‘The inner consultation’, and
the influential (especially given that candidates are examined on it) Royal College of General
Practitioners (RCGP) performance criteria check list.
Each model has its own criteria checklist of which elements are important and which should
be included in each consultation. One of the most helpful and intuitive is Roger Neighbour’s five
stage model: Connecting with the patient, Summarizing the patient’s reason for attending (as well
as their feelings, concerns, and expectations), Handing over to the patient the agreed plan, Safety
netting or advising what to do if something unexpected happens, and Housekeeping to ensure the
clinician stays in good shape for the next patient. The influence of this model is apparent by the
PREFACE vii
way some of his stages have entered common language usage, such as ‘housekeeping’ and ‘safety
netting’, and it should be possible to notice some of these stages in the case stories presented.
The RCGP expands some of these stages, for example, marking candidates on picking up cues
and responding to them, using psychosocial information and not just medical information and
explaining things appropriately with written information as a backup, and specifically checking
understanding. These are all useful techniques and some may be observed within some of these
case stories.
Medical protection groups have also expanded certain parts of the consultation, specifically
‘connecting’. The connection the doctor has with the patient is a key stage, and it makes a dif-
ference to absolutely everything, from the medical assessment to the ultimate outcome. A good
connection can benefit everyone. Everything from hospital décor to the doctor’s appearance,
voice, tone, and body language will all affect the patient’s first impression. To then have a doctor
who is actively listening, who is showing an interest in what the patient has to say, who has good
eye contact (and is not just looking at the computer), and who does not immediately interrupt
the presenting complaint will all enable an excellent consultation to proceed. If the doctor then
acknowledges what has been said by the patient by summarizing it briefly so that patient and
doctor are agreed on what the consultation will address, then this all creates a good basis for the
consultation to continue and for all further interactions. The consultation, and these consultation
models combine, to form a wide-ranging and fascinating subject, only briefly touched on here.
The microbiology relating to each topic also benefits from an overview (see Appendices 1, 2
and 3). Appendix 1: A table of medically important bacteria, describes the classification of
bacteria using, for example, positive and negative Gram stains, bacterial shapes, and growth
requirements. These characteristics are frequently mentioned in the cases. Appendix 1 also contrasts
the difference between bacterial classification for medical purposes and classification based on
phylogenetics.
Appendix 2: A table of medically important viruses, explains terms relating to virus
classification also frequently mentioned in the cases, for example single-stranded (ss) versus
double-stranded (ds) viruses or RNA versus DNA viruses. Appendix 2 also contrasts the
difference between viral classification for medical purposes and classification based on scientific
conventions related to taxonomy.
Appendix 3: Notification of infectious diseases, includes tables on notifiable diseases (again
frequently mentioned in the cases) as well as a description of the purpose and processes of noti-
fication.
This introduction is intended to allow a better understanding of the consultation process in
particular, as well as to point out the appendices on classification and notification. Knowledge
of the consultation models and of these appendices will enable a better understanding of what is
going on in each case, and this will allow examples of good practice to be picked out and used;
whether of history taking, examination, obtaining microbial specimens, or good use of the laboratory.
The cases contained within Learning Microbiology through Clinical Consultation will hopefully
allow the microbiology to be absorbed as easily as the clinical scenarios, but will at the very least
give a vivid picture of the consultation process.

Contents
List of infections and associated key microbes (Table P1.1) xiii
Contributors and Expert Reviewers xv
Abbreviations xvii
Chapter 1 Gastrointestinal
Case 1.1 Viral gastroenteritis 3
Case 1.2 Food-borne gastroenteritis 8
Case 1.3 Traveller’s diarrhoea 12
Case 1.4 Duodenal ulcer 16
Case 1.5 Diarrhoea in hospital 21
Case 1.6 Normal bowel flora 24
Case 1.7 Hepatitis A 27
Case 1.8 Hepatitis B 30
Case 1.9 Hepatitis C 34
Case 1.10 Threadworm infection 37
Chapter 2 Cardiovascular
Case 2.1 Infective endocarditis 43
Chapter 3 Respiratory
Case 3.1 Community-acquired pneumonia 49
Case 3.2 Pneumonia in the immunocompromised 53
Case 3.3 Exacerbation of chronic obstructive pulmonary disease 57
Case 3.4 Tuberculosis 60
Case 3.5 Influenza 65
Case 3.6 Bronchiolitis 69
Case 3.7 Croup 72
Case 3.8 Viral pneumonia 75
Chapter 4 Central nervous system
Case 4.1 Bacterial meningitis 81
Case 4.2 Viral meningitis 85
Case 4.3 Neurosyphilis 87