Clinical Microbiology for Diagnostic Laboratory Scientists

Sarah J. Pitt

• Publisher: Wiley-Blackwell
• Year: 2017
• ISBN:
  9781118745823
• Edition: 1
• Topic: Biowissenschaften
• Subtopic: Mikrobiologie

A modern, evaluative, and integrative approach to diagnostic microbiology encouraging problem-solving in the clinical laboratory context through the use of examples to illustrate clinical and diagnostic issues

Clinical Microbiology for Diagnostic Laboratory Scientists is designed to encourage readers to develop a way of thinking that can be applied to any diagnostic scenario in microbiology. Through consideration of a selected range of infections caused by pathogenic bacteria, viruses, fungi, protozoa, and helminths, the book encourages readers to explore connections between the available information about clinical symptoms, pathogenesis of infections, and the approaches used in laboratory diagnosis, in order to develop new insights.

The book begins with an introductory chapter that outlines the scope of clinical diagnostic microbiology and the key areas for the laboratory scientist to be aware of. The subsequent six chapters review a type of infection in depth, using particular pathogenic microorganisms to illustrate salient points. At the end of each chapter there are three exercises related to management of a diagnostic service and assessing the suitability of test methods to specific contexts. There are no right or wrong answers to these, but the reader can discuss them with their laboratory colleagues or university tutor.

• Makes extensive use of published research in the form of journal articles, publically available epidemiological data, professional guidelines, and specialist websites
• Stimulates the reader in critical appraisal of published evidence and encourages problem-solving in the laboratory
• Outlines the scope of clinical diagnostic microbiology and the key areas for the laboratory scientist to be aware of
• Considers topics relevant to professional scientists working in the area of diagnostic microbiology

Clinical Microbiology for Diagnostic Laboratory Scientists is ideal for post graduate scientists intending to pursue careers in diagnostic clinical microbiology and for biomedical scientists, clinical scientists, and full time students studying for upper level qualifications in biomedical science, microbiology, or virology.

1
Overview of Clinical Diagnostic Microbiology

1.1 Introduction

The scope of diagnostic microbiology has developed along with technological advances in laboratory science. In the nineteenth century, detection of organisms relied on light microscopy and a limited range of in vitro culture methods. Some of these techniques are still used to detect and identify bacteria and parasites, in some cases with little or no modification (e.g., Gram’s stain). The discovery of proteins and then later nucleic acids during the twentieth century, along with the advent of the electron microscope, opened up the microbial world. The ability to determine and characterise the exact cause of an infectious disease, and thus to devise control measures, treatments, and prophylaxes has reduced morbidity and premature mortality throughout the world. Indeed, some diseases – smallpox in humans and rinderpest in cattle – have been eliminated altogether.

The ever‐expanding range of known microorganisms has led to the separation of diagnostic microbiology into distinct specialist areas – bacteriology, virology, mycology and parasitology. The diversity of microorganisms necessitates the training of individuals to be experts in one particular type of organism and they are often considered separately during study. It is important to remember that microorganisms do not operate in isolation and that a patient can be infected with more than one pathogen simultaneously. Advances in technology, in particular automation, make it possible to test for markers across pathology disciplines (not just within microbiology) on one single specimen in relatively short turnaround times. This means that the diagnostic microbiologist must be aware of the implications of an eclectic mixture of results and should certainly be able to solve problems and make decisions about patients with a wide range of infections.

N.B: This book assumes microbiological knowledge to at least graduate level. There are some very good general textbooks available for those who would like to revise any areas. For example, Greenwood et al. (2012) provides a brief overview of a comprehensive range of organisms, while clinical features are addressed clearly and simply in Murray et al. (2013) and Goering et al. (2013). Laboratory aspects are covered by Ford et al. (2014) and Wilkinson (2011), which were both written by practising diagnostic microbiologists.

Point to consider 1.1: What do you think is the most important scientific discovery in microbiology during the last 100 years and why?

1.2 Organisation and Management of Diagnostic Microbiology Services

The configuration of pathology services seems to be constantly changing in response to management trends, as well as financial constraints. Technological advances mean that it is easier to identify microorganisms to the level of a strain within a species, in a much shorter amount of time than it was 30 years ago. The techniques available have also been developed such that many aspects of the laboratory work can be done in automated systems (e.g., Fournier et al., 2013). The graduate and postgraduate microbiology scientist must therefore be able to interpret ever more complicated data, while retaining a working knowledge of the principles behind the tests used to generate that information. As laboratory microbiologists develop expertise and are given more responsibility, they sometimes find themselves working in larger teams, while at other times they are concentrating on a specialised area with a small number of colleagues. Cooperation with staff across pathology and in other departments in the hospital and primary care is becoming increasingly important in the daily running of the diagnostic microbiology service. Also, responding to the requirements of external bodies such as those involved in public health surveillance, quality assessment and service monitoring can create enough work for a full‐time post. Employing organisations can come and go, while the people who staff the laboratories often stay the same. This can be disconcerting, but it is important to keep sight of the facts. Firstly, each sample received in the laboratory has been collected from a patient with a clinical problem which needs addressing such as, ‘Has there been an adequate immunological response to this course of a vaccine?’, ‘What is causing this rash?’ and ‘Why does this antimicrobial treatment appear to be ineffective?’ Secondly, microbiology is endlessly fascinating; organisms can change very quickly – rendering diagnostic methods and treatments out of date – and infectious diseases are always in the news!

Point to consider 1.2: How many news stories involving microorganisms have you noticed during the last seven days? Find one article and think carefully about how well it was reported. Which points of information do you think were communicated well? Where there were inaccuracies, can you think of reason for the misunderstandings?

1.3 Techniques

Some techniques used to isolate and identify microorganisms have not changed substantially since they were first introduced – which in some cases is well over 100 years ago. This is usually because they are still useful and cost effective in helping to isolate and identify microorganisms from clinical samples. Others have been superseded by methods which give a more accurate or rapid result. It is therefore useful to critically evaluate techniques and to challenge assumptions about them. Does a traditional technique such as the Gram’s stain still have a place in twenty‐first century routine diagnostic microbiology? Why did virology services phase out virus isolation in monolayer cell culture? Is ‘PCR’ really the answer to every search for the optimal microbiology test?

The principles behind each technique will not be considered in any detail within this book. Readers are referred to laboratory protocols or standard operating procedures as appropriate, along with Wilkinson (2011) and Ford et al. (2014) for details.

Table 1.1 outlines some of the discussion points to consider about a selection of the techniques commonly used in diagnostic microbiology settings. The suite of tests used to investigate a particular clinical problem depends on a range of factors, which may include workload, available space, skill mix of workforce and service user requirements, as well as cost.

Table 1.1 Comparison of selected techniques used in diagnostic microbiology departments to isolate and characterise microorg...