Clinical Microbiology for Diagnostic Laboratory Scientists

Book Preface

This book is intended for post‐registration and post‐graduate level scientists who are developing careers in diagnostic clinical microbiology. It is suitable for those who are working in hospital laboratories while studying for advanced qualifications, as well as full‐time MSc students. The aim is to prompt readers to make connections between the clinical symptoms, pathogenesis of infections and the approaches used in laboratory diagnosis. This is not a comprehensive account of all aspects of clinical microbiology, but a consideration of a range of infections caused by selected pathogenic bacteria, viruses, fungi, protozoa and helminths. The idea is to use these examples to illustrate clinical and diagnostic issues, to stimulate critical appraisal of published evidence and to encourage problem‐solving in the clinical laboratory context.

There is an introductory chapter, which outlines the scope of clinical diagnostic microbiology and the key areas for the laboratory scientist to be aware of. In the subsequent six chapters, a type of infection is reviewed in depth, using particular pathogenic microorganisms to illustrate salient points. As well as journal articles, there are references to publically available epidemiological data and professional guidelines throughout the book. This includes links to specialist websites. I hope that the reader will find the mixture of sources of information useful and a helpful place to start their own exploration of topics which interest them. 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 could discussthem with their laboratory colleagues or university tutor. Chapters 2 to 6 also include clinical case studies based on the content of the chapter. Application of appraisal and problem‐solving skills should lead to the solutions in each case, but the outline answers are provided in Appendix 1, so the reader can check their interpretation of the information.

Pathology laboratory services seem to be continually in the process of reorganisation and reconfiguration. The ways in which laboratory scientists are expected to work is changing, due to the possibilities afforded by new techniques. This often includes requirements for multi‐site working patterns and a more multidisciplinary outlook. However, the laboratory scientist should never lose sight of the point of their work, which is to help the patient. Microorganisms and the diseases that they are associated with are endlessly fascinating – and new pathogens are being discovered all the time! The graduate microbiologist can make a valuable contribution to patient care through questioning received wisdom, investigating different laboratory methods and evaluating research.

Sarah J. Pitt

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.