Medical Microbiology and Infection at a Glance. Stephen H. Gillespie

and Tropical Medicine. He was appointed senior lecturer at the Royal Free Hospital School of Medicine and subsequently professor. During this time, he led the clinical microbiology service for 16 years and subsequently served as the Regional Microbiologist for the Health Protection Agency for 6 years. In 2010, he was appointed the foundation Sir James Black Professor of Medicine at the University of St Andrews in 2010.

      His research focusses on all aspects of tuberculosis diagnosis and drug development. He has led multiple clinical trials to shorten tuberculosis treatment. He holds several patents for rapid drug susceptibility testing methodologies and has developed rapid molecular methods to measure and quantify the number of live organisms in patient samples.

      He has published more than 300 research papers and had authored or edited 15 books in microbiology, infectious diseases and antibiotic resistance research.

      Kathleen B. Bamford is a consultant medical microbiologist at the Royal Cornwall Hospital in Truro. She trained in medicine at the Queen's University Belfast with postgraduate training in Northern Ireland. She was appointed as a senior lecturer at the Queens University Belfast and spent a sabbatical year in the University of Texas Medical Branch at Galveston, Texas. Following 20 years as senior lecture, then Reader at Imperial College London and then as a consultant microbiologist at Imperial College Healthcare NHS Trust, she worked for a year at the Hillingdon Hospital before moving to Cornwall in 2019. She has a broad clinical experience in all aspects of medical microbiology, infection prevention and control, and has contributed nationally to training, advisory and regulatory roles.

      Her research interests have included mucosal infection and immunology, epidemiology, healthcare‐associated infection and antimicrobial resistance with publications in each of these areas. She remains committed to improving health by addressing the interactions between humans and the microbial world.

      Preface to the fifth edition

      Since the publication of the fourth edition, the pace of change in the world of infection has increased. We have seen a global pandemic of a novel pathogen and increasing fears about the risks of antibiotic resistance. These challenges are reflected in the scale of this revision where there has been a comprehensive update to epidemiological, diagnostic and therapeutic components throughout the book. New chapters on innate immunity, antibacterial, antiviral and antifungal therapy, non‐tuberculosis mycobacteria, response to emerging infections, and chronic respiratory infections have been added. The figures have been updated to reflect new information and many new figures created. The availability of information has changed since the first edition of this book was written. This revision was completed during the COVID‐19 pandemic and this event emphasized the importance of infection and infection control to every healthcare worker wherever they practice.

      Medical Microbiology and Infection at a Glance, Fifth edition, continues to provide a comprehensive introduction to the topic of human infection and to provide learners at all stages of their clinical life a framework upon which they can build comprehensive knowledge for clinical practice.

      Stephen H. Gillespie

      Kathleen B. Bamford

      About the companion website

      This book is accompanied by a companion website:

      www.wiley.com/go/gillespie/medical5e

      The website includes:

       Interactive self‐assessment case studies.

       Revision notes for each chapter.

1 Microbial pathogens, classification and concepts

      Humans are at risk of infection by hundreds of different microorganisms: viruses, bacteria, protozoa and helminths. Understanding their biology helps us to diagnose them, classify them, to better predict their behaviour in our patients.

Characteristics of bacteria

      Describing the components of bacteria is important to help us understand how they cause disease and how we can inhibit them with antibiotics. Unlike eukaryotic cells the bacterial cell wall is rigid, to protect the organism from environmental stress. Some have a thick peptidoglycan layer and cell membrane that stains blue with Gram stain, and others have three layers: inner and outer membranes, and a thinner peptidoglycan layer staining pink with Gram stain. Mycobacterial cells have a high proportion of lipid, including immunoreactive antigens and there are bacteria whose cell wall forms a spiral shape. Some require specialist stains.

Bacterial structural components

       Capsule: a polysaccharide layer that protects the cell from phagocytosis and desiccation.

       Slime: polysaccharide material secreted on the surface protecting organisms against immune attack and antibiotic action. It is formed when growing in a biofilm, which may occur on medical devices such as canulae, or in lungs damaged by bronchiectasis.

       Lipopolysaccharide: surface antigens that strongly stimulate inflammation and protect Gram‐negative bacteria from complement‐mediated lysis.

       Fimbriae or pili: specialized thin projections aiding adhesion to host cells. Escherichia coli, which causes urinary tract infections, binds to mannose receptors on ureteric epithelial cells via P fimbriae. Fimbriae are often immunogenic, varying between strains allowing repeated infections to occur (e.g. Neisseria gonorrhoeae).

       Flagella: a motility organelle that allows organisms to move to sources of nutrition and penetrate the host mucus. The number and position of flagella may help identification.

       Spores: metabolically inert bacterial forms adapted for long‐term survival in the environment, which are able to regrow under suitable conditions.

       Genetics: Bacteria have a single chromosome and lack a nucleus (prokaryotes). The DNA is coiled and supercoiled by the DNA gyrase enzyme system (see Chapter 7) and bacterial ribosomes differ from eukaryotic examples. Both of these features are targets for antibacterial therapy (see Chapter 7). Bacteria have accessory DNA in the form of plasmids, integrons, transposons and bacteriophages that can transmit antimicrobial resistance (see Chapter 9) and encode for pathogenicity factors.

Bacterial classification

      Bacteria are divided into genera and species based on the sequence of their DNA. Complex computer algorithms are used to compute genomic information allowing comparison between genera, species and strains. Using these techniques, it is possible to track transmission of individual bacterial strains (see Chapter 11).

      Gram reaction: Gram‐positive and Gram‐negative bacteria respond to different antibiotics. Other bacteria (e.g. mycobacteria) may require special staining techniques.

       Cell shape: Bacteria may