Acknowledgment
Thank you to Dr Maximillian Habibi and Dr Mark Hopkins, who reviewed Dr William Tong’s chapters. We are grateful for your help.
Abbreviations xiii
Contributors xxi
PART 1 BASIC BIOLOGY OF BACTERIA, VIRUSES, FUNGI AND PARASITES; HOST- PATHOGEN RELATIONSHIPS 1
1 The Biology of Bacteria 3
2 The Biology of Viruses 9
3 The Biology of Fungi 19
4 Parasites and Worms 25
5 The Host-Parasite (Microbe) Relationship 35
6 Basic Immunology 44
PART 2 MICROBIOLOGY/ VIROLOGY LABORATORY PRACTICE 55
7 The Use of the Laboratory in the Investigation, Management, and Prevention of Infection 57
8 Bacteriology Diagnostic Methods 64
9 Virological Diagnostic Methods 77
10 Fungal Diagnostics 86
11 Molecular Diagnostics 96
12 Laboratory Quality Control and Accreditation 105
PART 3 HEALTH AND SAFETY 113
13 Biosafety Categorisations and Containment Levels 115
PART 4 PRINCIPLES OF PUBLIC HEALTH IN RELATION TO COMMUNICABLE DISEASES 125
14 Key Communicable Diseases of Public Health Significance and UK Legislation 127
15 Vaccine-Preventable Diseases 136
PART 5 INFECTION PREVENTION AND CONTROL 141
16 Common Organisms Responsible for Healthcare-associated Infection (HCAI) 143
17 The Concept of Chain of Infection and Infection Control Principles 153
18 Antimicrobial Stewardship 161
19 Tools in Infection Prevention and Control 170
20 Sterilization and Decontamination 177
PART 6 IMPORTANT CLINICAL SYNDROMES 185
21 Sepsis—Recognition, Diagnosis, and Management in Adult Patients 187
22 Pyrexia of Unknown Origin (PUO) 193
23 Blood-Borne Viruses 199
24 Tuberculosis and Other Mycobacterial Infections 206
25 Multisystem Infections 213
26 Cardiovascular Infections 220
27 Skin and Soft Tissue Infections 230
28 Bone and Joint Infections 239
29 Upper and Lower Respiratory Tract Infections 245
30 Gastro-intestinal, Hepatic, Pancreatic, and Biliary Infections 251
31 Urinary Tract and Genital Infections including Sexually Transmitted Infections (STIs) 259
32 Infection of the Central Nervous System 266
33 Ocular Infections 279
34 Device-Associated Infections 286
35 Zoonotic Infections 290
36 Exanthemata 297
37 Pregnancy-Associated Infections 305
38 Infections in Neonates and Young Children 313
39 Infections in the Immunocompromised Host 319
40 Post-Infection Syndrome 325
PART 7 UNDERSTANDING USE OF ANTIMICROBIAL AGENTS 329
41 Mechanism of Action of Antimicrobial Agents 331
42 Use of Antimicrobials and Toxicity 339
43 Mechanisms of Antibiotic Resistance 347
44 Detecting Antimicrobial Resistance 354
45 Immunotherapy 363
46 Outpatient Parenteral Antimicrobial Treatment (OPAT) 369
47 Antivirals 375
PART 8 VACCINATION 383
48 Different Types of Vaccines 385
49 Vaccination Schedules 391
50 Vaccination of Specific Groups 397
51 Post-Exposure Prophylaxis 404
PART 9 THE MANAGEMENT OF HIV INFECTION 411
52 Epidemiology and Natural History of HIV 413
53 Laboratory Diagnosis and Monitoring of HIV Infection 422
54 Therapeutic Options for HIV Infection 428
55 Opportunistic Infections in HIV Infection 437
PART 10 TRAVEL AND GEOGRAPHICAL HEALTH 445
56 Geographical Pattern of Infectious Diseases and Infection Prevention for Travellers 447
57 Malaria 454
58 Fever in Returned Travellers 460
Index 467
Abbreviations
+ve positive
-ve negative
A&E Accident and emergency
ACDP Advisory Committee on Dangerous Pathogens
ACT Artemisinin combination therapy
ADEM Acute disseminated encephalomyelitis
AFB Acid fast bacilli
AHA American Heart Association
AMR Antimicrobial resistance
AMS Antimicrobial stewardship
ANTT Aseptic non-touch technique
APC Antigen-presenting cells
API Analytical profile index
ART Antiretroviral therapy
ASOT Antistreptolysin O Titer
AST Antimicrobial susceptibility test
ATLL Adult T cell leukaemia/lymphoma
ATP Adenosine triphosphate
ATS American Thoracic Society
BAL Broncho-alveolar lavage
BBV Blood-borne virus
BCG Bacillus Calmette-Guérin
BDG Beta-D-glucan
BNF British National Formulary
BP Blood pressure
BSAC British Association of Antimicrobial Chemotherapy
BSC Biological safety cabinet
BSE Bovine spongiform encephalopathy
BSI British Standards Institution
CA-MRSA Community-acquired MRSA
CAP Community-acquired pneumonia
cART Combination anti-retroviral therapy
cccDNA Covalent-closed-circular DNA
CCG Clinical Commissioning Groups
CCHF Crimean/Congo haemorrhagic fever
CDC Centers for Disease Control
CDI Clostridium difficile
xiv Abbreviations
cDNA Complementary DNA
CFS Chronic fatigue syndrome
CJD Creutzfeldt-Jakob disease
CL Containment level
CLO Campylobacter-like organism
CMV Cytomegalovirus
CN V Trigeminal nerve
CNS Central nervous system
CNS Coagulase-negative staphylococci
COPD Chronic obstructive pulmonary disease
COSHH Control of Substances Hazardous to Health
CPA Clinical Pathology Accreditation
CPE Cytopathic effect
CPE Carbapenemase-producing Enterobactericeae spp.
Cq Quantification cycle
CQC Care Quality Commission
CRE Carbapenem-resistant enterobacteriacae
CRO Carbapenem-resistant organisms
CRP C-reactive protein
CSF Cerebrospinal fluid
CSF Colony stimulating factor
CT Computed tomography
Ct Crossing threshold
CTLA-4 Cytotoxic T lymphocyte-associated protein 4
CVC Central venous catheter
CVID Combined variable immune deficiency
DAIR Debridement and retention of implant
DALY Disability-adjusted-life-years
DHFR Dihydrofolate reductase
DHR Dihydrorhodamine
DIC Disseminated intravascular coagulation
DIF Direct immunofluorescence
DIPC Director of Infection Prevention & Control
DMSA Dimercaptosuccinic acid
DNA Deoxyribonucleic acid
DoH Department of Health
DTP Diphteria, tetanus, and polio
DVT Deep venous thrombosis
EBV Epstein-Barr Virus
EFI European Federation of Immunogenetics
EIA Enzyme immunoassay
ELISA Enzyme-linked immunosorbent assay
ELISPOT Enzyme-linked immunospot
EM Electron microscopy
EORTC European Organisation for Research and Treatment of Cancer
EPI Expanded Programme on Immunisation
EPP Exposure-prone procedure
ESBL Extended spectrum betalactamase
ESC European Society of Cardiology
ESIMS Electrospray ionization-mass spectrometry
ESR Erythrocyte sedimentation rate
Abbreviations
EVD External ventricular drain
EWD Endoscope washer-disinfector
FBC Full blood count
FITC Fluorescein isothiocyanate
GAS Group A strep
GBS Group B strep
GCS Glasgow Coma Score
GCSF Granulocyte Colony Stimulating Factor
GDH-EIA Glutamate dehydrogenase enzyme immunoassay
GIT Gastro-intestinal tract
GM Galactomannan
GMC General Medical Council
GPEI Global polio eradication initiative
GPEI Glycopeptide-resistant enterococci
GUM Genito-urinary medicine
GVHD Graft versus host disease
H&E Haematoxylin and Eosin
HAART Highly active anti-retroviral therapy
HACEK Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella
HAP Hospital-acquired pneumonia
HBIg Hepatitis B immunoglobin
HBV hepatitis virus B
HCAI Healthcare-associated Infection
HCC Hepatocellular carcinoma
HCCA Alpha-4-cyano-4-hydroxy cinnamic acid
hCMV Human cytomegalovirus
HCV hepatitis virus C
HCW Healthcare worker
HEPA High-efficiency particulate air
HFMD Hand, foot, and mouth disease
hGISA heterogeneous glycopeptide-intermediate S. aureus
Hib Haemophilus influenzae type b
HICPAC Hospital Infection Control Advisory Committee
HII High-impact interventions
HIV Human immunodeficiency virus
HLIU High Level Isolation Unit
HNIg human normal immunoglobulin
HPT Health protection team
HRIg Human rabies immunoglobin
HSE Health and Safety Executive
HSE Herpes simplex encephalitis
HSV Herpes simplex virus
HTA Human Tissue Authority
HTIg Human tetanus immunoglobin
HUS Haemolytic uraemic syndrome
IA Invasive aspergillosis
ICED-IE ICED-infective endocarditis
ICED-LI ICED lead infections
ICP Intracranial pressure
ICPT Infection Control and Prevention Team
ID Infectious diseases
xvi Abbreviations
IDSA Infectious Diseases Society of America
IE Infective endocarditis
IFD Invasive fungal disease
IFU Instructions for use
IgG Immunoglobulin G
IgM Immunoglobulin M
IGRA Interferon Gamma Release Assay
IPC Infection prevention and control
IRIS Immune reconstitution inflammatory syndrome
ISAGA Immunosorbent agglutination assay
ISO International Standards Organization
ITN Insecticide-treated bed nets
ITP Idiopathic thrombyocytopenic purpura
IUGR Intrauterine growth restriction
IV Intravenous(ly)
IVDMDD In Vitro Diagnostic Medical Device Directive
IVDU Intravenous drug use
IVIg Intravenous immunoglobulin
JCVI Joint Committee on Vaccines and Immunisation
KOH Potassium hydroxide
KPC Klebsiella pneumoniae carbapenemase
KS Kaposi’s sarcoma
LAIV Live attenuated intranasal influenza vaccine
LDH Lactate dehydrogenase
LDT Laboratory developed test
LFT Liver function test
LP Lumbar puncture
LPS Lipopolysaccharide
LRINEC Laboratory Risk Indicator for Necrotizing Fasciitis
LTBI Latent TB infection
MAC Membrane attack complex
MAG3 Mercapto acetyl tri-glycine
MALDI-ToF Matrix-assisted laser desorption/ionization-Time of Flight
MAP Mean arterial pressure
MASPs Mannose-binding lectin-associated serine proteases
MAT Microscopic agglutination test
MBL Mannose-binding lectin
MBL Metallo-beta-lactamases
MC&S Microscopy, culture, and sensitivity
MDR Multi-drug resistant
MDR-TB Multidrug-resistant tuberculosis
MDT Multidisciplinary team
MHC Major histocompatibility complex
MHRA Medicines and Healthcare Products Regulatory Authority
MIC Minimum inhibitory concentration
MLSB Macrolides, lincosamides (clindamycin), and streptogramin B
MMR Measles, mumps, rubella
mRNA Messenger RNA
MRSA Meticillin-resistant Staphylococcus aureus
MS Mass spectrometry
MSM Men who have sex with men
MSU Midstream specimen of urine
MTB Mycobacterium tuberculosis
NAAT Nucleic acid amplifying test
NaTHaC National Travel Health Network and Centre
NBT Nitroblue-tetrazolium
NEC Necrotizing enterocolitis
NETs Neutrophil extracellular traps
NEWS National early warning score
NGS Next-generation sequencing
NICE National Institute for Health and Care Excellence
NNRTI Non-nucleoside reverse transcriptase inhibitor
NPV Negative predictive value
NRTI Nucleoside reverse transcriptase inhibitors
NTM Nontuberculous mycobacteria
NVE Native valve endocarditis
OCT Outbreak control team
OI Opportunistic infection
OLM Ocular larva migrans
OPAT Outpatient parenteral antimicrobial treatment
OPV Oral polio vaccine
PAMPs Pathogen-associated molecular patterns
PAN Polyarthritis nodosa
PAS Periodic acid shift
PBP2a Penicillin-binding protein
PCP Pneumocystis jiroveci pneumonia
PCR Polymerase chain reaction
PD Pharamcodynamic
PD-1 Programmed cell death protein 1
PEG Polyethylene glycol
PEP Postexposure prophylaxis
PET Positron emission tomography
PHI Primary HIV infection
PHT Public health team
PI Protease inhibitor
PICC Peripherally inserted central catheter
PII Periods of increased incidence
PIR Post-infection review
PIS Post-infection syndrome
PJI Prosthetic joint infection
PK Pharamcokinetic
PLHIV People living with HIV
PML Progressive multifocal leukoencephalopathy
PMR Polymyalgia rheumatica
PMTCT Prevention of mother-to-child transmission
PNA FISH Peptide nucleic acid fluorescence in-situ hybridization
PPD Purified protein derivative
PPE Personal protective equipment
PPV Positive predictive value
PPV23 Pneumococcal polysaccharide vaccine
PR Rectal examination
PrEP Pre-exposure prophylaxis
Abbreviations
PRRs Pathogen recognition receptors
PTFE Teflon
PTLD Post-transplant lymphoproliferative disease
PUO Pyrexia of unknown origin
PVE Prosthetic valve endocarditis
PVL Panton-Valentine leucocidin
PWID People who inject drugs
QA Quality assurance
QC Quality control
QMS Quality management system
qSOFA Quick Sequential Organ Failure Assessment
RA Rheumatoid arthritis
RBC Red blood cells
RCA Root cause analysis
rCTB Recombinant cholera toxin B
RDT Rapid diagnostic test
RIPL Rare and Imported Pathogens Laboratory
RITA Recent infection testing algorithm
RMP Registered medical practitioner
RNA Ribonucleic acid
RPR Rapid plasma reagin
RR Respiratory rate
RSV Respiratory syncytial virus (or bronchiolitis)
RT Reverse transcriptase
S Svedberg units
S/CO Signal-to-cutoff ratio
SAPO Specified Animal Pathogens Order
SARS Severe Acute Respiratory Syndrome
SCT Stem cell transplant
SD Standard deviation
SDGs Sustainable Development Goals
SFTS Severe fever with thrombocytopaenia syndrome
SIGN Scottish Intercollegiate Guidelines Network
SIRS Systemic Inflammatory Response Syndrome
SIV Simian immunodeficiency virus
SLE Systemic lupus erythematosus
SNHL Sensorineural hearing loss
SOFA Sequential Organ Failure Assessment
SOP Standard operating procedure
SPE Streptococcal pyrogenic exotoxin
SSI Surgical site infection
SSPE Subacute sclerosing panencephalitis
SSTI Skin and soft tissue infection
SUI Serious untoward incident
SVR Sustained virological response
TB Tuberculosis
TBE Tick-borne encephalitis
TCR T cell receptor
Th T-helper
TOE Transoesophageal echocardiogram
ToF Time of flight
Abbreviations
TORCH Toxoplasma, rubella, cytomegalovirus, and herpes simplex virus
TPPA Treponema pallidum particle agglutination
TSI Triple sugar iron
TSS Toxic shock syndrome
U&E Urea and electrolytes
UKAS UK Accreditation Service
ULN Upper limit of normal
URT Upper respiratory tract
UTI Urinary tract infection
UV Ultraviolet
VAP Ventilator-associated pneumonia
VDRL Venereal disease research laboratory
VFR Visiting friends and relatives
VHF Viral haemorrhagic fever
VIP Visual Infusion Phlebitis
VISA Vancomycin-intermediate Staphylococcus aureus
VP Ventriculoperitoneal
VRE Vancomycin-resistant enterococci
VZIG Varicella-Zoster immunoglobulin
VZV Varicella-zoster virus
WBC White blood cells
WCC White cell count
XDR-TB Extensively drug-resistant TB
XLD Xylose lysine deoxycholate
ZN Ziehl-Neelsen
Contributors
Fatima Ahmad, Biomedical Scientist, Department of Infection, Barts Health NHS Trust, London, UK
Sarfaraz Ameen, Anti-Microbial Pharmacist, Barts Health NHS Trust, London, UK
Gurtan Atamturk, Biomedical Scientist, Department of Infection, Barts Health NHS Trust, London, UK
Zahir O. E. Babiker, Assistant Professor and Consultant in Infectious Diseases, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
Marina Basarab, Consultant, Department of Infection, Barts Health NHS Trust, London, UK
Ruaridh Buchanan, Specialist Registrar in Microbiology and Infectious Diseases, Barts Health NHS Trust, London, UK
Duncan Clark, School of Life Sciences, University of Glasgow, Glasgow, UK
Martina N. Cummins, Clinical Director Infection Prevention and Control, Barts Health NHS Trust, London, UK
Subathira Dakshina, Specialist Registrar in Genitourinary Medicine, Barts Health NHS Trust, London, UK
Satya Das, Consultant, Barts Health NHS Trust, London, UK
Jayshree Dave, Consultant Microbiologist, HPA Specialist Microbiology Network (SMN), Public Health England
Heather Dolphin, Chief Biomedical Scientist, Barts Health NHS Trust, London, UK
Rohma Ghani, Specialty Trainee, Infectious Diseases, Barts Health NHS Trust, London, UK
Jennifer Henderson, Biomedical Scientist, Department of Infection, Barts Health NHS Trust, London, UK
Desmond Hsu, Specialist Registrar in Microbiology, Barts Health NHS Trust, London, UK
Mark Hopkins, Consultant Clinical Scientist, Department of Infection, Barts Health NHS Trust, London, UK
George Jacob, Consultant in Medical Microbiology, Royal Berkshire NHS Foundation Trust, Berkshire, UK
Angelina Jayakumar, Specialist Registrar in Infectious Diseases, Barts Health NHS Trust, London, UK
Anna Jeffery-Smith, Infectious Diseases and Virology Registrar, Barts Health NHS Trust, London, UK
Steve Kempley, Clinical Senior Lecturer in Paediatrics, Blizard Institute, Barts and The London, School of Medicine and Dentistry, London, UK
Palwasha Khan, Clinical Epidemiologist, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; Interactive Research and Development, Karachi, Pakistan
Jonathan Lambourne, Consultant in Infectious Diseases, Department of Infection, Barts Health NHS Trust, London, UK
Tim Linehan, Biomedical Scientist, Department of Infection, Barts Health NHS Trust, London, UK
Rohini J. Manuel, Consultant Medical Microbiologist, National Infection Service, Public Health England, London, UK
Sylvia Martin, Decontamination Lead, Barts Health NHS Trust, London, UK
Mark Melzer, Consultant in Microbiology and Infectious Diseases, Department of Infection, Barts Health NHS Trust, London, UK
Michael Millar, Consultant, Department of Infection, Barts Health NHS Trust, London, UK
Caoimhe NicFhogartaigh, Consultant in Infectious Diseases and Microbiology, Barts Health NHS Trust, London, UK
Anthony R. Oliver, Programme Manager at CliniSys, Chertsey, UK; Formerly Advanced Practitioner, Virology, Barts Health NHS Trust, UK
Chloe Orkin, Consultant Physician, Barts Health NHS Trust, London, UK
Sarah Parry, Specialist Registrar in Genitourinary Medicine and HIV, Department of Infection and Immunity, Barts Health NHS Trust, UK
Lynette Phee, Clinical Research Fellow, Blizard Institute, Queen Mary University of London; Specialist Registrar in Medical Microbiology and Virology, Barts Health NHS Trust, London, UK
Anna Riddell, Specialist registrar in Infectious Diseases and Virology, Barts Health NHS Trust, London, UK
Caryn Rosmarin, Consultant in Medical Microbiology, Department of Infection, Barts Health NHS Trust, London, UK
Marta Gonzalaz Sanz, Specialist Registar in Medical Microbiology, University College London Hospitals, Barts Health NHS Trust, London, UK
Shila Seaton, Bacteriology Scheme Manager, UK NEQAS for Microbiology, National Infection Service, PHE, Colindale, London, UK
Armine Sefton, Emerita Professor of Clinical Microbiology, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
Gee Yen Shin, Consultant Virologist, Public Health Laboratory London, Public Health England, London, UK
Stephanie J. Smith, Specialist Registrar in Medical Microbiology, Department of Infection, Barts Health NHS Trust, London, UK
Sherine Thomas, Consultant in Infectious Diseases, Department of Infection, Barts Health NHS Trust, London, UK
Simon Tiberi, Consultant, Department of Infection, Barts Health NHS Trust, London, UK
Cheuk Yan William Tong †, Consultant in Clinical Virology, Department of Infection, Barts Health NHS Trust, London, UK
Robert Serafino Wani, Consultant in Infectious Diseases and Microbiology, Department of Infection, Barts Health NHS Trust, Royal London Hospital, London, UK
David Wareham, Clinical Senior Lecturer/Honorary Consultant in Microbiology, Queen Mary University of London, Barts Health NHS Trust, London, UK
Mark Wilks, Clinical Scientist, Department of Microbiology, Barts Health NHS Trust, London, UK
Elizabeth Williams, Consultant in Sexual Health and HIV, Homerton Sexual Health Services, Homerton University Hospital NHS Foundation Trust, UK
Emily Zinser, Specialist Registrar in Immunology, Department of Immunology, Barts Health NHS Trust, London, UK
