Practical Clinical Microbiology and Infectious Diseases

Firza Alexander Gronthoud, MD, DTM&H, is a Consultant Microbiologist at the Royal Marsden NHS Foundation Trust, United Kingdom.

SECTION I Principles of Infection Management

1.1 Pillars of Infection Management

1.2 Diagnostic Stewardship

1.3 Antimicrobial Stewardship

1.4 Infection Prevention and Control

SECTION II Diagnosis of Infections

2.1 Commensal Flora

2.2 Diagnosing Bacterial Infections

2.3 Diagnosing Viral Infections

2.4 Diagnosing Invasive Fungal Infections

2.5 Diagnosing Parasitic Infections

2.6 Laboratory Detection of β-Lactam Resistance in Enterobacterales

2.7 Understanding the Antibiogram

2.8 Understanding Microbiology Culture Results

2.9 Understanding Serology

2.10 Understanding Molecular Diagnosis

SECTION III Treatment of Infections

3.1 Basic Principles of Antimicrobial Treatment

3.2 Basic Principles of Antifungal Treatment

3.3 β-Lactam Allergy

3.4 Antimicrobials in Pregnant Women

3.5 Antimicrobial Agents and Liver Injury

3.6 Antimicrobial Agents and Neurotoxicity

3.7 Antimcrobial Agents and Drug Interactions

3.8 Pharmacokinetic and Pharmacodynamic Considerations

3.9 Source Control

3.10 Antibiotic Treatment Failure

SECTION IV Special Problems

4.1 Acute Streptococcal Pharyngitis

4.2 Animal Bites

4.3 Asymptomatic Bacteriuria

4.4 Atypical Pneumonia

4.5 Bacterial Skin and Soft Tissue Infections

4.6 Bloodstream Infections

4.7 Bordetella pertussis

4.8 Breast Abscess

4.9 Bronchiectasis

4.10 Bronchitis

4.11 Brucellosis

4.12 Candiduria

4.13 Cardiac Implantable Device Infections

4.14 Chlamydia trachomatis

4.15 Cholangitis

4.16 Deep Neck Space Infection

4.17 Empyema

4.18 Encephalitis

4.19 Endocarditis

4.20 Neisseria gonorrhoeae

4.21 Hepatitis A

4.22 Hepatitis B

4.23 Hepatitis C

4.24 Hepatitis E

4.25 Histoplasmosis

4.26 Human Immunodeficiency Virus and Opportunistic Infections

4.27 Infections in Haematopoietic Stem Cell Transplants

4.28 Infections in the ICU

4.29 Infectious Diarrhoea

4.30 Influenza

4.31 Intra-Abdominal Infections

4.32 Invasive Candidiasis

4.33 Invasive Group A Streptococcal Infections

4.34 Invasive Pulmonary Aspergillosis

4.35 Keratitis

4.36 Lung Abscess

4.37 Measles

4.38 Meningitis

4.39 Near-Drowning-Associated Pneumonia

4.40 Neutropaenic Sepsis

4.41 Non-Resolving Pneumonia

4.42 Norovirus

4.43 Onychomycosis

4.44 Osteomyelitis

4.45 Otitis Externa

4.46 Pelvic Inflammatory Disease

4.47 Perianal Abscess

4.48 Pneumocystis jirovecii Pneumonia (PJP) in Patients with a Haematological Malignancy or Solid Organ Transplant

4.49 Pneumonia (CAP, HAP and VAP)

4.50 Post-Exposure Prophylaxis for Healthcare Workers Exposed to Blood-Borne Viruses

4.51 Post-Operative Infections

4.52 Prosthetic Joint Infections

4.53 Protatitis

4.54 Pyomyositis

4.55 Ringworm

4.56 Salmonella Carriage

4.57 Septic Arthritis

4.58 Septic Bursitis

4.59 Splenectomy: From Prophylaxis to Treatment

4.60 The Immunocompromised Patient

4.61 Typhoid Fever

4.62 Urinary Tract Infections

4.63 Uveitis

4.64 Varicella Zoster

SECTION V Difficult-to-Treat Organisms

5.1 AmpC, Extended Spectrum β-Lactamase and Carbapenemase Producers

5.2 Acinetobacter baumannii

5.3 Achromobacter xylosoxidans

5.4 Pseudomonas aeruginosa

5.5 Stenotrophomonas maltophilia

5.6 Staphylococcus aureus

5.7 Vancomycin-Resistant Enterococci

5.8 Helicobacter pylori

5.9 Clostridioides difficile

5.10 Actinomycosis

5. 11 Nocardia

SECTION VI Appendix

6.1 Syndromic Approach to Infections

6.2 Specimen Collection

6.3 Spectrum of Activity of Antibiotics

6.4 Doses of Common Antimicrobials

6.5 Pathogen-Specific Infection Control Precautions

6.6 Pillars of Infection Control

6.7 Transmission-Based Precautions