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  • General Principles of Clinical Microbiology

  • Approaches to Laboratory Analysis in Clinical Microbiology

  • Microbiology Techniques

    • Acid-Fast Stain (AFB Smear, Kinyoun Stain)

    • Albert Stain

    • Blood Cultures

    • Blood Culture Key Points

    • Culture Media for Bacterial Pathogens

    • Darkfield Examination

    • Giemsa Stain

    • Gonorrhea Detection

    • Gram Stain and Common Pathogens

    • India Ink Preparation

    • KOH Preparation

    • Malaria Smear

    • Molecular Microbiology

    • Nasopharyngeal swabs

    • Nucleic Acid Amplification Tests

    • Pinworm Preparation (Cellophane Tape Test)

    • Sputum Culture

    • Stool Culture

    • Stool for Ova and Parasites

    • Syphilis Testing

    • Urine Culture

    • Vaginal Wet Preparation

    • Viral Detection Methods

  • Common Infections and Empiric Therapy

    • Bacterial

    • Viral

    • HIV-1

    • Fungal

    • Parasitic

    • Tick-borne

  • Common Clinical Microbiology Applications

    • Catheter-Related Bloodstream Infection

    • Central Nervous System Infection

    • Hepatitis

  • HIV Testing and Screening

    • Infectious Diarrhea

  • Infective Endocarditis Prophylaxis

    • Pulmonary Infections and COVID-19

    • Sepsis

    • Skin and Soft Tissue Infections

    • Streptococcal Pharyngitis

    • Urinary Tract Infection (UTI, Non-CAUTI)

    • Catheter-Associated Urinary Tract Infection

  • Bioterrorism and Select Agents

  • Isolation Protocols

Chapter update by Morgan McCoy, MD, PhD, Vaneet Arora, MD, MPH, D (ABMM), Rose Jung, Pharm D, Steven A. Haist, MD, MS, and Leonard G. Gomella, MD


Clinical microbiology has become increasingly complex, requiring interpretive judgment in spite of, and in many cases due to, the advent of laboratory automation and integration of genomics and proteomics. Diagnostic stewardship, which involves appropriate selection of the patient, specimen, and test, is critical in getting results that are accurate, significant, and clinically relevant. Some of the most common tests performed on patients are the procurement of tissue or body fluids for direct detection of pathogenic organisms to prove or disprove the presence of infection. The results of these tests are critical in guiding the selection of antibiotics for targeted therapy.

The three basic questions that need to be answered from the laboratory are: Is this an infection? If yes, what is the organism? And lastly which antimicrobial agent will likely work against this agent? The clinical microbiology laboratory provides answers to these questions. Several clinical microbiology principles must be considered when ordering or interpreting the tests:

Severity or Degree of Risk: There is a difference between an otherwise healthy patient with a complaint of dysuria consistent with a urinary tract infection (UTI) versus a patient with neutropenia and a high fever. The first needs a simple urinalysis with a routine bacterial culture. The second needs more extensive testing that may involve specimens from multiple sites and appropriate radiologic studies. The second patient also needs prompt treatment with empiric broad-spectrum antibiotics while waiting on test results because she is at high risk of septicemia and death.

Choice of Antibiotics: Initiation of antibiotics that broadly cover a newly recognized infection in a timely and appropriate manner is often lifesaving. Selecting the wrong antibiotic, the wrong dose, an improper route of administration, or delaying treatment can increase morbidity and mortality. While initially a broad-spectrum antibiotic may be employed, ...

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