Principles of laboratory diagnosis

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Richard Davis
Ph.D., D(ABMM), MLS(ASCP) · Microbiology and Infectious Disease contributor
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Table of Contents
High-yield summary

Learning goals

  • Compare direct examination, culture, serologic, and molecular methods for identifying microorganisms.

  • Differentiate diagnostic approaches for bacteria vs. viruses.

  • Understand how to select appropriate microbiologic diagnostic tests.

 

Direct examination

  • Uses stains (Gram, Acid-fast, fluorescent) to visualize organisms directly from specimens.

  • Low sensitivity/specificity; risk of false positives/negatives.

  • Gram stain: differentiates Gram-positive (purple) vs. Gram-negative (pink) based on peptidoglycan.

  • Key morphologies: cocci in chains (Strep), clusters (Staph), rods (Enterobacterales), diplococci (Neisseria).

 

Culture techniques

  • Gold standard for bacterial and fungal diagnosis.

  • Media types: nutritive (e.g. chocolate agar), selective (e.g. MTM), differential (e.g. blood agar, MacConkey).

  • Allows for antimicrobial susceptibility testing and downstream identification.

 

Biochemical identification

  • Catalase: Staph (+), Strep (-).

  • Coagulase: S. aureus (+), CoNS (-).

  • Optichin: S. pneumoniae sensitive.

  • Oxidase: Pseudomonas (+).

 

Serology

  • Detects host antibodies (IgM = acute, IgG = past infection/vaccine).

  • Used for viruses and some parasites.

  • Methods: lateral flow, ELISA/EIA.

  • Limitations: delayed response, cross-reactivity.

 

Molecular testing (NAAT/PCR)

  • Detects pathogen DNA/RNA directly from specimen.

  • High sensitivity and specificity; rapid results.

  • Applications: syndromic panels, viral load, resistance mutations.

  • Real-time PCR: cycle threshold (Ct) correlates with pathogen load.

 

USMLE tips

  • Gram stain is foundational for bacterial classification.

  • Culture is gold standard but slow; molecular tests are faster and more sensitive.

  • Serology useful for viral and parasitic infections; interpret IgM vs. IgG.

  • Know test metrics: SN, SP, PPV, NPV.

  • PCR = high sensitivity; Ct value inversely related to pathogen load.

Learning goals

  1. Describe considerations used to select microbiologic diagnostic tests
  2. Compare and contrast direct examination, culture, serologic, and molecular laboratory methods for identifying microorganisms in terms of the benefits and limitations of each
  3. Compare and contrast laboratory methods used to identify and characterize bacteria versus viruses

Study materials

These materials are not required; they are supplementary to large group session. They are intended as a curated guide to content focused on the learning objectives. There are both textbook and video resources for this session for students to use per their preference. For each reference, I have designated the learning goal addressed with a and number.

Click the  book icons below to go to the library resources listed.

  • Sherris Medical Microbiology, 8e

    Chapter 4: Principles of Laboratory Diagnosis of Infectious Diseases
    2  This chapter provides overview of the common laboratory methods used for identifying microorganisms. Review the summary boxes/blue boxes for review of key points.
    1   High-yield sections: Good discussion of the value of proper specimen collection.

  • Murray Medical Microbiology, 9e

    Chapter 4: Microscopy and In Vitro Culture
    2 Chapters 4 and 6 provide a ‘deeper dive’ into laboratory methods: microscopy, culture, and immunologic tests.

     High yield:
    Table 4-1: Table of the different stains used in microbiology with a description of principle applications. This is provided for reference and to give some familiarity of the different stains that you will encounter (not required to memorize details of this table)
    Table 4-2: Table of the different types of bacterial culture media, which highlights nutritive, selective, and differential agars. This is provided for reference and to give some familiarity of the different types of media that you will encounter (not required to memorize details of this table). The associated text provides further definition of these types of agar and description of how and why they are used.

  • Murray Medical Microbiology, 9e

    Chapter 6: Serologic Diagnosis
    2 Chapters 4 and 6 provide a ‘deeper dive’ into laboratory methods: microscopy, culture, and immunologic tests.

     High yield:
    Table 6-1: Table of the various immunological lab test methods with brief description and some examples. This is provided for reference and to give some familiarity of the different types of immunologic tests you will encounter (not required to memorize details of this table).

  • Principles and Practices of Infectious Diseases, 9e

    Chapter 16: The Clinician and the Microbiology Laboratory: Test Ordering, Specimen Collection, and Result Interpretation
    Note: This text and chapter is designed as a primary reference for practicing infectious disease physicians and clinical laboratory directors and is largely beyond the scope of this course.
     High-yield section: Figure 16.1 and related explanation of MALDI-TOF, a transformative technique in clinical microbiology.