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Microbiology

Sterile Fluids

This section covers the key elements of bacteriological analysis for body fluids from normally sterile sites. Understanding the appropriate procedures, identifying potential contaminants, and recognizing the pathogenicity of infecting organisms is critical for patient care

Specimen Sources

  • Normally Sterile Sites: The presence of microorganisms in these fluids signals an infection
  • Specific Examples
    • Pleural Fluid (Thoracentesis): Pleural space
    • Peritoneal Fluid (Paracentesis): Peritoneal cavity
    • Pericardial Fluid (Pericardiocentesis): Pericardial space
    • Vitreous/Aqueous Humor: Fluids from the eye
    • Synovial Fluid (Arthrocentesis): Joint space
    • Amniotic Fluid (Amniocentesis): Fluid surrounding the fetus
  • Critical Aspects
    • Aseptic technique
    • Adequate volume
    • Prompt transport

Indigenous Organisms Associated with Mucosal Surfaces and Skin

  • Significance: Important for distinguishing between contaminants and true pathogens
  • Specific Sites and Examples
    • Upper Respiratory Tract: Viridans streptococci, Neisseria spp., Corynebacterium spp.
    • Gastrointestinal Tract: Enterococcus spp., Enterobacteriaceae, Bacteroides spp.
    • Genitourinary Tract: Staphylococcus epidermidis, Enterobacteriaceae, Candida spp.
    • Skin: Staphylococcus epidermidis, Staphylococcus aureus, Corynebacterium spp., Propionibacterium acnes, Malassezia spp.
  • Clinical Relevance: These organisms can be contaminants

Colony Morphology and Identification of Major Pathogens

  • Key Steps: Direct Gram stain, culture, and identification
  • Culture Media: Blood agar (BAP), chocolate agar (CHOC), anaerobic media (as needed)
  • Incubation: 35-37°C, with or without CO2, for specific time periods
  • Examination
    • Gram Stain: Quick method to reveal morphology
    • Colony Morphology: Examining the appearance of bacterial colonies
  • Identification
    • Based on the laboratory results
  • Major Pathogens and Characteristic Findings (Examples)
    • Streptococcus pneumoniae: Alpha-hemolytic, lancet-shaped diplococci
    • Haemophilus influenzae: Requires X and V factors to grow
    • Neisseria meningitidis: Gram-negative diplococci, oxidase-positive
    • Escherichia coli: Lactose-fermenting
    • Listeria monocytogenes: Beta-hemolytic, tumbling motility
    • Staphylococcus aureus: Beta-hemolytic, coagulase-positive
    • Enterobacteriaceae (Other than E. coli): Variable lactose fermentation, oxidase-negative
    • Beta-hemolytic streptococci: Group A, Group B, etc
    • Enterococcus spp.: Growth on bile esculin
    • Pseudomonas aeruginosa: Produces a blue-green pigment, oxidase-positive
    • Acinetobacter spp.: Gram-negative coccobacilli, oxidase-negative
    • Clostridium perfringens: Produces double-zone hemolysis

Molecular Methods

  • Enhanced Diagnostics: Valuable for rapid diagnosis and to confirm results
  • Principles
    • PCR: Amplifies specific DNA sequences
    • RT-PCR: Detects RNA viruses
    • Multiplex PCR: Detects multiple pathogens simultaneously
    • Next Generation Sequencing (NGS): High-throughput sequencing
  • Applications
    • Detecting a large variety of bacteria, fungi, viruses
    • Detecting resistance genes
  • Advantages: High sensitivity, rapid results
  • Limitations: Cost, technical expertise, does not always provide susceptibility information

Organism Pathogenicity

  • Understanding Pathogenicity: Crucial for understanding infections
  • Key Components
    • Etiology: Causative agent
    • Transmission: How it spreads
    • Virulence Mechanisms: How it causes disease
  • Pathogenicity in Action: The ability to
    • Colonize
    • Invade
    • Evade
    • Produce harmful substances
  • Examples
    • S. pneumoniae: Capsule, adhesins, pneumolysin
    • H. influenzae: Capsule, endotoxin
    • N. meningitidis: Capsule, endotoxin, adhesins, outer membrane proteins
    • E. coli: Adhesins, capsule, endotoxin
    • L. monocytogenes: Internalins, listeriolysin O, ActA
    • Staphylococcus aureus: Adherence, enzymes, immune evasion, toxins
  • Relevance to Diagnosis, Treatment, and Prevention: All aspects of the pathogen are important
  • Summary of Pathogenicity
    • Clinical Presentation: Determines what happens
    • Diagnosis: Determines the type of tests that should be used
    • Treatment: Helps choose the proper treatments
    • Prevention: Helps with all strategies for prevention