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Microbiology

Indeginous Surface Organisms

While the body fluids from normally sterile sites are themselves sterile, understanding the indigenous organisms that colonize the mucosal surfaces and skin is crucial for interpreting culture results. These organisms can be potential contaminants or pathogens in certain clinical scenarios. This understanding enables the laboratorian and clinician to differentiate between true infections and contamination, guiding appropriate patient management

General Principles

  • Normal Flora as a Source of Potential Contaminants: Most of the body’s mucosal surfaces and the skin harbor diverse microbial communities. During procedures to collect sterile body fluids, these organisms can contaminate the samples
  • Differentiating Contamination from Infection: Distinguishing true infection from contamination is critical. The presence of organisms in a sterile body fluid is significant, but must be interpreted with clinical context
  • Factors that Influence the Significance of an Isolate
    • Clinical Context
    • Specimen Source
    • Number of Organisms
    • Gram Stain Results
    • Isolation of the same organism repeatedly
    • Response to Treatment
  • Importance of Identifying the Organism: The ability to identify the potential contaminants and to perform susceptibility testing is essential for making informed decisions
  • Pathogens Can Cause Disease: Normal flora can cause infection under specific circumstances (e.g., when the host’s immune system is compromised, when the organisms enter a normally sterile site)

Indigenous Organisms on Mucosal Surfaces

Upper Respiratory Tract

  • Primary Colonization Site: The nasopharynx and oropharynx harbor a diverse array of organisms
  • Common Organisms
    • Viridans streptococci
    • Neisseria spp.: (non-pathogenic species)
    • Staphylococcus epidermidis: and other CoNS
    • Corynebacterium spp.: (diphtheroids)
    • Moraxella catarrhalis
    • Haemophilus spp. (non-encapsulated)
    • Various anaerobes, including Peptostreptococcus spp., Fusobacterium spp., Prevotella spp.
  • Clinical Significance
    • Potential Contaminants: Can contaminate CSF collected via lumbar puncture
    • Pathogens: Can cause pneumonia if aspirated into the lungs, can cause endocarditis

Gastrointestinal Tract

  • Abundant and Complex Flora: The GI tract harbors a diverse bacterial community
  • Common Organisms
    • Enterococcus spp.
    • Enterobacteriaceae (e.g., Escherichia coli, Klebsiella spp.)
    • Bacteroides spp.
    • Clostridium spp.
    • Lactobacillus spp.
    • Candida spp.
  • Clinical Significance
    • Potential Contaminants: Can contaminate peritoneal fluid, especially after bowel perforation or surgery
    • Pathogens: Can cause peritonitis, bloodstream infections, and intra-abdominal abscesses

Genitourinary Tract

  • Lower Urinary Tract: Contains a variety of organisms
  • Common Organisms
    • Staphylococcus epidermidis
    • Corynebacterium spp.
    • Lactobacillus spp.
    • Streptococcus spp.
    • Enterococcus spp.
    • Enterobacteriaceae (e.g., E. coli, Klebsiella spp.)
    • Candida spp.
  • Clinical Significance
    • Potential Contaminants: Can contaminate amniotic fluid during amniocentesis
    • Pathogens: Can cause infections of the urinary tract

Skin

  • Surface and Deep Flora: The skin harbors a wide range of microorganisms
  • Common Organisms
    • Staphylococcus epidermidis
    • Staphylococcus aureus
    • Corynebacterium spp.
    • Propionibacterium acnes (now Cutibacterium acnes)
    • Micrococcus spp.
    • Malassezia spp.
    • Candida spp.
  • Clinical Significance
    • Potential Contaminants: Frequently contaminate all sterile body fluid samples, during collection
    • Pathogens: Can cause infections when skin barrier is breached or when organisms enter a normally sterile site

Interpreting Results and Differentiating Contamination

  • Contamination vs. Infection
    • Contamination: Isolation of a small number of organisms, typically from the normal flora, with no supporting clinical evidence of infection
    • Infection: Isolation of a significant number of organisms, especially a known pathogen, with clinical signs and symptoms
  • Key Factors
    • Clinical Presentation: The patient’s symptoms and physical examination findings are essential
    • Number of Organisms: Significant growth (e.g., pure culture, heavy growth) is more likely to indicate infection
    • Multiple Isolates: If the same organism is isolated from multiple samples or at different times, the probability of infection increases
    • Gram Stain Results: The appearance of organisms on Gram stain can provide a clue to the source
    • Correlation with Other Laboratory Results: WBC count, protein, and glucose levels in the body fluid should be correlated with culture results
    • Antibiotic Use: If the patient is already on antibiotics, the presence of an organism in the culture may indicate resistance or a secondary infection

Examples of Interpretation

  • Pleural Fluid
    • Staphylococcus epidermidis isolated from a single culture with no clinical evidence (fever, pleuritic chest pain, etc.) - likely contamination
    • Streptococcus pneumoniae isolated in pure culture with an elevated WBC count and the presence of pneumonia - likely infection
  • Peritoneal Fluid
    • Escherichia coli isolated from a patient with symptoms of peritonitis - likely infection
    • Corynebacterium spp. isolated in low numbers, with a clear fluid - likely contamination
  • Synovial Fluid
    • Staphylococcus aureus isolated from a patient with a swollen, painful joint - likely septic arthritis

Key Terms

  • Normal Flora: The microorganisms that colonize the body’s surfaces
  • Indigenous Organisms: Organisms that are naturally present in a specific environment
  • Contamination: The presence of organisms in a sample that were not present in the patient
  • Pathogen: An organism that can cause disease
  • Mucosal Surface: A membrane that lines a body cavity
  • Gram Stain: Staining technique used to differentiate bacteria
  • Culture: The growth of microorganisms in a laboratory setting
  • Pleural Fluid: Fluid from the pleural space
  • Peritoneal Fluid: Fluid from the peritoneal cavity
  • Synovial Fluid: Fluid from a joint
  • Sepsis: A life-threatening organ dysfunction caused by a dysregulated host response to infection
  • WBC Count: White blood cell count
  • Protein: a large molecule found in body fluids
  • Glucose: A sugar used for energy
  • Pure Culture: A culture where only one type of organism is growing
  • Biofilm: A community of microorganisms that adhere to a surface and are encased in a matrix of extracellular substances
  • Opportunistic Pathogen: An organism that causes disease primarily in a host with a weakened immune system