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Microbiology

Urine

This section covers the essential steps involved in the microbiological analysis of urine specimens, from collection to the interpretation of results. The goal is to provide accurate and timely information to clinicians for the diagnosis and management of urinary tract infections (UTIs)

Specimen Sources and Collection

  • Overview: Proper specimen collection is the foundation of accurate urine culture results. The method of collection influences the likelihood of contamination and the ability to recover the causative pathogen
  • Key Specimen Sources
    • Midstream Clean-Catch: The most common method, emphasizing patient education on cleaning the perineal area and collecting a mid-stream sample to minimize contamination
    • Catheterized Urine: Used when patients cannot void voluntarily, involves sterile catheter insertion to collect urine
    • Suprapubic Aspirate: The most sterile method, involving direct aspiration of urine from the bladder
    • Nephrostomy Tube: Used for urine collection from a catheter in the kidney
  • Critical Considerations
    • Sterility: Prevent contamination from the patient’s skin, collection container, or collection technique
    • Timing: Collect the specimen at a time that minimizes contamination and maximizes the likelihood of detecting the pathogen
    • Transport and Storage: Prompt transport and appropriate storage (refrigeration) to preserve bacterial viability

Colony Morphology and Identification of Major Urinary Pathogens

  • Overview: This stage involves isolating and identifying the bacteria present in the urine sample
  • Procedure
    • Inoculation: Urine is inoculated onto appropriate agar plates (e.g., Blood Agar Plate (BAP), MacConkey Agar (MAC)) using a calibrated loop
    • Incubation: Plates are incubated under appropriate conditions
    • Colony Examination
      • Macroscopic Observation: Assessing colony characteristics (size, shape, color, texture, elevation, opacity, hemolysis)
      • Microscopic Examination: Gram staining to determine Gram reaction, cell shape, and arrangement
  • Identification Methods
    • Presumptive Identification: Based on colony morphology, Gram stain, and rapid tests (e.g., catalase, oxidase)
    • Further Identification: Biochemical tests, commercial kits, automated systems, and molecular methods (e.g., MALDI-TOF MS, PCR) are used to confirm the identity of the organism
  • Key Urinary Pathogens
    • Enterobacteriaceae: E. coli (most common), Klebsiella pneumoniae, Proteus mirabilis, Enterobacter spp., Citrobacter spp., Serratia marcescens
    • Enterococcus spp.: Enterococcus faecalis, Enterococcus faecium
    • Streptococcus agalactiae (Group B Streptococcus, GBS)
    • Candida spp.: Candida albicans, Candida glabrata, Candida parapsilosis
    • Staphylococcus saprophyticus

Correlation of Colony Counts with Clinical Significance

  • Overview: Determining the clinical significance of the culture results based on the number of bacteria isolated (colony count), patient symptoms, and other clinical data
  • Key Concepts
    • Colony-Forming Units (CFU/mL): The measure of the number of viable bacteria in the urine
    • Clinical Significance: The relevance of the lab findings in relation to the patient’s symptoms, medical history, and other diagnostic information
    • Significant Bacteriuria: A colony count above a threshold, typically associated with UTI symptoms
    • Asymptomatic Bacteriuria: Presence of bacteria without symptoms
    • Contamination: Bacteria from improper collection, not a true infection
  • General Guidelines
    • Significant Bacteriuria: Generally ≥ 10^5 CFU/mL (clean-catch), ≥ 10^3 CFU/mL (catheterized), or any growth (suprapubic aspirate)
    • Possible Contamination: Often < 10^3 CFU/mL, or mixed flora (multiple organisms)
    • Asymptomatic Bacteriuria: ≥ 10^5 CFU/mL (in two consecutive clean-catch specimens)
  • Reporting: Report the identified organism, colony count, antibiotic susceptibility profile, and a comment on the clinical significance

Correlation of Culture with Urinalysis Results

  • Overview: Integrating the findings from both the urine culture and urinalysis to provide a comprehensive assessment of the patient’s condition
  • Urinalysis Components and Correlation
    • Physical Examination: Color, Clarity, Odor
    • Chemical Examination: Leukocyte Esterase (WBCs), Nitrite, Protein, Blood (Hematuria), Glucose, Ketones
    • Microscopic Examination: WBCs (Pyuria), RBCs (Hematuria), Bacteria, Casts, Crystals
  • Examples of Correlation
    • Typical UTI: Positive leukocyte esterase, positive nitrite, pyuria, significant growth of a uropathogen in culture
    • Possible Contamination: Relatively normal urinalysis, mixed bacterial flora, low colony counts in culture
    • Asymptomatic Bacteriuria: Normal or mild urinalysis changes, significant bacteriuria in culture
    • Pyelonephritis: Positive leukocyte esterase, pyuria, WBC casts, significant growth of a uropathogen in culture
  • Clinical Implications: Integrated information is used for:
    • Diagnosis of UTIs
    • Selection of appropriate antibiotics
    • Monitoring treatment response
    • Differentiating between infection, contamination, and other urinary tract disorders
  • Comprehensive Reporting: Laboratory reports should provide both urinalysis and urine culture results together, along with an interpretation of the findings