microbial identification

Cards (16)

  • normal flora
    • beneficial effects
    • competition for resources w/ invading pathogens
    • aid in digestion
    • production of antimicrobial substances
    • harmful effects
    • can overgrow and become pathogenic
    • immunocompromised pts, eradication of harmless competitors (like yeast)
    • can cause infection when displaced from their normal site in the body to another
    • called opportunistic infections
  • normally sterile body sites
    • blood
    • CSF (cerebral spinal fluid)
    • pericardial fluid
    • synovial fluid/bone
    • pleural fluid
    • peritoneal fluid
    • microorgansims identified from normally sterile sites are usually treated
    • lack of growth of an organism does not always indicate absence of an infection
    • growth of an organisms does not always indicate presence of an infection
    • as a result, cultures ALWAYS need to be clinically correlated to pt presentation, and when available, imaging studies
  • when growth does NOT representation true infection
    • contamination of a sample w/ bacteria
    • contamination of blood draws w/ low virulence skin bacteria (CoNS, Corynebacterium spp.)
    • colonization w/ a microorganisms
    • MRSA and/or VRE + pts
    • typically put into isolation
  • when lack of growth does not rule out infection
    • antibiotics given prior to culture being drawn
    OR
    • clinical signs/symptoms and/or imaging indicate infection
  • microbial identification
    • direct visualization of the microogranism
    • gram stain
    • acid fast stain, etc.
    • culture
    • growing bacteria in enriched media in vitro
    • media can be non-selective or selective
  • examples of common single enzymes and metabolic tests
    • coagulase test
    • distinguishes btwn coagulase negative staphylococci (ie. S. epidermidis) and coagulase positive staphylococci (S. aureus)
    • lactose fermentation
    • lactose fermenters (E. coli, Enterobacter, etc) vs. non-fermenters (Pseudomonas, etc)
  • automated systems
    • computer sensors utilize fluorescent technology to monitor for presence of growth --> microbial detection
    • automated antimicrobial susceptibility tests
    • commercial examples: Vitek, Microscan, Phoenix
  • matrix-assisted laser desorption/ionization (MALDI) time of flight (TOF) mass spectrometry
    • accurate and fast bacterial identification --> compares "protein fingerprint" of the bacteria to a database
    • no susceptibility information
  • polymerase chain reaction (PCR)
    • fast turnaround time (faster than cultures)
    • qualitative detection (pos or neg) --> no susceptibilities
    • high sensitivity/specificity
    • examples:
    • most gram+ and gram- bacteria
    • antimicrobial resistance genes
    • mycobacteria
    • STDs
    • viruses
  • serology
    • detection and quantification of antibodies or antigens directed against a specific pathogen or its components --> no actual detection of microorganism
    • advantages
    • microorganisms that are hard to grow in lab (eg, Legionella, Treponema) or difficult to obtain specimen fr. site of infection (eg, H. pylori)
    • used to confirm immunity to many vaccines (eg, Hep B)
    • drawbacks:
    • may not differentiate btwn active vs. past infection (eg, Treponema)
    • antibodies usually take a few months to develop and will not be present during acute infection (ie, HIV)
    • no susceptibilities
  • culture
    • can it identify a microbe? yes
    • turnaround time to ID - a little fast (+)
    • susceptibilities? yes
  • automated systems
    • can it identify a microbe? yes
    • turnaround time to ID - fast (++)
    • susceptibilities? yes
  • MALDI-TOF
    • can it identify a microbe? yes
    • turnaround time to ID - very fast (+++)
    • susceptibilities? no
  • PCR
    • can it identify a microbe? yes
    • turnaround time to ID - very, very fast (++++)
    • susceptibilities? no
  • serology
    • can it identify a microbe? yes
    • turnaround time to ID - fast (++)
    • susceptibilities? no