microbial identification

• 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