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• non selective media 


  non differential allowing growth of many types of bacteria e.g blood agar
• selective media


  selects for growth of desired organism, inhibiting growth of non desired organisms
• differential media 


  takes advantage of biochemical properties of target organisms leading to a visible change when target organics are present
• 2 ways to identify bacteria/fungal biochemical phenotype

  manual biochemical identification strips or automated biochemical identification instrument (MALDI-TOF MS)
• kirby - bauer disc diffusion method

  swap organism over agar plate, put antibiotics discs of knows concentration on agar, let grow overnight and disc diffusion gives zone of inhibition to measure susceptibility
• MIC (minimum inhibitory concentration)


  minimum concentration of antibiotic which inhibits visible growth go the organism
• MBC (minimum bactericidal concentration)


  minimum concentration of antiobitic which kills the organism
• clinical microbiology workflow


  bacterial / fungal culture, biochemical phenotype, antimicrobial susceptibility testing (only more PCR etc if unidentified bacteria)
• MALDI-TOF MS


  an automated biochemical phenotype identification instrument, mass spectrometry to determine bacertia based on mass/charge ratio
• 6 keys for collection quality microbial specimen

  1. represent diseased area (except blood antibody)
  2. quality and quantity
  3. avoid preventable contamination
  4. collect in right container, kept at right temp
  5. collect before antimicrobials given
  6. sent to lab with detailed info
• sensitivity 


  the proportion of those who have the disease correctly identified as having the disease
• specificity 


  the proportion of those without the disease who are correctly identified by the test as not having the disease
• PPV


  proportion of those the a positive test who have the disease
• NPV 


  proportion of those with a negative test who don't have the disease
• sensitivity calc


  TP / TP + FN
• specificity calc


  TN / TN + FP
• PPV calc


  TP / TP + FP
• NPV


  TN / TN + FN
• problem with interpreting positive test results for a rare condition

  a prevalence decrease PPV drops dramatically, more false positive than true positives
• diagnosis of pneumonia - specimen type

  usually septum, bronchoalveolar lavage (tube down wash out part of lung) more accurate used for severe cases
• diagnosis of pneumonia - sample quality

  good quality = >25 neutrophils and <10 squamous epithelial cells (from upper respiratory)
• diagnosis of pneumonia - antigen detection 


  S.pneumonia detected by lateral flow assay (RAT), 70% sensitivity, 90% specificity
• diagnosis of pneumonia - antibody detection

  after 4 weeks have antibodies specific to organism, 4 fold rise in antibody levels implies recent infection (but to late not useful)
• PCR advantages for NA detection

  sensitive to low NA levels, can detect killed bacteria, rapid
• PCR disadvantage 


  very sensitive so can get false positive if contaminated
• diagnosis of pneumonia - NA detection

  PCR either real time of endpoint to detect DNA products
• real time PCR


  DNA production detected in real time as they accumulate by fluorescence signal using probe to match target sequence
• end point PCR


  DNA production detected by gel electrophoresis