Clinical Microbiology

• Microbiology section

  • Responsible for the identification of pathogenic microorganisms and for hospital infection control.
• The Microbiology Section is divided into:

  • Bacteriology
  • Mycology
  • Virology
  • Parasitology
• Biological Safety Level

  • As part of Laboratory Safety, CDC has classified microorganisms into various biosafety categories.
• Biological Safety Level

  BSL 1

  • no known pathogenic potential for immunocompetent individuals
  • NO RISK
  • Example: Bacillus subtilis
• Biological Safety Level

  BSL 2

  • this category includes the most common microorganisms associated with laboratory acquired infections
  • MODERATE RISK
  • Examples: Staphylococcus aureus, HBV, HIV, enteric pathogens like Salmonella spp. and Shigella spp.
• Biological Safety Level

  BSL 3

  • used to study infectious agents or toxins that may be transmitted through air and cause potentially lethal infections
  • Examples: Mycobacterium tuberculosis, Brucella spp., Coccidiodes immitis, Rickettsiaea and Arboviruses
• Biological Safety Level

  BSL 4

  • used to study infectious agents or toxins that pose a high risk of aerosol-transmitted laboratory infections and life threatening disease
  • no vaccine or therapy is available
  • Examples: Filovirus and Arenavirus
• Chemical Germicide Categories

  1. Sterilization
  2. Disinfection
• Chemical Germicide Categories

  Sterilization

  • complete destruction or removal of all living forms, including their spores
• Chemical Germicide Categories

  Sterilization Types

  1. Moist Heat
  2. Dry Heat
  3. Filtration
• Chemical Germicide Categories

  Sterilization (Moist Heat)

  a.) Autoclave

  b.) Tyndallization

  c.) Pasteurization

  d.) Boiling
• Chemical Germicide Categories

  Sterilization (Moist Heat)

  Autoclave

  • steam under pressure
  • 121°C at 15 psi for 15-30minutes
• Chemical Germicide Categories

  Sterilization (Moist Heat)

  Tyndallization

  • 100°C for 30mins for 3 consecutive days
• Chemical Germicide Categories

  Sterilization (Moist Heat)

  Boiling

  • 100°C for 15-30 minutes
• Chemical Germicide Categories

  Sterilization (Dry Heat)

  Oven

  • 160-180°C for 1-2 hrs, for glasswares
• Chemical Germicide Categories

  Sterilization (Dry Heat)

  Incineration

  • most common for disposal of infectious wastes (870-980°C)
• Chemical Germicide Categories

  Sterilization (Dry Heat)

  Flaming

  • for loops and needles
• Chemical Germicide Categories

  Sterilization (Dry Heat)

  Cremation

  • burning materials into ashes, to control disease
• Chemical Germicide Categories

  Sterilization (Filtration)

  Seitz Filter

  • used to filter heat labile fluid
• Chemical Germicide Categories

  Sterilization (Filtration)

  Membrane Filter

  • aka. cellulose filter
• Chemical Germicide Categories

  Disinfection

  • to destroy or irreversibly inactivate bacteria, viruses and fungi but not necessarily the spores on inanimate object
• Chemical Germicide Categories

  Disinfection (Antiseptic)

  • 70% ethyl/ isopropyl alcohol
  • Iodophors (iodine + detergent)
  • Chlorhexidine
  • Hexachlorophene
• Chemical Germicide Categories

  Disinfection (Disinfectants)

  • Sodium hypochlorite
  • QUATS - quaternary ammonium compounds
• Clinical Specimens

  (Blood)

  • Avoid normal skin flora while collecting blood for culture
• Clinical Specimens

  (Blood)

  • Most common anticoagulant for blood collection: Sodium Polyanethol Sulfonate (SPS)
• Clinical Specimens

  (CSF)

  • Samples are collected in sterile tubes usually numbered 1 through 3, representing the order in which the sample was collected:

  • Tube No. 1 - chemistry

  • Tube No. 2 - microbiology

  • Tube No. 3 - hematology

  • Tube No. 4 - additional testing (Microbiology, chemistry, serology or hematology)
• Clinical Specimens

  (Throat and Nasopharyngeal Swabs)

  • Specimen of choice to detect carrier state of: Neisseria meningitidis and to detect presence of Bordetella pertussis and Haemophilus influenzae
• Clinical Specimens

  (Sputum)

  • May often be contaminated with normal flora so it is important to evaluate the quality of specimen.
• Clinical Specimens

  (Sputum)

  • Note the number of Squamous epithelial cells/ LPF and PMNs to evaluate acceptability of specimen.
• Clinical Specimens

  (Sputum)

  • Collected ideally in morning when it is most concentrated.
• Clinical Specimens (Urine)

  • Specimen of choice for bacterial culture is Midstream Clean Catch
  • Catheterized for those unable to produce
  • Suprapubic urine for anaerobic culture
• Clinical Specimens (Urine)

  • Escherichia coli - major cause of UTI
  • Staphylococcus saprophyticus - cause of UTI among young females
• Clinical Specimens

  (Stool)

  • Used for the detection of enteric pathogen
• Clinical Specimens

  (Genital Tract Specimens)

  • To detect presence of sexually transmitted pathogen
• Tests performed in the Microbiology Section

  Acid-fast bacillus (AFB) Culture

  • Detects acid-fast bacteria, including Mycobacterium tuberculosis
• Tests performed in the Microbiology Section

  Blood Culture

  • Detects bacteria and fungi in the blood
• Tests performed in the Microbiology Section

  Culture & Sensitivity (C & S)

  • Detects microbial infection and determines antibiotic treatment
• Tests performed in the Microbiology Section

  Fungal Culture

  • Detects the presence of and determines the type of fungi
• Tests performed in the Microbiology Section

  Gram Stain

  • Detects the presence of and aids in the identification of bacteria
• Tests performed in the Microbiology Section

  Occult Blood

  • Detects nonvisible blood (performed on stool samples)