Week 1: Overview of Micro + Lab Safety Flashcards
What are purposes of the clinical microbiology lab?
- Isolate and ID pathogenic organisms from specimen
- Give clinicians info
- Use in conjunction with medical history (physical exam, x-rays…etc) to help diagnose
- Result in patient treatment + care
Infectious disease
Infectious diseases are illnesses caused by germs (such as bacteria, viruses, and fungi) that enter the body, multiply, and can cause an infection.
Infection
Pathogenic introduction/invasion of body tissues and their multiplication
Colonization
Formation of a population of microorganisms in the host that does not cause disease.
True pathogen
An infectious agent that causes disease in virtually any susceptible host.
Opportunistic pathogen
Potentially infectious agents that rarely cause disease in individuals with healthy immune systems. It can only cause disease in situations that compromise the host’s defenses, such as the body’s protective barriers, immune system, or normal microbiota.
Nosocomial pathogen
Hospital-acquired
Virulence
Degree of pathology caused by an organism. The extent of the virulence is usually correlated with the ability of the pathogen to multiply within the host; may be affected by other factors; the disease-evoking power of a microorganism.
What are virulence factors that help pathogens attach to the host?
- Pili
- Adherence proteins
- Biofilms
What are virulence factors that help pathogens invade the host?
- Trauma
- Inhalation
- Medical devices
- Production of enzymes
What are virulence factors that help pathogens survive in the host?
- Avoid phagocytes, capsules, antigenic variation
- Inhibit immune response
Difference between endotoxin and exotoxin?
Endotoxin: Lipid portions of lipopolysaccharide (LPS), which are part of the outer membrane of the cell wall of Gram-negative bacteria. Released by dead bacteria.
Exotoxin: Proteins produced inside pathogenic bacteria, usually Gram-positive but some Gram-neg. Secreted or released by living bacteria
Give detail about exotoxins
- Specific toxins target specific host cells and vary with bacterial species
- Some kill host cell and help spread bacteria while some destroy/interfere with specific intracellular activities
- Heat labile
- Example: toxin that causes necrotizing fasciitis
Give detail about endotoxins
- Effects to host include: disruption of clotting factor, fever, activate complement + immune systems, blood cell changes
- Heat stable
- Example: Gram-negative septicemia
List 3 types of bacterial toxins
- Enterotoxin
- Neurotoxin
- Extracellular enzymes
Explain enterotoxins
- Target intestinal mucosa
- Endotoxin or exotoxin
- E.g., Staph food poisoning
Explain neurotoxins
- Target nerve tissue
- Exotoxin only
- E.g., tetanus toxin
Explain extracellular enzymes
- Proteases and hyaluronidases
- Liquefy hyaluronic acid of connective tissue matrix and aid in bacterial spread into tissues
Define normal flora
Microbes found in/on specific body site and usually do not cause infectious disease
List sterile body sites (no indigenous microbial flora)
- CNS, brain
- Blood, tissues, organs
- Inner and middle ear
- Lower respiratory tract
- Kidneys, bladder
- Uterus
List signs of inflammation
- Swelling
- Redness
- Heat
- Pain
- Pus
List examples of direct transmission
- Congenital
- Sexual contact
- Hand-to-hand contact
- Droplet
- Breaches to protective barriers
List examples of indirect transmission
- Fomites
- Water
- Food
- Animal or insect
- Airborne
What is the most important step in clinical micro and why?
Organism recovery! Improper specimen collection can result in misleading info
What are timing factors in specimen collection?
- Early acute phase: must collect during fever spike for best chance of true positive. After could lead to false negative
- Collect before antibiotics given to patient
Proper collection devices and specimen containers?
- Keep specimen moist
- Sterile (except stool specimens)
- Proper aerobic/anaerobic environment
- Leak-proof
Where must specimen come from?
Site of infection. Collect with minimal contamination, sufficient quantity, and proper label
Transport conditions for urine, stool, blood, swabs, and special media?
Urine: Refrigerate or boric acid (prevents microbe overgrowth) if delayed transport
Stool: Use Cary-Blair transport media for bacteria. Ova/parasites use formalin + modified PVA
Blood: SPS to prevent clotting
Swabs: Stuart’s or Amie’s transport medium
Special media: JEMBEC system chocolate agar with CO2 generator capsule for N. gonorrhoeae
Transport medium should…?
- Preserve viability without allowing multiplication of bacteria
- Maintain pH
- Prevent drying
Specimens should be delivered within what time from to laboratory?
30 minutes
What renders specimens unacceptable?
- Unlabeled, mislabeled, doesn’t match requisition -> reject
- Contamination due to leakage
- Inadequate quantity
- Unpreserved specimen more than 2hrs old
- Improper transport media
- Improper source for type of culture
- Improper culture type
- Improper transport environment
Ways we protect ourselves in the lab?
- Engineering controls (BSC, HEPA, sharps containers)
- Work practices (hand washing, aseptic technique, decon…etc)
- PPE (lab coat, gloves, goggles, needle re-sheathing device, fitted N-95)
Sterilization
Removes ALL forms of life, including spores
-Incineration
-Dry heat
- Bacti-cinerator
-Filtration
- Hot air oven
-Moist heat-steam under pressure
Disinfection
Removes pathogens but **not necessarily all* of them, or spores
- Boiling, pasteurizing, UV light
- Phenols, alcohols, detergents, bleach
Antiseptic
Disinfectants applied to living tissue such as Listerine or iodine
Give examples of BSL-1 microbes
B. subtilis, E.coli, S. cerevisiae
Give examples of BSL-2 microbes
Hepatitis A virus, S. progenies, Borrelia burgdorferi, Salmonella
Give examples of BSL-3 microbes
Mycobacterium tuberculosis, SARS, yellow fever, hantaviruses, West nile virus, rabies virus, Yersinia pestis
Give examples of BSL-4 microbes
Smallpox, Ebola
What is a class I BSC?
Unsterilized room air enters and circulates within cabinet. Exhaust air is filtered by HEPA filter. BSL-1
What is a class II BSC?
- Sterilize both air entering and circulating with cabinet along with exhaust air
- Most hospital micro labs use this one
- “Laminar flow hood”
- BSL-2 and BSL-3
What is a class III BSC?
- Highest level of safety
- All air entering and leaving cabinet is HEPA-sterilized
- Entirely enclosed system
- Handle specimens with rubber gloves sealed to cabinet
- BSL-4
