Introduction to Microbiology

• Microbiology is the study of organisms that are small and generally require a microscope to be seen.
• Microbiology includes the study of bacteria, fungi, parasites, viruses, toxins, and prions. Fungi, parasites and bacteria are considered living entities, whereas viruses, toxins, and prions are considered non-living entities.

Important Figures in Microbiology

• Anthony Van Leeuwenhoek is considered the "Father of Microbiology" for building the first microscope.
• Louis Pasteur disproved the theory of "spontaneous generation", developed vaccines, and invented pasteurization using the word "microorganism".
• Robert Koch is known as the "Father of the Germ Theory of Diseases" and developed Koch's postulates.
• Ignaz Semmelweiss introduced hand hygiene practices that greatly impacted healthcare.
• Florence Nightingale established aseptic practices in nursing and was a statistician and researcher.
• Joseph Lister introduced carbolic acid (phenol) to sterilize surgical instruments and patient's skin, earning him the title "Father of Modern Surgery".

Koch's Postulates

• The microorganism must be found in abundance in all organisms suffering from the disease.
• The microorganism must be isolated from a diseased host organism and grown in pure culture.
• The cultured microorganism should cause disease when introduced into a healthy organism.
• The microorganism must be re-isolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Biological Classification (Taxonomy)

• Life is organized into a hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species (Specific).
• There are 3 Domains: Bacteria, Archaea, and Eukaryota.

Prokaryotes vs. Eukaryotes

• Prokaryotes: Have no nucleus.
• Eukaryotes: Have a nucleus.

Microbes and Human Disease

• Bacteria (Prokaryotes):
  • Can cause disease.
  • Examples: Chlamydia & Chlamydophila, Mycoplasma & Ureaplasma, Rickettsia.
• Fungi & Parasites (Eukaryotes): Examples: Yeasts and molds
• Viruses and Prions: Can still be considered as microorganisms

Bacterial Cell Structure

• Cell Envelope: All bacteria have a cell wall and cytoplasmic membrane.
• Cytoplasm: Where functions for cell growth, metabolism, and replication are carried out.
• Ribosomes: Are the powerhouses of all cells.

Symbiotic Relationships

• Mutualism: Both species benefit.
• Commensalism: One species benefits, and the other is not affected.
• Parasitism: One species benefits, and the other is harmed.
• Competition: Neither species benefits.

Terms

• Parasite: An organism that lives on or in a host.
• Autotroph: Bacteria that create their own energy, fueled by light or chemical reaction.
• Heterotroph: Organism that cannot produce its own food.

Oxygen Requirements of Bacteria

• Obligate Aerobes: Require oxygen and cannot survive without it.
• Facultative Aerobes: Use oxygen but can survive without it.
• Aerotolerant Anaerobes: Don't use oxygen but can grow in its presence.
• Obligate Anaerobes: Unable to use oxygen and cannot survive if it is present.
• Micro-aerophiles: Use oxygen but only at very low concentrations.

Specimen Processing

• Transport media: To stabilize the bacteria and the microbiome of the specimen from the time it's collected to being processed.
• UTM: Universal Transport Medium
• STI: Sexually Transmitted Infection
• BV: Bacterial Vaginosis
• MRSA: Methicillin-resistant Staphylococcus Aureus
• HAI: Hospital Acquired Infection
• CAP: Community Acquired pathogen /Infection
• TSA: Triptic Soy Agar
• CFU: Colony Forming Unit
• AFB: Acid Fast Bacilli
• VRE: Vancomycin Resistant Enterococcus
• SAF: Sodium Acetate Formalin
• C&S: Culture and Susceptibility

More Terms

• ESBL: Extended spectrum beta-lactamase
• DIC: Disseminated Intravascular Coagulation
• Bacteremia: Bacteria in the blood
• EBV: Epstein-Barr Virus
• SPS: Sodium polyanetholsulfonate
• Culture medium: A nutrient material for the growth of microorganisms in a laboratory
• Inoculum: Introduction of microbes into or onto the culture media to initiate growth
• Culture: Is to grow microorganisms
• C&S: Which antibiotics will kill any pathogens

Agar Concentrations in Media

• Liquid (0.05-0.1%) - Slows mixing of fluid, reduces convection currents.
• Semi-Solid (0.2-0.5%) - Motility testing, prevents dispersion of acid/alkaline products.
• Solid (1-2%) - Solidification.
• Solid (2-5%) - Prevents swarming growth.

Types of Media

• Basic Media: Containing only basic necessities of nutrition
  • Examples: TSA, Nutrient agar, BHIA, Columbian Agar base, Mueller-Hinton Agar, Nutrient broth
• Enriched Media: Basic medium + added nutrients, can grow most bacteria, even fastidious ones
  • Examples: Blood Agar, Chocolate Agar, Thioglycollate broth
• Selective Media: Suppress the growth of some organisms while allowing growth of others.
  • Example: Thayer Martin Agar, NYC agar, Campylobacter Agar
• Differential Media: Allows groups of bacteria to be visually distinguished by appearance.
  • Examples: Blood Agar, CNA, MacConkey, Sorbitol MAC
• Enrichment Media: To recover Salmonella from fecal specimens
  • Examples: Selenite broth, Carrot broth
• Parasite: An organism that lives in or on another species
  • Ectoparasite: A parasite that lives on the outside of another organism (causes infestation)
  • Endoparasite: A parasite that lives within another organism (causes infection)
• Parasitology: The study of parasites, their host and the relationship within them.
• Symbiosis: Close long-term relationship between species
• Host: The organism from which a parasite obtains nutrients and in which some or part of the parasite's life cycle is completed.

Types of Parasites

• Protozoa: Single celled eukaryotic organism (i.e. Ciliata/Giardia)
• Helminths: Worm-like organisms (i.e. roundworm/flatworm)
• Ectoparasites: Organism that infest in skin (i.e. lice/bed bugs)
• Mycology: The study of fungi. Eukaryotic organisms
• Mycoses/Mycosis - Diseases caused by fungi
• BW: Bronchial Washing
• BAL: Bronchoalveolar Lavage
• BSC: Biological Safety Cabinet
• Gram-pos: Appears purple under microscope
• Gram-neg: Appears pink under microscope
• BAA - Brucella anaerobic Agar
• PM - Preventative Maintenance
• PHAC - Public Health Agency of Canada
• PSOS - Pathogen Safety data sheet
• API - Analytical Profile Index
• "Motility and standard 0.5-0.43
• "Ready the card every 15 minutes
• AST - Antimicrobial Susceptibility Testing
• Epidemiology - the study of the factors that cause disease and determine disease frequency and distribution.
• Endemic - Same disease in some area
• Epidemic - Disease in one large area
• Pandemic - Lots of disease cat the whole world
• 5 stages of infectious disease:
  • Incubation period - Time between contact or exposure
  • Prodromal phase - The appearance of early signs and symptoms
  • Acute phase - The peak of disease. Immune response starts responding.
  • Period of decline - Replication of the infectious agent is brought under control. Symptoms start to resolve.
  • Convalescent phase - The patient recovers.

Infections

• Lytic infection: When a microorganism infects a host and creates copies of itself to go forth and multiply
• Latent infection: Organism remains dormant within host
• Local infection: An infection that is limited to a specific part of the body (UTI, pneumonia)
• Systemic infection: An infection in w/o the pathogen is distributed throughout the body
• Morbidity: The rate of incidence of a disease.
• Mortality: The death rate of the disease
• IPAC: Infection Prevention and control
• ARO: Antimicrobial resistant organisms
• ESBL: Extended Spectrum beta-lactamase
• CPE: Carbapenemase producing Enterobacteriaceae
• Immunization: Process by which an individual's immune system becomes strengthened against microbial agents
• Vaccine: A biological preparation that improves immunity to a particular disease
  • Inactivated vaccine: Use a killed version of a microbe that cause a disease
  • Live attenuated vaccine: Is made from a "wild" virus or bacterium made weaker by repeated culturing
  • mRNA vaccine: Teach cells to make proteins that trigger an immune response
  • Subunit vaccine: Contains harmless and purified pieces (proteins) of the undesirable organism to trigger immunity
  • Recombinant vaccine: Made by combining the genetic material from two microorganisms
  • Polysaccharides vaccines: Target an immune response to bacteria that are encased in a layer of sugar
  • Toxoid vaccines: Use an inactivated toxin (harmful product) made by bacterium or virus
  • Vector vaccine: When pieces of genetic material from a harmful microbe are inserted to an attenuated (weakened) harmless bacterium or virus which becomes the carrier
• Herd immunity: When the vaccination of a large part of population to a disease provides protection for individuals