BASI WEEK 7 Notes PDF

Bacteria Structure and Growth lecture 3 interrelated areas of bacterial taxonomy - - - Bacterial Morphology Size - bacteria are small and rely on diffusion Shapes - various shapes of bacteria Most common shapes: - - Other common shapes: - - - - Arrangement of bacteria:...

Bacteria Structure and Growth lecture 3 interrelated areas of bacterial taxonomy - - - Bacterial Morphology Size - bacteria are small and rely on diffusion Shapes - various shapes of bacteria Most common shapes: - - Other common shapes: - - - - Arrangement of bacteria: - - - - Diplo - pair Strepto - chain Some bacteria have no defined shape called pleomorphic Arrangements: cell that divides in two or more planes give rise to clusters or packets to be describes as - tetrades: packets of 4 cells - Cell membrane: Bacterial cell membranes have a fluid mosaic model, but do not contain **sterols** Bacterial Cell Wall: - - Function of Cell wall is different from cell membrane: - - - - Virtually all bacterial cell walls have **peptidogylcan** - - - Clincal relevance : Peptidoglycan - - 1. a. b. 2. c. Antibiotics that target the cell wall are called cell wall inhibitors These only affect cells that are actively growing, as these synthesize petidoglycan Lysozyme, found in tears, saliva, mucus degrades glycine backbone of peptidoglycan - - Classification of most bacteria into two groups Gram Stain: can differentiate bacteria using two stains: crystal violet, safranin red (differential stain) **Gram negative - thin peptidoglycan layer** - **Gram positive - thick peptidoglycan layer** - - Peptidoglycan thickness defines most bacterial cells as being gram positive or gram negative - helps with initial identification of an organism knowing this allows - - Not all bacteria that have gram + or gram - cell wall - - - - So there are 3 main types of cell walls in bacteria gram - gram + acid-fast Gram - Negative Cell Walls - - - - - - - clinical relevance of LPS (lipopolysaccharide) O antigen: outer portion of LPS - - Core polysaccharide: - Lipid A: embedded in the outer and has Toxin Activity - - - - LPS can bind to receptors on various cells causing release of cytokines and pro-inflammatory mediators resulting in symptoms of **septic shock** Outer membrane of gram negative cell walls - - - - - Periplasmic Space of Gram negative cell walls - - Gram Positive Cell walls - - - - - - - - - - - Acid-Fast Cell Walls contain 2 things Mycolic Acid Layer:polymers of long-chain fatty acids and other lipids - - Tetrameric Porins - Acid-Fast Organisms - - - - Bacterial internal and external structure: many can be called virulence factors External structures: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Internal Structures - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Binary Fission: how bacteria replicate 1. 2. 3. 4. Measuring Bacterial grow Optical density (OD) - - Colony-Forming Unity (CFU) - - Biomass - - Bacterial Growth Curve LAG phase: Zero population growth - - - - - LOG phase: exponential population growth - - - - - - Late LOG phase: transition to stationary phase - - - Stationary Phase - - - - - Death/decline phase - - - Why is it important to know what the organism needs? - - - First step is to isolate the organism in pure culture - - - Bacterial cultivation - media medium can be liquid (broth) or (semi) solid (gel) solid media contains agar - cells are immobilized - each cell will grow into an isolated colony Types of media: - - - - - Defined Media: - - - - - Complex (undefined) media: - - - - Enriched media - - Selective media - - - Differential media: - - - Using medica to detect fermentation MacConkey agar: differential and selective contains bile salts and crystal violet: inhibit gram + cells Selctive for Gram - cells Neutral red - ph indicator If anything grows it is gram - - Fastidious organisms - - - - - - Obligate vs Facultative obligate: - - Facultative: - - Environmental Factors - - - - - Most pathogenic bacteria are mesophiles - - Low temp challenges - - High Temp challenges - - PH - most pathogens are neutrophiles, ph 7.0 Acidophile- lactobacilluc, coxiella burnetil Alkaliphile - Bacillus spp, Vibrio cholerae Oxygen - - - - - - - - CO2 capnophiles- require high CO2 levels many pathogens are capnophilic Water Availability/Osmotic Pressure - - - - - Microbial Pathogenicity lecture PCR - - Colonization - - Infection - - Disease - - - - - Signs and symptoms of disease signs - Symptoms - Conjunctivitis - - different organisms can lead to disease of similar signs and symptoms - same organism can lead to disease with different signs and symptoms - Stages of disease depends on severity and duration of disease and varies with - - - Incubation stage - - - - - Prodromal warning - - - - Acute Stage - - - - - - - Decline Stage - - - - Convalescent stage - - opportunistic pathogens - - - Virulent pathogens - - - Mechanisms of bacterial virulence tissue damaging metabolites - - Invasins or spreading factors - - - adhesins - - Toxins - - Exotoxins - Enterotoxins - - E-B Exotoxins - - - - - Superantigens - - Membrane active exotoxins - - - Virulence mechanisms - - - - Evasion by antigenic variation microbe will: - - - Antigenic drift - - - Antigenic shift - influence A - - - Antigenic Switching - - **Fungal Agents: Structure and Biology Lecture** Kingdom Fungi: Unicellular, multicellular, Eukaryotic (similar to our genetics), heterotrophic - lost of fungi opportunistic infections are present when immune system is weakened or broken Fungi are eukaryotic organsims that reproduce asexually through spores. Fungi Structure - - - - Cell Wall - - - - Cell Membrane - - - - - Specific features of fungi linked to determinants of pathogenicity - - - - - - Isolation and lab culture - - - Direct detection - - - - - - - - Molds - - Mycoses - - - - Primary pathogens - - - - Opportunistic pathogens - - - Candida - - - Antifungal therapy - - Antifungal agents 1. 2. 3. 4. most fungi are resistant to antibacterial drugs most antifungal agents are toxic to humans Treatments Nystatin - - - Amphotericin B - - - Azoles - - - - Terbinafine - - Echinocandins - - - Intro to Viruses/Structure What is a virus? - - - Viruses do not have their own ability to encode their own ribosomes. This is the key difference between bacteria and virus Virus infected cell (alive) Virion/viral particle Virus structures - - - - - - - Viral replication is **Host cell dependent** **Entry**: 1. 2. 3. **Replication** 4. CPE cytopathic effects in viral culture cells die from viral replication Viral culture measures whether infectious virions are present PCR detects viral DNA while Reverse Transcripticase detects Viral RNA Antigen test - measures whether viral protein is present two main things virus needs to do 1. 2. Viruses can have RNA or DNA genomes - - DNA vs RNA polymerase RNA is prone to replication errors DNA not prone to replication errors RNA viruses use rna dependent rna polymerase (RdRp) (RNA -\>RNA) Retroviruses use reverse transcriptase (RNA - DNA) to replicate RdRp and reverse transcriptase lack proofreading mechanisms - introduce errors and mutations give rise to variants and resistance to treatment Make viral protein Boltimore classification (if you can classify you can use proper treatment) - - - - - - - - - - - - Virus Architecture classification - - Families of viruses - helpful to group because drugs work based on families of viruses Valacyclovir completely inhibits and inactivates viral DNA polymerase for herpes virus Viral Virulence Virulence: is the relative capacity to cause damage to the host Determined by both the host and virus (primarily the host) Cannot compare the virulence of different viruses Mutations in viral genes can change viral properties Principles of infection control - - 3 most important rules of infection control 1. 2. 3. Respiratory pathogens transmission - - - - - Respiratory precautions - How long SARS COV-2 lasts on surface - - - - Terms Septic Aseptic Antiseptic Biocide Bacteriostatic Bactericidal Sterilization- absolute inactivation or removal of all microbes, including spores - - - Disinfection: killing, inhibiting, or removal of microorganisms that may cause disease - - Antisepis: chemical control of microbes on living tissues - not inanimate objects Autoclaves: how do you know the autoclave is working? - - Time: how long it takes to sterilize depends on: - - Common chemical and standard precautions - critical items - penetrate tissues and contacts bone, blood, or normally sterile sites: requires sterilization Semi-critical: contacts but does not penetrate tissues: requires sterilization or high level disinfection, sterilization required if the item is heat tolerant Non-critical - casual contact only - Standard precautions - Ebola virus in the eye: one of his eye had turned from a blue to a green color - - - Challenge of Prions: Prions are novel disease agents - - - Antibiotics lecture 1 How do you choose the right drug? Infectious agent? Patient/history? drug resistance cost adverse effects Antimicrobial Resistance Lecture Why we are doomed! Resistance - - - - - **Kirby Bauer Test** - - - - - - - - - - - **Broth Dilution Test** - - - Determines: - - - - - - - - If bacteria are still alive in all test tubes: they are bacteriostatic and can't kill off the bacteria Need bactericidal for immunocompromised individuals because immune system can\'t clear off the bacteria **Development of resistance** 1. 2. a. i. ii. iii. **Specific mechanisms of resistance** 1. a. 2. b. 3. c. d. 4. e. f. g. h. **Resistant to "all"** **Factors contributing to antibiotic resistance** - - - - - - - - - - - Antibiotic failures are not always due to resistance - - -