Microbiology Core Notes Year 1 PDF

MICROBIOLOGY  Prokaryotic & Eukaryotic Pathogens The Black Death A gram negative bacteria that was blood borne and transmitted via black rats and their fleas 5.2 billion people died in the 20th century due to multiple factors Infectious diseases account of 1/3 of deaths Factor...

MICROBIOLOGY  Prokaryotic & Eukaryotic Pathogens The Black Death A gram negative bacteria that was blood borne and transmitted via black rats and their fleas 5.2 billion people died in the 20th century due to multiple factors Infectious diseases account of 1/3 of deaths Factors affecting us Antimicrobial Resistance (AMR) Ineffective vaccines Immune dysfunction (sepsis) What we need is: new antibiotics, vaccines, synthetic antibodies Medical microbiology is microbiology that affects medicine Terminology Nomenclature Pathogenesis: origination and development of a disease Kingdom Molecular pathogenesis: study of molecules in a disease state Phylum Microbial pathogenesis: ability of microbes to cause infection Class Host-Pathogen interaction: how microbes sustain themselves Order in hosts Family Disease aetiology: study of causes of the disease Note: fungi and Protozoa follow bionomial Microbial aetiology: a microbe is the cause of disease nomenclature while viruses and prions dont Microbial disease: disease caused by microorganisms Infectious disease: disease caused by microbial invasion/ multiplication Communicable disease: ID that spreads through a given path Contagious disease: ID is communicable between hosts Taxonomy is the science of naming, identifying, and classifying organisms Phylogeny is the representation of evolutionary history and relationships between groups of organisms JOIN THE DARKSIDE Differences between prokaryotes and eukaryotes Characteristics used for diagnosis Morphology (shape) Cellular and population arrangements Characteristics (gram + gram - ) Biochemical properties (antibiotic resistance, composition, growth, etc.) Presence/absence of certain structures (flagella) Detailed genetic makeup (specific gene sequences) Bacterial shapes Bacilli- rod shaped (Escherichia coil) Cocci- spherical (staphylococcus aureus) Ovococci- oval type of cocci (enterococcus faecalis) Spirillium- curved rods (campylobacter jejuni) Spirochaetes- spiral rods (treponema pallidium) Vibrio- comma shaped rods (vibrio cholera) Monocistronic means coding for only I protein Bacterial arrangements (eukaryotes) Strepto- chains of cocci Polycistronic means coding for multiple proteins Staphylo- clusters of cocci (prokaryotes) Diplococci- pairs of cocci The reason why eukaryotes are monocistronic is because eukaryotic mRNA are shorter than bacterial mRNA meaning they can’t provide more information for coding A cistron is a gene Eukaryotes are intronic because they have introns while prokaryotes do not. The reason being is introns were eventually lost from prokaryotes for efficiency (since introns don’t contain useful DNA there is no need for them). Take but don't harm JOIN THE DARKSIDE Bacterial capsule Lies outside the cell wall and is made up of polysaccharides (glucose) It is there for immune resistance and absorption of moisture Bacterial cell wall Determines shape of bacteria It is made of a couple sugars that are linked together by small amino acid chains The shape of bacteria determines growth, motility, reproduction It handles the passage of large molecules by restricting them Resists osmotic pressure Helps in immune system evasion Assembles proteins Gram positive and Gram negative bacteria Cellular stains differentiate the cell wall differences under a microscope Gram negative bacteria are surrounded by a thin peptidoglycan wall surrounded by 2 cell membranes Gram positive bacteria are surrounded by a thick peptidoglycan wall with only one membrane Flagella/Flagellum Allow bacteria to “swim” (move) They are present in many bacteria but not all Made up of flagellin which is a globular protein (a flagellum is made up of 20000 flagellin) Fimbriae/fimbria Not all bacteria have them Found in gram positive and negative They are long filamentous protein structure located on the surface of bacterial cells Made of single protein called fimbrillin (short) They attach to surfaces allowing bacteria to bind receptors and take over cells Pilae/pilus Only found in gram negative Hollow on the inside Made of thousands of copies of pilin (a protein) Longer than fimbrae shorter than flagella Involved in cell interactions, genetic exchange, twitching motility (form of movement) Viruses (parasite) Acellular and has no metabolic capacity Has to use host cells machinery do its activities Shape is either helical or icosahedral Very specific for its host Virion is the ineffective from of the virus JOIN THE DARKSIDE Classification of viruses Life cycle of a virus Based on host, disease vectors, location, shape, biochemical and genetic makeup Fungi Eukaryotes Grow by binary fission (division) and as hyphae (mold) Hyphae are filaments that make up a fungi Hyphae can branch and cluster creating a huge unnderground group called mycelium The cell wall of a fungi is made of chitin (it folds in itself creating hydrogen bonds) They have a membrane but no cholesterol instead they have ergosterol Bacteria don’t have ergosterol They grow at a pH of 5 Low moisture Able to grow at high osmotic pressure Their classification depends on habitat, type of mycelia, and how they grow and reproduce Protozoa Some have cell walls There are different forms that allow them to perform different functions They are unicellular eukaryotes Found in almost every habitat Can ingest complex food particles through the cytosome JOIN THE DARKSIDE  The Human Microbiota Gram positive is stained blue Gram negative is stained red The gram stain binds to sugars of the cell wall When cell walls are exposed to safranin and crystal violet + iodine in the gram negative cell wall alcohol dissolves fat and some of rheumatoid arthritis crystal violet. The wall gets broken. But in gram positive it stays in tact because of the thick peptidoglycan Bacterial pathogens are heterotrophs (can’t produce their own food) They require: water, sugar, protein, salt, and essential supplements Phases of bacterial growth: 1. Lag phase: adapts to environment 2. Log phase: adaptation is complete and optimal conditions for growth 3. Stationary phase: nutrients, O2 and pH become compromised and toxic products start growing 4. Death phase: nutrients, O2, and pH are depleted and toxin levels lead to death Ideal temp and pH for most bacteria is 5-45 degrees and 4.5-9.5 pH. Aerobe: needs oxygen to grow Anaerobe: doesn’t need oxygen to grow Bacteria growing in different arrays of growth media (places where the bacteria grow) 1. General growth medium: contains nutrients for a wide array of bacteria (allows growth for everything) 2. Selective medium: contains nutrients for selected organisms 3. Differential medium: contains nutrients for growth and differentiation of various organisms (can see more than 1 bacteria at a time) Microbiota Body contains 10x more bacteria than cells Terms Microbiota: taxonomic classification (culture, biochemistry, 16s rRNA) Microbiome: includes all microorganism, genomes, biotic and abiotic factors Metagenome: collection of genomes and genes from member if a Microbiota (has plasmids) JOIN THE DARKSIDE Facts Microbiota makes up 1-3% of our body weight (most are bacteria) Human viruses and viruses called bacteriophages are there The Healthy Microflora Beneficial effects of Microbiota 1. Maturation of immune system 2. Contributes to immune development 3. Source of essential nutrients 4. Production of antibacterial bacteriodicins 5. Maintenance of pH The host provides them with shelter, food, and transport Staphylococcus epidermidis is a sort of “healthy” flora on our body surfaces 1 in 3 in the population carry staphylococcus aureus Dry areas of the body typically have fewer organisms (staphylococcus epidermidis) Moisture areas have more (staphylococcus aureus, candida spp) Fatty areas (or limited o2 areas), hair follicle areas, sebaceous glands and sweat have anaerobic organisms (propionibacterium acnes and diptheroids) Mouth Microbiota 20,000,000,000 bacteria in mouth Salivary microbiome is affected by diet, genes, and environment Examples: streptococcus spp, veillonella spp, etc. The type of feeding has an effect on the type of Microbiota Microbiota is found accommodating in our GI tract as we move from the stomach to colon. We also acquire microbiota at birth. Some of the notable "microbiota acquired at birth : propionic bacterium; lactobacillus; staphylococcus. The microbiota we are born with changes as we grow. Some of the microbiota we die with are: firmicutes, bacteroidetes, actinobacteria, proteobacteria. Microbiota is also known to be distributed geographically. JOIN THE DARKSIDE  The Mycobiome More bacteria as we get older Fungal microbials found an organism and their preferred environments 1. Candida: wet/moist area (more common in female vaginal area) 2. Malasezzia: dry 3. Aspergillu: dry and acidic Pityriasis/Tinea versicolor One of the infections caused by the mycobiome could be pityriasis versicolor caused by malasezzia furfur (on skin). It causes scaly skin & discoloured patches (sometimes itchy). It is mostly prevalent on the chest, abdomen, back & neck. Aspergillus, Candida, Cryptococcus, fusarium, malasezzia, Saccharomyces are all prevalent in clinical practice. Co-presence and exclusion Some (yet few microorganisms form links across different parts of the body. Microorganisms that are closelyrelated occur in the same niche. However, exclusion networks also exist between micro-organisms that are less related. These organisms either thrive together or one prevails. Streptococcus is prevalent in the oral cavity. Bacteroidetes is the signature gut bacterium. In the vagina, one either has prevotella, or lactobacillus. On the skin, one either has propionibacterium or staphylococcus. In the mouth, one has Streptococcus or tannerella. But, prevotella is found with treponema in the mouth Dysbiosis It is the imbalance in the different types of organism in your body GI tract disorders: inflammatory bowel disease (IBD); most common forms are Crohn’s disease & ulcerative colitis. Patients exhibit decreases microbial population and functional diversity (lower firmicutes, higher bacteroidetes) Similar thing happens with IBS and colorectal cancer Metabolic disorders: Obesity (increased firmicutes, decreased bacteroidetes) Type 2 diabetes CNS related disorders: Early colonization of intestinal tract Clostridium difficile infections- enterocolitis Gram positive It is easier to kill an active infection JOIN THE DARKSIDE Clostridium difficile dysbiosis Mild diarrhoea -> pseudomembranous colitis -> sepsis like picture -> death The path to dysbiosis Solution to C. difficile Problem Molecular pathogenesis is the solution - Diagnosis is not easy: breath testing, blood testing, still evaluation, and imaging tests Cure= antibiotics and nutritional supplements (B12) Gut tells brain what to feel JOIN THE DARKSIDE