Microbiology and Immunology PDF

# Topic 1: Introduction to Medical Microbiology. ## History | Date | Invention/Discovery | Autor's | Comment | |---|---|---|---| | 1590 | Microscope | Hans and Zacharias Jansen, Hans Lippershey | wrote a book (Micrographia) describing fleas, roots, head lice, insects,... | | 1665 | cells | Robert...

# Topic 1: Introduction to Medical Microbiology. ## History | Date | Invention/Discovery | Autor's | Comment | |---|---|---|---| | 1590 | Microscope | Hans and Zacharias Jansen, Hans Lippershey | wrote a book (Micrographia) describing fleas, roots, head lice, insects,... | | 1665 | cells | Robert Hooke | Observed animalcules (protozoa) from teeth plaque | | 1677 | Microorganisms | Anton Van Leeuwenhoek = Father of Microbiology | + bacteria, sperm, blood cells,... | | 1796 | Vaccination/ immunology | Edward Jenner = coined the word vaccine from the latin "vacca" | Through smallpox | | 1846 | He implement mandatory hand washing and chlorine disinfection of instruments | Ignaz Semmelweis | By studying maternal mortality after labor, he implemented mandatory hand washing. + instrument disinfection by chlorine | | 1864 | Pasteurization | Louis Pasteur | Heating beer, milk, alcohols | | 1867 | Phenol= sterilize surgical instrument and clean wounds | Sir Joseph Lister | applied Louis Pasteur's principles | | 1876 | Postulate 1-4 that microbes are the causative agent of any given infection or disease | Robert koch | by working on B. anthrax | | 1892 | Foundation of virology | Dimitri Ivanoski | By infected tobacco leaves | | 1910 | Concept of chemotherapy + Salvarsan, an arsenic treating syphilis | Paul Ehrlich | | | 1928 | Discover penicillin (penicillium notatum) | Alexander Fleming | A fungi with antibacterial properties | | 1931-1938 | Developed the electron microscope | Max Knoll, Ernst Ruska | | ## Importance of Microbiology. - Bacteria appeared approximately 3.5 billion years ago. - Microbes are involved in photosynthesis - account for >50% of the earth's oxygen. Decomposition - nutrient recycling - Microbes are used in food industry, to synthesize medicines and vaccines, and bioremediate contaminated water. - Microbes are responsible for diseases in humans and animals → link between microorganisms and disease. - Robert Koch verified the germ theory, which states that many diseases are caused by microorganisms and not by sins, bad character, poverty or other social problems - What are the main differences between countries with respect to causes of death? Vaccination and antibiotics ## Epidemics, Pandemics, Endemics: - **Epidemics**: unexpected increase in the number of disease cases in a specific region → - **Pandemic**: when the virus covers a wide area. Ex Covid 19 - **Endemics**: disease consistently present but limited to a particular region. Ex Malaria - History's most deadly pandemics ## Healthy Microbiome - Human fetus lives in a sterile environment → infant are exposed to bacteria, archaea, fungi and viruses from the mother and the environment. Over the next few years, communities of organisms (microbiota or normal flora) form on the surfaces of the skin, nose, oral cavity, intestines, and genitourinary tract. - Humans share a core microbiome (95%) at specific site: nose, skin, mouth, intestine and vagina. - The most personal microbiome is found in the intestine and mouth. - Microorganisms affect ALL aspects of our existence→ recently named the “the last organ" - The host provides a place to colonize, nutrients, and some protection from unwanted species (innate immune responses). The microbes provide: - stimulate innate and regulatory immunity, - needed metabolic functions, - prevent colonization with unwanted pathogens. - If the microbiota gets unbalanced a dysbiosis is produced. This leads to chronic inflamation and potentially cancer. ## The microbial word - The domains are clustered on the basis of 16S rRNA sequence and are further divided into: - Kingdom ## There are four main types of microorganisms in Medical Microbiology ### Bacteria - This domain includes a group of phylogenetically related prokaryotes distinct from Archaea - It is estimated that bacterial species on Earth number in the hundreds of thousands, of which only about 5500 have been discovered and described in detail. - Bacteria are prokaryotes (lacking a formal nuclear structure) - Their DNA is usually a single molecule, generally covalently closed and circular (bacterial chromosome) - Sometimes they carry extra-chromosomal DNA (plasmids) - Bacterial cells are smaller than eukaryotic cells, usually less than 2 micrometres in diameter - Responsible for many serious human and animal infections (syphilis, faringitis, endocarditis, anthrax,...) ### Fungi - 2nd most common category after insect - Fungi are everywhere. There are approximately 1.5 million different species of fungi on Earth, but only about 300 of those are known to cause disease in humans, - Fungi are eukaryotes - They live outdoors in soil and on plants and trees as well as on many indoor surfaces and on human skin. - Mild fungal skin diseases can look like a rash and are very common. - Fungal diseases in the lungs are often similar to other illnesses such as the flu or tuberculosis. - Some fungal diseases like fungal meningitis and bloodstream infections are less common than skin and lung infections but can be deadly. ### Parasites - A parasite is an organism that lives on or in a host and gets its food from or at the expense of its host. - There are three main classes of parasites that can cause disease in humans: protozoa, helminths, and ectoparasites. - Protozoa are microscopic, one-celled organisms that can be free-living or parasitic in nature. They are able to multiply in humans, which contributes to their survival and also permits serious infections to develop from just a single organism. - Helminths are large, multicellular organisms that are generally visible to the naked eye in their adult stages. Like protozoa, helminths can be either free-living or parasitic in nature. In their adult form, helminths cannot multiply in humans. - Ectoparasites: ticks, fleas, lice, and mites that attach or burrow into the skin and remain there for relatively long periods of time (e.g., weeks to months). ### Virus - Viruses are genetic elements that can replicate independently of a cell's chromosomes but not independently of cells themselves. - Sub microscopic entities consisting of a single nucleic acid surrounded by a protein coat and capable of replication only within the living cells of bacteria, animals or plants. - Obligate Intracellular Parasites - Viruses are characterized by having an extracellular state, known as virion, in this extracellular state the virus particle is metabolically inert and does not carry out respiratory or biosynthetic functions. - The origin of modern viruses is unclear. There are two hypotheses: - They could be fugitive pieces of nucleic acid belonging to a larger body that broke off and became active, therefore, new viruses are being formed frequently and many do not have ancestors. - The viruses once lived outside the host cells, but with time due to its parasitic lifestyle, lost the genes required to live outside the host. - DNA or RnA viruses but not both - Envellope virus (prot) vs naked virus (prot + lipidic coat) - The structure of virions is quite diverse, presenting differences in size, shape, and chemical composition. - The nucleic acid of the virion is always located within the particle, surrounded by a protein coat called the capsid (coat, shell). - The protein coat is always formed of a number of individual protein molecules, called structural subunits, which associate to form morphological units or capsomers. - The complete complex of nucleic acid and protein is called the virus nucleocapsid. If the nucleocapsid is enclosed in a membrane the virus is enveloped. Otherwise is called naked virus. - Classification depen on : - Species that infect: animal viruses, plants, bacteria,... - Presence or absence of lipid envelope - Symmetry of the nucleocapsid - Depending on the type of nucleic acid (DNA or RNA) - Depending on the number of nucleic acid strands, their structure and the polarity of the viral genome. ## TAXONOMY - A system for organising, classifying and naming living organisms. - The primary concerns of taxonomy are classification and nomenclature. - Modern biologists currently use the three-domain (archaea, bacteria and eukarya) taxonomic system developed by Dr. Carl Woese in 1990. ### Domain: Bacteria - The domains are classified in phyla, classes, orders, families, genera, and species, plus subtypes if any. For example: - Phylum: Proteobacteria - Class: Gamma proteobacteria - Order: Coccidioides - Family: Enterobacteriaceae - Genus: Escherichia - Species: E. coli - Subtype: Serovar O157 ### Species - The “basic unit” of taxonomy, representing a specific, recognized type of organism is the SPECIES. - For sexually reproducing organisms, a fundamental definition of “species” has been reproductive compatibility - Organisms within a genus generally share 93% similar rRNA - Organisms within a species generally share 97% similar rRNA - This definition fails for many microbial species (including bacteria), because they do not reproduce sexually. ## Species in non-sexually dividing organisms - A population of cells with similar characteristics - Clone: A population of cells derived from a single cell (genetically identical) - Strain: A subgroup within a species with one or more characteristics that distinguish it from other subgroups in the species (not genetically identical) ## Binomial system of nomenclature - Scientific or Systematic Name: - Genus name + species name - Italicized or underlined - Genus name is capitalized and may be abbreviated - Species name is never abbreviated. - A genus name may be used alone to indicate a genus group; a species name is never used alone - example: - B. subtilis - Bacillus - subtilis ## Examples ### Bacterial classification - Bacteria are single celled microbes. The cell structure is simpler than that of other organisms as there is no nucleus or membrane bound organelles. - Classification can be done on the basis of: - Morphology - Structure - Metabolism ### Bacterial morphology - **Coccus**: round shape - **Bacilli**: elongated, rod-shape - **Other shapes** - Vibrio → diarrhea(death risk) - Spirillum → not pathogen in human ### Spirochetes - Siphylis =STD - Treponema pallidum - Shape of the cell is referred to as its morphology - Bacteria vary in size from 0.1 to 50 micrometres ### Bacterial structure - Intracellular structures: - Bacterial chromosome - Plasmids (not always) - Ribosome (70S): two subunits, 30S and 50S - Cell membrane (no cholesterol) - Extracellular structures - Flagella - Pili - Cell wall - Capsule (not always) - Flagella = No good if they have flagella because they move away from antibiotics: - long helical filaments extending from the cell surface, - made (mainly) of a protein called flagellin - involved in chemotaxis (positive and negative) - Pili, also known as Fimbriae = More stiky they are ...more pathogen - short, rigid and numerous - involved in: - Attachment to other bacteria and/or host cells - Avoid phagocytosis and immune recognition - The main structural component of the cell wall is a peptidoglycan (also known as murein). - It is a mixed polymer of hexose sugars (N-acetylglucosamine and N-acetylmuramic acid) and amino acids ### Gram pattern - In 1882, Christian Gram devised a bacterial staining method to visualize bacterial groups. - Bacteria are classified according to their cell wall as Gram-positive or Gram-negative. #### Gram positive and negative structure - In Gram-positive the peptidoglycan forms a thick (20-80 nm) layer, external to the cell membrane, and may contain other macromolecules. - In Gram-negative species the peptidoglycan layer is thin (5-10 nm) and is overlaid by an outer membrane, which contains lipopolysaccharides and lipoprotein - The periplasm is the space between the inner and outer membrane in Gram-negative bacteria. In Gram-positive bacteria a smaller periplasmic space is found between the inner membrane and the peptidoglycan layer. #### Lipopolysaccharide - Conserved structure in all Gram-negative bacteria - Essential for structural integrity and viability of the bacteria - LPS is also known as endotoxin because it induces a strong immune response in the host. - It has also been implicated in other aspects of bacterial ecology, such as surface adhesion. #### Other cell wall compartment - **Teichoic acids**: typically have a backbone of (polyol-phosphate)n, usually with sugars and/or the amino acid D-alanine as substituents. They are probably involved in uptake of Mg2+ by the cell. Only present in Gram positives. - **Teichuronic acids**: similar polymers found in capsules or LPS in some Gram negative bacteria. - **Other**: Lipids, proteins... #### Capsule - Capsule = Sugar layer hyding the bacteria - Capsule → meningites - No capsule → otites - Same genu - External to the cell wall there may be an additional capsule of high molecular weight polysaccharides that give a slimy surface. - Very important in virulence, as protects the microorganism from the host immune system. ## Bacterial nutrition and metabolism - It is a process by which chemical substances (nutrients) are acquired from the environment and used in cellular activities. - Bacteria take up small molecules such as amino acids, oligosaccharides and small peptides across the cell wall. - Transport of nutrients into the cytoplasm is achieved by the cell membrane using facilitated diffusion or active transport. - Gram-negative species can also take up larger molecules after preliminary digestion in the periplasmic space ## Microbial metabolism: - From the Greek word metabole, meaning change. - Metabolism - the sum of the biochemical reactions required for energy generation AND the use of energy to synthesize cell material from small molecules in the environment. - Why is important? - Because we want to know how to inhibit metabolism to control bacterial growth ### Metabolism - Two components: - **Anabolism** - biosynthesis - building complex molecules from simple ones - requires ENERGY (ATP) - **Catabolism** - degradation - breaking down complex molecules into simple ones - generates ENERGY (ATP) - 3 Biochemical Mechanisms Utilized - Aerobic Respiration - Anaerobic Respiration - Fermentation ### METABOLIC DIVERSITY - Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: - Source of energy. - Source of carbon. - Source of electron acceptors (energy production) - These requirements can be combined: - In every possibility there is bacterias - All pathogen bacteria are in the last group→ chemoorganotrophes - All pathogenic bacteria are organotrophs - They obtain energy by oxidizing preformed organic molecules (carbohydrates, lipids and proteins) from their environment ## 3. Energy Production - Three Biochemical Mechanisms Utilized: - Aerobic Respiration - Anaerobic Respiration - Fermentation ### Aerobic respiration - Molecular Oxygen (O2) serves as the final e- acceptor - O2 is reduced to H2O - 3 Coupled Pathways Utilized - Glycolysis - Kreb's Cycle or Tricarboxylic Acid Cycle or Citric Acid Cycle - Respiratory Chain or Electron Transport Chain (ETC) ### Anaerobic respiration - Utilizes same 3 coupled pathways as Aerobic Respiration - Used as an alternative to aerobic respiration - Final electron acceptor something other than oxygen: - NO3-: Pseudomonas, Bacillus. - SO4-: Desulfovibrio - CO3-: methanogens - Lower production of ATP because only part of the TCA cycle and the electron transport chain operate. ### Fermentation - Incomplete oxidation of glucose or other carbohydrates in the absence of oxygen - Uses organic compounds as terminal electron acceptors - Effect a small amount of ATP - Production of ethyl alcohol by yeasts acting on glucose - Formation of acid, gas & other products by the action of various bacteria on pyruvic acid