Introduction to Microbiology PDF

Objectives Introduction to Microbiology 108- 2nd Yr PharmD Dr. Omamah Alfarisi Feb 2024 Introduction By the end of this lecture, students are expected to: Distinguish prokaryotes and eukaryotes Identify the, morphology, taxonomy, and structure of bacteria Differentiate between gram-positive and gram...

Objectives Introduction to Microbiology 108- 2nd Yr PharmD Dr. Omamah Alfarisi Feb 2024 Introduction By the end of this lecture, students are expected to: Distinguish prokaryotes and eukaryotes Identify the, morphology, taxonomy, and structure of bacteria Differentiate between gram-positive and gram-negative bacteria Identify the general process of bacteria pathogenicity and virulence Identify the mechanisms of energy production by bacteria Identify some of the major methods for bacterial identification Introduction membrane Microorganism is an organism that can be seen only through a microscope Bacteria, protozoa, fungi Viruses are not considered living organisms but maybe included in microorganism They can be found in every ecosystem and in close association Few of these microorganisms are pathogenic i.e.: cause disease either through direct infection or by producing toxin or both. IMucous Most infectious disease is initiated by colonization (the establishment of proliferating microorganisms on the skin or mucous membranes). The major exceptions are diseases caused by introduction of organisms directly into the bloodstream or internal organs. 6 The fate of this colonization may be: 1) elimination of the microorganism without affecting the host; 2) infection in which the organisms multiply and cause the host to react by making an immune or other type of response or 3) a transient or prolonged carrier state. 4) Infectious disease occurs when the organism causes tissue damage and impairment of body function. Prokaryotes vs eukaryotes ttm in bac.iarche bac.larchea Characteristics Prokaryotic Cells Chromosome Usually single, circular Nucleus No nuclear envelope or nucleoli Membrane bound, nucleoli present Membrane-bound organelles Not present Present (examples include mitochondria and endoplasmic reticulum) Cell wall Usually present, many contain peptidoglycan Present in plant cells, no peptidoglycan Plasma membrane No carbohydrates, most lack sterols Sterols and carbohydrates present Ribosome 70S Average size 0.2–2 mm in diameter Emt C Eukaryotic Cells Multiple six 80S (70S in organelles) 10–100 mm in diameter Prokaryotic Pathogens: Prokaryotes are mainly divided into bacteria and archaea Typical bacteria: Rigid cell wall, bacteria maintain a definite shape, though they vary as shape, size and structure. Individual bacteria can assume one of three basic shapes: spherical (coccus), rodlike (bacillus), or curved (vibrio, spirillum, or spirochete). Nearly all bacteria, with the exception of the mycoplasma, have cell wall surrounding the cell membrane that determines the shape of the organism. Atypical bacteria: Group of bacteria that cannot be detected on Gram stain due to absence of some structural elements. Some also differ in their metabolic processes. Examples are Mycoplasma, Chlamydia, and Rickettsia. IT FIi i aero None Prok. non Eukar. Eukaryotic pathogens: Fungi: Its contain a well-defined nucleus, mitochondria, Golgi bodies, and endoplasmic reticulum. Most fungi exist as either yeasts or molds; however, some fungi can assume either morphology. no not Viruses: in 8867,8 d I Helminths: so Group of worms that live as parasites, multicellular, eukaryotic organisms with complex body organization to Obligate intracellular parasites that do not have a cellular structure; rather consist of genetic molecules either DNA or RNA surrounded by a protein coat. Protozoa: Single-celled, nonphotosyntetic, eukaryotic organisms. Free living or parasitic III 0 e Prions: Prions consist of a cell-coded protein (PrP: prion protein) altered in its conformation and by point mutations. They are infectious and can cause normal cellular PrP to assume the pathological configuration leading to diseases. 1 1 Normal Flora we Harmed Up until the time of birth, the human fetus lives in a sterile environment By the time of birth, the infant gets exposed to microorganisms from the surrounding Over years, microorganisms resides in surfaces: skin, oral, nasal cavity, GI and genitourinary tract, However Blood and other body organs are sterile 2. Transient Flora 1. Resident Flora E 9pm Constantly present, (or at a given age) Cannot be removed permanently E.g: E.coli in the intestine É i Varies over time Can be removed permanently E.g: Pneumococcus in nasopharynx Can be pathogenic Normal Flora: What can go wrong? I ff.gg Some Flora act as pathogens if they reach a site where they don’t normally inhabitate e.g: normal flora of intestine E.coli may cause Urinary tract infectionsimmunecimmunoderenet (UTI) When individuals are immunocompromised, normal flora can overgrow and become pathogenic. Abnormal multiplication of normal flora can cause diseases such as enteritis and endotoxic shock Some pathogens can overgrow for example when normal bowel flora are depleted by antibiotic therapy; will lead to overgrowth by the pathogenic bacteria Clostridium difficile in the GI, causing diarrhea aÉ Antibiotics kill harmful bacteria during infections. But they also a ect the good gut bacteria. When good bacteria decrease (due to antibiotics), Clostridium di cile (C. di ) can grow excessively. C. di produces toxins, causing gut irritation. This leads to diarrhea. Normal Flora: Advantages I IE5I aYisno enemies Prevent the colonization of body by pathogens (how?) Second, some bacteriane of the bowel produce antimicrobial substances to which the producers themselves are not susceptible. Some produce Vit. K and some Vitamin B and aid in the digestion and nutrients The bacterial colonization of a new-born infants act as a powerful stimulus for the development of the immune system YEg Normal flora: I atypical I Bacterial Morphology spnirias 0 Bacteria es ae ceneneedd Bacterial Structure IIjYopYaYm.c Bacteria Taxonomy factor meme o g membrane All bacteria are prokaryotes The cell envelop: Capsule: (not all bacteria) momma Organized polysaccharide layer Mediate adherence to surfaces, help evade host barrier and immune response Protect bacteria from antibodies and phagocytosis o o Cell wall: Peptidoglycan layer (thick in gram +, thin in Gram -) Cell cytoplasmic membrane: Composition: phospholipid bilayer; polar phosphate groups on the outside of the bilayer and nonpolar lipid chains on the inside. Similar to eukaryotes but contains no steroids (e.g: cholesterol) Function: act as a permeability barrier to the cytoplasm controlling the type and amount of molecules that move in or out of the cell g 01 o Figg am Bacterial Structure I III Cell wall: Peptidoglycan (Sugar + amino acid) Sugar and amino acid polymer that forms the basis of cell wall N-acetyl glucosamine (NAG) and N-acetylmuramic acid (NAM) crosslinked with oligopeptides Component of almost all bacterial walls (exception: mycoplasmas) Thickness of cell wall determines Gram staining.Heart'nocenwan NAG NAM P E P NAG NAG NAM P E P NAM NAG NAM P P E E P P P E P NAG NAM NAG NAG P E P NAM NAG t.mn Difference between Gram + and Gram – Bacteria Gram positive bacteria (stains blue- violet purple) Gram negative bacteria (red) Have a Thick multi-layered peptidoglycan cell walls, No outer membrane (only cytoplasmic membrane) Teichoic acids (TA): covalently linked to peptidoglycan and Lipoteichoic acid (LTA) which is covalently linked to cytoplasmic membrane: essential to cell viability Play a role in pathogenesis (adherence) Both are common surface antigens that distinguish bacterial serotypes Thin peptidoglycan layer Have outer lipid membrane: maintains the bacterial structure, and impairs the permeability of: large molecules (e.g: proteins such as lysozyme) hydrophobic molecules (e.g: some antimicrobials). Provides protection from adverse environmental conditions. The outer membrane has the porin channel that allows passage of metabolites and small hydrophilic antimicrobials. Has periplasmic space II f Cell wall contain virtually non lipopolysaccharide content Periplasmic space is absent I AppendageD Bacterial Structure Appendages: hair-like appendages that project from the cell wall Flagella: long rope-like propellers composed of helically coiled protein subunits (flagellin) anchored in the bacterial membranes through a hook. I Bacterial structure Pili & fimbriae: Pili (sometimes called fimbriae): p ggg shorter and thinner than flagella function as attachment structures that promote adherence- virulence factor Fimbriae and pili are thin, protein tubes originating from the cytoplasmic membrane of many bacteria. Both are able to stick bacteria to surfaces, but pili are typically longer and fewer in number than fimbriae. They are found in virtually all Gram-negative bacteria but not in many Gram-positive bacteria. am Spores: Under harsh conditions, bacteria can convert from a vegetative state to a dormant state, or spore Some gm + (e.g: Bacillus (e.g., Bacillus anthracis) and Clostridium (e.g., Clostridium tetani or botulinum) bacteria are spore formers. Gm negative don’t produce spores Don’t confuse spore production with toxin production ! IT II L Lipopolysaccharide (LPS), imbedded in the outer membrane: The lipid portion of the LPS (lipid A), is toxic to humans and animals (endotoxin). The polysaccharide portion of the LPS is antigenic and can therefore be used to identify different strains and species. can Pathogenesis & Virulence Factors Entry into the host: Bacterial pathogenicity: The first step of infectious process Via several ports: respiratory, GI, urogenital tract, damaged skin Bacteria that have outer polysaccharide capsule have better chance of surviving these primary defense (e.g: Streptococcus pneumoniae and Neisseria meningitidis) Pathogenicity: The ability of the microorganism to induce disease in the host ovarian Virulence: the number of microorganism needed to cause the disease in 50% of the population who are exposed to the pathogen For example, Whereas 100,000 of Salmonella is needed to cause diarrhea in the gastrointestinal (GI) tract, only 100 Shigella is need to cause diarrhea. The ability of the pathogen to cause the disease depends on different factors some related to the pathogen’ virulence factors and others related to the host’s immune system. The mechanism through which the infectious process takes place can vary widely between bacteria but general steps are required to cause the disease. É Pathogenesis & Virulence Factors Biofilm formation: aggregates of microorganisms in which cells are embedded in a self-produced matrix of extracellular polymeric substances protecting the bacteria from the host removal and antimicrobial drugs O mom C Host-mediated pathogenesis: The pathogenesis of many bacterial infections is caused by the host response rather than by bacterial factors. The tissue damage in these infections is caused by various immune cells and mediator at the site of infection or in the blood- stream. Often the host response is so intense that host tissues are destroyed, allowing remaining bacteria to proliferate. o Antigenic variation: A successful pathogen must evade the host’s immune system that recognizes bacterial surface antigens. One important evasive strategy for the pathogen is to change its surface antigens either by switching off and on those antigens or changing them. Adherence to cell: o Some bacteria (e.g: Escherichia coli) use pili to adhere to the surface of host cells. Group A streptococci have similar structures (fimbriae). Invasiveness: reason The ability of pathogen to enter/penetrate host cell or mucosa Invasiveness is facilitated by several bacterial enzymes, e.g: collagenase and hyaluronidase They degrade components of the extracellular matrix, providing the bacteria with easier access to host cell surfaces. Many bacteria express membrane protein known as “invasion” that interact with some host cells to facilitate their uptake. Toxins: o O Toxigenicity refers to an organism’s ability to make toxins For bacteria, there are two categories of toxins, the exotoxins and the endotoxins: Exotoxin: Produced by Gm+ or Gm- 498 ane Endototxin: Gm- 5 Proteins produced inside pathogen as part of their growth and metabolism Secreted out of the pathogenic cell Heat labile (60-80 C) Highly toxic F it.mnEiger Lipid portion of lipopolysaccharide (LPS) that is part of the outer membrane Not release outside the pathogenic cell Heat stable (250C) Moderate toxic Mechanisms for energy production by bacteria Aerobic o eggs Requires Presence of oxygen for energy production O2 is the terminal electron acceptor of the electron transport chain ox Anaerobic Absence of O2 inorganic compounds (e.g: nitrate or sulfate) are the terminal electron acceptor of the electron transport chain. Can be either the main mechanism of the bacteria (obligate anaerobes) or in some can be used as an alternative to aerobic respiration (facultative organisms) born Fermentation Presence or Absence of O2 organic compounds are terminal electron acceptor. Energy produced by fermentation is less than that produced by aerobic and anaerobic respiration How to identify the bacteria Microscopy methodsEgg.IE Gram Staining: The most important differential technique: Gram-positive bacteria stain blue-violet, Gram + cells have a thick layer of peptidoglycan in the cell wall that retains the primary stain, crystal violet. Gram-negative bacteria stain red: Gm - cells have a thinner peptidoglycan layer that allows the crystal violet to wash out on addition of ethanol. Gram staining is almost always the first step in the preliminary identification of a bacterial organism. While Gram staining is a valuable diagnostic tool, not all bacteria can be definitively classified by this technique. mmicroscop o 0 atepicaebac.cannorxe.gmycobacteria monocenwa nora Fg Immune Detection Culturing methods: Microscopy methods Acid-fast stain (Ziehl-Neelsen technique): m.am nopa nocenwan Used to stain mycobacteria, which do not “take” gram or methylene blue stains due to the amounts of lipids in their cell walls. Since mycobacteria cannot be destained with HCl-alcohol, they are called acidresistant rods. The mycobacteria are stained red and everything else blue. H Fluorescence microscopy E A fluorochrome absorbs shortwave light and emits light with a longer wavelength. The stained particles appear clearly against a dark background in the color of the emitted light. 0 I Culturing is a method of multiplying microbial organisms by letting them reproduce in predetermined culture medium under controlled laboratory conditions. Microbial cultures are basic diagnostic methods “gold standard” Culturing is required in most cases to detect and identify bacteria. Nutrient mediums are either liquid (nutrient broth) or gelatinous (nutrient agar, containing 1.5–2% of the polysaccharide agarose). to Molecular Methods (genetic material identification): The main objective is direct recognition of pathogen-specific DNA nucleotide sequences in the test material. These methods are used in particular in the search for bacteria that are not culturable, are very difficult to culture, or proliferate very slowly. Immunologic Detection (antigen-antibody identification): Depends on the concept of antigen-antibody binding. It uses a prior knowledge of known antigens and/or antibodies to identify the intended pathogen. A. Direct detection of bacterial antigens: Antigens specific for particular species or genera can be detected directly by means of polyclonal or monoclonal antibodies present in the test material. This allows for rapid diagnosis. B. Serological identification serum antibodies: when the direct pathogen antigen is not known, identification of the serum antibodies produced as a result of the pathogenic antigen is way of determining current or past infection with a specific pathogen.