Microbiology I Lecture Notes - Second Stage - PDF

Microbiology I Pharmacy department Lecture -1 Second Stage Medical Microbiology I Introduction to microbiology..... Microorganisms/microbes: are microscopic living organisms which are very diverse...

Microbiology I Pharmacy department Lecture -1 Second Stage Medical Microbiology I Introduction to microbiology..... Microorganisms/microbes: are microscopic living organisms which are very diverse and invisible by naked eye. They can be found in nearly every environment. The life in our planet is impossible without microbes due to their important role in generation of energy. Bacteriology The bacteria—small single-celled prokaryotic organisms Mycology The fungi, a group of eukaryotes that includes both microscopic eukaryotes (molds and yeasts) and larger organisms (mushrooms, puffballs) Protozoology The protozoa—animal-like and mostly single-celled eukaryotes Parasitology Parasitism and parasitic organisms—traditionally including pathogenic protozoa, helminth worms, and certain insects. Virology Viruses—minute, noncellular particles that parasitize cells Phycology or Algology Simple photosynthetic eukaryotes, the algae, ranging from single-celled forms to large seaweeds. Morphology The detailed structure of microorganisms. Physiology Microbial function (metabolism) at the cellular and molecular levels. Taxonomy Classification, naming, and identification of microorganisms Microbial. Genetics, Molecular Biology The function of genetic material and biochemical reactions that make up a cell’s metabolism Microbial Ecology Interrelationships between microbes and the environment; the roles of microorganisms in the nutrient cycles and natural ecosystems The Importance of Microorganisms Benefits -Basis of food chain. -Photosynthesis. -Digestion, synthesis of vitamins. -Manufacture of food and drinks. -Synthesis of chemical products. -Recycling sewages. -Use of microbes to control crop pests. 1 Microbiology I Medical microbiology: the field of microbiology that deal with study of pathogenic microorganisms and their interactions with human as causative agents of infectious diseases, with the prevention, diagnosis and treatment of these diseases. It covers the branches of bacteriology, virology, mycology, parasitology and immunology. Types of microbial pathogens: The pathogenic organisms of infectious diseases can be classified into four major groups of organisms: viruses, bacteria, fungi and parasites. Differences between these groups are listed in table number (1). Table (1): Comparison between main groups of major pathogens. Virus Bacteria Fungi Parasite Size smallest larger and more larger than larger than infectious complex than bacteria bacteria agents viruses (20 nm-300 nm) Cell type particle Prokaryote Eukaryote Eukaryote No. of cell acellular Unicellular Uni- Uni- /multicellular /multicellular Cell wall - + + - Type of DNA or RNA DNA and RNA DNA and RNA DNA and RNA Nucleic acid Nuclear - - + + membrane No true true nucleus true nucleus nucleus Organelles - Only small + + Ribosomes Replication Replicate only Binary fission budding or Mitosis within living mitosis cells 2 Microbiology I Generally microbes can be divided into two categories: Cellular microbes and the acellular microbes 1- In the cellular camp: we have the bacteria, archaea, fungi, and the protists Cellular microbes can be either unicellular, where one cell is the entire organism, or multicellular, where hundreds, thousands or even billions of cells can make up the entire organism. 2- In the acellular camp: we have the viruses and other infectious agents, such as prions and viroid. Normal microbial flora: are permanent residents of certain body sites, especially skin, mouth, nose, colon and vagina, without causing any disease. It includes various non-pathogenic bacteria and yeasts, while all viruses and most parasites are usually not considered as members of normal flora, although they present in asymptomatic individuals. The members of normal flora vary in both number and kind from one site to another; although it is extensively populates many areas in the body, the internal organs are sterile. Normal flora should be differentiated from carrier state and colonization: Carrier state: an individual who harbors a potential pathogen, and can be a source of infection to others; whether it is asymptomatic infection or a person recovered from a disease and continue to carry and shed the organism for a long period. Colonization: an acquisition of a new organism, that may cause an infectious disease or may be eliminated by the immune system. The normal flora has 3 roles in the body: 1- They can cause disease, especially in immunocompromised individuals or when it changes its anatomical location. 2- Constitute a protective host defense mechanism, as it prevent colonization of pathogenic organisms and produce inhibitory substances. 3- They may serve a nutritional function, as the intestinal bacterial flora produce many vitamins B and vitamin K 3 Microbiology I Prokaryotes vs. Eukaryotes: All types of cells can be divided into two different types according to the nucleus: Prokaryote and Eukaryote. The differences between them are : 1. The eukaryotic cell has a true nucleus with multiple chromosomes surrounded by a nuclear membrane. The prokaryotic cell has not true nucleus but has single circular loosely chromosome in cytoplasm lacking nuclear membrane. 2. All types of cells contain both types of nucleic acid (DNA and RNA) , except viruses contain one type of nucleic acid, either DNA or RNA. 3. The prokaryotic organisms are only unicellular, whereas eukaryotic organisms either unicellular or multicellular. 4. Eukaryotic cells contain cellular organelles (such as mitochondria, lysosome, large80s ribosome, Golgi apparatus and others), whereas prokaryotic cells contain no organelles except small 70s ribosome. 5. Most prokaryotes have rigid cell wall that contain peptidoglycan, whereas eukaryotes not contain peptidoglycan but have flexible cell membrane, except fungi and plant cells have cell wall. 6. The prokaryotic cell (eg; bacteria) replicate by binary fission, whereas most eukaryotic cells replicate by mitosis. During which one parent cell divided to make two progeny cells. In contrast, viruses produce many copies of nucleic acid and protein , then reassemble into multiple progeny viruses. 4 Microbiology I Eukaryote 5 Microbiology I Scientific nomenclature: Scientific nomenclature for organisms as illustrated by Carolus Linnaeus, consist of two parts: genus and species. First name for genus and second name for species. First letter of genus must be written in capital, whereas first letter of species must be written in small form. The Latinized name of genus and species for any organism must be written in Italic form or place line under each genus and species. Example: Staphylococcus aureus or Staphylococcus aureus Bacillus anthracis or Bacillus anthracis Classification of Organisms Hierarchy of Taxonomic Categories DOMAIN Kingdom Phylum or Division Class Order Family Genus Specie 6 Microbiology I History of Microbiology (IMPORTANT CONTRIBUTIONS) Antony van Leeuwenhoek (1632 – 1723) who invented the first microscope (50 –300x), was the first to accurately observe and describe microorganisms. Louis Pasture known as ‘Father of Microbiology’ (1822-1895) He was a professor of chemistry in France. His studies on fermentation led him totake interest to work in Microbiology He had proposed the principles of fermentation for preservation of food Introduced sterilization techniques and developed steam sterilizer, hot air oven and autoclave Described method of pasteurization of milk Contributed for vaccine development against several diseases Postulated “germ theory of disease” Robert Koch known as ‘Father of Bacteriology’ (1843-1901). He got Nobel prize in year 1905 for the discovery of tubercle bacilli Introduced solid media for culture of bacteria and use of agar Methods of isolation of bacteria in pure culture Described hanging drop method for motility of organism. Discovered bacteria like anthrax, cholera and tubercle bacilli Introduced staining techniques by using aniline dyes Koch’s postulates and Koch’s phenomenon was given by him Edward Jenner known as ‘Father of Immunology’. Developed the first vaccine of world, the small pox vaccine. Used cowpox virus to immunize children against smallpox Alexander Fleming, Scotland (1928) discovered penicillin Selman Waksman, Ukraine (1944) discovered streptomycin Charles Chamberland (1851-1908) discovered viruses and their role in disease. 7 Microbiology I Characteristics of Microbes & Bacterial Structure….. 1- Size of Microbes: Microbes vary in size ranging from 10 nm (nanometers) to 100 mu (micrometers) to the macroscopic. Viruses in nm = 10-9 m (meter) Bacteria in M m = 10 -6 m Helminthes in mm = 10-3 m 8 Microbiology I 2- Shapes and arrangements of Bacteria Depending on their shape, bacteria are classified into several varieties 1. Cocci are spherical or oval cells 2. Bacilli are rod shaped cells 3. Vibrio are comma shaped curved rods and derive their name from their characteristics vibratory motility. 4. Spirillum are rigid spiral forms. 5. Spirochetes (from speira meaning coil and chaite meaning hair) are flexuous spiral forms 6. Actinomycetes are branching filamentous bacteria, so called because of a fancied resemblance to the radiating rays of the sun when seen in tissue lesions 7. Mycoplasma are bacteria that are cell wall deficient and hence do not possess a stable morphology. They occur as round or oval bodies and as interlacing filament ts. Bacteria sometime show characteristic cellular arrangement or grouping. According to the plane of cellular division, cocci may be arranged in pairs (diplococci), chains (streptococci), groups of four (tetrads) or eight (sarcina), or grape like clusters (staphylococci). 9 Microbiology I 10 Microbiology I 3- BACTERIAL STRUCTURE five essential structural components: a nucleoid (DNA), ribosomes, cell membrane, cell wall, and outer membrane. Non-essential structural components : capsule , flagella , pili and spore The outer layer or cell envelope consists of two components, a rigid cell wall and beneath it a cytoplasmic or plasma membrane. The cell envelope encloses the protoplasm, comprising the cytoplasm, cytoplasmic inclusions such as ribosomes and mesosomes, granules, vacuoles and the nuclear body. 11 Microbiology I 1- Cell wall Beneath the external structures is the cell wall. It is very rigid & gives shape to the cell. Its main function is to prevent the cell from expanding & eventually bursting due to water uptake. Cell Wall constitutes a significant portion of the dry weight of the cell and it is essential for bacterial growth & division. The cell wall cannot be seen by direct light microscopy and does not stain with simple stains. It may be demonstrated by micro dissection, reaction with specific antibodies, mechanical rupture of the cell, differential staining procedures or by electron microscopy. Outermost component common to all bacteria - Multilayered structure located external to the cytoplasmic membrane - Composed of an inner layer of peptidoglycan and an outer membrane that varies in thickness and chemical composition depending upon the bacterial type The membrane has four important functions: (1) active transport of molecules into the cell. (2) energy generation by oxidative phosphorylation. (3) synthesis of precursors of the cell wall. (4) secretion of enzymes and toxins. 12 Microbiology I CELL WALLS OF GRAM-POSITIVE AND GRAM-NEGATIVE BACTERIA The structure, chemical composition, and thickness of the cell wall differ in gram-positive and gram-negative bacteria 1. The peptidoglycan layer is much thicker in gram-positive than in gram-negative bacteria. 2. Some gram-positive bacteria also have fibers of teichoic acid, which protrude outside the peptidoglycan, whereas gram-negative bacteria do not. 3. Gram-negative bacteria have a complex outer layer consisting of lipopolysaccharide, lipoprotein, and phospholipid 4. Between the outer-membrane layer and the cytoplasmic membrane in gram- negative bacteria is the periplasmic space, which is the site, in some species, of enzymes called B -lactamases that degrade penicillin and other B-lactam drugs. 13 Microbiology I Outer Membrane Outer membrane is found only in Gram-negative bacteria, it functions as an initial barrier to the environment and is composed of lipopolysaccharide (LPS) and phospholipids Lipopolysaccharide Lipopolysaccharide (LPS) of the outer membrane of the cell wall of gram-negative bacteria is endotoxin Responsible for fever and shock (especially hypotension) Called endotoxin because it is an integral part of the cell wall, in contrast to exotoxins, which are actively secreted from the bacteria The LPS is composed of three distinct units : 1. A phospholipid called lipid A, which is responsible for the toxic effects 2. A core polysaccharide of five sugars linked through ketodeoxyoctulonate(KDO) to lipid A 3. An outer polysaccharide consisting of up to 25 repeating units of three to five sugars ,This outer polymer is the important somatic, or O antigen of several gram-negative bacteria that is used to identify certain organisms in the clinical laboratory 14 Microbiology I Peptidoglycan The term "peptidoglycan" - peptides and the sugars (glycan) that make up the molecule A complex, interwoven network that surrounds the entire cell Composed of a single covalently linked macromolecule Found only in bacterial cell walls Provides rigid support for the cell, maintaining the characteristic shape of the cell, and allows the cell to withstand media of low osmotic pressure, such as water 15 Microbiology I Teichoic Acid Fibers of glycerol phosphate or ribitol phosphate are located in the outer layer of the gram-positive cell wall Ability to induce septic shock when caused by certain gram-positive bacteria Mediate the attachment of staphylococci to mucosal cells. Gram-negative bacteria do not have teichoic acids The functions of Teichoic acid 1- gives negative charge 2-major antigenic determinant 3- transport ions 4- anchoring 5- external permeability barrier 16  Microbiology I 2- Cytoplasmic membrane Cytoplasmic membrane is present immediately beneath the cell wall, found in both Gram positive & negative bacteria and it is a thin layer lining the inner surface of cell wall and separating it from cytoplasm. It acts as a semipermeable membrane controlling the flow of metabolites to and from the protoplasm. 3- Cytoplasm The cytoplasm is a Colloidal system containing a variety of organic and inorganic solutes containing 80% Water and 20% Salts, Proteins. They are rich in ribosomes, DNA & fluid. 4- Mesosomes A large invaginations of the plasma membrane, irregular in shape. a. increase in membrane surface, which may be useful as a site for enzyme activityin respiration and transport. b. may participate in cell replication by serving as a place of attachment for the bacterial chromosome. 5- periplasmic space is between the cell membrane and the cell wall. It contains enzymes and other proteins, such as chemoreceptors for sensing the environment. 6- Ribosomes They are the centers of protein synthesis. They are slightly smaller than the ribosomes of eukaryotic cells 7- Nucleus 1-The area of the cytoplasm in which DNA is located. 2-DNA of prokaryotes is a single, circular molecule 3-Contains no nuclear membrane, no nucleolus, no mitotic spindle, and no histones 4-Bacterial DNA has no introns, whereas eukaryotic DNA does 8- Granules Serve as storage areas for nutrients and stain characteristically with certain dyes 17 Microbiology I 9- Capsule Gelatinous layer covering the entire bacterium Composed of polysaccharide Sugar components of the polysaccharide vary from one species of bacteria to another The capsule is important for four reasons: 1. Determinant of virulence of many bacteria since it limits the ability of phagocytes to engulf the bacteria 2. Specific identification of an organism can be made by using antiserum against the capsular polysaccharide. 3. Capsular polysaccharides are used as the antigens in certain vaccines 4. Play a role in the adherence of bacteria to human tissues, which is an important initial step in causing infection. 10- Pili (Fimbriae) Hair like filaments that extend from the cell surface Shorter and straighter than flagella Composed of subunits of pilin, a protein arranged in helical strands Found mainly on gram-negative organisms Pili have two important roles: 1- Mediate the attachment of bacteria to specific receptors Fimbriae (singular = fimbria) are pili used to attach the bacteria to target cells ( in infection) or to surfaces, where they form a biofilm. 2-Role of sex pilus during conjugation DNA can be transferred between bacteria by conjugation, which is initiated when sex pili on the donor cell attach to and draw in the recipient cell. 18 Microbiology I 11-Flagella Long, whip like appendages that move the bacteria toward nutrients and other attractants, a process called chemotaxis, they are composed of flagellin protein. Flagellated bacteria have a characteristic number and location of flagella: Some bacteria have one, and others have many, in some, the flagella are located at one end, in others, they are all over the outer surface 12- SPORES Highly resistant structures formed in response to adverse conditions Importance of spores lies in their extraordinary resistance to heat and chemicals. As a result of their resistance to heat, sterilization cannot be achieved by boiling, Steam heating under pressure (autoclaving) at 121°C, usually for 15-20 minutes, is required to ensure the sterility of products for medical use 19 Microbiology I Endospore Function Endospores are ultimately protection for the bacterial genome Spores form within the cell and contain a full copy of the bacterial genome Endospores are not a form of reproduction, because only one new cell germinates from each spore – Spores can be variable in size and location within the cell Spores are produced only by a few genera – Anthrax – Bacillus species including anthracis (anthrax) and cereus (endotoxin causes ~5% of food poisoning) – Clostridium – species including tetani (tetanus), perfringens (gangrene), and botulinum (botulism: food poisoning from improperly canned food The sporulation process begins when nutritional conditions become unfavorable, depletion of the nitrogen or carbon source (or both) being the most significant factor. The endospore is able to survive for long periods of time until environmental conditions again become favorable for growth. The endospore then germinates, producing a single vegetative bacterium These spores are resistant to bactericidal agents and adverse physical conditions. Each spore can give rise to only one endospore which play a role in heat resistance. Spores consists of three layers namely core, cortex and spore coat 20 Microbiology I 21 Microbiology I Characteristics of B 22 Microbiology I Q1/ What are the main human body organs free from microflora (sterile) ? Q2/ What are the microorganisms (microflora) can produce vitamins ? 23