introduction to Microbiology


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introduction to Microbiology

  1. 1. Microbiology  MODULE TITLE: INTRODUCTION TO MEDICNE  MODULE CODE:BM-IM401/1  Course title: Microbiology Course Instructor: Meka A. MSc. 1
  2. 2. Course Objectives At the end of the course the students should be able to:      Describe the historical development of microbiology and the natural history of microbial diseases Explain the rationale for classifying microbes into bacteria, fungi viruses, parasites Classify microorganisms and illustrate their cellular/anatomic characteristics in general Discuss the Unique differentiating features of eukaryotes and prokaryotes Identify the source and spread of microbes 2
  3. 3.  Describe The nature of bacteria  Discuss the morphological differences and Growth requirement of bacteria, nomenclature and classification of bacteria Explain biology of protozoa Describe medically important helminths, ectoparasites Discuss the nature and properties of viruses Explain brief appraisal of pathogenicity of viruses Describe nature of fungi : basic structures and classification Identify sterilization and disinfection methods List the different mechanisms of disinfection and sterilization        3
  4. 4. Introduction  Microbiology     Is the study of microorganisms Microorganisms are all single-celled microscopic organisms and include the viruses, which are microscopic but not cellular Microbial cells differ in a fundamental way from the cells of plants and animals microorganisms are independent entities that carry out their life processes independently of other cells 4
  5. 5.  The science of microbiology revolves around two interconnected themes: (1) understanding the living world of microscopic organisms, (2) applying our understanding of microbial life processes for the benefit of humankind and planet Earth 5
  6. 6. Microorganisms The main types of medically important microorganisms: 1. Bacterium, 2. Fungus, 3. Virus, 4. Protozoan, 5.Helminth. 6
  7. 7. Historical development of microbiology and the natural history of microbial diseases  Microorganisms are visible with the help of magnifying lenses (ex. Microscope) → Microscope is the tool of microbiologist. Microbiology started after the discovery of magnifying lenses. Microscope has two major roles: i. Magnification- Enlarging the size ii. Resolution – showing the fine details (scattering)   7
  8. 8.  Progress In Microscopy    1590 Hans & Zacharius Janssen: Lense makers 1665 Robert Hooke- views and describes fungi 1676 Anthony van Leeuwenhoek observed first microscopic organism, blood cells and protists 8
  9. 9. Robert Hooke and early microscopy The first descriptions of Microorganisms by Robert Hooke in Micrographia in 1665 9
  10. 10.  Microorganisms were first observed by Antonie van Leeuwenhoek, using a primitive microscope 10
  11. 11. (a) A replica of Antoni van Leeuwenhoek’s microscope. (b) Van Leeuwenhoek’s drawings of bacteria, published in 1684. Even from these simple drawings we can recognize several shapes of common bacteria: A, C, F, and G, rods; E, cocci; H, packets of cocci 11
  12. 12. Photomicrograph of a human blood smear taken through a van Leeuwenhoek microscope. Red blood cells are clearly apparent 12
  13. 13. Progress in Tools • 1883 Carl Zeiss and Ernst Abbe make advancements in microscopy lenses and techniques. • 1931 Ernst Ruska- first electronic microscope  Christian Grham – the use of stains 13
  14. 14. Summary of types of Microscope  Microscopy  Bright Field Light Microscopy  Dark Field Microscopy  Phase Contrast Microscopy  Fluorescent Microscopy  Electron Microscopy  Transmission Electron Microscopy - TEM  Scanning Electron Microscopy - SEM 14
  15. 15. 15
  16. 16. Investigator Nationality Date Contributions Robert Hooke English 1664 Discovery of microorganisms (fungi) Antoni van Leeuwenhoek Dutch 1684 Discovery of bacteria Edward Jenner English 1798 Vaccination (smallpox) Louis Pasteur French Mid- to late 1800s Mechanism of fermentation, defeat of spontaneous generation, rabies and other vaccines, principles of immunization 16
  17. 17. Investigator Nationality Date Contributions Joseph Lister English 1867 Methods for preventing infections during surgeries Ferdinand Cohn German 1876 Discovery of endospores, preventing culture media from contamination Robert Koch German Late 1800s Koch’s postulates, pure culture microbiology, discovery of agents of tuberculosis and cholera Martinus Beijerinck Late Dutch 1800s to 1920 Enrichment culture technique, discovery of many metabolic groups of bacteria, concept of a virus 17
  18. 18. Factors that contributed to the dev’t of Microbiology 1. Controversy between the supporters of Abiogenesis (Theory of spontaneous generation) and Biogenesis 2. The Germ Theory of Diseases 18
  19. 19. The controversy  Spontaneous Generation  Living things arise from non-living matter spontaneously  Biogenesis  Living things arise from pre-existing life form 19
  20. 20. Theory of Spontaneous generation  Early belief that some forms of life could arise from vital forces present in nonliving or decomposing matter. ex. flies from manure, etc 20
  21. 21. Theory of Biogenesis  Some of the Supporters of Biogenesis  Francesco  Lazaro  Louis Redi Spallanzani Paster 21
  22. 22. Challenges to spontaneous generation  Does Spontaneous Generation work?  Francesco Redi’s Experiment (1600’s)  Problem: Did rotting meat produces maggots spontanously?  Experiment: Used 3 jars: 1.Covered 2.Uncovered 3.Meshed & closed  Result: No growth in boiled and closed jar. 22
  23. 23. Lazaro Spallanzani’s Experiment  Spallanzani's Problem :What causes microbes to form in decaying broth? Hypothesis: Microbes come from the air. Boiling will kill microorganisms. Experiment: Spallanzani put broth into four flasks  Flask 1 was left open  Flask 2 was sealed  Flask 3 was boiled and then left open  Flask 4 was boiled and then sealed Result: No growth only in Flask 4.  Conclusion: Life arise from pre-existing form.    23
  24. 24.  Spallanzani is best known for his experiments to disprove abiogenesis. He showed having boiled a broth and then sealed the container, no microorganisms would grow  That is, broth did not spontaneously produce microorganisms 24
  25. 25. Louis Pasteur’s Experiment Louis Pasteur did an experiment to show bacteria do not arise spontaneously.  He showed microbes caused fermentation and spoilage, and disproved spontaneous  25
  26. 26. Louis Pasteur’s Experiment 26
  27. 27. Louis Pasteur’s Exp.      Pasteur’s work also led to the development of effective sterilization Food science also owes a debt to Pasteur, as his principles are applied today in the preservation of milk and many other foods by heat treatment (pasteurization). Pasteur’s fame from his rabies research was legendary and led the French government to establish the Pasteur Institute in Paris in 1888 Originally established as a clinical center for the treatment of rabies and other contagious diseases, the Pasteur Institute today is a major biomedical research center focused on antiserum and vaccine research and production 27
  28. 28. Significances of the controversy  Existence   of microorganism in two forms: Vegetative - heat labile Spore form – resistance to heat  Spores and sterilization  Aseptic technique  Sterilization techniques    “Pasteurization” Heat Chemical 28
  29. 29. History of Microbiology cont… Spores and sterilization • Some microbes in dust and air were resistant to high heat. • Spores were later identified. • The term “sterile” was introduced which meant completely eliminating all life forms from objects or materials. 29
  30. 30. Microbiology as a science  Developed through accumulation of knowledge following scientific methods. Scientific Method involve:  Identification of problem/gap of knowledge • Hypothesis • Experimentation • Results • Conclusion or theory 30
  31. 31. Natural History of Microbial Diseases    Even as early as the sixteenth century it was thought that something that induced disease could be transmitted from a diseased person to a healthy person. After the discovery of microorganisms, it was widely believed that they were responsible, but definitive proof was lacking Improvements In sanitation by Ignaz Semmelweis and Joseph Lister provided indirect evidence for the importance of microorganisms in causing human diseases 31
  32. 32. Do Microbes Cause Disease? • 1546 Girolamo Fracastoro wrote about “contagion” – communicable disease  Mainly philosophical as the existence of MOs were not known  Proposed that disease are transmitted by: 1. direct contact 2. through air 3. through inanimate objects such as clothes   1835 Agostino Bassi de Lodi linked a fungi with a silkworm disease– the first recognized contageous agent of animal disease! but it was the work of a German physician, Robert Koch (1843–1910) that give experimental support to the concept of infectious disease 32
  33. 33. Germ theory of disease  Germ Theory is the concept that microorganisms can cause disease, and this theory is the foundation of modern medicine.  Many diseases are caused by the growth of microbes in the body and not by sins, bad character, or poverty, etc.  Robert Koch was a man who dedicated his life to finding the causes of infectious diseases 33
  34. 34.  Koch was convinced that microbes caused some diseases  However, to test this idea, he needed to isolate the causative agent.  Almost all samples from diseased animals or any natural surface contained many different microbes and it was impossible to tell which one was the problem.  A method was needed to separate these different bacteria. The most common method of isolation was to continually dilute a sample in liquid broth in hopes only one type of microbe would be found  A major contribution to bacterial techniques was the development of methods using solid medium for the cultivation of bacteria. 34
  35. 35. Robert Koch’s Experiment  Robert Koch (1843-1910) verified (realized)the Germ theory (and formulated Koch’s postulates). 35
  36. 36. Experiment  Figure 36
  37. 37. Koch’s Postulates In 1876 Robert Koch – cultivates Anthrax using blood serum and published postulates: 1. The disease agent must be present in every case, and absent in healthy individuals. 2. The agent must be isolated and cultured in vitro (i.e. cultivated in a laboratory environment). 3. Disease must be produced when a pure culture is inoculated into susceptible host 4. The agent must be recoverable from infected host 37
  38. 38. Exceptions to Koch’s postulates 1. Many healthy people carry pathogens but do not exhibit symptoms of the disease. 2. Some microbes are very difficult or impossible to grow in vitro(in the laboratory) in artificial media. Eg. Treponema pallidum 3. Many species are species specific. Eg. Brucella abortus cause abortion in animals but no report in humans. 4. Certain diseases develop only when an opportunistic pathogen invades immunocompromised host 38
  39. 39. Contribution of Koch discoveries    The establishment of the fact that disease are caused by microorganisms, Koch's laboratory also developed methods of pure culture maintenance and aseptic technique. Aseptic technique involves:  the manipulation of pure cultures in a manner that prevents their contamination by outside microorganisms.  Equally important, aseptic technique prevents their spread into the environment 39
  40. 40. Contribution of Koch disc…     The postulate not only offered a means for linking the cause and effect of an infectious disease, but also stressed the importance of laboratory culture of the putative infectious agent These discoveries led to the development of successful treatments for the prevention and cure of many diseases, thereby greatly improving the scientific basis of clinical medicine and human health and welfare 40
  41. 41. Contribution of Koch disc…..      Koch announced his discovery of the cause of tuberculosis M. tuberculosis in 1882 and published a paper on the subject in 1884 in which his postulates are most clearly stated. For his contributions on tuberculosis, Robert Koch was awarded the 1905 Nobel Prize for Physiology or Medicine. Koch had many other triumphs in medicine, including discovering the organism responsible for the disease cholera and developing methods to diagnose exposure to M. tuberculosis (the tuberculin test) 41
  42. 42. History con…..    Martinus Beijerinck (1851–1931)&Sergei Winogradsky (1856– 1953) greatest contribution to the field of microbiology was their clear formulation of the enrichment culture technique In 1929 Alexander Fleming observed that molds can produce a substance that prevents the growth of bacteria. His discovery, an antibiotic called penicillin, was later isolated and produced commercially to protect people against the harmful effects of certain microorganisms. 42
  43. 43. The Modern Era of Microbiology      In the 1940s microbiology expanded into the fields of molecular biology and genetics. Viruses were found to be simple microbes that could be studied quantitatively, and they were used to study the nature of DNA In the early 1970s, genetic researchers discovered recombinant DNA. Scientists found that DNA could be removed from living cells and spliced together in any combination. They were able to alter the genetic code dictating the entire structure and function of cells, tissues, and organs. 43
  44. 44. The development of early techniques in microbiology Year Event 1664 Robert Hooke is the first to use a microscope to describe the fruiting structures of molds. He also coined the term cell when using a microscope to look at cork, as the dead plant material in cork reminded him of a jail cell. 1673 Anton van Leeuwenhoek, a Dutch tradesman and skilled lens maker, is the first to describe microbes in detail. 1872 Ferdinand Julius Cohn publishes landmark paper on bacteria and the cycling of elements. In it is an early classification scheme that uses the name Bacillus. 1872 Oscar Brefeld reports the growth of fungal colonies from single spores on gelatin and the German botanist Joseph Schroeter grows pigmented bacterial colonies on slices of potato. 44
  45. 45. 1877 Robert Koch develops methods for staining bacteria, photographing, and preparing permanent visual records on slides. 1881 Koch develops solid culture media and the methods for obtaining pure cultures of bacteria. 1882 Angelina Fannie and Walther Hesse in Koch's laboratory develop the use of agar as a support medium for solid culture. 1884 Hans Christian Gram develops a dye system for identifying bacteria [the Gram stain]. 1887 First report of the petri plate by Julius R. Petri. 1915 M. H. McCrady establishes a quantitative approach for analyzing water samples using the most probable number, multiple-tube fermentation test. 45
  46. 46. Microbial Taxonomy       Previously living organisms grouped into five kingdoms: plants, animals, fungi, protists, and bacteria. DNA sequence-based phylogenetic analysis, on the other hand, has revealed that the five kingdoms do not represent five primary evolutionary lines Instead, cellular life on Earth has evolved along three primary lineages, called domains. Two of these domains, the Bacteria and the Archaea, are exclusively composed of prokaryotic cells. The Eukarya contains the eukaryotes, including the plants, animals, fungi, and protists. 46
  47. 47. Microbial Taxonomy con…  Definition Taxonomy : is a system for organizing, classifying & naming of living things. • Primary concerns of taxonomy are:  classification,  nomenclature, and  identification 47
  48. 48. Microbial Taxonomy con…   Classification is the organization of organisms into groups on the basis of either phenotypic similarity or evolutionary relationships The hierarchical nature of classification is that species is made up of one to several strains, and similar species are grouped into genera (singular, genus). Similar genera are grouped into families, familiesm into orders, orders into classes, up to the domain, the highestlevel taxon. 48
  49. 49. Microbial Taxonomy cont….  Nomenclature – giving a two word name (Binomial) (Genus and species name)  Identification – assigning to the corresponding taxa or group using the existing system of classification set 49
  50. 50. Microbial Taxonomy cont…. Nomenclature: • Binomial nomenclature: naming organisms using the genus and species name together  It is (scientific) • Genus – always capitalized(Ex. Bacillus, ) • species – use lowercase (ex. subtilis) • Both italicized or underlined -Bacillus subtilis, or - Bacillus subtilis, or - B. subtilis 50
  51. 51. Microbial Taxonomy cont… Levels of Classification: • Kingdom/Domain • Phylum or Division • Class • Order • Family • Genus • species 51
  52. 52.      The polyphasic approach to taxonomy uses three kinds of methods—phenotypic, genotypic, and phylogenetic—for the identification and description of bacteria Phenotypic analysis examines the morphological, metabolic, physiological, and chemical characteristics of the cell Genotypic analysis considers characteristics of the genome These two kinds of analysis group organisms based on similarities They are complemented by phylogenetic analysis, which seeks to place organisms within an evolutionary framework 52
  53. 53. Microbial Taxonomy cont… Domains 1. 2. ►Developed after the five-kingdom system Eubacteria -true bacteria, with true peptidoglycan Archaea –odd bacteria that live in extreme environments, high salt, heat,etc 3. Eukarya- have a nucleus, & organelles 53
  54. 54. Microbial Taxonomy cont…. Approaches in Microbial Taxonomy  Classical  Molecular (Phenotypic) (Genotypic) 54
  55. 55. Classical Approach to microbial taxonomy  Cell morphology  Cell shapes, cell grouping  Physiological  Tolerance characteristics to salt, pH, temperature  Biochemical characteristics  Carbohydrate source, etc fermentation, utilization of nitrogen  Serology  Antigen type 55
  56. 56. Molecular (Genotypic) Approaches  Plasmid profiling  DNA-DNA  DNA hybridization sequencing ►All involve Molecular techniques  PCR (Polymerase Chain Reaction)  DNA/Plasmid Extraction, purification, etc 56
  57. 57. Bacteria:     Bacteria: This domain includes the kingdom of the heterotrophic eubacteria and includes all human pathogen bacteria. The other kingdoms, for instance that of the photosynthetic cyanobacteria, are not pathogenic. 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. 57
  58. 58. Eucarya:     Eucarya: This domain includes all life forms with cell possessing a genuine nucleus. The plant and animal kingdoms (animales and plantales) are all eukaryotic life forms Pathogenic eukaryotic microorganisms include fungal and protozoan species 58
  59. 59. Bacteria • No membrane bounded organelles • Cell wall made of Peptidoglycans • Antibiotic sensitivity • Reproduction by Binary fission • DNA with no Histones • 70S ribosome  Some are parasitc, others are beneficials (food, antibiotic, industry, agriculture, environment, medical), some are pathogenic (Salmonella, Shigela), still some others are toxin producing(Clostridium, S.aurus), 59
  60. 60. Fungal general characteristics           They are achloropyllus Without true root, stem, and leaf, no vascular system Heterotrophic mode of nutrition(they digest and ingest) They follow both sexual and asexual mode of reproduction Some are parasitic;(smuts, rust, athletes foot, ringworm); others are beneficial(antibiotic, food, industry), some form associations(lichen, Mycorrhiza, termites), some produce toxins which is potent chemical to human, animal and other vertebrates, Some are still poisonous(Amanita spp.) Some are still disease causing Mycosis (athletes foot, ring worm,) 60
  61. 61. Major groups of fungi Fungi • Classification based on: – Morphology – Reproduction _Nutrition, Habitat, life cycle, growth   Molecular The major Fungal divisions are:  Zygomycetes  Ascomycetes  Basidiomycetes  Deutromycetes /fungi imperfecta/ mitosporic 61
  62. 62. Medically important protozoa • Amoeboid protozoa – Causes brain infections • Flagellated protozoa – Example: Giardiasis • Apicomplexan protozoa – Example: Malaria 62