Microbiology Lecture Notes PDF

Lecture : 1 Dr. Alaa’ Turki Lecturer (PhD Microbiology) 2024-2025  Micro= very small, What is Microbiology? Bio= life, logy= science The study of microorganis...

Lecture : 1 Dr. Alaa’ Turki Lecturer (PhD Microbiology) 2024-2025  Micro= very small, What is Microbiology? Bio= life, logy= science The study of microorganisms and their activities [Nutrition, Multiplication, Pathogenicity,…. etc]. Is the study of all living organisms that are too small to be visible by the naked eye.  What are Microorganisms or Microbes? They are very small organisms [Viruses, Bacteria, Fungi, and Protozoa] that are too small to be seen with the naked eye, they are observed with the aid of the microscope. Microorganisms are commonly known as GERMS.  Nature of Microorganisms or Microbes? o Most microorganisms are harmless. o Some microorganisms found in the body are beneficial to us. o When a microorganism enters a part of the body other than where it is intended to be, it can be harmful; e.g. E. coli from the colon (breaks down waste/makes vitamin K) can enter the urinary tract and cause an infection, and become a Pathogen Microorganisms that cause disease. What are the  What is Medical Microbiology? Medical Microbiology, also known as Clinical Microbiology is a science dealing with the study of microorganisms (parasites, fungi, bacteria, and viruses) capable of infecting and causing diseases in humans, [deal with the etiology, pathogenesis, laboratory diagnosis, specific treatment and control of infection (immunization)].  Microbiological nomenclature [Naming] Binomial nomenclature also called Binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, both use Latin grammatical forms, the 1st part of the name [generic name] identifies the genus to which the species belongs is written with a Capital letter, while the 2nd part [specific name] identifies the species within the genus is written with a small letter, and both are write in italics or underlined. Staphylococcus aureus Pseudomonas aeruginosa  The history of microbiology Before the discovery of microorganisms, there were TWO kingdoms of living things: Plant and animal. [First microbes were observed in 1673]. Robert Hooke (1635-1703): English scientist First report of cell structure in 1665, when cut a thin slice of cork, & examined it with homemade microscope. He saw what looked like Little boxes, which he named CELL.  Antoni van Leeuwenhoek (1632-1723) : Dutch merchant & scientist He is considered the Father of Bacteriology First person to observe and record living microbes used His single-lens microscope. He wrote scientific papers describing his observations of bacteria, algae, protozoa, & fungi as Animalcules [tiny animals]  The history of microbiology (Cont.) ORIGIN OF LIFE Theories or hypotheses There are two hypotheses: Spontaneous generation or Abiogenesis: living organisms can arise spontaneously from non-living things. OR The organisms originate directly from nonliving matter. “Life from nonlife” Abiogenesis [ a=not, bio=life, genesis=origin] Biogenesis: the living organisms arise from life. “Life from life”  The history of microbiology (Cont.) Many believed in spontaneous generation: Herodotus Living organisms could arise from non living matter [crocodiles from mud]. Van Helmont He believed that that maggots originated from meat  The history of microbiology (Cont.) Biogenesis [Disproving Spontaneous Generation] Many scientist performed different theories and experiment to disprove Spontaneous Generation. Francesco Redi Lazzaro Spallanzani [An Italian doctor] [an Italian scientist] 1626-1697 They proved through the experiments that the Microbes came from other microbes. These results suggested that the spontaneous generation was wrong and false.  The history of microbiology (Cont.) Many scientists have made significant contributions to development of Microbiology; and the following are the notable ones: Louis Pasteur [A French Scientist] 1822-1895 Father of Modern Microbiology He coined term “ Microbiology “, aerobic and anaerobic. Disproved the Spontaneous Generation theory, proved microbes only come from other microbes (life from life) [Biogenesis]. Invented the processes of Pasteurization for sterilization. Showed that microbes are responsible for fermentation [which is the conversation of sugar to alcohol]. Development of vaccines against rabies. Microbial growth is also responsible for spoilage of food. Demonstrated that anthrax caused by bacteria & also produced the vaccine for the disease.  The history of microbiology (Cont.) Robert Koch [German physician & microbiologist] 1843-1910 Father of Medical Microbiology He perfected the technique of isolating bacteria in pure culture. He discovered and isolated the causative agents of Anthrax [Bacillus anthracis] , Cholera [Vibrio cholerae] , & Tuberculosis [ Mycobacterium tuberculosis]. Robert Koch and Louis Pasteur led to discover the GERM THEORY The diseases are caused by microorganisms  The history of microbiology (Cont.) 1884 Robert Koch developed rules still used today to identify microbes that cause specific diseases. Known as “Koch's postulates” Are sequence of experimental steps to relate a specific microbe to a specific disease.  The history of microbiology (Cont.) Koch's postulates criteria 1- The microorganism must be present in all cases of the disease. 2-The pathogen can be isolated from the diseased host and grown in pure culture. 3-The pathogen from the pure culture must cause the disease when inoculated into a healthy, susceptible laboratory animal. 4-The pathogen must be re-isolated from the new host and shown to be the same as the originally inoculated pathogen. Koch's postulates Microorganisms are isolated from dead animals Microorganisms are grown in pure culture & Microorganisms are identified Microorganisms are injected into healthy animal Disease is reproduced in second animal Microorganisms are grown in pure culture and Identification of identical microorganism.  The history of microbiology (Cont.) Alexander Flemming (1881-1955) He discovered Penicillin from Pencillium notatum that destroy several pathogenic bacteria. John Tyndall (1820-1893) He discovered highly resistant bacterial structure [Endospore]. Developed the sterilization process Tyndallization to kill the spores. Richard Petri (1852-1921) He developed the Petri dish (plate), a container used for solid culture media.  Importance of microbiology for Nursing Why microbiology is needed for Nursing ?? o Nurses are involved in controlling infection in hospital, so nurses must know about Microbiology for:  Isolation of causative agents  Determination of antibiotic sensitivity and drugs for treatment  Prevention of infectious diseases by vaccine and immunization  Provides knowledge on Sterilization and Disinfection o Microbiology helps the nurse to know about normal flora and harmful microorganisms to human being, as well as how they can cause disease.  Importance of microbiology for Nursing (Cont.) o The nurse needs to know different organisms that cause diseases in the human, their effects, and modes of transmission.. etc. Microbiology helps the nurse to achieve this. o Microbiology helps the nurse to know how to render and keep certain instruments aseptic in order to prevent the cross infection. o Studying Microbiology also helps the nurse to recognize the signs and symptoms of the infection. o Microbiology also gives the knowledge to nurse how to handle patients and his sample infected with diseases to protect themselves from pathogenic microorganisms. Classification Organisms Prokaryotic Eukaryotic All other forms of life Bacteria Archaea Protozoa or Fungi Protista & VIRUSES Animalia Plantae Viruses: Very small, simplest, non-living organisms outside the host. Viruses are considered as to be microorganisms, but they are different form of other organisms because they reproduce only in body of host cells (e.g. human, ….), they are obligate intracellular parasites. Viruses are considered neither prokaryotes nor eukaryotes because they lack the characteristics of living things, except the ability to replicate only in living cells.  Structure of viruses Consist of a strand of nucleic acid [DNA or RNA not both] surrounded by a protein coat (capsid). Sometimes have an envelope [membrane of lipid, surrounding the protein]. They may also have a tail.  Prokaryotes Bacteria Archaea -Unicellular prokaryotes with cell -Unicellular prokaryotes without wall containing peptidoglycan. peptodoglycan in cell wall. -Exist in most environments -Exist in extreme environments (hot and salty). They are differing in some structural, biochemical and physiological characteristics Prokaryotic cells: are cells that do not have a true nucleus & most other cell organelles. Prokaryotes: are unicellular organisms, & they are found in all environments. Bacteria and archaea are prokaryotes. Prokaryotes are smaller in size when compared with Eukaryotes.  Eukaryotes Animal Plant Fungi Protozoa Eukaryotic cells: are cells that contain a nucleus & organelles, & are enclosed by a plasma membrane. Eukaryotic cells: are larger & more complex than prokaryotic cells. Organisms: that have eukaryotic cells include protozoa, fungi, plants and animals.  Differentiate between Eukaryotes Prokaryotes Characteristics Eukaryotic Prokaryotic Size large small Nucleoid Nucleus surrounded by a nuclear membrane. Yes [no true nucleus no nuclear membrane] Cytoplasm Yes Yes [gel-like substance supports the parts of the cell] Ribosomes produce proteins. larger smaller Flagella some Yes [tail-like structures, enable the organism to move] Pili No Yes [small hair-like structures, help adhere to surfaces]  Characteristics Eukaryotic Prokaryotic Cell membrane (plasma membrane), is a biological membrane surrounds the cytoplasm of living cells, Yes Yes separating the intracellular components of the cell from extracellular environment. Membrane-bounded bodies called organelles [Golgi body, Endoplasmic reticulum (rough & smooth), Yes No & Mitochondria] Chromosomes [DNA] Several One long DNA strand Cell wall [No] animal Yes [yes] plant Lysosomes contain a variety of enzymes [yes] animal No [No] plant Capsule, a sticky layer of carbohydrates, protect from No Yes phagocytic cells of the immune system Examples Animal, Bacteria, plant, fungi archaea  Eukaryotes FUNGI Fungal Cells Fungal cells have a cell wall, but their cell wall is made of chitin. Some fungi have septa, which are holes that allow organelles and cytoplasm to pass between them. Fungi are eukaryotes, have DNA & RNA, with a nucleus & a cell wall. They are non-motile.  Medical fungi can be divided into: True Yeasts: unicellular, reproduce asexually by budding & sexually with formation of spores [Cryptococcus spp]. Molds: multicellular consisting of mycelia [um], which composed of filaments called hyphae [Aspergillus]. Yeast like fungi: have pseudo mycelium [Candida] Protozoa Single cell eukaryotic motile organisms. The most important groups of protozoa medically are: A-Amoeba: Entamoeba species. Mode of Motility: pseudopodia. C- Sporozoa: intracellular infection. (Malaria) D- Mastigophora: Mode of Motility is the Flagella. Gastrointestinal Tissue and blood flagellates: Urogenital flagellates: flagellates: Giardia intestinalis Trichomonas vaginalis Trypanosoma , Leishmania.  What are the Branches of Microbiology? Bacteriology: study of bacteria. Parasitology: study of parasite. Immunology: study of immunity. Virology: study of viruses. Mycology: study of fungi. Prokaryotes Single cell organisms (prokaryotes) Have both DNA & RNA Have cell wall Divide by binary fission. No nucleus No mitochondria. Nucleoid or bacterial chromosome contains a closed circle of double stranded DNA, highly folded & compacted.  Classification of Bacteria Bacteria can be classified according to Morphology [size and shape], Arrangement, and Staining into the following groups: 1- Filamentous bacteria: Streptomyces. 2- True bacteria: Cocci: Gram positive: Staphylococcus, Gram negative: Neisseria. Bacilli: Gram positive: Bacillus, Gram negative: Brucella 3- Spirochetes: Slender , spiral bacteria Treponema 4- Mycoplasma: The Smallest bacteria that lack of a rigid cell wall. 5- Rickettsiae [lacks teichoic acid] 6- Chlamydiae[lacks peptidoglycan]: obligate intracellular parasites  Morphology Size: bacterial cells are about one-tenth the size of eukaryotic cells. Size range from 1-10 μm in length & from 0.2-1 μm in width. Morphology 1-Cocci 2-Bacilli 3-Vibrios 4-Spirochetes 5-Spirilla  Arrangement Single Pairs Tetra Chain Clusters  Staining [Gram stain] Gram stain: it is one of the most useful staining procedures used in bacteriology to classify bacteria. Discovered in 1884 by Gram (Hans Christian Gram (1853-1938), Danish scientist and physician), using TWO dyes in sequence, each of a different color, he found that bacteria fall into TWO main groups: Gram positive Gram negative bacteria appear in bacteria appear in violet [blue] color. red [pink] color. Cell wall is a structure or wall surrounds the bacterial cell. Chemical nature of bacterial cell walls Cell wall is a multi-layered structure located external to the cytoplasmic membrane. The most important structure in the bacterial cell wall is the Peptidoglycan [murein], which it responsible of cell wall rigidity. Peptidoglycan is an unique macromolecule consists of : 2 amino sugars * N-acetyl-glucosamine = NAG N- acetylmuramic acid = NAM 4 amino acids ** L-alanine = L-ala D-glutamic acid = D-glu Diaminopimelic acid= DAP D-alanine = D-ala Linked by polypeptide bonds Almost all bacteria can be divided into two large groups based on cell wall peptidoglycan and permeability factor. Characters Gram + Gram - Peptidoglycan Thick (80%) Thin (20%) Teichoic acids [acid polysaccharides provide rigidity to Present Absent the cell wall] links to peptidoglycan Lipo Teichoic acid [Regulator of autolytic wall Present Absent enzymes] links to plasma membrane Lipopolysaccharideor endotoxin, Lipid A portion of Absent Present LPS is responsible for the endotoxic activities Periplasmic space[area between the outer membrane Absent Present & the plasma membrane]. Outer membrane Absent Present Lipid Very low Very high Porine [proteins] form channels through membrane Absent Present  Reagents of Gram stain Dye Action Time Crystal violet primary stain 1min Iodine mordant 1min 95% Ethyl alcohol decolonization 10 sec Safranin Safranin 1min Gram stain procedure 1min 1min 10 sec 1min