Clinical Bacteriology - Brief History of Microbiology PDF

CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________...

CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________ Lecture | AJDC | Batch 2024 BRIEF HISTORY OF MICROBIOLOGY THE FIRST OBSERVATION THE DEBATE OVER SPONTANEOUS GENERATION After van Leeuwenhoek discovered the “invisible” world of microorganisms, the scientific community became interested in the origins of these tiny living things. Many scientists and philosophers believed that some forms of life could arise spontaneously from non-living matter (Spontaneous Generation). People thought that: a) toads, snakes, and mice could be born of moist soil; b) flies could emerge from manure; c) maggots could arise from decaying corpses. FRANCESCO REDI Prison cell a strong opponent of spontaneous generation Italian physician Founder of Experimental Biology 1668 — demonstrated that maggots do not arise spontaneously from ROBERT HOOKE decaying meat, as was commonly believed. 1665 an Englishman 1. Redi filled 3 jars with decaying reported to the world that life’s smallest meat and sealed them tightly. structural units were “little boxes,” or “cells,” as he called them 2. He arranged 3 other jars able to see individual cells with a similarly but left them open. microscope that he had developed Hooke’s discovery marked the beginning of Maggots appeared in the open vessels after flies entered the jars and the Cell Theory. laid their eggs The sealed containers showed no forms of life. CELL THEORY – “All living things are “Father of Microbiology” Still, his antagonists were not convinced; they claimed that fresh air composed of cells.” was needed for spontaneous generation. Though Hooke’s microscope was capable of showing protozoans and probably bacteria, He set up a 2nd experiment, in he lacked the staining techniques that would which 3 jars covered with a fine have allowed him to see such small microbes net instead of being sealed clearly. No larvae appeared in the gauze-covered jars, even though air was present. 1632-1723 — ANTON VAN LEEUWENHOEK Maggots appeared only if flies were Dutch glass merchant and amateur scientist allowed to leave their eggs on the one of the first to actually observe meat. microorganisms through magnifying lenses Redi’s results were a serious blow to (invented the first single lens microscope the long-held belief that large forms or simple microscope) of life could arise from non-life. wrote a series of letters to the Royal Society of London describing the “animalcules” he JOHN NEEDHAM saw through his simple, single lens The case for spontaneous generation of microorganisms was microscope strengthened in: JOHN NEEDHAM Born September 10, 1713 Died December 30, 1781 (aged 68) 1745 — John Needham found that, even after he heated nutrient fluids (chicken broth/corn broth) the cooled solutions were soon teeming with microorganisms. Needham's Experiment his detailed drawings of “animalcules” in rainwater, in liquid in which peppercorns had soaked, and in material taken from teeth scrapings have since been identified as representations of bacteria and protozoans. proponent of the “Theory of Spontaneous Generation” also known as “Theory of Abiogenesis” = life came from abiotic factors “Father of Microbiology” He claimed that the microbes developed spontaneously from the fluids Spearheaded the observation Taken from abiotic factors of microorganisms  CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________ Lecture | AJDC | Batch 2024 LAZZARO SPALLANZANI Pasteur’s unique design allowed air to pass into the flask, but the curved 1765 - Lazzaro Spallanzani neck trapped any airborne microorganisms that might contaminate the Italian scientist = suggested that broth. (Some of these original vessels, which were later sealed, are on microorganisms from the air probably had display at the Pasteur Institute in Paris. They still show no sign of entered Needham’s solutions after they were contamination more than 100 years later.) boiled Pasteur showed that microorganisms can be present in non-living showed that nutrient fluids heated after being matter — on solids, in liquids, and in the air. sealed in the flask did not develop microbial growth. He demonstrated conclusively that microbial life can be destroyed by heat and that methods can be devised to block the access of airborne Spallanzani’s Experiment microorganisms to nutrient environments. Needham responded by o these discoveries form the basis of the aseptic techniques claiming that the “vital force” Pasteur’s work provided evidence that microorganisms cannot originate necessary for spontaneous from mystical forces present in non-living materials. generation had been Rather, any appearance of “spontaneous” life in non-living solutions destroyed by the heat and was can be attributed to microorganisms that were already present in the kept out of the flasks by the air or in the fluids themselves. seals. Scientists now believe that a form of spontaneous generation probably This intangible “vital force” was given all the more credence shortly after did occur on the primitive earth when life first began, but they agree that Spallanzani’s experiment when Laurent Lavoisier showed the this does not happen in our present environmental conditions. importance of oxygen to life. Spallanzani’s observations were criticized on the grounds that there GOLDEN AGE OF MICROBIOLOGY was not enough oxygen in the sealed flasks to support microbial life. 1857 – 1914 (Tuff lock – Tub Thor) 1. rapid advances led to the establishment of microbiology as a science THE THEORY OF BIOGENESIS 2. discoveries of the agents of many diseases The spontaneous generation issue was still 3. relationships between microorganisms and disease unresolved in 1858, when RUDOLF 4. the role of immunity in the prevention and cure of disease. VIRCHOW (German scientist) challenged 5. microbiologists studied the chemical activities of microorganisms, spontaneous generation with the concept of improved techniques for microscopy and the culturing of BIOGENESIS. microorganisms, and developed vaccines and surgical techniques “Living cells can arise only from pre-existing living cells” FERMENTATION & PASTEURIZATION Arguments about spontaneous generation A group of French merchants asked Pasteur to find out why wine and continued until 1861, when the issue was resolved experimentally by Louis Pasteur (French scientist). beer soured. They hoped to develop a method that would prevent spoiling when those beverages were shipped long distances. At that time, many scientists believed that air converted the sugars in LOUIS PASTEUR these fluids into alcohol. demonstrated that microorganisms are indeed present in the air and that they can air sugars (wine & beer) —————> alcohol contaminate seemingly sterile solutions, but air itself does not give rise to microbial life. Pasteur found instead that microorganisms (Yeast) convert the sugars to alcohol in the absence of air. → FERMENTATION 1st experiment: Yeast sugars —————> alcohol 1. He filled several short-necked flasks with beef broth and boiled them (no air) (focused on air) Souring and spoiling, which occur late, are caused by a different 2. Some were left open and allowed to cool. group of microorganisms, which are bacteria. a. these flasks were found to be contaminated with microbes o In the presence of air, bacteria change the alcohol in the beverage 3. The other flasks, sealed after boiling. into vinegar (HAc). a. remained free of microorganisms (Needham’s) bacteria alcohol ——————————>. Vinegar/Hac 2nd experiment: (with air) 1. Place the boiled broth in open-ended long-necked flasks (swan flasks) Pasteur’s solution to the spoilage problem was to heat the alcohol just 2. Then, he bent the necks into S-shaped curves. enough to kill most of the bacteria; the process does not greatly affect 3. The contents of these flasks were then boiled and cooled. the flavor of the beverage. ▪ the broth in the flasks did not decay and showed no signs of life after days, weeks, and even months. PASTEURIZATION – now commonly used to kill potentially harmful bacteria in MILK as well as in some alcoholic drinks Figure 1.12 Pasteur’s experiments with “swan-necked”" flasks THE GERM THEORY OF DISEASE Louis Pasteur => one of the proponents of the Germ Theory of Disease (a specific microorganism causes a specific infectious disease); 1865 silkworm disease Agostino Bassi = another silkworm disease was caused by 1835 a fungus Joseph Lister (English surgeon) introduced antiseptic 1860s technique Ignaz Semmelweis (Hungarian physician); 1840s Father of Handwashing  CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________ Lecture | AJDC | Batch 2024 LOUIS PASTEUR The Germ Theory of Disease Exemptions to the “Koch’s December 11, 1843 — May 27, 1910 Postulates” developed vaccine to prevent chicken cholera, anthrax and swine Certain pathogens will not grow on artificial media. These pathogens erysipelas (a skin disease) which brings serious economic problems in include viruses, rickettsias, and chlamydias, and the bacteria that France during his time. cause leprosy and syphilis – violate 2 and 4 developed the rabies vaccine oViruses – embryonated chicken eggs/stem lines oRickettsias/Chlamydia – special type of bacteria ROBERT KOCH – 1876 oLeprosy – foot pods of mice/armadillos (rodent) a German scientist oSyphilis – specific media discovered that Bacillus anthracis produces spores and can resist adverse conditions Many pathogens are species-specific, meaning that they infect only one developed the method of fixing, staining and species of animal (zoonotic infections – animals) photographing bacteria Certain diseases, called synergistic infections, are caused not by one developed methods of cultivating bacteria on particular microorganism, but by the combined effects of 2 or more solid media discovered M. tuberculosis and V. cholerae different microorganisms. – number 2 Certain pathogens become altered when grown in vitro. Some become Vertical photomicroscopic apparatus of the less pathogenic, while others become nonpathogenic. Thus, they will Koch's drawing of the anthrax bacillus type Koch used to photograph the anthrax no longer infect animals after being cultured on artificial media – at / various stages of development. bacillus. number 2 and 3 Suggested further readings: 1. How Robert Hooke Discovered the Existence of Cells https://www.differenttruths.com/science- technology/how-robert- hooke-discovered- the-existence-of-cells/ 2. Anton van Leeuwenhoek https://discoveries- project.weebly.com/anton- van-leeuwenhoek.html worked on tuberculin (a protein derived from M. tuberculosis) used as a skin test valuable in diagnosing TB. contributed to the germ theory of diseases through “Koch’s Postulates” o An experimental procedure to prove that a specific microorganism is a cause of a specific disease (published 1884). o This gave a tremendous boost to the development of microbiology culture and identification of organisms in the laboratory. “KOCH’S POSTULATES” 1. A particular organism must be found in all cases of the disease and must not be present in healthy animals or humans. 2. The microorganisms must be isolated from the diseased animal or human and grown in a pure culture in the laboratory. 3. The same disease must be produced when microorganisms from pure culture are inoculated into a healthy susceptible laboratory animal. 4. The same microorganisms must be recovered from the experimentally infected animals and grown again in a pure culture.  CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________ Lecture | AJDC | Batch 2024 MICROBIAL CLASSIFICATION INTRODUCTION: WHAT IS MICROBIOLOGY? 6. When bacteria are referred to as a group, their names are neither MICROBIOLOGY capitalized nor underlined. Greek E.g. staphylococci, gonococci, “mikros” small 7. The plural of genus is genera. “bios” Life E.g. There are many genera within the Enterobacteriaceae family “logia” / “logos” study of 3. CLASSIFICATION the study of organisms that are so small they cannot be seen with the A. Classification by Phenotypic and Genotypic Characteristics naked eye The traditional method of placing an organism into a particular genus MICROORGANISMS (“microbes”) – ubiquitous and species is based on the similarity of all members for a number of phenotypic characteristics. MICROBES In the diagnostic microbiology laboratory, this is accomplished by Acellular infectious Agents Cellular Microorganisms testing each bacterial culture for a variety of metabolic characteristics Prokaryotes Eukaryotes and comparing the results with those listed in established charts. -prokaryotic -eukaryotic cells Epidemiologists constantly seek means of further subdividing bacterial cells (no (true nucleus, species in order to follow the spread of bacterial infections. Prions true animal and plant) Species may be subdivided into: Viruses nucleus) subsp Algae Subspecies Bacteria based on phenotypic differences Fungi Archaea serovar Protozoa Serovarieties based on serologic differences 1. TAXONOMY biovar Biovarieties refers to the classification and grouping of organisms based on biochemical test result differences is based on genotypic (genetic) and phenotypic (observable) based on susceptibility to specific bacterial Phage typing similarities and differences. phages o Phenotypic – classify based on shape (circular, rod-shaped) B. Classification by Cellular Type Formal Levels of Bacterial Classification: Bacteria Prokaryotes, Eukaryotes, and Archaeobacteria: (Cell organization) Cell organization TAXA oanother method of classifying organisms Kingdom oorganisms fall into 3 distinct groups based on type of cell organization Division/Phylum and function: Class Order Prokaryotes E.g. Bacteria Family Micrococcaceae e.g. Fungi, algae, protozoa, animal cells & plant Eukaryotes Genus Staphylococcus cells Species/specific epithet aureus Archaeobacteria “Did King Philip/David Come Over For Good Spaghetti?” 1. PROKARYOTES E.g. Bacteria non-compartmentalized 2. NOMENCLATURE Pathogenic bacteria – are prokaryotic cells that infect eukaryotic hosts provides naming assignments for each organism. Standard Rules for Denoting Bacterial Names: Targeting antibiotic action against unique prokaryotic structures and 1. The family name is capitalized and has an –aceae ending functions inhibits bacterial growth while avoiding harm to eukaryotic E.g., Micrococcaceae, Enterobacteriaceae host cells. This is one reason pharmaceutical companies have been so successful 2. The genus name is capitalized and is followed by the species name, in developing effective antibiotics against bacterial pathogen but have which begins with a lowercase letter; both the genus and species been less successful in finding effective against parasites, medically should be italicized in print but underlined in script. important fungi, and viruses, which are eukaryotic like their human host. E.g. Staphylococcus aureus (in print; typewritten) 2. EUKARYOTES Staphylococcus aureus (in script) E.g. Fungi, algae, protozoa, animal cells & plant cells more complex than that of prokaryotic cells larger (10x) and contains membrane-encased organelles (covering) or 3. Genus name is abbreviated by using the first letter of the genus followed by a period and the species epithet. compartments that serve various functions though different organelles, they serve common purpose E.g. S. aureus 4. The genus name followed by the word species may be used to refer 3. ARCHAEOBACTERIA to the genus as a whole. appears to be more closely related to eukaryotic cells than to E.g. Staphylococcus species prokaryotic cells found in microorganisms that grow under extreme environmental 5. Species abbreviated sp (singular) or spp (plural) is used when the conditions the cell envelope and enzymes of Archaeobacteria have been designed species is not specified. for survival under stressful conditions.  CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________ Lecture | AJDC | Batch 2024 COMPARISON OF EUKARYOTIC AND PROKARYOTIC CELL STRUCTURES EUKARYOTIC CELL STRUCTURE 1. Cytoplasmic Structures (within the cytoplasm) a. Nucleus separated from the cytoplasm; has nuclear envelope command center of the cell; relays instructions has chromatin (if not dividing); chromosome (for cell division) chromatin is linear 46 chromosomes; 22 pairs of autosomes, 23 rd pair sex chromosome DNA is the blueprint of life; contains the genes, genes carry the traits Chromatin Chromosome Hazy; non compact compact 2. Cell Envelope Structures b. Nucleolus a. Plasma Membrane (cell membrane) The presence of STEROLS is a trait of eukaryotic cell membrane produces rRNA to produce ribosomes Animal cell – cholesterol Fungi cell – ergosterol; antifungal drug c. Nuclear membrane Selective permeable – toxic substances cannot go out nuclear pore – ribosomes will travel through these Potassium is needed inside, does not allow exit from cell Glycolipid – cell recognition d. Endoplasmic Reticulum = RER, SER highway INTEGRAL PERIPHERAL Rough ER Smooth ER Glycoprotein For regulate and transport Has ribosomes No ribosomes Carbohydrate component only combines with the cell to cell attachment e. Golgi apparatus/complex/body glycolipid to form the Identity markers packager of proteins GLYCOCALYX proteins (nonfunctional) will be modified/matured to be functional Phospholipid; polar head, nonpolar tails f. Ribosomes Cholesterol stabilizes the cell membrane Integral; peripheral proteins - regulate movements, identity true site of protein synthesis proteins are needed for growth of tissues markers, enzymes, anchoring sites exocytosis – via vesicles CYTOPLASMIC/PLASMA MEMBRANE g. Mitochondria 2 coverings Powerhouse of the cell – produces ATP ATP – energy currency of the cell h. Centrioles Used in the division of cells; migrates to opposite poles of the cell Form in between them mitotic spindle fibers during cell division NOT FOUND IN NEURONS i. Lysosomes Digestive enzymes to digest foreign material (antigen) b. Cell wall Plant, fungi – have a cell wall j. Peroxisomes Animal – none Breaks down free radicals Has catalase c. Motility Organelles Hydrogen peroxide will be broken down to water and oxygen c.1. cilia - shorter c.2. flagella - longer k. Chloroplasts Found in plants *Basal body / Kinetosome Contains chlorophyll; energy – small structure located at the base of cilia / flagella Counterpart of mitochondrion – here microtubule proteins involved in movement are anchored  CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________ Lecture | AJDC | Batch 2024 PROKARYOTIC CELL STRUCTURES Gram Positive Cell Wall (+) Gram Negative Cell Wall (-) with thick peptidoglycan 1. Cytoplasmic Structure with thin peptidoglycan/ layer (MUREIN layer) – the a. Nucleoid murein layer and a different principal component of the Area/space occupied by the chromosome cell wall structure gram-positive cell wall Not a true nucleus, no nuclear membrane Circular chromosome (plasmid) Peptidoglycan Layer / Murein Layer o consists of glycan (polysaccharide) chains of alternating NAG & NAM b. DNA consisting of a single circular chromosome units Plasmid NAG N-acetyl-D-glucosamine NAM N-acetyl-D-muramic acid c. Mesosomes Energy producer; like mitochondria PEPTIDOGLYCAN ON CELL WALL Inserted in the infoldings of bacteria d. Ribosomes Protein synthesis e. Cytoplasmic granules Food storage Allows for recognition Babes Ernst granules f. Endospores/Spore Promote survival Withstand extreme environment Bacilli/Rod-shaped – spore-formers 3 layers Clostridium tetani - terminal b. Cell wall Gram (+) cell wall: g. Plasmids anchored to Teichoic PROKARYOTIC CELL STRUCTURE the acid peptidoglycan anchored to Lipoteichoic the plasma acid membrane Gram (-) cell wall o Outer membrane ▪ additional structure outside the peptidoglycan ▪ consists of proteins, phospholipids, lipopolysaccharides (LPS) ▪ O- somatic polysaccharide ▪ Lipid A - endotoxin 2. Cell Envelope Structures a. Plasma membrane - same with eukaryotic - does not contain sterols (Except: MYCOPLASMA) b. Cell Wall 2 Major Types of Cell Wall categorized according to their staining characteristics: 1. Gram positive type 2. Gram negative type Outer membrane Functions: Periplasmic space  CLINICAL LESSON | 01 BACTERIOLOGY _______________________________________________________________________________________ Lecture | AJDC | Batch 2024 to hydrophobic compounds and harmful d. Cell appendages Barrier substances 1. Flagella – most are rod-shaped; some spiral allows water-soluble molecules to enter a. Atrichous Sieve b. Monotrichous through protein-lined channels called PORINS Attachment c. Amphitrichous that enhances attachment to host cells d. Lophotrichous Sites e. Peritrichous o Lipopolysaccharide (LPS) – contains 3 regions: 1. Antigenic O-specific polysaccharide 2. Core polysaccharide 3. Inner Lipid A / Endotoxin – responsible for producing fever and shock conditions GRAM-NEGATIVE CELL WALL GRAM (+) & GRAM (-) CELL WALL GRAM POSITIVE GRAM NEGATIVE Composed of 2 layers: 1. Inner peptidoglycan Thick peptidoglycan - thin (10-20% murein) layer (90-100% murein) 2. Outer membrane - thicker Teichoic acid – Regions of the outer membrane: anchored to the Lipopolysaccharides (LPS) peptidoglycan a. Lipid A (endotoxin) *Axial filament – functions like a flagellum b. Core polysaccharide Lipoteichoic acid – c. O-specific polysaccharide anchored to the Phospholipid plasma membrane 2. Pili / Fimbriae Polypeptide hair like protein structures that aid in attachment to the surfaces Periplasm consists of gel-like matrix a. Common pili – adherence pili Periplasm is containing nutrient-binding of proteins and b. Sex pili – not related to reproduction; but in CONJUGATION not visible degradative and detoxifying enzymes o transfer of the F plasmid (conjugation) o gene transfer EXOTOXIN VS. ENDOTOXIN o donor – F plus (fertility/sex pili) EXOTOXIN ENDOTOXIN o recipient – F minus Gram (+) organisms, except Listeria Gram (-) organisms o PLASMID is transferred (extrachromosomal DNA) from F plus Metabolic prod’n of bacteria Released when to F minus released to the surrounding tissues. cells are lysed o Implications – antibiotic resistance Composed of proteins or short Composed of lipids o https://www.youtube.com/watch?v=ycgBXmJw83U peptide (lipid A) Heat labile (weak) THE PILI / FIMBRIAE Heat stable except Staphylococcal enterotoxin Can be converted to toxoid Not easily converted (weaker form of the vaccine) to toxoid Detoxified by formaldehyde Not detoxified c. Surface Polymers highly organized structure Capsule anti-phagocytic structure; slide unorganized structure serve either: Slime a. to inhibit phagocytosis, or layers b. to aid in adherence to host tissues or synthetic implants  CLINICAL LESSON | 01 BACTERIOLOGY Lecture | AJDC | Batch 2024 _______________________________________________________________________________________ PROKARYOTES VS. EUKARYOTES PROKARYOTES EUKARYOTES Without true nucleus With true nucleus Not bound by a membrane Bound by a membrane Circular chromosome made up One or more paired of linear of DNA and histone-like chromosome made up of DNA proteins, except Borrelia and and histones Streptomyces Mitosis, Meiosis, Budding Binary fission formation CW made up of peptidoglycan, Animals and Protozoans lack except Mycoplasma and CW; Ureaplasm Plants – cellulose; (pleomorphism) Fungi and Algae - chitin Cell membrane is phospholipid Cell membrane is phospholipid bilayer w/o CHO and sterols bilayer with CHO and sterols Cellular organelles absent (e.g. Cellular organelles present mitochondria, ER, Golgi bodies) Cytoplasmic membrane is the Mitochondria – site of energy site of energy prod’n. production Free ribosomes – site of Endoplasmic reticulum is the CHON site of CHON synthesis synthesis 70s (Svedberg unit) – 80s ribosomal size size of ribosome