Introduction to General & Clinical Microbiology Lecture Notes PDF

Introduction to General & Clinical Microbiology Outline Microbial Communities Support and Affect All Life on Earth The Human Body Has Its Own Microbiome Microbiology Then: The Pioneers The Microbial World Is Cataloged into Unique Groups Microbiology Now: Challenges Remain ...

Introduction to General & Clinical Microbiology Outline Microbial Communities Support and Affect All Life on Earth The Human Body Has Its Own Microbiome Microbiology Then: The Pioneers The Microbial World Is Cataloged into Unique Groups Microbiology Now: Challenges Remain  Microbes & Microbiology Biology is the study of living organisms. Microbiology is an advanced biology course. Microbiology is the study of microbes, which are extremely small (microscopic) living organisms and certain nonliving entities. Living microbes are known as cellular microbes or microorganisms; examples include bacteria, archaea, some algae, protozoa, and some fungi. Non-living microbes are known as acellular microbes or infectious particles; examples include viroids, prions, and viruses. Microbes are ubiquitous (i.e., they are found virtually everywhere). The microbes that cause disease are sometimes referred to as “germs.” The scientific term for disease-causing microbes is pathogens. Microbes that do not cause disease are called non-pathogens; the vast majority of microbes are non-pathogens. Microbes that live on and in our bodies are referred to as our indigenous microbiota. Some members of our indigenous microbiota are opportunistic pathogens. Opportunistic pathogens are microbes that can cause disease, but usually do not; they can be thought of as microbes that are awaiting the opportunity to cause disease. Pathogens cause two categories of diseases: infectious diseases and microbial intoxications.  Acellular and Cellular Microbes flow chart shows the classification of microbes. Microbes are divided into two: Acellular infectious agents and Cellular microorganisms. Acellular infectious agents are prions and viruses. Cellular microorganisms are further divided into two: Prokaryotes and Eukaryotes. Prokaryotes are archaea and bacteria. Eukaryotes are algae, protozoa, and fungi.  Microbiology Carolus Linnaeus developed a taxonomic system for naming plants and animals and grouping similar organisms together. Leeuwenhoek’s microorganisms can be grouped into six categories: Bacteria Archaea Fungi Protozoa Algae Small multicellular animals A concept chart shows the relationship between microbiology and its various disciplines. Microbiology deals with cellular and noncellular organisms. Cellular organisms consists of the following disciplines namely, bacteriology (bacteria and archaea), phycology (algae), protozoology (protozoa), mycology (fungi), and parasitology (multi cellular animals). A noncellular organism includes virology (viruses) and other infectious agents.  How Can Microbes Be Classified? Bacteria and Archaea Unicellular and lack nuclei Much smaller than eukaryotes Found everywhere there is sufficient moisture; some isolated in extreme environments Reproduce asexually Bacterial cell walls contain peptidoglycan, though some lack cell walls. Archaeal cell walls are composed of polymers other than peptidoglycan. Fungi Eukaryotic (have membrane-bound nucleus) Obtain food from other organisms Possess cell walls Include: Molds—multicellular; grow as long filaments; reproduce by sexual and asexual spores Yeasts—unicellular; reproduce asexually by budding; some produce sexual spores How Can Microbes Be Classified? Protozoa Single-celled eukaryotes Similar to animals in nutrient needs and cellular structure Live freely in water; some live in animal hosts Asexual (mostly) and sexual reproduction Most are capable of locomotion by: Pseudopods—cell extensions that flow in direction of travel Cilia—numerous short protrusions that propel organisms through its environment Flagella—extensions of a cell that are fewer, longer, and more whiplike than cilia Algae Unicellular or multicellular Photosynthetic Simple reproductive structures Categorized on the basis of pigmentation and composition of cell wall Other organisms of importance to microbiologists Parasites Viruses Categories of Diseases Caused by Pathogens chart describes how the two categories of diseases, Infectious disease and microbial intoxication, are caused by pathogens.  Why Study Microbiology? Microbes play significant roles in our lives; they are essential for life on this planet. Photosynthetic algae and bacteria (such as cyanobacteria) produce much of the oxygen in our atmosphere. Microorganisms are involved in the decomposition of dead organisms and waste products. Saprophytes are organisms that live on dead and/or decaying organic matter. The use of microbes to clean up toxic wastes and other industrial waste products is known as bioremediation. Many microbes play essential roles in various elemental cycles, such as the carbon, nitrogen, oxygen, sulfur, and phosphorus cycles. Algae and bacteria serve as food for tiny animals; they are important links in food chains. Microbes that live in the intestinal tracts of animals aid in the digestion of food and produce beneficial substances. For many years, microorganisms have been used as “cell models”; the more the scientists learned about microbial cells, the more they learned about cells in general. Microbes are used in many industries, such as food, beverage, chemical, and antibiotic industries and in genetic engineering. In genetic engineering, a gene(s) from one organism is inserted into a bacterial or yeast cell; the cell that receives the new gene(s) is then capable of producing the gene product(s) coded for by the new gene(s). The use of living organisms or their derivatives to make or modify useful products or processes is called biotechnology.  Microbes as Saprophytes Microbes and Nitrogen Fixation An illustration depicts the nitrogen cycle. Nitrogen-fixing bacteria that live on or near the roots of legumes convert the nitrogen gas in the air into ammonia into the soil. Nitrates then replenish the soil nutrients and the nitrogen gas returns to the air. An illustration shows saprophytes and organic materials getting Microbes and the decomposed into the soil as nitrates, phosphates, sulfates, Food Chain ammonia, carbon dioxide, water, and other chemicals. An illustration depicts the food chain. Tiny living organisms such as algae are eaten by small fish, small fish are eaten by larger fish, the larger fish is consumed by a human being.  First Microorganisms on Earth Fossils of primitive microorganisms date back about 3.5 billion years. Candidates for the first microorganisms on Earth are archaea and cyanobacteria. Infectious diseases of humans and animals have existed for as long as humans and animals have inhabited the planet. Earliest known account of pestilence occurred in Egypt in about 3180 BC.  The Marine Microbiome Is One of the Largest Microbiomes on the Planet Oceans and seas cover >70% of planet Earth. Marine microbiome includes 3 x 1029 microbes. 90% marine biomass Viruses most abundant: 10X more than bacteria Dominant agents affecting life on Earth Courtesy of Rachel Parsons, Bermuda Institute of Ocean Science. A light micrograph shows a cluster of several large and small dots found in one drop of seawater. The large dots represent bacterial cells and the small dots represent virus.  The Soil Microbiome Shapes the World Around Us Microbes associated with plants, soil animals, and the soil itself Ubiquitous in all environmental niches 1013 microbes per kilogram of moist farming soil Drivers of soil chemistry Protect soil health Help feed the world as drivers of agriculture © Alexander Gold/Shutterstock. A culture dish filled with soil granules and several small patches of bacteria and fungi.  The Atmospheric Microbiome Carries a Diverse Community of Bacteria and Fungi 9,000 to 300,000 microbes per cubic meter of air 315 bacterial species identified in air masses 10 km above surface of the Earth Work together with marine microbes in the formation of clouds Support the formation of raindrops and snowflakes Affect chemical composition of air and influence weather cycles © Khamkhlai Thanet/Shutterstock. A culture dish with white circular patches representing fungi and smaller dots representing bacteria.  The Deep Earth Microbiome Is Home to Vast and Unusual Communities of Microbial Life Found 5 km into land subsurface and below seafloor Bacteria and fungi that live in inhospitable conditions Extreme heat, no light, sparse nutrients May represent 70% of all microbes and >50% of Earth’s biomass Recycle minerals and stabilize biogeochemical health of planet Courtesy of Jennifer Magnusson/IODP. The Human Microbiome (1 of 2) 38 trillion microbes The pie chart 4000 different species of bacteria and shows the fungi on and in the body composition of microbiome in More than the number of human human. A. The cells forming the body (30 trillion) data from the chart in percent Microbiome varies among people due are as follows. to physiological differences, age, diet, Bacterial cells: 49. and geographic location. Fungal cells: 8. Human cells: 43. Newborns are colonized during the birthing process and from environmental contact. The Human Microbiome (2 of 2) The photo shows the unique microbial Some microbes are temporary community corresponding to different anatomical (transient). areas. B. The different GI tract microbes: anatomical areas of the human body that possess Help prevent infectious disease a unique microbiome are Aid in breakdown of food labeled as follows: Nasal, oral, skin, gastrointestinal, Provide essential nutrients and and urogenital. vitamins humans can’t make Communicate with brain and immune system May influence obesity, asthma, and allergies Courtesy of NIH Medical Arts and Printing. Pioneers in the Science of Microbiology Robert Koch (1843–1910) Anton van Leeuwenhoek (1632–1723) Louis Pasteur (1822–1895) German physician who made “Father of Microbiology” French chemist who made numerous numerous contributions to contributions to microbiology microbiology Not a trained scientist! Investigated different fermentation Made significant contributions to the Made many simple single-lens products germ theory of disease microscopes Developed the pasteurization process Discovered that Bacillus anthracis Observed “animalcules” Discovered life forms that could exist produced spores without oxygen (anaerobes) Developed methods of fixing and (bacteria and protozoa) Developed several vaccines, including staining bacteria rabies and anthrax vaccines Developed methods to cultivate bacteria  Koch’s Postulates 1. A particular microbe must be found in all cases of the disease and must not be present in healthy animals or humans. 2. The microbe must be isolated from the diseased animal or human and grown in pure culture in the laboratory. 3. The same disease must be produced when microbes from the pure culture are inoculated into healthy susceptible laboratory animals. 4. The same microbe must be recovered from the experimentally infected animals and grown again in pure culture. If an organism fulfills Koch’s Postulates, it has been proven to be the cause of that particular infectious disease. Koch’s Postulates helped prove the germ theory of disease. Koch gave a tremendous boost to the development of microbiology by stressing laboratory culture and identification of microorganisms. Circumstances do exist in which Koch’s Postulates cannot be fulfilled. An illustration depicts Koch’s postulate in four steps. 1. An illustration shows a sick rat. The text reads the microorganism must always be found in similarly diseased animals but not in healthy ones. 2. An illustration shows a culture sample is collected in the petri dish. The text reads the microorganism must be isolated from a diseased animal and grown in pure culture. 3. An illustration shows cultured organism is injected to healthy rat. The text reads the isolated microorganism muse causes the original disease when inoculated into a susceptible animal. 4. An illustration shows a culture sample is collected in the petri dish. The text reads the microorganism can be re-isolated from the experimentally infected animal. Table 1.2 Other Notable Scientists of the Golden Age of Microbiology and the Agents of Disease They Discovered Scientist Year Disease Agent Edwin Klebs 1883 Diphtheria Corynebacterium diphtheriae (bacterium) Theodor Escherich 1884 Traveler’s diarrhea; bladder infection Escherichia coli (bacterium) Albert Fraenkel 1884 Pneumonia Streptococcus pneumoniae (bacterium) David Bruce 1887 Undulant fever (brucellosis) Brucella melitensis (bacterium) Anton Weichselbaum 1887 Meningococcal meningitis Neisseria meningitidis (bacterium) A. A. Gartner 1888 Salmonellosis (form of food poisoning) Salmonella species (bacterium) Shibasaburo Kitasato 1889 Tetanus Clostridium tetani (bacterium) Dmitri Ivanovsky and 1892 Tobacco mosaic disease Tobamovirus tobacco mosaic virus Martinus Beijerinck 1898 Blank Blank William Welch and George 1892 Gas gangrene Clostridium perfringens (bacterium) Nuttall Alexandre Yersin and 1894 Bubonic plague Yersinia pestis (bacterium) Shibasaburo Kitasato Kiyoshi Shiga 1898 Shigellosis (a type of severe diarrhea) Shigella dysenteriae (bacterium) Walter Reed 1900 Yellow fever Flavivirus yellow fever virus Robert Forde and Joseph 1902 African sleeping sickness Trypanosoma brucei gambiense (protozoan) Dutton What Is an Organism? An organism is any living system consisting of one or more cells. A microorganism is a living system consisting of an extremely small (microscopic) cell that has the following features common to all living things: Hereditary material Complex biochemical patterns Reproduction Response to stimuli Evolutionary adaptations A microorganism can be prokaryotic or eukaryotic. Microorganisms are found in all three domains of life. The Prokaryotes: Bacteria and Archaea (1 of 3) >200,000 prokaryotes have been described; may be millions of species in nature. Bacteria are extremely prevalent and are the most studied group in microbiology. Mostly unicellular but some form filaments. Majority associate in biofilms. Most have a rigid cell wall. Common cell shapes are spheres, spirals, and rods. Courtesy of Dr. Rodney M. Donlan and Janice Carr/CDC. The Prokaryotes: Bacteria and Archaea (2 of 3) Most bacteria obtain food from the environment. Some are important decomposers involved with nutrient cycling. Some do photosynthesis instead. Bacteria are also widely studied because: Many are disease pathogens. Many species are responsible for food spoilage. Many species are useful in the food industry. Courtesy of CDC. The Prokaryotes: Bacteria and Archaea (3 of 3) Archaea superficially resemble bacteria but are evolutionarily unique. Many were originally isolated from extreme environments: Yellowstone hot springs (extreme heat) The Dead Sea (extreme salt) Acid mine drainage (extreme low pH) Also found in temperate soil, water, and animal digestive tracts © Eye of Science/Science Source. None known to be pathogenic The Microbial Eukaryotes: Protists and Fungi (1 of 2) Protists include protozoa and single- celled algae. >200,000 species 10–50X larger than prokaryotes May be free-living or live in association with plants or animals Algae can perform photosynthesis and have cell walls. Several protozoans are clinically important human pathogens. © Lebendkulturen.de/Shutterstock. The Microbial Eukaryotes: Protists and Fungi (2 of 2) 125,000 species of Fungi have been described, probably 6 million exist. Nonphotosynthetic; many are decomposers. Two forms: single-celled yeasts and filamentous molds Generally not pathogenic, some are opportunists. Important sources of antibiotics Responsible for some food flavor, such as cheeses Courtesy of Pinterest. Other Infectious Agents: The Viruses Estimated >100 million types of virus Acellular, not considered organisms Genetic material either DNA or RNA but not both Protein coat surrounds genetic material. Must infect an organism to replicate because lack of metabolic machinery Crucial role in evolution of organisms Only a fraction are human pathogens. Courtesy of CDC.  Global Mortality from Infectious Diseases 15 million annual deaths across the globe from infectious diseases 16% of all deaths World Health Organization (WHO) declared a global emergency four times since 2010. Threefold increase in infectious disease outbreaks over 30-year period Data from World Health Organization. World Health Statistics 2011. Retrieved from https://www.who.int.whosis/whostat/2011/en/. Accessed February 7, 2019. A horizontal bar graph shows the global mortality rate from infectious diseases. The graph plots infectious diseases Drug-Resistant Pathogens Declining effectiveness of many antibiotics Bacteria evolve through beneficial mutations. Bacteria can acquire resistance genes from other bacteria. Antibiotics are abused and misused by medical professionals and patients leading to superbugs. Few new drug discoveries Courtesy of CDC. Emerging and Reemerging Diseases Emerging diseases arise in the human population for the first time. 75% spread to humans from animals. 1 or 2 new diseases identified yearly. 40 infectious diseases of humans were not known a generation ago. Most humans will be susceptible due to lack of immunity. Epidemics and pandemics may result. Reemerging diseases had been under control in the past but are showing a resurgence. May be due to drug-resistance or geographic range expansion Most prominently includes tuberculosis and gonorrhea Combat through outbreak surveillance, hygiene and sanitation compliance, and developing new vaccines and antimicrobial drugs Emerging and Reemerging Diseases Courtesy of NIAID A world map shows the newly emerging, re-emerging/resurging, and deliberately emerging infectious diseases recorded over the last 30 years across the globe. Bioterrorism Intentional or threatened use of biological agents to cause fear or inflict death/disease Bioterror agents are mostly bacteria, viruses, and microbial toxins (e.g., anthrax attack 2001). Many can be spread widely through the air and water to affect large populations. Combat by early detection systems, measures to protect the public, and effective treatments © Photodisc. The Climate Crisis and Infectious Disease How will changes in temperature and rainfall patterns affect the frequency and distribution of infectious diseases? Mosquito-borne diseases (malaria, dengue fever) kill 1 million annually If mosquitoes expand their range, tropical and subtropical diseases may be seen in temperate regions. More people may then die. Warming ocean waters can lead to increased spread of waterborne diseases (cholera, leptospirosis). Koko Nakajima/NPR.  The Golden Age of Microbiology What Causes Disease? Gram’s stain The most widely used staining technique One of the first steps to identify a bacterium How Can We Prevent Infection and Disease? Semmelweis and handwashing Lister’s antiseptic technique Nightingale and nursing Snow—infection control and epidemiology Gram positive cells are round and Jenner’s vaccine—field of immunology approximately 1 micrometer in diameter. Gram negative cells are rod shaped and Ehrlich’s “magic bullets”—field of chemotherapy approximately 5 micrometers in length.  Table 1.3 Fields of Microbiology (1 of 3) Disciplines Subject(s) of Study Basic Research Blank Microbe Centered Blank Bacteriology Bacteria and archaea Phycology Algae Mycology Fungi Protozoology Protozoa Parasitology Parasitic protozoa and parasitic animals Virology Viruses Process Centered Blank Microbial metabolism Biochemistry: chemical reactions within cells Microbial genetics Functions of DNA and RNA Environmental microbiology Relationships between microbes and among microbes, other organisms, and their environment  Table 1.3 Fields of Microbiology (2 of 3) Disciplines Subject(s) of Study Applied Microbiology Blank Medical Microbiology Blank Serology Antibodies in blood serum, particularly as an indicator of infection Immunology Body’s defenses against specific diseases Epidemiology Frequency, distribution, and spread of disease Etiology Causes of disease Infection control Hygiene in health care settings and control of healthcare-associated infections Chemotherapy Development and use of drugs to treat infectious diseases Applied Environmental Microbiology Blank Bioremediation Use of microbes to remove pollutants Public health microbiology Sewage treatment, water purification, and control of insects that spread disease Agricultural microbiology Use of microbes to control insect pests Table 1.3 Fields of Microbiology (3 of 3) Disciplines Subject(s) of Study Industrial Microbiology Blank (Biotechnology) Food and beverage technology Reduction or elimination of harmful microbes in food and drink Pharmaceutical microbiology Manufacture of vaccines and antibiotics Recombinant DNA technology Alteration of microbial genes to synthesize useful products (genetic engineering) The Modern Age of Microbiology (1 of 9) What Are the Basic Chemical Reactions of Life? Biochemistry Began with Pasteur’s work on fermentation and Buchner’s discovery of enzymes in yeast extract Kluyver and van Niel—microbes used as model systems for biochemical reactions Practical applications: Design of herbicides and pesticides Diagnosis of illnesses and monitoring of patients’ responses to treatment Treatment of metabolic diseases Drug design  The Modern Age of Microbiology (2 of 9) How Do Genes Work? Microbial genetics Molecular biology Recombinant DNA technology Gene therapy Microbial genetics Avery, MacLeod, and McCarty determined genes are contained in molecules of DNA. Beadle and Tatum established that a gene’s activity is related to protein function. Translation of genetic information into protein explained Rates and mechanisms of genetic mutation investigated Identify methods cells use to control genetic expression  The Modern Age of Microbiology (4 of 9) How Do Genes Work? Molecular biology Explanation of cell function at the molecular level Pauling proposed that gene sequences could: Provide understanding of evolutionary relationships and processes Establish taxonomic categories to reflect these relationships Identify existence of microbes that have never been cultured Woese and Fox determined cells can be categorized as bacteria, archaea, or eukaryotes. Cat scratch disease caused by unculturable organism Recombinant DNA technology Genes in microbes, plants, and animals manipulated for practical applications Production of human blood-clotting factor by E. coli to aid hemophiliacs Gene therapy Inserting a missing gene or repairing a defective one in humans by inserting desired gene into host cells The Modern Age of Microbiology (6 of 9) What Role Do Microorganisms Play in the Environment? Bioremediation uses living bacteria, fungi, and algae to detoxify polluted environments. Recycling of chemicals such as carbon, nitrogen, and sulfur Causation of disease  The Modern Age of Microbiology (7 of 9) How Do We Defend Against Disease? Serology The study of blood serum Von Behring and Kitasato—existence in the blood of chemicals and cells that fight infection Immunology The study of the body’s defenses against specific pathogens Chemotherapy Fleming discovered penicillin. Domagk discovered sulfa drugs. Figure 1.22 The Effects of Penicillin on a Bacterial “Lawn” in a Petri Dish The petri dish has numerous bacteria, Staphylococcus, growing throughout the dish, except in an area around a large fungus colony, Penicillium, on one side. This clear area is the zone of inhibition.