Clinical Microbiology Lecture Notes PDF

Welcome to Clinical Microbiology BIOL 205 Chapter 1 - Course Introduction Introduction to Microbiology Microorganisms or Microbes are organisms that are too small to be seen with the unaided eye include bacteria, fungi, protozoa, microscopic algae, and viruses My goals f...

Welcome to Clinical Microbiology BIOL 205 Chapter 1 - Course Introduction Introduction to Microbiology Microorganisms or Microbes are organisms that are too small to be seen with the unaided eye include bacteria, fungi, protozoa, microscopic algae, and viruses My goals for today Why are microbes important? To introduce the general concepts and overarching themes we will cover during this course Most importantly, why are microbes important to you and your future career Why should you care? History of Microbiology 1665: Robert Hooke examined cork with a crude microscope and reported that living things are composed of little boxes, or “cells” Beginning of cell theory: All living things are composed of one or more cells 1676: Anton van Leeuwenhoek published his observations of “Animalcules” (or “tiny animals”) viewed through magnifying lenses Probably the 1st person to view microbes History of Microbiology Up until ~160 years ago many believed in spontaneous generation: the hypothesis that life arises from nonliving matter; that a “vital force” is necessary for life 1858: Rudolf Virchow proposed biogenesis: the hypothesis that living cells arise only from preexisting living cells History of Microbiology 1861: Pasteur disproves spontaneous generation History of Microbiology 1861: Pasteur disproves spontaneous generation Microbes present in nonliving matter (air, solids, liquids) Microbes can be destroyed by heat Methods can be used to prevent microbial contamination – Aseptic techniques  History of Microbiology First Golden Age of Microbiology Beginning with Pasteur's work, discoveries included: The relationship between microbes and disease The “germ theory of disease” – microbes cause disease Koch’s postulates – specific diseases are caused by specific microbes Immunity Protection from disease by vaccination or disease recovery  History of Microbiology Second Golden Age of Microbiology Chemotherapy – Treatment of disease with chemicals Synthetic drugs Antibiotics – chemicals produced by bacteria and fungi that inhibit or kill other microbes Penicillin – The first antibiotic discovered History of Microbiology We are currently in the Third Golden Age of Microbiology Previous discoveries have expanded the field into several new areas of study Field The Study of Bacteriology Bacteria Mycology Fungi Parasitology Protozoa and parasitic worms Virology Viruses Microbial How microbes inherit traits genetics The relationship between Microbial microorganisms and their ecology environment Immunology Immunity Molecular How DNA directs protein synthesis biology  Microbes and Life Microbes are essential for life as we know it and the processes that support life Basis of the aquatic food web Recycle chemical elements by breaking down organic compounds (decomposition) Perform majority of planet’s photosynthesis Phytoplankton (i.e. cyanobacteria) carry out around 70% of the photosynthesis on the earth Only bacteria convert atmospheric nitrogen (N2, useless to most organisms) to ammonia (NH3, used by most organisms) Microbes and Human Welfare Microorganisms provide essential models that give us fundamental knowledge about life processes Used as “model organisms” in research Humans utilize and harness microorganisms and their products Produce chemical products such as ethanol, acetone, and vitamins Produce fermented foods such as vinegar, cheese, bread, soy sauce, and of course, alcohol Used in processes such as sewage treatment, bioremediation, and even pest control Microbes and Human Welfare Biotechnology is the use of biological processes (especially involving microbes) for practical applications, such as producing foods and chemicals Recombinant DNA technology enables bacteria and fungi to produce a variety of things they naturally could not Products used in manufacturing (e.g., cellulose) and disease treatment (e.g., insulin) Vaccines Gene therapy to replace missing or defective genes in human cells Microbes and Human Disease – Pathogens!!! The vast majority of microbes are beneficial; only a minority (~5%) are pathogenic (disease causing) Pathogens – microbes that can cause disease and that carry out all or part of their life cycle in the infected host Disease – a condition that impairs normal functioning and typically shows distinguishing signs and symptoms Infectious disease – disease caused by pathogens (bacteria, viruses, fungi, etc.) invading a susceptible host (humans, plants, etc.) Microbes and Human Disease Knowledge of pathogenic microorganisms allows humans to Prevent disease Understand causes and transmission of disease to prevent epidemics Why should microbiology be taken seriously? Healthcare professions are on the front lines against the absolute worst pathogens Lab strains of Microbes in nature Hospital/healthcare associated microbes microbes Microbes and Human Disease Emerging infectious diseases (EIDs): new diseases and diseases increasing in incidence Due to numerous factors Mutation of existing organisms Spread to new geographic locations Increased human exposure to pathogens Antibiotic-resistance Viral Infections infections Zika virus disease Methicillin-resistant Middle East respiratory syndrome Staphylococcus aureus (MRSA) (MERS) Multi-drug-resistant Coronavirus disease 2019 (COVID- tuberculosis (MDR-TB) 19) Clostridium difficile H5N1 influenza (bird flu) Ebola hemorrhagic fever (EHF)  Microbes and Human Disease Biofilm: community of Biofilm on a piece of plastic microbes in which the cells stick to each other and Serratia liquefacie usually to a surface, and ns also has a protective slime- like outer layer. Capsula Grow on rocks, pipes, teeth, r materia medical implants…pretty l much anywhere Plastic Biofilms can cause infections and are often resistant to antibiotics Our Natural Defenses Resistance is the ability of the body to ward off disease When a pathogen invades a host and overcomes the host's resistance, disease results Resistance factors include skin, stomach acid, and natural antimicrobial chemicals (e.g. interferon) Another major resistance factor are the microbes normally present in and on a healthy human body called the normal microbiota (normal flora) Begin to be acquired as newborns and may colonize the body indefinitely An average adult is composed of ~30 trillion body cells (3 x 10 13), but over 40 trillion bacterial cells (3 x 1013) live on or in the human body The Human Microbiome Microbiome – all the microorganisms in an environment Each human microbiome is composed of that humans normal microbiota Benefits Help to maintain good health Can prevent growth of pathogenic microbes May help train the immune system to discriminate threats Understanding the human Appanna V.D. (2018) The Human Microbiome: The Origin. In: Human Microbes - The Power Within. Springer, Singapore microbiome is of great importance The Human Microbiome Project (Began – 2007) Goal of determining the makeup of typical microbiota of various areas of the body Secondary goal of understanding relationship between changes in microbiome and human diseases The National Microbiome Initiative (Began – 2016) Explores the role microbes play in different ecosystems Naming Microorganisms System of scientific nomenclature (naming) still used today was created in 1735 by Carolus Linnaeus, the "father of modern taxonomy." Escherichia coli or Escherichia coli (Genus) (Species) Scientific names Two part names that are italicized or underlined (not both!) Genus name is first and the first letter is capitalized Specific epithet or species name is second and is lowercase Naming Microorganisms Scientific names Are “Latinized” and used worldwide May be descriptive or honor a scientist Escherichia coli Honors the discoverer, Theodor Escherich Describes the bacterium's habitat—the large intestine, or colon Staphylococcus aureus Describes the clustered (staphylo-) spherical (coccus) cells Describes the gold-colored (aureus) colonies Naming Microorganisms After the first use, scientific names may be abbreviated with the first letter of the genus and the full specific epithet (still italicize or underline both). For example: Escherichia coli and Staphylococcus aureus are found in the human body. E. coli is found in the large intestine, and S. aureus is on the skin.  Classifying Microorganisms 8 Major microbe groups Domain Archaea found in all three domains Archaea of life (two exceptions) Domain Domain Bacteria Eukarya Bacteri Fungi a Protozoa Multicellul ar Animal Nonliving Parasites Viruses Algae Prions Microbe Types