Microbiology Lecture 1 2024-2025 PDF

Microbiology ASC_4_489 Dr Claire Atkinson 2024/25  Welcome to Microbiology ASC_4_489 Dr Claire Atkinson Senior Lecturer in Biomedical Science  Code of conduct- General rules 1. If you have questions/comments, please fe...

Microbiology ASC_4_489 Dr Claire Atkinson 2024/25  Welcome to Microbiology ASC_4_489 Dr Claire Atkinson Senior Lecturer in Biomedical Science  Code of conduct- General rules 1. If you have questions/comments, please feel free to ask 2. Respect everyone in the module, during lectures and labs 4. I’ll do my best to make the lecture as interactive as possible, but it is up to you to make it so. 3. If you need any help with the module, please ask in the General channel in the TEAMs site and tag me, I’ll do my best to answer within 48hrs. If your question is general, please use MyAccount 5. All questions are welcome  Microbiology Define the term microorganisms, demonstrate an understanding of the major taxonomic groups and be able to distinguish the key features of prokaryotic and eukaryotic cells. Explain and apply the fundamental aspects of microbiology such as growth of populations, structure, physiology, biochemistry, nutrition, identification, classification and control of microbes, sterilization and disinfection. Discuss the importance of microbiology and microorganisms in disease and public health (Knowledge and Understanding) Develop knowledge of the pathogenic mechanisms of a range of microorganisms, as well as antimicrobial and antiviral therapy, including drug resistance (Knowledge and understanding) Understand the significance of microbial advances to the study health and disease and basic concepts of Immunology (Intellectual Skills) Recognise and apply the theory of microbiological laboratory health and safety and demonstrate competence in aseptic techniques and a variety of standard microbiological practical skills (Practical Skills) Analyse and manipulate quantitative data and to demonstrate adherence to Laboratory  General Information able: s:. 2hrs lecture + tutorial. 2 will be revision (online) b tutorial: There are a series of micro labs which are COMPULSORY, you will need to attend le to complete your lab book. sments: b book (50%) MCQ/SAQ (50%) ass mark for the module is 40%, but no individual component (Lab or Exam) can be be leader/ Lecturers: Dr. Claire Atkinson ([email protected]) m: Moodle /TEAMs  Labs (50%) Pre-session: make sure you read the lab book and any associated material. Complete the virtual lab All LABS WILL BE IN J202 - YOU WILL NEED A MICROBIOLOGY LAB COAT WHICH WILL BE SUPPLIED BEFORE YOUR 1ST SESSION. Lab 1 - Environmental sampling Introduction to staining and microscopy Aseptic technique and inoculation Lab 2 - Selective and differential growth media Serial dilutions and viable count Assessment is via a lab book, you will need to complete an electronic copy and hand it before the deadline  Engagement If you have a disability or medical condition and need an adjustment to allow you to fully participate in this module (e.g. different format of literature, clear communication for lip reading, breaks for medication, etc.) please tell me so that arrangements may be made. If you encounter any difficulties that affect your ability to progress this module/course tell me. For the lab, if you are pregnant, immune-compromised or are taking immunosuppressant drugs, please speak w me so that arrangements may be made. If you encounter any difficulties that affect your ability to progress this module/course tell me.  Reading List CORE 1. Madigan, M.T, Bender, K.S, Buckley, D.H, Sattley, W.M, & Stahl, D.A. (Global Edition). Brock Biology of Microorganisms. Pearson (edition 2019 and 22) 2. VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Mosby, Elsevier. 3. Willey, J, Sherwood, L & Woolverton, C.J. (2020). Prescott’s Microbiology (11th Edition). McGraw-Hill 4. Cappuccino JG and Welsh C. Microbiology: a laboratory manual (2018) OPTIONAL 5. Slonczewski J.L, Foster J.W and Foster E. (2020).Microbiology: An Evolving Science. W.W. Norton & Co (5th Edition) Questions  Lecture 1 Introduction to Microbiology Dr. Claire Atkinson  Learning objectives By the end of the lecture you should be able to answer the following questions What are the origins of microbiology and microscopy? What are the origins and evolution of microorganisms? How do we classify microorganisms? How do microorganisms impact upon health and disease? How do we encounter microorganisms in everyday life?  What is Microbiology?  Study of microorganisms: living organisms that are too small to be seen by naked eye (bacteria, virus, fungi, archaea, yeast)  Variety of techniques used for  Visualization  Identification  Study of microbial function  Science of microbiology  Originated with invention of the microscope. Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Small, but how small? Few bacteria are actually bigger than some eukaryotic cell So small, that a human cheek cell has some ‘resident’ bacteria 1000X. Bacteria smaller than the nucleus of the cell. Can we use size to separate microorganisms?. If I have I have filters for 220 nm, 450nm, 1000nm VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Small, but how small? https://www.youtube.com/watch?v=E6TFuTGcPjc Microscopy The History of the Microscope - YouTub  Seeing is believing: Microscopy Zaccharias and Hans Janssen Anton van Leeuwenhoek (1632–1723) Dutch eyeglass makers Native of Holland In about 1590 produced the first compound Father of microscopy microscope Observed protozoans and bacteria “Animalcules”(1676-1st Bacteria) Robert Hooke (1635–1703) English scientist Improved the design and capability of the compound light microscope Observed insects, sponges, protozoans, and more Micrographia (1665) Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition  Where life is coming from??? Abiogenesis: The origination of living organisms from lifeless matter; such genesis as does not involve the action of living parents; spontaneous generation. Do microbes spontaneously appear, or are they the cause of decay and fermentation? Firmly believed that living Scientists started doubting and developed experiments things can come from to contradict abiogenesis nonliving matter Louis Pasteur and the swan-necked flasks The spoilage of liquid was caused by particles in the air rather than the air itself. These experiments were important pieces of evidence supporting the idea of germ theory of disease. Led to the technique - Pasteurization Do you know other things that get pasteurized? Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition  Germ Theory of Disease Suspicion that microorganisms cause not only spoilage and decay but also infectious disease Childbirth deaths Linked maternity infections Expanded protocols linked to dirty hands to contamination of hands with aerosol disinfection of physicians Required chlorine solution Introduced aseptic wash. techniques Odor… Oliver Wendell Holmes (1809-94) Ignaz Semmelweis Joseph Lister (1818-65) (1827-1912)  Germ Theory of Disease: existence of infectious organism. Louis Pasteur/Robert Koch Koch’s postulates Robert Koch Investigation of anthrax (1876-77) Edward Jenner Convinced of the existence of infectious Smallpox Immunization: Microorganisms. start of immunology Endospores from antrax. (1796) Cowpox lesion material (with Vaccinia virus) into a small incision, provide protection against smallpox Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Brief history of microbiology 5. Questions?  Microscopy Light Microscopes Use visible light and optical lenses Either simple or compound Ocular lens Dissection and stereomicroscopes Objective lens Final magnification: Multiply the enlarging Low power: for observing power of both the ocular and objective whole objects lenses Bright-field microscope Example: ×10 times ×4 = ×40 Background is lighter than observed specimen Most specimens require fixing and staining for bright- field microscopy VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Microscopy Dark-field microscope Phase-contrast microscope Used to view unfixed, unstained specimens Used to view unfixed, transparent specimens Such as living organisms Effective for observation of cytoplasmic Background dark, specimen bright streaming, motility, and the dynamic states of cell organelles Cheek cells Cheek cells VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Microscopy Fluorescence microscopes Pseudomonas Ultraviolet illumination Visualization of specimens that contain naturally fluorescent substances or that have been stained with fluorescent stains/dyes Used in diagnosis of infectious diseases Used in microbial ecology Applied to identify specific antibodies in response to antigens VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Microscopy Confocal microscopes Sharper images Allows visualization of different planes of a specimen Often by using a laser for illumination Image can be displayed three-dimensionally with “electronic staining”  Microscopy Electron Microscopes (EM) Neuron Transmission electron microscopy (TEM) Electron beam goes through specimen and magnetic field instead of optical lenses Special preparation, sectioning, and staining Two-dimensional images Good internal detail Pictures are referred to as electron micrographs VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Microscopy Electron Microscopes Campylobacter Scanning electron microscopy (SEM) No sections Scans the surface of an object Three-dimensional image Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Microscopy Microscopes and resolution Physiology Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Questions? Why do we study Microbiology: diversity Shapes/ sizes/arrangement/staining/energy source/ temperature/pH/pressure/ oxygen requirements Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition  Classification of Microorganisms Fossil records show that the first living organisms were prokaryotic (3.5-4 billion years ago) From them all other organisms EVOLVE. Eukaryotes (2.2billion years) 5-100 million species of organisms! Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Alberts. Molecular Biology of the cell. (2014)  Domains of life How do we distinguish if they are different microorganism? Phenotypic (how they look like: size, shape Organization, color) Analytic (their composition) Genotypic (their genetic information-rRNA) Bacteria Archaea Eukarya How do we name a new Protists microorganism? Fungi Plants Animals Leboffe, M.J & Pierce, B.E. (2015) Microbiology: Laboratory Theory and Application  Classification of Microorganisms Prokaryotes No membrane-bound organelles, such as a nucleus (pro, before; karyon, nucleus) Archaea, bacteria Eukaryotes (microorganism) With membrane-bound cell organelles Algae, fungi, protozoans Other Viruses, viroids, prions Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Alberts. Molecular Biology of the cell. (2014)  Taxonomy The formal system of organizing, classifying, and naming living organisms Domain(3) /Kingdom (6) Phylum (division for bacteria) Class Order Family Genus Species Strain Binomial (scientific) nomenclature: established by Linnaeus Escherichia coli VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Taxonomy Each organism has at least two names: the genus and species Scientific names are italicized or underlined The Genus is capitalized and the species is in lower case After the first use, scientific names may be abbreviated with the first letter of the genus Escherichia coli E. coli  Domains of life Bergey’s Manual of Systematic Bacteriology Baltimore Classification of viruses – based on RNA DNA genomes, ss or ds and sense or antisense replication How do we name a new microorganism? International Committee on Taxonomy of Viruses (ICTV) International Committee on systematics of prokaryotes VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Microorganisms in Health and Disease Microbial ecology Often deals with biofilms- organized into complex communities of different microorganisms, found in variety of surfaces (medical devices, industrial piping, natural aquatic systems) Interactions Mutualism: Both organisms benefit Commensalism: the waste product of one serves as source of energy for the other Synergism: Both organisms dependent on each other to access the nutrients Parasitism: One organism benefits and the other is harmed  Microorganisms in Health and Disease Normal flora versus pathogens Foodborne diseases Organism/toxin contamination Waterborne diseases- Floods Organism contamination Airborne diseases Aerosols – can you think of an airborne disease ? Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Foodborne and Waterborne Disease 5.  Airborne Disease 5. Covid19-----Coronavirus (SARS-Co-V2)  Applied Microbiology Food production Yogurt, bread, cheese (different microorganism for different cheese), pickets, vinegar Alcoholic beverages Wine, beer Treatment of water supplies Indicator organisms Pharmaceutical agents Penicillin Insulin Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Allison Ramsey and Mary Staicu: The accident that changed the world | TED Talk  Applied Microbiology Agriculture Soil microbes, nitrogen cycle Bioremediation Petroleum-digesting bacteria Energy Fuel cells, ethanol, methane Forensics Medicine, criminal justice, epidemiology, bioterrorism Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition  Applied Microbiology Allison Ramsey and Mary Staicu: The accident that changed the world | TED Talk Questions? BREAK QUIZ What originated the study of Micro- organisms? 1. Abiogenesis 2. The invention of the Microscope 3. The Swan Neck experiment 4. The boiled broth experiment 5. None of the above All Micro-organisms are? 1. Prokaryotes 2. Eukaryotes 3. Non living 4. Visible only with a microscope 5. Living What theory was created by Pasteur? 1. Bacteria 2. Wheat 3. Germ 4. Fermentation 5. none of the above _______ postulates contain 4 basic rules? 1. Lous 2. Koch 3. Newton 4. Pasteur 5. Fleming How did Koch test that microbes were causing disease? 1. He studied them under a microscope 2. He exposed humans to microbes 3. He ingested microbes 4. He exposed animals to microbes What microscope has the largest magnification? 1. Light microscope 2. phase contrast microscope 3. Electron microscope 4. Fluroscent microscope 5.Dark field microscope Which of the following is not a microorganism? 1. Bacteria 2. Fungi 3. virus 4. insect 5.yeast  Tutorial Lab Safety Dr. Claire Atkinson  Laboratory Safety *Ask yourself, "What am I working with? What are the hazards? RISK ASSESSMENT *Come prepared – read your lab manual before the lab *Prevent potential exposure. dress for work in the laboratory. Wear clothing and shoes that cover exposed skin and protect you from potential splashes. Tie back long hair, jewellery, or anything that may catch in equipment. Never eat food, drink beverages, chew gum, apply cosmetics (including lip balm), or handle contact lenses in the laboratory. Laboratory Safety  PPE Gloves Generally latex Nonlatex available because of allergies Respiratory protection Various types Clothing Laboratory coats at all times Eye protection Mandatory in many laboratories Footwear Closed shoes  Laboratory Safety Equipment 1. Fire extinguishers 2. Fume hoods General purpose hoods Radioisotope hoods Biosafety cabinets Perchloric acid hoods 3. Autoclave 4. Eyewashes and safety showers 5. Refrigerators/freezers 6. Disposal of hazardous waste Leboffe, M.J & Pierce, B.E. (2015) Microbiology: Laboratory Theory and Application Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc.  Waste Disposal Broken glass Biohazardous Sharp wastes s Leboffe, M.J & Pierce, B.E. (2015) Microbiology: Laboratory Theory and Application Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier  Chemicals in the Laboratory Standards for the safe use and handling of chemicals Control of substances hazardous to health (COSHH) MSDSs for each chemical in each laboratory Potential risk Storage Disposal What to do if…….  Laboratory Safety Biosafety—involves biological agents Bacteria Viruses Fungi Other microorganisms and their toxins All can adversely affect human health Mild allergic reactions Serious medical conditions  Laboratory Safety Advisory Committee on Dangerous Pathogens (ACDP) Guidance: Biological Agents: Managing the Risks in Laboratories and Healthcare Premises Protection Against Blood-Borne Infection in the Workplace: HIV and Hepatitis Transmissible Spongiform Encephalopathy Agents: Safe Working and the Prevention of Infection Management and Control of Viral Haemorrhagic Fevers Health and Safety Commission (HSC) / Health and Safety Executive (HSE) Guidance: Safe Disposal of Clinical Waste Biological Agents: Managing the Risks in Laboratories and Healthcare Premises  Biosafety Levels (BSLs) BSL 1 Working with microorganisms that generally do not cause disease in healthy humans Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc.  Biosafety Levels (BSLs) BSL 2 Laboratories designed to work with agents that may be considered a moderate risk to the personnel. Containment devices, administrative controls, and more strict guidelines than in BSL 1 Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc.  Biosafety Levels (BSLs) BSL 3 Applies to clinical, diagnostic, teaching, research, production laboratories using original or exotic agents These agents are potentially causing serious disease or lethality Increased laboratory safety Increased training of laboratory personnel Limited access to the laboratory Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc.  Biosafety Levels (BSLs) BSL 4 Required when working with exotic agents Agents with a high risk of aerosol transmission Infections that are life threatening. Staff in these laboratories have specific training Facilities handling these agents are in separate buildings or in controlled areas—completely isolated from all other areas Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc. Biosafety Levels (BSLs) Summary Leboffe, M.J & Pierce, B.E. (2015) Microbiology: Laboratory Theory and Application  TASKS: Week 1 Think about what you have learnt today Read you lab book in preparation for next week Create a list of microbiological terms