MMI 133 Lecture 1 Notes - Medical Microbiology for Health Professionals PDF

MMI 133 Lecture 1 Nuts and Bolts & Beginnings  MMI 133: Medical Microbiology for Health Professionals Dr. Judy Gnarpe (pronounce all letters) 6-020D Katz Group Centre Department Medical Microbiology & Immunology Faculty of Medicine & Dentistry College of Health Scienc...

MMI 133 Lecture 1 Nuts and Bolts & Beginnings  MMI 133: Medical Microbiology for Health Professionals Dr. Judy Gnarpe (pronounce all letters) 6-020D Katz Group Centre Department Medical Microbiology & Immunology Faculty of Medicine & Dentistry College of Health Sciences Email: [email protected]  A little bit about me: Undergrad at the U of A in Medical Laboratory Science (eons ago, obviously) PhD at University of Uppsala, Sweden – Clinical Microbiology (eons ago) Worked for 23 years in Sweden at hospital lab as clinical microbiologist Along the way married a Swede Moved back to Edmonton 1999 with my Swede Research on C. pneumoniae while here 1999-2003 Teaching from 2003 on – health professionals: Nurses, pharmacists, dental hygienists, medical and dentistry students, lab residents  My girls Frankie 3 yr Gracie 9 yr.  Session 1 Objectives 1. Introduction to MMI 133 2. Introduction to eclass 3. Introduction to microbiology 4. Relative sizes of organisms 5. Student should be familiar with the naming of bacteria based on their morphology 6. Gram staining: how we differentiate bacteria  Course Objectives 1. differences between microorganisms; how they cause disease (and why) 2. how antimicrobials act to inhibit microbes 3. knowledge about the clinical conditions associated with infection 4. ramifications of epidemiology, spread and prevention of infection  Textbook = (4th edition)Medical Microbiology for Health Professionals (Gnarpe) Do you need it? – Yes if you want to be able to answer the questions on the assessments and the assignment it is required. The exams are open book. There are also readings that need to be done for the course. Where do I get the text? – New at the U of A bookstore; new in paperback or electronic version at Kendall Hunt.com (link https://he.kendallhunt.com/gnarpe). – There are two copies of the 4th ed. on reserve at the Sperber Health Sciences library (ECHA) eClass: Necessary to use for course!!!!! all lecture handouts and information can be found and downloaded from eclass general course information, schedules, eClass help files lecture recordings case studies, videos, practice exams self-assessment quizzes , puzzles, cool and uncool games (self assessment quizzes are not for marks) GRADES: assignment and exam marks link to U of A library,-info on cheating, plagiarism assignment drop box exams ( all online) Zoom and Yuja where the lecture recordings are  The assignment can be uploaded to the assignment portal in eclass early but should not be handed in late. The due date is Dec 5 at midnight. Late assignments will be deducted 10% per day and after 2 days will not be accepted, resulting in a mark of “0”. This Photo by Unknown Author is licensed under CC BY-SA  Where do the marks come from? Midterm 1 (Oct 1 ) = 25% Midterm 2 (Oct 31 ) = 25% Assignment (due Dec 5) = 10% Final exam (Dec 16) = 40% Bonus mark of 1% for completing the quiz on student code of ethics by Sept 20 at midnight. Must get 80% or higher for mark, but you can do the quiz as many times as you need to.  This course is not graded on “the curve”, but rather on natural breakpoints. What does the curve mean? : ~6% of students in a first year course should get an F. Is this desirable? Marks are lined up at the end of the year and we look for the most likely spots to break in terms of grades. For example: A+ 100,100, 98,98,98,98,98, 97,97,97,97,97,97,96,96,96,96,96, 95, 94,94,94,94,94,93,93,93,93,93,93,93,92,92,92,92,92,92,92,92,91, A 91,91,91,91,91,91,90,90,90,90,90,90,90,89,89,89,89,89,88.88,88,88, 88, 88,88,88,88,88, 87,87,87, 86,86,86,86,86,86,86,86,86, 85,85,85, 85,85,85,85,85,85, A- 84,84,84,84,84,84,84,84,83,83,83,83,83,83,83,83 82, 81,81,81,81,81,81,81,81,81,81 *** note this is only an example and not the marks you will need in reality.  5 Major Categories of Microbiology 1. Bacteriology: study of bacteria 2. Virology: study of viruses 3. Mycology: study of fungi and yeast 4. Parasitology: study of protozoa (amoeba etc) and metazoa (worms) 5. Immunology: study of immunity (resistance to infection) Do you think Microbiology is BORING? © S Hnatko, MD, U of A  Bacteria + Infections © PHIL 1941, CDC – Cutaneous Diphtheria  Virus + Infection www. images.md © Bernardo Raigosa, MD, DermAtlas, Johns Hopkins University Parasites + Infection © PHIL 373 CDC  Fungus + Infections © PHIL 15439 CDC, Lucille K George © PHIL 12529 CDC, Lucille K George Lecture 1 Part 2 Getting started  Universal Ancestor Bacteria Archaea Eukarya G- bacteria Fungi Methanogens G + bacteria Animals & Us Extreme Halophiles Cyanobacteria Amoeba Hyperthermophiles Chloroplast Plants Mitochondrion Microspora A. Size © PHIL 5260 CDC © J Gnarpe, DrMedSci PHIL 11212 Drs. C Goldsmith and A. Balish, CDC  Sizes of organisms Prion smallest Virus Bacteria Micro - & macro- Fungi scopic Parasites largest Mammals We’ll start with bacteria….  Are bacteria BAD? What would happen if we didn’t have any bacteria associated with our body? -We have a complex ecosystem in our bodies: -Healthy adult has 10 trillion bacteria in the gut which is about the same number of body cells -We provide shelter and nutrients to bacteria, they provide services: -E.g. milk contains sugars in form of “glycans”. We cannot use these for food unless there are bacteria present that break down the glycans to usable sugars. -E.g. production of Vitamin K and Vitamin B12 -E.g. protection against disease producing bacteria -ETC.  But- there are some “nasties” Imbalance in bacterial flora due to previous treatment with antibiotics Infection with some strains of bacteria that have virulence factors which cause them to damage tissue Immunocompromised individuals at more risk for infection because we need to have a good immune system to keep everything in balance So let’s get on with learning about this!  Example: Escherichia coli Kingdom: Monera (bacteria) Do not need to Phylum: Proteobacteria know Class: Gamma Proteobacteria Order: Enterobacterales Family: Enterobacterale Genus: Escherichia Species: coli (E. coli) Need to know Subspecies EHEC (O157:H7) EPEC ETEC, etc  B. Bacterial Naming classified into families on the basis of the relatedness of genetic information (use rRNA for typing) Family → Genus → Species  Subspecies Important to know both Genus and Species names  * Note capitalization convention and italics Genus, species ❑ Staphylococcus aureus (S. aureus) Staphylococcus epidermidis (S. epidermidis) Staphylococcus sp. (all types of Staphylococcus) ❑ Salmonella typhi (S. typhi) Salmonella enteritidis (S. enteritiditis)  Bacterial Shape (morphology) ❑ Cocci o Staphylo-, strepto-,, diplo- ❑ Bacilli o Diplo, strepto, cocco- ❑ Spiral bacteria o Vibrio, spirillum, spirochaete  Spiral and Curved Bacteria PHIL 6631 CDC Vibrio cholerae ©J. Gnarpe, DrMedSci  How do we tell bacteria apart if they are the same shape? Differential stains (separate bacteria into different groups): GRAM STAIN: divides most bacteria into two groups ACID FAST STAIN: used for mycobacterium (e.g. TB bacteria) ❑ most important practical distinction to know about bacteria is the staining characteristic: GRAM’S STAIN ❑ still used as one of the major diagnostic tests used to identify disease causing bacteria ❑ based on cell wall structure: amount of peptidoglycan (structural mesh) in the bacterial cell wall IMPORTANT: Read your text about Gram staining Make slide from sample and fix (heat or methanol) PHIL 15353 CDC Mae Melvin Add Crystal Violet (“primary stain”) PHIL 3433 CDC Dr. Michael Rein Wash crystal violet off after 1 min PHIL 3426 CDC, Dr Michael Rein  Add Iodine – “mordant” PHIL 3427 CDC Dr. Michael Rein  Wash iodine off after 1 min PHIL 3435 CDC Dr. Michael Rein Decolourize with acetone/alcohol PHIL 3437 CDC Dr Michael Rein Add counterstain (safranin) PHIL 3436 CDC Dr. Michael Rein  After safranin washed off, dry slide PHIL 3434 CDC Dr Michael Rein  Crystal Violet Bacterium Crystal violet (unstained sticks in peptidoglycan of but fixed) all bacteria Mechanism published 2013, American Chemical Society, Wilhelm et al, DOI: 10.1021/acshembio.5b00042 Iodine Iodine is the mordant and complexes with CV in the peptidoglycan mesh. Crystal violet –Iodine complex precipitates in PG layer  Peptidoglycan is 10- 20X thicker in G+ - Peptidoglycan is compressed in Gram+ Gram + Acetone-alcohol wash - disrupts peptidoglycan and associated G-outer membrane Gram - * Peptidoglycan is thinner in G- and (Holes in outer the mesh is attached to the outer membrane and membrane with lipoprotein disruption of peptidoglycan) Counterstain the G- with a contrasting dye i.e. Safranin Gram + Cross sections Gram – (only safranin)  Summary: Gram staining Fig 2.1 Medical Microbiology for Health Professionals  Summary ❑ Many different organisms can cause human disease ❑ Bacteria are prokaryotic organisms (before nucleus) Plants, mammals, birds, reptiles and amphibians, fungi and we humans are eukaryotes ❑ Bacteria have different shapes and often are named accordingly ❑ Bacteria have a naming system that is dependent on their genetic relatedness ❑ The Gram stain is used to divide bacteria into two major groups (G+ and G-).