DPAS 5200a25 Day 3 Bact Viruses PDF

DPAS 5200a25 Day 3 Intro to Bacteria And Viruses  Before anything else… a bit of inspiration for the study of infectious agents. Screen Shot 2013-02-15 at 4.21.55 PM.png  TODAY’S Instructional OBJECTIVES: DAY 2: Bacteria/Virus physiology 1. Describe the basic...

DPAS 5200a25 Day 3 Intro to Bacteria And Viruses  Before anything else… a bit of inspiration for the study of infectious agents. Screen Shot 2013-02-15 at 4.21.55 PM.png  TODAY’S Instructional OBJECTIVES: DAY 2: Bacteria/Virus physiology 1. Describe the basic structure of bacteria and of viruses. 2. Translate the nomenclature used in bacteriology. 3. List the ways that bacteria are classified and subcategorized. 4. Describe the role of normal flora in human resistance to infection. 5. Define the concepts of specific and nonspecific immunity, host immunity, virulence, and mutability (immunity also covered in PAS 6120) 6. Explain the two basic models for viral life cycles (lytic, lysogenic) 7. Describe the pathophysiologic mechanisms utilized by bacteria and viruses in infection  The life cycle of bacteria Bacteria are prokaryotes– cells with no membrane-bound organelles like the nucleus, ER, or Golgi. Their life cycle is simple, as Dr. Bassler described: 1. Grow 2. Replicate your DNA 3. Divide 4. repeat Many bacteria divide once every 20 minutes in an exponential fashion. Over 7 hours, if all the population’s needs are met, 1 bacterium can create a 1 million- bacterium population. Over 24 hours, one E. coli bacterium could (theoretically) give rise to enough E. coli to coat the globe. Fortunately, bacteria do not usually “max” their reproductive capacity like that. CONTROLLERS OF BACTERIAL GROWTH:  Limits on resources (nutrients, water)  Limits of environmental area (space)  Absence of environmental requirements (temp, pH, etc…)  Presence of predators or defense systems The typical pattern, even in absence of predatory (immune system) sources, is to multiply up to a “carrying capacity.”  Classification of Bacteria Bacteria are classified according to four major characteristics: ▪ Shape and arrangement: coccus, bacillus, spiral ▪ Gram stain reaction: gram-positive and gram- negative ▪ Biochemical and growth characteristics We will ▪ Aerobic and anaerobic discuss ▪ Spore formation these. ▪ Biochemical profile ▪ Antigenic structure: antigens in cell body, capsule, flagella  Classification of Bacteria: This is a human construct- a way of describing the bacteria that is encountered.* the next few slides will describe ways we classify bacteria. Gram-positive bacteria do not all use the same nutrients. *Very similar to ways we Rods don’t all have the describe humans: same reproduction time. White vs. black vs. brown Hair color/ hair amount Language spoken/understood Not all cocci like to grow in Omnivore, vegetarian, vegan the same environment. Heat tolerant vs heat intolerant Burns easily vs tans easily  Classification criteria– GROWTH PREFERENCES: Bacteria often are classified according to how they can be grown in the lab. Type of culture media: what kind of nutrient plates will they grow on? Tolerance to suboptimal conditions Fastidious organisms: can be grown only on enriched media under carefully controlled conditions of temperature and acidity (pH) Hardy organisms: can grow on relatively simple culture media under a wide variety of conditions Oxygen requirements: Aerobic organisms: grow best in the presence of oxygen (O2) Anaerobic organisms: only grow when O2 is low or absent Facultative Anaerobes grow equally well under any O2 conditions  Classification criteria– STRUCTURAL FEATURES: Bacteria often are classified according to what they look like.  Flagella: hair-like processes covering the surface of some bacteria; responsible for the organism’s motility  Spores: a dormant, extremely resistant bacterial modification formed when the bacterium is in adverse conditions  Spores can germinate and give rise to actively growing bacteria once conditions become favorable  If a bacterium can be induced to produce spores, that tells you something about its identity. C. Tetani rods with spores  Antigenic Structure An ANTIGEN is the part of an invading organism that mammals create antibodies to.  They usually are pieces of the bacterium’s cell body, capsule, wall, or flagellum. These aren’t magic– they’re just a portion of the bacterium that:  your body is exposed to, and  your body’s immune system recognizes as “not you.” A piece of an invading organism is most likely to act as an antigen when: It is biochemically very different from its host, and The host is most likely to get exposed to it (e.g. the bacterium’s cell wall rather than its nuclear membrane) Identifying the structure of a organism’s antigenic portion is exceptionally helpful! This structure often is unique to the organism, or to its family. One can test for an organism by looking for evidence of its antigens One can use antigens to make vaccines against particular organisms Humans and Bacteria: Vocab! a love/hate relationship  Normal Flora: the “assist” to your immune system This is lactobacillus, a normal finding in the GI tract and other places Normal Flora establish themselves within hours of birth. The many roles of normal GI flora: Endocrine Reviews December 1, 2010 vol. 31 no. 6 817-844 Innate immunity Acquired immunity Perform metabolic functions for us Related to insulin sensitivity, hunger, BMI, lipid storage and more  Normal flora assist in maintaining a non-infected environment by making the “peri-human” environment unavailable to pathogens. Normal flora often create a layer of glycoprotein and polysaccharide molecules (mucous layer) that is difficult for pathogens to penetrate. Once penetrated, though, it’s important to get the normal flora to re-establish a presence. One significant protection against bacterial overgrowth is ensuring a healthy “normal flora” population. Ex: this graph illustrates three different treatments for C difficile. Treatment B worked better than any antibiotic in C diff treatment. Do you know what the treatment is? “normal flora transplantation” Fecal transplantation “Normal” also means absence of overpopulation of any particular type of bacterium- even a normal one. Example: normal vaginal flora vs bacterial vaginosis Top: normal squamous cells on a vaginal smear, with few coccobacilli and lots of lactobacilli. This is associated with a normal vaginal discharge. Bottom: “clue cells”: no lactobacilli seen, and an abundance of coccobacilli. This is associated with copious watery, often smelly discharge. It’s not that the coccobacilli are abnormal; It’s that the number of them should not be very high.  Bacterial vaginosis Lactobacilli produce an acid that keeps the vaginal pH around 3.8-4.2. This is normal; it hinders infection by other bacteria/yeast/viruses. Decrease in the lactobacilli population shifts the vaginal pH over 4.5. When this happens, there’s a risk for: 1. Overgrowth of coccobacilli 2. Sometimes, overgrowth of yeast 3. An environment more susceptible to other pathogenic organisms Candida Occasionally, it’s the presence of a pathogenic organism that kills the lactobacilli, thus tipping the pH. Other times, antibiotics have killed the lactobacilli, causing the pH shift. Trichomonas How would you define the role of coccobacilli in bacterial vaginosis?  In contrast… Obligate pathogens are never a normal finding and never benign.  Human Immunity: there’s both nonspecific (innate) immunity and specific (acquired) immunity. Nonspecific Immunity: anti-infection protections that are not geared toward a specific organism Includes: Physical barriers like skin pH shifts and compartmentalization The inflammation process Normal flora  Acquired Immunity Active and passive Passive acquired immunity comes from the administration of antibodies specific to a particular organism The antibodies are NOT made by the host (in other words, “borrowed antibodies.”). The immunity goes away when the lifespan of the antibodies is over. This results in no long-term immunity. Passive immunity can come from: innoculations with IgG from mother to fetus or baby when antibodies pass through the placenta (IgG) and/or breast milk (IgA). 23  Acquired Immunity Active and passive Active acquired immunity is an immune response to a vaccine or pathogen that causes the individual to create their own set of specially- coded immune system cells, and stimulates the production of memory cells that recognize the organism if it returns. This immunity (at least theoretically) lasts forever MORE ON ACTIVE IMMUNITY IN PAS 6120 (pathophys I). 24  Antibiotics  Antibiotics come from:  Living organisms  Lab synthesis  Antibiotic resistance comes from:  Over-prescribing  Inappropriate prescribing  Overuse as feed supplement for livestock  Improper use  Spread of resistant strains worldwide  How do Antibiotics Work? Know these mechanisms  Some inhibit synthesis of bacterial cell wall and cell membrane “Something—cillin”  Penicillin family: penicillin, methicillin, nafcillin, oxacillin, amoxicillin, ampicillin, piperacillin, ticarcillin “Cepha-something  Cephalosporin: cephalexin, cefoxitin, ceftazidime, ceftriaxone; vancomycin, bacitracin  Some inhibit the bacteria from making proteins it “Something—mycin” or “something- needs micin”  Macrolides and aminoglycosides  Some work by inhibiting bacterial reproduction  Some turn off bacterial enzymes Any of these that I ask you will be kept VERY basic! Antibiotic Resistance  How do Pathogens become resistant to antibiotics?  Development of resistant strains  Spontaneous mutation  Plasmid-acquired resistance  Mechanisms for circumventing effects of antibiotics  Develop enzymes (penicillinase)  Change cell wall structure  Change internal metabolic machinery  Antibiotic Sensitivity Tests Tube dilution method:  measures the highest dilution of an antibiotic that can still inhibit growth of a bacterium in a test tube sensitive Disk method:  Growth of bacterium on a plate is resistant inhibited around the disk with antibiotic it is sensitive to  Growth continues when a disk has an antibiotic the bacterium is resistant to  Plasmids and Plasmids are small circular DNA molecules Resistance that are separate from the main bacterial chromosome Some contain “the F factor”– a gene that allows conjugation to happen. When a plasmid contains the F- Factor, bacterial genes can be transferred from one bacterium to another via conjugation. When the two bacteria separate, both may contain the F Factor.  Some contain an “R factor” – a gene that codes for some type of antibiotic R- and F- factors resistance. can co-exist on  R Factors can be transferred during bacterial the same plasmid. conjugation  BACTERIAL CONJUGATION: one way Plasmids are Transferred Bacterium with a plasmid and the gene Finds another bacterium, creates a mating bridge, Now, both bacteria possess the plasmid. for the “F Factor” and transfers a copy of its plasmid to bacterium #2. If the plasmid contains the gene for penicillin resistance, you now have two resistant bacteria, and both can use the F-Factor to spread this resistance.  BACTERIAL TRANSFORMATION: Bacteria also can absorb “stray” DNA from their surroundings by endocytosis DNA fragment from a destroyed bacterial cell Bacterial chromosome  Break! Next up: viruses Viral Life Cycles Here’s the Herpesvirus: Phospholipid membrane Protein coat DNA interior  Viral Replication Screen Shot 2013-02-19 at 4.21.28 PM.png The viral “life” cycle can be lytic or lysogenic, or sometimes change from one to the other.  Lytic Viral replication:  Viruses have genetic material surrounded by a protein coat and (sometimes) a membranous envelope  Viral proteins bind to receptors on a host’s target cell  Viral nucleic acid enters the cell When activated, viral DNA triggers viral duplication, using the host’s molecules and organelles  The host cell is destroyed, and newly replicated viruses are released to continue the infection  Lysogenic Cycle the “trojan horse” cycle Lysogenic viruses get into cells, then insert themselves into the cell’s genome. Every time the cell divides, the viral DNA is copied. The host cell remains alive and unaffected– for now. Once a large number of cells are “carriers”, a trigger (environmental?) causes the virus to “go lytic”, creating millions of viruses and destroying the host cell. Image: https://courses.lumenlearning.com/suny-microbiology/chapter/the-viral-life-cycle/ Lysogenic Viruses are sometimes linked to cancer UNCONTROLLED CELL GROWTH CAN HAPPEN: If a virus inserts itself in the middle of a DNA area important for control of cell division If a virus inserts itself in the middle of the gene for a “correction” protein If a virus prevents certain DNA from being read, or causes it to be read too readily Examples: HIV HPV http://www.livescience.com/10023-viruses-cancer-previously-thought.html  Lytic vs. Lysogenic Viral Reproduction- Summary: Lytic cycle Lysogenic cycle ▪ Viral particles are ▪ Viral DNA is inserted into the host produced using host chromosome by recombination cell components ▪ The inserted phage DNA is called a prophage or provirus ▪ The host cell lyses, and viruses are ▪ Viral DNA is duplicated along with the host released chromosome during each cell division ▪ Most prophage genes are inactive ▪ Environmental signals can cause a prophage to come out of the DNA, and move into a lytic cycle (quorum sensing?)  RNA Viruses an RNA virus: Enters the cell releases its RNA genome with an enzyme that converts the viral RNA into a mRNA particle Creates more mRNA, as well as making new viral RNA Performs Protein synthesis of new virus shells using its host’s machinery Assembles lots of viral particles Gets released by shedding or bursting the cell And Sometimes uses a reverse transcriptase to convert itself to DNA and incorporate into the host’s chromosomes (lysogenic)  RNA Viruses mutate fast! DNA synthesis uses a protein that has a “proofreader”. RNA synthesis has no “proofreader”. If a “mistake” is made while making an RNA virus, the If a “mistake” is made while making a mistake stays as a mutation. DNA virus, the proofreader (DNA Polymerase) almost always fixes it. Sometimes those mutations make viruses more pathogenic.  COVID-19: an RNA Virus Consists of Spike proteins, an envelope, a membrane, and a length of mRNA. Spike Protein– a protein optimized for binding to human ACE2 receptors– found on human respiratory epithelium cells (and other human cells!!) This site mutates frequently  Human Immunodeficiency Virus: a retrovirus with a lysogenic cycle  HIV is a retrovirus, consisting of A membrane coating Its RNA genome Reverse transcriptase, an enzyme that produces DNA from an RNA template Image © 2009 Pearson Education, Inc. Acute HIV infection: Initial HIV symptoms occur while the virus is in a lytic phase. These symptoms hit within days of initially acquiring the virus. After this, the virus goes into a lysogenic cycle: It sheds minimally, but over several years. It incorporates itself into host cell DNA This incorporation is lethal for Helper T cells.  Chronic HIV infection: During the chronic HIV infection, Viral load in the bloodstream starts LOW and slowly gets higher Antibodies to various viral antigens are HIGH Helper T cell (CD4) counts start out adequate, but go down as the viral load goes up. https://kids.frontiersin.org/articles/10.3389/frym.2022.912547  How Helper T cells “Help”: (CD4 is another name for Helper T cell) (we’ll cover the details of B and T cells in Pathophysiology) Some of the An APC presents helper T’s an antigen activate attached to an phagocytes. MHC. Some of the B cells become memory cells as It activates a It activates a well. helper T cell, cytotoxic T cell, which which proliferates. proliferates. Some of the Some of the Lots more helper T’s Some of the helper T’s activate Cytotoxic T’s: become Memory helper T’s activate LOTS of cytotoxic they seek and LOTS of B cells. T cells. T cells. destroy.  Without Helper T Cells: Some of the An APC presents helper T’s an antigen activate attached to an phagocytes. MHC. Some of the B cells become memory cells as It activates a It activates a well. helper T cell, cytotoxic T cell, which which proliferates. proliferates. Some of the Some of the Lots more helper T’s Some of the helper T’s activate Cytotoxic T’s: become Memory helper T’s activate LOTS of cytotoxic they seek and LOTS of B cells. T cells. T cells. destroy.  HIV is one of many EMERGING VIRUSES: viruses that have the potential to rapidly increase in incidence The characteristics of Emerging Viruses: Mutation- most commonly RNA viruses Contact between species- rapid mutation can help viruses from other animals can spread to humans Spread from isolated populations- people isolated from others for hundreds of years may have viruses that mutated in a way that other humans haven’t encountered. Spread to areas with overcrowding and/or poor sanitation- more opportunity for exposure, and less protection against exposure Questions?