Principles of Immunization Lecture Notes PDF

Principles of immunization Learning outcomes/goals After this lecture section you should be able to: Name different vaccination strategies Understand the concept of ‘herd immunity’ Appreciate vaccine hesitancy, but place it in perspective Textbook sections to support learning:...

Principles of immunization Learning outcomes/goals After this lecture section you should be able to: Name different vaccination strategies Understand the concept of ‘herd immunity’ Appreciate vaccine hesitancy, but place it in perspective Textbook sections to support learning: 24.1 (part), 24.2 (part), 24.6 Antibodies display antigenic specificity (also called ‘immunologic specificity’) The degree to which an antibody recognizes an antigen And can distinguish between several similar-looking antigens Earliest clues about immunologic specificity came from smallpox Survivors of the disease didn’t get smallpox again Someone who had a mild case of smallpox, you pick the Variolation scabs, grind them and dry them in the sun, you give it to children to help them be immune to it. prtects agsint future disease. Vaccination – where did the name come from? Fig. 24.6 Cross-protection Inoculation of cowpox worked to protect against smallpox But why do we get so many colds in our lifetimes? And why do we need a ‘flu shot every year, and a COVID shot every 6 months? The viruses mutate fast so they become resistant to the vaccines. Prevention is better than cure Suffering an infection with a pathogen results in an immune response to the pathogen and (usually) acquired immunity driven protection against subsequent infection For some nasty pathogens, this comes at the risk of high morbidity and sometimes, mortality It also comes with the risk of infecting others nearby Leading to epidemics or even pandemics Instead, we can trick the body into seeing a pathogen and raising an immune response without the risk of pathogen-mediated disease This is immunization (an example of which is vaccination) Vaccination works because of our adaptive immune response where does the name vaccine come from? vaca is latin for cows (you can get protection from cows), edward jenner immunizing people with cow pox lesions. Vaccinations come in 4 basic types: 1: Killed whole organisms Good examples are vaccines against hepatitis A, and the earliest polio vaccine (Salk vaccine) Benefits: easy to produce, many antigens are presented to the immune system for a robust response Jonas Salk Drawbacks: Complete inactivation of the organism can be difficult to achieve The Cutter Incident (1955) was a tragedy caused by the Cutter Laboratory, which manufactured the Salk vaccine in the 1950s. Some batches were incorrectly tested and passed, and contained live virus Over 250 cases of polio were attributed to this event Many cases of paralysis resulted Legislation was introduced to stop this happening again Vaccinations come in 4 basic types: 2: live attenuated organisms These are organisms that have been weakened in some way before administration, to give the immune system the upper hand Benefits: the pathogen infection process is appropriate (antigens are presented in the right part of the body, see later); many antigens are presented to the immune system for a robust response Drawbacks: Can be difficult to produce; Contraindicated for those who are immunocompromised; cold chain distribution usually required they need to be kept in the cold and maintaining this temp is not cheap Examples: BCG, Sabin polio vaccine Vaccinations come in 4 basic types: 3: Subunit vaccines no pathogen, just the antigen present These are selected, purified antigenic components of pathogens Benefits: Usually easy to produce; no chance of infection Drawbacks: Can be hard to find a protective antigen Examples: Streptococcus pneumoniae capsular antigen, viral capsids from human papillomavirus, toxoid vaccines What are toxoids? many pathogens produce toxins which produce disease Note: some subunit vaccines contain subunits of antigens from multiple pathogens, for efficiency Vaccinations come in 4 basic types: 4: nucleic acid vaccines (e.g. mRNA vaccines, viral vector vaccines) mRNA vaccines contain mRNA that codes for a specific antigen, that is wrapped in a lipid layer and injected mRNA that codes for an antigen, encased by a lipid layer and is injected Gets taken up into the cell and the cell briefly makes the target antigen, long enough for antigen to stimulate an immune response Benefits: Once set up, super-easy to manufacture, and relatively quick to get to market; no chance of infection Drawbacks: Cold chain distribution required; very poor public understanding/excessive fearmongering Examples: Spikevax and Comirnaty against SARS-CoV-2, upcoming mRNA vaccines against Zika virus and influenza TABLE Recommended Immunization Schedule for Children and Adolescents a 24.5 Age of administration Why so many vaccinations Vaccine Birth 1 month 2 months 4 months 6 months 9 months 12 months 15–18 months 24 months 4–6 years early 11–12 years in childhood? Hepatitis HepB HepB HepB HepB series b B Rotavirus Rota Rota Rota Diphtheri DTaP DTaP DTaP DTaP DTaP Tdap a, tetanus, acellular c pertussis Haemophi Hib Hib Hib Hib lus influenzae d type b Inactivate IPV IPV IPV IPV d poliovirus Measles, MMR MMR MMR mumps, rubella Varicella Varicella Varicella Meningoc Administer to high-risk children MCV4 occal e (ACWY) Meningoc MenB occal (B) (10–12 yr) Pneumoc PCV13 PCV13 PCV13 PCV13 PPSV23 f occal g Influenza Influenza (yearly) Hepatitis HepA (2-dose series) He pA h A Human HPV (9–12 papilloma i yr) virus j COVID-19 2-dose  The need for repeated doses increases production of IgG I: Boosting response Most vaccines are given once to a naïve individual, then again, a few weeks or months later – why? The first dose leads to early synthesis of IgM followed by IgG The second shot is a ‘booster’ shot and results in a rapid response because memory B cells were formed during the first response The booster shot ensures sufficient antibodies with sufficient reactivity towards antigen will be circulating in the body, protecting against reinfection Fig 24.12 The need for repeated doses II: overcoming antigenic changes Some pathogens change their antigens rapidly A vaccine primes the body against an antigen that may be lost or changed into something else within a short space of time Examples: SARS-CoV-2, influenza; we need a slightly different vaccine to fit the new antigens, as soon as the virus mutates (which is often) Text Nature Reviews Primers  The need for repeated doses III: waning memory Memory T cells and memory B cells have long lifespans, but not indefinite As they replicate, they can lose specificity for their cognate antigen Eventually they become unprotective This is why you need e.g. a tetanus shot every 10 years Text Getting the right exposure Live attenuated vaccines are often superior to inactivated, subunit or mRNA vaccines – why? A live pathogen activates the immune system appropriately Example 1. Salk (dead) and Sabin (live attenuated) polio vaccines Normally polio is transmitted through the fecal-oral route Replicates in the gut mucosa, moves to regional lymph nodes you can’t give live attenuated vaccines to those and induces viremia; some replicated virus can attack the who are immunocompormised nervous system and cause paralysis Salk vaccine is injected: the antibody response is protective against paralysis, but does not elicit the mucosal response Later, a person can get a mild form of the disease through the fecal-oral route …And they can easily pass on this infection to unvaccinated people, often unknowingly  Getting the right exposure, continued Example 2. COVID-19 mRNA vaccines are injected: the antibody response is protective against severe disease, but does not elicit the typical lung mucosal response A person can still get a mild form of disease through natural infection ‘Breakthrough infection’; they can still pass the infection on to others what the point of getting the covid vaccineif you could get covid any ways: you are protected from the severe version of the disease  Herd immunity Do all people within a community need to be vaccinated in order for protection of the community? No – vaccinating a large part of the community effectively interrupts the transmission of the disease How much of a community needs to be vaccinated to afford herd immunity depends upon many factors including transmission rate, population density etc. Works well for diseases such as mumps, rubella, measles. Does not work for tetanus. Why? tetanus is not transmitted from person to person, but it’s acquired from the enviroenment Herd immunity is important as it protects immunocompromised people who cannot tolerate, or do not respond to vaccinations For these individuals, vaccination is not an option, and they rely on the vaccination of others Text Vaccine hesitancy this is a huge problem when jenner was admisistrating his vaccine, people thought they would turn into cows if they go the vaccine A particular problem at the moment (largely because of the social media megaphone, and lack of fact-checking) Not new – Jenner’s work promoted public hysteria in the 18th century People believed cowpox would turn them into cows Fig 1.20 It’s the combination Let’s face it, no-one enjoys vaccination! of needles and infectious agents that at first glance But it’s worth considering the alternative – serious seems terrifying infectious disease and the potential to cause an epidemic No medical procedure is without risk, but social media has blown risk way out of proportion to benefit Now people who are not trained in the scientific method are encouraged to ‘do their own research’; few people know how to fact-check effectively no medical procedure comes without risk  Antibiotics Learning outcomes/goals After this lecture section you should be able to: Understand fundamental concepts of antibacterial agents such as spectrum of activity and antibiotic susceptibility Describe the major classes of antibacterial agents and their mechanisms of action Appreciate the phenomenon of antibiotic resistance, and the mechanisms of action Understand why AMR is such a current threat Textbook sections to support learning: 27.1, 27.2, 27.3 (not ‘Biofilms and the mystery of antibiotic persisters’, or ‘Fighting resistance and finding new drugs’) NB we will not cover antivirals and antifungals in this course, except in passing Antibiotics save lives! Many of you would not be alive today had antibiotics not been available to save you Infections we consider minor today often killed their victims even just 80 or 90 years ago Common deadly infections included: pneumonia, tuberculosis, skin infections, tooth infections, syphilis Fig 27.1  We usually think of Alexander Fleming when considering antibiotic discovery The truth is, people used molds and soil microbes as home remedies for centuries prior to the discovery of penicillin Ernst Duchesne originally discovered the antibiotic properties of Penicillium molds – but was never credited for this Alexander Fleming rediscovered penicillin, but it didn’t really garner much interest Howard Florey and Ernst Chain are credited with purification of penicillin Fleming, Florey and Chain won the Nobel Prize for Medicine in 1945 for this work Gerhard Domagk’s contribution A German physician (1895-1964) who worked at Bayer His 6-yr old daughter developed a serious infection after a pinprick Her life was in grave danger Domagk injected her with a dye called Prontosil Prontosil was being investigated as a possible antimicrobial Fig. 27.2 No activity on plates, but antimicrobial activity in mice Prontosil cured Domagk’s daughter – how? answer on next slide  Prontosil is metabolized to sulfanilamide by the body PABA is a pre-cursor of folic acid, an essential B vitamin Humans cannot synthesize folic acid (we get it from our food) Bacteria can synthesize folic acid Sulfanilamide inhibits the enzyme that makes folic acid, thereby interrupting bacterial metabolism Prontosil, and later, sulfanilamide itself, and then the class of ‘sulfa drugs’ went on to save hundreds of thousands of lives  ROZH 101 Monday 9th Dec 7-9 pm FINAL EXAM 70 multiple choice, 15 matching terms, 5 true or false, 1 short answer section for the independent assignment Waksman’s contribution Selman Waksman (1888-1973), USA, screened 10,000 strains of soil bacteria for antimicrobial activity Paid off – he discovered streptomycin! (or was it his PhD student…?) MICR*3430 Advanced Methods in Microbiology – includes screening soil bacteria for novel antibiotics (using more modern tools) Maybe you can help discover a new antibiotic! Antibiotics exhibit selective toxicity It seems obvious now, but at the dawn of the antibiotic discovery era, the idea that a drug should be selectively toxic against a pathogen (and leave the host alone) was considered innovative! Selective toxicity is possible because there are key elements of microbial physiology that eukaryotic cells do not share E.g. : Peptidoglycan Ribosomes (structurally different between prokaryotes and eukaryotes) Spectrum of activity No single antimicrobial drug affects all microbes Antimicrobials are classified according to activity Antifungal, antibacterial, antiprotozoan, antiviral The term ‘antibiotic’ is usually reserved for compounds that affect bacteria Some agents affect a small number of target organisms Narrow spectrum Some affect a much larger number of target organisms Broad spectrum Some antibiotics kill a bacterium Bactericidal cidal means to kill Some antibiotics prevent growth of a bacterium, but do not kill it Bacteriostatic Why are these effective, if they don’t kill the pathogen? suspends the growth and buys you time for the immune system to take care of it.  Measuring drug susceptibility Antibiotic effectiveness depends on The organism being treated The attainable tissue levels of the drug The route of administration Fig. 27.3 In vitro, we can measure the minimum inhibitory concentration (MIC) of an antibiotic against its target Fig. 27.5 Serial dilution in a 96-well plate E-strips (MIC strip tests) Kirby-Bauer disk diffusion assay What is the major downside of all of these tests? they take time, you don’t see the results of these tests for atleast a day so the pateint coul dbe dying in this time Fig. 27.4 Antibiotic mechanisms of action Classic targets of antibiotics include: Cell wall synthesis Cell membrane integrity DNA synthesis RNA synthesis Protein synthesis Metabolism cell wall inhibitors: peptidoglucan is unique to bacteria Cell wall Antibiotics Recall: peptidoglycan is unique to bacteria and thus an excellent target for antibiotics The process has several steps – each is a separate target for different antibiotic classes. Essentially: 1) Sugar molecules N-acetylmuramic acid (NAM) and N-acetyl glucosamine (NAG) are made in the cytosol 2) Linked together by a transglycosylase enzyme at the cell wall 3) Then side chains of adjacent NAM molecules are then cross- linked by a transpeptidase to provide rigidity to the cell wall Fig 27.8 Fig 27.8 Case History: Meningitis Beta-lactam antibiotics Derived from fungi, consist of a beta lactam ring structure to which a number of R groups can be added Each R group provides different properties (stability, spectrum of activity) Transpeptidase and transglycosylase enzymes involved in cell wall building are also called penicillin binding proteins Fig 27.9 A clue to their mechanism of action! penicillin in an unstable molecule, but ampicillin is How do beta lactam antibiotics work? stabel Resistance to beta-lactam antibiotics Two basic mechanisms: 1) Inheritance of a gene that codes for a beta lactamase gene E.g. New Delhi metallo-beta-lactamase 1 (NDM-1), greatly feared by clinicians Can be overcome in some cases by beta lactamase inhibitors such as clavulanic acid this acid is good at inhibiting beta-lactamses 2) Inheritance of a gene that codes for an altered PBP that does not bind the antibiotic E.g. MRSA, codes for a PBP with very low affinity for beta lactam antibiotics The arms race… Cephalosporins, another type of beta-lactam antibiotic, have been continuously synthetically altered to combat the development of resistance But the microbes are quick to adapt! Some of these antibiotics are therefore deliberately only used in worst case scenarios, to slow down the development of resistance Fig. 27.10 Other antibiotics that target cell-wall synthesis Bacitracin: binds to the bactoprenol lipid carrier and inhibits transport of the peptidoglycan monomers to the growing chain Very toxic and can only be used topically Cycloserine: inhibits the two enzymes that make a precursor peptide of the NAM side-chain Useful for the treatment of tuberculosis Vancomycin: binds to the D-Ala-D-Ala terminal end of the disaccharide unit & prevents bindings of transglycosylases and transpeptidases Some bacteria have incorporated D-lactate into the D-Ala terminus to develop resistance Drugs that affect bacterial membrane integrity Remember the MAC? Poking holes in bacterial cell walls is a great way to kill bacterial cells! Gramicidin: a cyclic peptide that inserts into the bacterial membrane Polymyxin: Binds to both outer and inner membranes of G- bacteria, disrupting the inner membrane like a detergent Unfortunately, both gramicidin and polymyxin also have activity towards mammalian cell membranes, and so can only be used topically Daptomycin: aggregates in G+ bacterial membranes to form channels Very effective against MRSA (for now)  Drugs that affect DNA synthesis and integrity Sulfa drugs (referred to as ‘antimetabolites’): Interfere with nucleic acid synthesis by preventing the synthesis of tetrahydrofolic acid (THF), an important cofactor in the synthesis of nucleic acid precursors All organisms, including humans, use THF to synthesize nucleic acids, so why are sulfa drugs selectively toxic to bacteria? because we use THF, only bacteria can make it Quinolones: target microbial topoisomerases, enzymes that are Sulfa drugs were among the first antibiotics developed and saved essential for catalyzing changes in DNA countless lives during WWII topology to allow replication and transcription Not often used – turns out they are toxic to mitochondria (why?) mitochondria genome? use the saem mechanisma/enzymes to replicate their Drugs that affect DNA synthesis and integrity (cont.) Metronidazole: an example of a pro-drug Activated on reduction by microbial flavodoxin or ferrodoxin, found in microaerophilic and anaerobic bacteria Nicks DNA at random once activated Not effective against aerobic bacteria this drug is activated through reduction it only affects anaerobic organism RNA synthesis inhibitors Best examples: rifampicin and actinomycin D Only rifampicin is used clinically Binds to the exit tunnel of bacterial RNA polymerase, blocking RNA from exiting the polymerase structure Halts transcription Turns bodily secretions bright orange while in use! Fig 27.15 Protein synthesis inhibitors Bind and interfere with the function of bacterial rRNA Bacterial ribosomes and eukaryotic ribosomes have fundamentally different properties – bacterial ribosomes are thus useful antibiotic targets Recall: ribosomes catalyze the linkage of amino acids during translation, using mRNA as the code and tRNAs as the source of amino acids Bacterial ribosomes are made up of small (30S) and large (50S) subunits Why does 30S + 50S = 70S?! S stands for svedberg units, when you add them together they come togterh really closely, so they don’t function additively, but are a little less than that Fig. 8.17 Targeting the 30S subunit Aminoglycosides: Bind 16S ribosomal RNA (part of the 30S ribosome) and causes translation misreading of mRNA Resulting peptides are jumbled or truncated Tetracyclines: Bind to and distort the ribosomal A site (that accepts incoming tRNAs) Can interfere with bone development in fetuses and young children Targeting the 50S subunit Macrolides and lincosamides: inhibit translocation of the growing peptide chain Chloramphenicol: inhibits peptidyltransferase activity Can depress production of blood cells in the bone marrow in some people – aplastic anemia Oxazolidinones: Bind to the 23S rRNA component of the 50S ribosome and prevent formation of the protein synthesis 70S initiation complex Streptogramins: 2 types; both bind to the peptidyltransferase site Usually, types A and B are used together and act synergistically Targeting aminoacyl tRNA synthetases Mupirocin: binds to bacterial enzymes that attach amino acids to the end of tRNA molecules, halting protein synthesis Used topically in creams to treat infections caused by G+ bacteria Cannot be used internally because it is rapidly degraded in the bloodstream antibiotic resistance is not a problem in the soil The problem of antibiotic resistance Many antibiotics are derived from nature (e.g. soil bacteria) AMR is not necessarily a problem there because the substances are usually used sparingly by the organisms that make them Antibiotic resistance has become a problem in medicine because we have consistently used high concentrations of antibiotics for long periods of time Exerting selective pressure on bacteria to evolve Fig. 27.19 www.nature.com  Antibiotic resistance strategy 1: Keep antibiotics out of the cell Destroy the antibiotic before it can enter the cell E.g. beta-lactamases Decrease membrane permeability across the outer membrane (express narrower pores) E.g. flouroquinolone resistance Pump the antibiotic out of the cell using specific transporters E.g. tetracycline resistance Can be particularly dangerous if the efflux pump can export many types of antibiotics, despite differing antibiotic structures Antibiotic resistance strategy 2: Prevent antibiotics from binding their target Modify the target so that it no longer binds the antibiotic E.g. modify shape of PBPs or ribosomal proteins Add modifying groups to the antibiotic so that the antibiotic is inactivated E.g. aminoglycoside resistance, through production of enzymes that change antibiotic structure Antibiotic resistance strategy 3: Dislodge an antibiotic bound to its target Ribosome protection or rescue Some G+ organisms can make proteins that bind to ribosomes and dislodge or prevent the binding of antibiotics that bind near the peptidyltransferase site From Ero et al. https://doi.org/10.1002/pro.3589 Summary of resistance strategies Resistance may be: Intrinsic Natural resistance, e.g. G- bacteria and vancomycin Acquired through genetic mutations The gene encoding the antibiotic target acquires a mutation that creates drug resistance Acquired through receipt of an antibiotic resistance gene A resistance gene is carried on a mobile genetic element such as a plasmid, transposon, or integron Fig. 27.20 How antibiotic resistance spreads Text From: Mancuso et al. Pathogens 2021, 10:1310 Back to the Amazon… You might think that previously uncontacted Amerindian tribes who have never had any exposure to antibiotics would have microbiomes devoid of antibiotic resistance genes You’d be wrong! Living close to the soil means that these people harbour many antimicrobial resistance genes It turns out that many antibiotic resistance genes originated in the environment They are ancient Human activity and travel has amplified and disseminated them Even Fleming predicted AMR would become a problem… ”…the microbes are educated to resist penicillin and a host of penicillin-fast organisms is bred out... In such cases the thoughtless person playing with penicillin is morally responsible for the death of the man who finally succumbs to infection with the penicillin-resistant organism. I hope this evil can be averted.” June 1945 Antibiotics and your microbiome As we talked about, your microbiome exists in a state of ecological balance Antibiotics have the potential to destroy that balance Collateral damage A huge number of diseases are now recognized to be associated with a lack of diversity in the gut microbiome So, should we take antibiotics? Yes! They are lifesaving drugs, if used appropriately Why are we in the mess we are in? We have not used antibiotics appropriately since their development Especially during the ‘golden age’ of antibiotic discovery Antibiotics have been used in enormous quantities in agriculture Antibiotics are often prescribed inappropriately (In some countries, they are not regulated at all!) Patients often don’t take antibiotics appropriately Bacteria often exist in biofilms where resistant strains can persist Pharmaceutical companies have no desire to develop new antibiotics Antibiotic stewardship Antibiotics should never be used to treat viral infections (Most respiratory tract infections are viral in nature) Do not use an antibiotic to trat an infection if the patient’s microbiome includes strains that are already resistant Not often tested Know which antibiotic resistant strains are prevalent within a community before prescribing Consider how long a patient needs to take a given antibiotic Use narrow-spectrum antibiotics wherever possible Screen infectious agents for AMR genes Ensure patients with chronic infections (e.g. tuberculosis) maintain antibiotic regimen until their infection is cleared