Microbiology Exam 3 Study Guide PDF

Lecture 11: Lab Diagnostics Favorite Movie Aliens or Breakfast Club Acapella for why she is not there in Kingston Ontario Define sensitivity and specificity - Both measures of ability to test to correctly classify a person having a disease or not having a disease - Sensitivity: Refers test...

Lecture 11: Lab Diagnostics Favorite Movie Aliens or Breakfast Club Acapella for why she is not there in Kingston Ontario Define sensitivity and specificity - Both measures of ability to test to correctly classify a person having a disease or not having a disease - Sensitivity: Refers test ability designate individuals with disease as positive. Highly sensitive test= few false negative results fewer cases of disease of disease missed - Specificity: Refers ability to designate an individual who does not have the disease as negative. Highly specific test-few false positive results few incorrect diagnoses Describe immunological methods including: agglutination tests,EIAs/ELISAs, ICAs - Agglutination tests: - Antibodies have 2 antigone binding sites - Can attach to one or more antigens - Antibody binds antigen in a clump - Testing either antigen or antibody patient sample - Tiny synthetic beads coated antigens - EIAs/ELISAs: - Uses enzyme bound antibody to detect presence of antigen - Enzyme labeled antibody added to sample - Variable region binds specific antigen - Addition substrate allows detection substrates: chromogen, alkaline phosphatase, horseradish peroxidase - ICAs - Simple device detect presence/absence antigen or antibody - Combination of chromatography - Separation of components sample based on difference to movement through sorbent - And immunological reactions (antibody-antigen) Define POCT and state the pro/cons - Medical diagnostic testing at or near the point of care  - Performed by clinicians - POCTS for infection often based ICAs - Pros: Efficiency, Speed/diagnose of treatment, portable, relatively easy to use - Cons: cost, processing errors, sample shortage/collection sensitivity (less sensitivity than lab methods) Reliability (higher margin of error) Describe polymerase chain reaction (PCR) - DNA template - Sensitive enough detect DNA of single cell/virion in sample - Creates billions copies genes few hours - Highly specific: only DNA that is exact match primers amplified - Applications: gene sequencing genetic disorders diagnosing infections Describe DNA microarrays and explain how they are used in clinical diagnostics - Based ability of ssDNA to hybridize (bond) to complementary ssDNA - Short ssDNA molecules (oligos) bound glass slide microscopic array - If complementary DNA molecules they will bind and can be visualized by detector - Useful for: panel test, blood culture panels/specific GP bacteria GN bacteria or yeast species, Respiratory panels (respiratory viruses) Compare and contrast common diagnostic methods for infectious disease - Culture show morphology fungi and bacteria but can take a long time for growth - Microscopy show morphology bacteria and fungi do not work for viruses - Immunological methods are able to use antibodies to identify specific proteins - Molecular methods: Detection of DNA/RNA used to diagnose viruses Lecture12: Antimicrobials and AMR  Define: empiric therapy and prophylaxis - Empiric therapy is commonly started protect patient - Prophylaxis: process that prevents infection or disease in a person at risk For each drug class, identify: cellular target (mode of action) and whether they are bacteriostatic or bactericidal - See note cards Identify the 3 drug classes that are considered beta- lactam drugs - Penicillins - Cephalosporins - Carapemens Explain the significance of MRSA, VRSA, and CRE - They are among resistant microbes of greatest concern Define the spread of AMR describe the 3 methods of HGT that occur in bacteria HGT - Transformation- take up new DNA from environment - Transduction- genes transported between bacterial cells by bacteriophages (viruses) - Conjugation- sharing DNA through physical connection (sex pilus) Describe the three mechanisms by which antibiotic resistance may develop AMR - Target Alteration- bacterial protein changes (mutates) drug is no longer effective - Drug inactivation- acquire new proteins (acquire new genes) - Drug reducing considerations inside the cell- Limited drug entry or pumping drugs out Lecture 13:Respiratory Infections- viral Define:sinusitis, pharyngitis, epiglottitis, laryngitis, bronchitis, croup,stridor, pneumonia, dyspnea, viral variant, viral strain - Sinusitis is inflammation of the sinuses and nasal membranes - Pharyngitis is the Inflammation of the pharynx at the back of the throat - Epiglottitis is inflammation or swelling of the epiglottis which can be life threatening - Laryngitis is the inflammation of the larynx or the voice box that causes hoarse sounding voice - Bronchitis is the when the bronchi become inflamed resulting coughing and other symptoms - Coup is an infection upper respiratory system making it hard to breathe - Stridor is a high pitched breathing sound (partial obstruction of the upper airway) - Pneumonia is a Lung infection where air sacs fill with fluid making it hard to breathe - Dyspnea is the medical term for shortness of breath - Viral variant is a mutation of the virus compared to the original strain - Viral strain is if the mutations are enough to causes new function of the virus compared to the original Describe the factors that limit infection of the respiratory system - Mucus membrane - Goblet cells and mucus - Ciliated epithelial cells - Muscolalitary escalator - MALT - Adenoids and tonsils - Alveolar macrophages  - Normal microbiota State where normal flora is found in the respiratory system - Nasal cavity - Pharynx - Varies person to person Compare and contrast the symptoms of common colds and influenza - Share symptoms of fatigue, chest discomfort, and stuffy nose - The flu is more abrupt in presentation of symptoms where cold symptoms are more gradual - A fever is rare for a cold but common for the flu - Aches are common for the flu but not likely for the cold - A headache is rare for the cold but common for the flu Describe the various strategies for immunization against RSV (elderly,pregnant people, newborns) - Adults over 60 should have RSV vaccine late summer to early fall - Babies should be given RSV antibodies if mothers not vaccinated while pregnant October-March - Pregnant people should be vaccinated 32-36 weeks September- january Discuss how influenza A strains are subtyped and named - Based on the number of glycoprotein spikes - Hemagglutinin and Neuraminidase - H1N1(swine flu) - H2N2 - H3N2 Discuss antigenic drift versus antigenic shift and the emergence of new influenza viral strains - Emergence of new strains of influenza virus is common because RNA viruses geomone can mutate quickly and they have the ability to mix and match genome mutates quickly - Antigenic Drift is where there are random mutations and minor changes to H/N spikes  - Antigenic Shift is major genetic changes with major altercations in viral antigens and can allow for pandemics Compare and contrast SARS, MERS, and COVID19 and associated pandemics - SARS is a severe acute respiratory syndrome coronavirus first outbreak november 2002 first identified in china - MERS is a middle east respiratory syndrome coronavirus first outbreak 2012 in the middle east start - COVID-19 is a naval coronavirus first identified in china and first outbreak december 2019 For each viral disease describe: causative agent, genome (RNA/DNA),transmission, diagnosis, treatment, and vaccine type (if currently available). See cards Lecture 14:URTI Explain why children are more prone to developing otitis media - They have shorter eustachian tubes - The less drainage of fluid allows bacterial infection to develop Explain how superantigens function as virulence factors - They target T helper cells which causes non-specific activation of the immune system and overstimulation the immune system - Cause massive inflammation that is harmful to the host - Usually pyrogenic Define sequelae and how they relate to treatment of GAS bacterial pharyngitis - Sequelae is a condition that is the consequence of a previous disease or injury  - GAS Bacterial pharyngitis can lead to scarlet fever, rheumatoid fever and heart disease or AGN which is why it is important to treat right away Describe the Lancefield classification system for Streptococcus spp. - Agglutination reaction with different antibodies - Reaction with “A” means group A strep (streptococcus pyogenes) - Reaction with “B” antibody means group B strep (streptococcus agalactiae) - No reaction with antibodies tested means streptococcus pneumoniae Identify Lancefield group for: S. pyogenes, S. agalactiae and S. pneumoniae - Reaction with “A” means group A strep (streptococcus pyogenes) - Reaction with “B” antibody means group B strep (streptococcus agalactiae) - No reaction with antibodies tested means streptococcus pneumoniae Describe the mechanism for rise in macrolide Resistance in GAS - Acquiring erythromycin resistance - Horizontal gene transfer - New gene Macrolide efflux pump - That will pump out macrolide drugs Differentiate the following terms: antigen, antibody, antitoxin, and toxoid - Antigen is a foreign substance that can bind to a receptor and trigger an immune response - An antibody is a protein made by the immune system to destroy foreign substances  - An antitoxin is a solution of antibodies that can neutralize a specific toxoid - A toxoid is a toxin that is no longer pathogenic Describe how antitoxin is produced and how it can treat diphtheria - Antitoxin is produced by antibodies coming together and can be used to treat diphtheria by neutralizing the diphtheria toxin from the vaccine antitoxin solution of antibodies For the diseases covered, describe: causative agent(s) (including Gram morphology), transmission, transmission precautions (if applicable), disease features, diagnosis, treatment, and vaccine type (if available) See cards Lecture 15: LRTI Describe/differentiate the types of specimens collected from the LRT - Exporated Sputum is easy, noninvasive and the most common type used. It can be commonly contaminated with microbiota and more challenging to interpret the results - Bronchoalveolar lavage is invasive and less frequently used. Bypass the oropharyngeal cavity no microbiota from the mouth and it is less challenging to interpret the results Describe/differentiate laboratory tests for diagnosing LRTIs - Bacterial culture/smear comes back in 2-3 days routine for every Sputum/BAL or tissue aspirate tested. The sample is rejected if too many squamous epithelial tissue is present - Fungal culture and smear takes 2-4 weeks and is recommended only if a fungal infection is suspected. - An acid fast culture and smear takes 2-8 weeks and is recommended only if mycobacterium is suspected  Given the staining results (Gram /acid fast/ fungal smear) from a sputum sample, correctly identify the most likely etiological agent - Aspergillus fumigatus Describe the conditions that might cause a sputum sample to be rejected and why this has clinical significance - If there are too many squamous epithelial cells because those are the normal skin cells of the mouth that could have normal microbiota. Hoping to find immune cells and bacteria not in the salvia Compare and contrast the forms of Tuberculosis - Latent TB is where there is formation of granuloma in the tubercle and calcium deposits in the chest x-ray positive chest x-ray the disease does not progress and the bacteria can remain for years - Active TB is when the immune system becomes weakened and the bacteria inside the granuloma is released. Have cough, bloody sputum, weight loss fatigue, night sweats and chest pain. High communicable with 60% mortality rate Describe methods for detecting exposure to M. tuberculosis versus diagnosing Tuberculosis - Tuberculin Skin test with 15mm or higher meaning there is a risk or TB exposure or not - Interferon Gamma Assay is used to mix the patient's blood with M. Tuberculosis antigens level INF is measure if past exposure higher number if INF will be released - TST or IGRA does not mean active infection need to do medical examination, physical exam,chest x-ray acid fast and culture smear (8 weeks) also order NAAT (3 hours) Compare and contrast typical and atypical pneumonia - In Typical pneumonia there is consolidation in the chest x-ray. The bacteria is either gram positive or negative and is ⅘ causes - An agent is often not successfully cultured from the sputum is ⅕ cases Compare/contrast ubiquitous vs endemic fungal pathogens (including examples)  - Ubiquitous fungal pathogens grow in varied environments and they are opportunistic pathogens causing infection in immunocompromised people (Example Aspergillus) - Endemic fungal pathogens grow in specific geographical areas. Characterized by thermal dimorphism and they are true pathogens that can cause infections in healthy people (valley Fever) For diseases covered, describe: causative agent(s) (including Gram, AFB or fungal morphology), transmission, transmission precautions, disease features, diagnosis, treatment, and vaccine type (if available) See cards Lecture16:Skin Infections-viral exanthems Describe the innate factors that limit infection of the skin - Melanin which has antimicrobial properties - Perspiration which has an acidic pH and high salt concentration that washes away microbes - Lysozyme an enzyme in sweat that breaks down peptidoglycan - Sebum: an oily substance produced by the sebaceous glands with low pH lipids and proteins that moisturize - Skin microbiome Define the following terms: lesion, rash, exanthem, vesicle/vesicular rash,macule, papule, maculopapular rash, purpura, petechiae, and ulcer See cards Differentiate between primary infection and reactivation events for VZV and HSV1  - Chicken pox from VZV appears as a vascular rash all over the body after the reactivation shingles appears on the band of skin where the virus was stored in the nerve. Reactivation HSV1 in oral herpes keeps coming back in the same spot Describe viral latency as it relates to viral replication and explain why latency is more common among DNA viruses - Viral latency is where the virus is laying dormant inside host cells and is not actively replicating. More common in DNA viruses because DNA can integrate into the host cell genome resulting in stable persistence and controlled gene expression during latency. RNA viruses rely on rapid replication cycles Describe the function of nucleoside analog drugs and explain why acyclovir is an effective treatment but not a cure for VZV or HSV1 - Inhibits viral replication by miminicing normal nucleotides - Cannot cure because cannot be used in the latency phases when the drugs cannot reach them. For each viral disease describe: Causative agent (RNA/DNA; naked/envelope), transmission/transmission precautions, disease features,diagnosis, treatment, and vaccine type (if currently available) See cards Lecture17:Skin Infections–bacterial and fungal Define: abscess, pyoderma, folliculitis, furuncle, carbuncle, cellulitis,impetigo, erysipelas, necrosis, necrotizing fasciitis, gangrene - Abscess is a collection of pus it may form in a variety of body sites - Folliculitis is an infected hair follicle  - Furuncles are small abscesses located deep in hair follicles - Carbuncles are connected furuncles - Cellulitis is an infection of lower dermis subcutaneous fat with raised painful swollen skin - Impetigo: is superficial pus filled vesicles crust over into honey colored lesions - Erysipelas are affecting the dermis and the superficial lymphatics. Painful very red appearance Raised defined borders can be progression from impetigo - Necrosis is tissue death due to loss of blood flow - Necrotizing fasciitis is Rare invasion wound infection disease flesh eating disease - Gangrene specific necrosis in an extremity foul smelling Describe/differentiate laboratory tests for diagnosing skin/wound infections - Routine culture and smear takes 2-3 days routine for every tissue swab or fluid test - Anaerobic culture and smear takes 7 days recommended for closed wounds and abscess - Fungal culture and smear takes 2-4 weeks recommended only if fungal infection is suspected - Acid-fast culture and smear takes 2-8 weeks and is only recommended if mycobacterium is suspected Describe key tests for differentiating Staphylococcus and Streptococcus - A catalase test distinguish staphylococcus (+) from streptococcus( -) Describe the clinical significance of the terms: coagulase -positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS) - Coagulase positive staphylococcus is typically going to staphylococcus aureus which is going to be more highly pathogenic - Coagulase negative staphylococcus are going to be less virulent but may still cause infections in immunocompromised patients  Given the smear and/or culture results from a skin/wound sample, identify most likely causative agent - Staphylococcal aureus Describe the mode of action of antifungal drugs: azoles, nystatin and amphotericin B - Azoles inhibit enzymes that build ergosterol. - Nystatin and Amphotericin B bind to the ergosterol and disrupt the membrane integrity that can lead to cell lysis For the diseases covered, describe: causative agent(s) (including Gram morphology), transmission, transmission precautions (if applicable), disease features, diagnosis, treatment, and vaccine type (if available) See cards Short answer Exam 3 questions: 1. Describe the use of immunological methods for diagnosing infectious disease. Include: principle (how it works), TAT, one advantage,one disadvantage, and give one example (5points). They work by using laboratory techniques involving the antigens with specific antibodies. They are fast and work in a few minutes to a few hours.One advantage is that they are fast and easy to use. One disadvantage is that they have lower sensitivity and specificity than culture. One example is an ELISA test 2.Describe the use of nucleic acid methods for diagnosing infectious disease.Include: principle (how it works), TAT, one advantage,one disadvantage,and give one example. (5points) Laboratory technique that involves the detection or amplification of Nucleic acids DNA or RNA. Takes 30 minutes to a few hours.One advantage is that it is very sensitive and specific. One disadvantage is that it is expensive. An example is PCR 3.Describe the various strategies for immunization against RSV. Include the type of vaccine and immunization strategy for each of the following: people>60yrs, pregnant people, newborns. (4 points) - Adults over 60 should have RSV vaccine late summer to early fall - Babies should be given RSV antibodies if mothers not vaccinated while pregnant October-March - Pregnant people should be vaccinated 32-36 weeks September- january 4.Define sequelae and superantigen. Describe how they relate to bacterial pharyngitis. List two sequelae of bacterial pharyngitis and describe the conditions. (5points) Sequelae is a condition that is the consequence of a previous disease or injury. Bacterial pharyngitis can cause potential sequelae such as scarlet fever or rheumatic fever. Scarlet fever is having a red sandpaper like rash. Rheumatic fever is the activation of immunity for the heart, skin, joints and the nervous system. A superantigen causes the immune system to overreact and release lots of cytokines and active T helper cells. Bacterial pharyngitis can have a potential superantigen that is an erythrogenic toxin which causes inflammation and dilation of the skin leading to skin rash. 5. Describe antitoxin - be sure to include details on the following: what type of molecule it is, how it is produced, how it can treat diphtheria and whether antitoxin treatment provides passive or active immunity. Define toxins. (5points) Toxins anything that causes harm. An antitoxin is a protein antibody. Antitoxins are typically produced in horses by injecting an toxin and then having antibodies produced in blood that are collected to be antitoxin that can be used in order to treat the same toxin. The diphtheria antitoxin is an antibody injection that neutralizes the diphtheria toxin. Antitoxin treatment is an example of passive immunity. 6.Describe latent tuberculosis infection (LTBI) and active tuberculosis relative to symptoms and transmission. Name and describe two tests that diagnose LBTI and one test that can diagnose active TB. (5 points) Latent tuberculosis is where the disease does not progress since the bacteria can remain for years. Latent tuberculosis is not contagious. Latent TB can be diagnosed by the tuberculin skin test or IGRA. Active tuberculosis the patient will develop a cough, blood sputum, weight loss, fatigue. Night sweats and chest pain. Active tuberculosis is highly communicable and is airborne transmission. A chest x-ray can be used to diagnose active TB 7. Malik is a 20-year-old college student who presents with shortness of breath and a dry cough. He reports these symptoms have been present for 4 weeks, but that he has been able to continue going to classes and keeping up a normal routine. All tests for viral pathogens are negative.A chest X-ray shows no signs of consolidation. (5 points) What is your diagnosis? Walking Pneumonia What is the causative agent? Mycoplasma pneumoniae What is the best test to diagnose the infection? Serology or NAAT If you were to request a routine bacterial culture on a sputum sample for this patient, what results would you expect and why? An agent is not likely to be successful cultured in atypical pneumonia because mycoplasma pneumoniae is slow growing 8. Kara is a 37-year -old woman undergoing chemotherapy as part of her treatment for breast cancer. She presents to her physician with a painful band of vesicular rash across her back. Her spouse, Abby, is 12-weeks pregnant and reports never having had a similar vesicular rash or any vaccinations as a child. Kara and Abby also have a 2 -yr old son, Caleb who has not been vaccinated. (5 points) What is your diagnosis for Kara? Shingles What is the causative agent? VZV What test(s) would you use to confirm your findings? NAAT What are your concerns for Abby? She is pregnant and has not been vaccinated. She could develop chicken pox and pass it to the baby as well because it is vertical transmission/ What are your concerns for Caleb? He has not been vaccinated for chickenpox and could develop the infection from his mom. He will be worse off because he does not have any antibodies to help fight the infection 9.Describe Gram morphology of Staphylococcus and Streptococcus species.Once the Gram stain is complete, describe the key lab tests/results required to differentiate between Staphylococcus and Streptococcus species. Discuss why Staphylococcus aureus is referred to as Coagulase-positive Staphylococcus and the clinical significance of the term. (5 points) Both Staphylococcus and Streptococcus are gram positive with staphylococcus being a cluster of cocci and streptococcus being in chains. They are distinguished from each other by a catalase test where staphylococcus is positive and streptococcus is negative. Staphylococcus aureus is referred to as coagulase positive because it has the coagulase enzyme which is significant because clinical it is going to be more pathogenic than coagulase negative staphylococcus. 10. Define antimicrobial resistance and describe the 3 methods of horizontal gene transfer that occur in bacteria. (7 points) Antimicrobial resistance occurs when microbes over time mutate to be less effective against drugs to treat them - Transformation- take up new DNA from environment - Transduction- genes transported between bacterial cells by bacteriophages (viruses) - Conjugation- sharing DNA through physical connection (sex pilus) 11.Describe the three mechanisms by which antibiotic resistance may develop and provide a specific example of each. (6 points) - Target Alteration- bacterial protein changes (mutates) drug is no longer effective. Cells that have PBP2 are resistant to beta-lactam - Drug inactivation- acquire new proteins (acquire new genes). Cells that express beta lactamase have an enzymes will inactivate beta lactam drugs - Drug reducing considerations inside the cell- Limited drug entry or pumping drugs out. An efflux pump mefA in GAS 12.Describe the function of nucleoside analog drugs and explain why acyclovir is an effective treatment but not a cure for VZV or HSV1. (3 points) - Inhibits viral replication by miminicing normal nucleotides - Cannot cure because cannot be used in the latency phases when the drugs cannot reach them. The virus is not able to replicate anymore but there is viral DNA in the nucleus of the cell that can remain latent to start an infection like for VZV being latent and becoming chickenpox and oral herpes able to come back.