Microb 2800 1st editionFinal Exam Study GuideLecture 1 (4/9)Disease logistics- Sign- any objective evidence of disease (measurable)- Symptom- the subjective evidence of disease as sensed by the patient- Syndrome- when a disease can be identified or defined by a certain complex of signs and symptomsSteps of a disease1. incubation period2. Prodromal stage- when you are the most contagious 3. period of invasion/height of infection- feel the worst but mostly inflammatory responses4. convalescent period- recovery periodStudy of disease in populations- epidemiology- the study of frequency and distribution of disease - Infectious dose- the number of organisms needed to set up an infection- mortality rate- number of deaths due to a disease- morbidity rate- the number of persons infected with a disease- Reservoirs- where it is found in the environmento water sources, soil, etc.- Vector- movement of organisms between a reservoir and a hosto drinking, fleas, ticksClassifications- Sporadic- few, isolated cases- endemic- native to a region- epidemic- spread but potentially unrelated- pandemic- world wideNosocomial infections- acquired during a hospital stay- cathetersDiagnosis of Microbial Pathogens- staining- apply chemical dyes or molecules that bind to specific pathogen macromolecules and direct examinationo gram staining- based on PPGo acid fast staining- based on lipid content of membrane  for gram n/a  contain mycolic acid (a wax) Look for pink spots- Growth/colony morphology- select correct media to show growth resultso SLOW- physiological/biochemical traits- metabolic and chemical analysis unique to an organismo ex: sorbitol, indole- Serology detection- antibodies- genetic detection- DNA from a certain organismDNA mutations- point mutant= single base change- silent- base change that does not change the amino acid codon- nonsense- stop codon, ends protein early- missense- changes codon to different AA- frame shift- disrupts normal triplet reading by insertion or deletion- **takes a lot of mutations to lead to an effectDNA sharing- transformation- pick up free DNA- transduction- injected DNA (moved by virus)- conjugation- sharing DNA (pass DNA via bridges between cells)- transposons- Jumping DNA (rearrangements)Modifying DNA- restriction endonucleases- cut DNA at specific spots- Ligase- glue DNA back togetherUsing genetics as a diagnostic= RFLPLecture 2 and 3 (4/14 and 4/16)Infectious diseases of the respiratory tractDefenses- Hairs (cilia), mucus, coughing, sneezing, swollowing- secretes IgANormal Biota- Strep Pyogenes (GAS)- H. Flu- Strep Pneumo- N. Meng- Staph Aureus Diseases of the Upper Respiratory Tract- Rhinitiso “common cold”o No fevero Symptoms due to immune responseo CC: Rhinoviruso VF: penetrate mucus, binds sialic acid and ICAM (allows virus to enter cell and replicate)- Enterovirus D68o More severe than a coldo “summer colds or pre flu”o low grade fever- Sinusitiso “sinus infection:o nasal congestion, pressureo opaque discharge with white, brown, yellow or green= bacterialo VFs: biofilmo Z-pack- Acute otitis mediao “ear infection”o pain in earo loss of hearingo us or fluid in middle earo can lead to eardrum rupture or meningitiso CC: Strep Pneumo (G+) or H. Flu (G-) lives in throat, can crawl up and cause diseaseo VF: capsule- Pharyngitiso “strep throat”o pain and swelling, reddened mucosa, swollen tonsils, white packetso CC#1: Group A strep VFs: M-protein adhesion (stick and stay) Scarlet fever (has an extra toxin) sandpaper like rash high fever children Rheumatic fever cross reaction between strep M-protein and heart muscle damage to heart valves and circulatory system arthritis in joints Glomerulonephritis Type 3 Hypersensitivity nephritis/kidney failure Toxic shock syndromeo CC#2: Viral less severe  hoarsenesso CC#3: fusobacterium necrophorum gram - (rare) adolescent/young adults lead to lemierres syndrome (blood infection) Use PEN Resistant to Z- packs - Diptheriao Sore throato loss of appetiteo low grade fevero Pseudomembrane (piles of dead cells) form on tonsilso Asphyxiation (membrane clogs airway)o CC: Corynebacterium diptheriae (gram + rod)o gram stain of XY or Chinese charactero ELEK test: black colonieso treatment: antitoxin- Pertusiso “whooping cough” paroxysmal stage coughing with a whoop sound long recovery (weeks/months) secondary infections possibleo CC: bordetella pertusis (gram - coccobacilli)o Tracheal cytotoxin: AB toxin, kills ciliated nasopharynx cellso pertussis toxin: unregulated cAMP (export)o clogs airway- Croupo infection of voice box and windpipeo “barking” cougho “stridor” or squeaking noise- pulling air in faster than normalo CC: parainfluenza viruso Steeple sign (narrowing of trachea)- RSV infectiono fever lasting 3 dayso blueing from airway inflammationo CC: respiratory syncytial virus (RNA virus)o “triple whammy of RSV”o forms syncytial cells - Influenzao headache, chills, fever, body aches(from cell breakdown)o cell breakdown product=cytokine storm responsible for systemic symptomso largest cause of death id from secondary bacterial infectionso VFs: hemogglutinin (HA and Neuraminidase (NA) capsid proteins- Influenza variationo yearly changes=antigenic drifto epidemic changes- antigenic shift- Metapeumoviruso hMPVo similar to fluo common in children and older adultso found as influenza negative and RSV negative- Coronaviruseso “Sudden acute respiratory syndrome” (SARS)o “Middle east respiratory syndrome” (MERS) symptoms range from mild cough/cold to swift, severe respiratory collapse shortness of breatho SARS coronavirus- gone in 2005o Novel coronavirus- MERS-CoVo Super spreaders- people that shed tons of virusLower respiratory infections- Tuberculosiso transmission via aerosolo CC: mycobacterium tuberculosis or mycobacterium avium intracellulare (MAC)o Gram n/a- need acid fast staining look for red snapper rodso produces “bread crumb” colonieso VFs: cord factor and proton pump allows for intracellular growtho Primary TB ID= 10 macrophages ingest bacterium and escape phagolysosomal destruction which leaves cell debris to form granulomas hard calcified lesions of infected cells + PPD - CXRo Secondary TB reactivation/escape causes large immune response mediated by T cells Cytokine release from T cells leads to Caseous (liquefying) Necrosis “cottage cheese” in lungs fever,