Microbiology Exam Notes

Applied Immunity

Types of Acquired Immunity

• Artificially acquired active immunity
• Naturally acquired passive immunity
• Naturally acquired active immunity
• Artificially acquired passive immunity
• Naturally acquired active immunity
• Artificially acquired active immunity

Vaccines

• Attenuated bacteria: Live bacteria weakened or modified not to cause disease.
  • Example: Typhoid Fever
• Attenuated virus: Live virus weakened or modified not to cause disease.
  • Example: OPV
• Inactivated (Whole agent): Has entire pathogen composition but is inactivated.
  • Example: Flu shot containing whole influenza virus
• Toxoid: Inactivated toxin (exotoxin).
  • Example: Tetanus shot in DTaP
• Protein subunit: Only a part of the pathogen.
  • Example: Hepatitis B shot has capsids, Gardasil for HPV
• Conjugated: Attaches capsule (sugar) to an inactivated toxin since sugar alone won't trigger the immune system; then the immune system will produce antibodies for both.
  • Example: Prevnar 13 or Pneumovax 23 (The # means strains protected)
• DNA: Injection or gene gun.
• mRNA: mRNA packaged in Lipid nanoparticle delivery (fat bubble).
  • Example: Gene gun COVID-19
• Diseases eradicated so far: Only smallpox, polio is closer now.
• Vaccines & Autism:
  • Thimerosal is a mercury-based preservative used in early vaccines, believed to cause autism.
  • A study from Denmark proved thimerosal had no effect on vaccinated individuals.
  • UC Davis study showed affluent areas have high autism rates because they are highly educated and likely to diagnose their children.
  • Dr. Wakefield's study claimed that the measles shot causes autism but was not published and was proved he did it for monetary interest, which caused him to lose his license.

Immunological Diagnostic Tests

• Know the basics of the following tests (what it detects & how it’s set up):

ELISA (Enzyme-Linked Immunosorbent Assay)

• Advantages:
  • Sensitivity: Even nanograms can be detected.
  • Specificity: Only binds to specific AB/AG.
• Direct ELISA
  • Detects Antigen (Ag)
    • Positive Reaction:
      1. Patient's Ag is added.
      2. Patient's Ag settles down.
      3. Monoclonal Enzyme-linked Ab is added and binds to the patient's Ag.
      4. Substrates are added and bind to enzyme-linked Ab, causing a color change.
    • Negative Reaction:
      1. Patient's Ag is added.
      2. Patient's Ag settles down.
      3. Monoclonal Enzyme-linked Ab is added and does not bind to the patient's Ag.
      4. Substrates are added and do not bind to enzyme-linked Ab, so no color changes.
• Indirect ELISA
  • Detects Antibodies (Abs)
    • Positive Reaction:
      1. Manufactured Ag is added.
      2. Patient's Abs are added and bind to Ag.
      3. Enzyme-linked Ab is added and binds to Ab.
      4. Substrates are added and bind to enzyme-linked Ab, so color changes.
    • Negative Reaction:
      1. Manufactured Ag is added.
      2. Patient's Abs are added and do not bind to Ag.
      3. Enzyme-linked Ab is added and does not bind to Ab.
      4. Substrates are added but do not bind to enzyme-linked Ab, so no color change.
• Sandwich ELISA
  • Detects Antigen (Ag)
    • Positive Reaction:
      1. Monoclonal Abs are added.
      2. Patient's Ag is added and binds to Monoclonal Abs.
      3. Enzyme-linked Ab is added and binds to the antigen.
      4. Substrates are added and bind to enzyme-linked Ab, so color changes.
    • Negative Reaction:
      1. Monoclonal Abs are added.
      2. Patient's Ag is added and does not bind to Monoclonal Abs.
      3. Enzyme-linked Ab is added and does not bind to the antigen.
      4. Substrates are added and do not bind to enzyme-linked Ab, so no color changes.

Antimicrobial Drugs

Ideal Antimicrobial Drug Characteristics

1. Selective toxic to the microbe but nontoxic to host cells.
2. Microbicidal (kill) rather than microbistatic (slow).
3. Remains potent long enough to act and is not broken down or excreted prematurely.
4. Doesn’t lead to the development of antimicrobial resistance.
5. Readily delivered to the site of infection.
6. Reasonably priced.
7. Doesn’t disrupt host health by causing allergies or predisposing the host to other infections.

Natural Antibiotics

• Bacteria: Streptomyces and Bacillus
• Molds: Penicillium and Cephalosporium

Spectrum of Activity

• Spectrum = range of activity of the drug

  1. Narrow = small range; targets specific components in certain microbes
  2. Broad = great range; targets common components of microbe

Antibiotic Targets

1. Cell Wall Inhibitors
2. Disrupt cell membrane structure or function
3. Inhibits nucleic acid synthesis
   • Target DNA
   • Target RNA
4. Inhibit protein Synthesis
   • Target 30s
   • Target 50s
5. Block metabolic pathway

Antibiotic Classes and Mechanisms

Cell Wall Inhibitors (Beta Lactams)

• Mode of Action: Contains 3-Carbon and 1- Nitrogen Ring that resembles a component required to make cell wall so bacteria incorporate it and then it will have cidal effect. Block enzymes PBP (needed to build peptidoglycan)
• Specific Cellular Target: Peptidoglycan
• Examples:
  • Natural Penicillins:
    • Penicillin G (injectable): Syphilis
    • Penicillin V (oral): Oropharyngeal infections
  • Semi-synthetic Penicillins:
    • Amoxicillin: Middle Ear Inflammation, Streptococcal pharyngitis, mostly Gram (+), resistant to stomach acid
    • Methicillin: Staphylococcus aureus, discontinued because MRSA developed resistance
  • Cephalosporins (begin with prefix ceph-, kef-, cef-):
    • Its beta-lactam ring is resistant to beta-lactimase compared to penicillin
    • Only 5th Gen is effective against MRSA
    • 1st Gen: Cephalothin
    • 2nd Gen: Cefaclor
    • 3rd Gen: Cefixime
    • 4th Gen: Cefepime
    • 5th Gen: Ceftaroline

Non-Beta Lactam Cell Wall Inhibitors

• Vancomycin
  • Mode of Action: Interferes with Alanine amino acids in cross bridge of cell wall
  • Specific Cellular Target: Cross-Bridge (peptide part) of Cell Wall
  • Clinical Use: Treat MRSA, given before surgery, ineffective against gram (-) because outermembrane blocks it because of being too big
• Isoniazid
  • Mode of Action: Block production of enzymes for mycolic acid production to form cell wall
  • Specific Cellular Target: Mycolic Acid
  • Clinical Use: Treatment of Tuberculosis
• Ethambutol
  • Mode of Action: Interferes with integration of mycolic acid into cell wall
  • Specific Cellular Target: Mycolic Acid
  • Clinical Use: Treatment of Tuberculosis
  • Issues with patient compliance since treatment is too long
  • DOT
  • Syngergy with Isoniazid

Cell Membrane Inhibitors

• Mode of Action: Disrupts cell membrane
• Not common since humans have cell membrane too, topical otherwise toxic, small range only gram (-)
• Examples: Polymixin in: 1.) Polysporin 2.) Neosporin A,B,C,D,E (B most common)

Protein Synthesis Inhibitors - 30s

• Aminoglycosides
  • Mode of Action: Changes shape of 30s Ribosome
  • Specific Cellular Target: 30s of Ribosome
  • Examples:
    • Streptomycin = toxic: Tuberculosis
    • Tobramycin (inhaler): Pseudomonas
    • Amikacin: Gram (-), bone infections
  • Synergistic with beta-lactam
  • Cons: ear damage, broad
• Tetracyclines
  • Mode of Action: Block docking site of tRNA on 30s Ribosome
  • Specific Cellular Target: Docking site of tRNA in 30s Ribosome
  • Examples:
    • Natural: Tetracycline
    • Semi-Synthetic: Doxycycline, Minocycline, Tigecycline
  • Broad
  • Streptomyacin produces Tetracyclin
  • Tetracycline has 4 hexagon rings
  • Cons: ● Ca ions disable it.
  • Clinical Use:
    • Intracellular parasitic bacteria: Chlamydia, Rickettsia (Rocky mountain fever)
    • Pneumonia
    • MRSA
    • Lyme Disease

Protein Synthesis Inhibitors - 50s

• Cloramphenicol
  • Mode of Action: Blocks 50s Ribosome so peptide bonds cannot form in amino acids
  • Specific Cellular Target: 50s Ribosome
  • Broad, Toxic so given as last resort, cant breastfeed while on it
  • Backup drug for Salmonella, Pink Eye
  • Anemia: Reversible and Aplastic
• Macrolides
  • Mode of Action: Blocks movement of 50s Ribosome along mRNA
  • Specific Cellular Target: 50s Ribosome movement
  • Examples: Ertythromycin, Azithromycin (Z-PAK), Clarithrimycin
  • For Penicillin-allergic pts, G (+) infections (Staph and Strep), Intracellular and respiratory infec, Chlamydia Trachomatis (mom to child)
  • Short Regimen so pt complete it, longer half-life, binds to GI Tract receptors causing Diarrhea
  • Erythrocites: US mandates eye drops to newborns

Antimetabolites

• Mode of Action: Shut down metabolic pathways, Analog of PABA/Vitamin B
• broad range, 3% are allergic
• Specific Cellular Target: PABA Dihydrofolic Acid
  • Examples:
    • Sulfonamides: Sulfisoxazole, Sulfamethoxazole (SMX):( Protozoan infections)
    • Trimethoprim (TMP): Analog of Dihydrofolic acid, Tree = pnemumonia, Mouth = gastrointestinal tract infec., Pee = UTI\ Synergism with the former. SxT

Nucleic Acid Inhibitors

• Mode of Action: Shut down DNA/ RNA
  Specific Cellular Target: DNA Gyrase
• * Fluoroquinolones
  • Targets DNA Gyrase which is needed for DNA replication during binary fission
    • Examples: Ciprofloxacin, Norfloxacin, Livofloxacin, Ofloxacin
  • Broad, cidal effect, cant be taken with multi-vitamins
  • Ciproflaxin be cautious causes tendon rupture and CNX, Toxic so cant be prescribed 18 under, Gram (-), MRSA urogenital & GI tract (diarrhea), Drug-resistant pneumococci
• Rifampin
  • Inhibits RNA polymerase to block synthesis of mRNA
    • Tuberculosis and ALL listed below:
    • R: Rifampin
    • I: Isoniazid
    • S: Streptomyacin
    • E: Ethambutol
    • red-orange urine

Antimicrobial Drug List from Lecture

Cell Wall Inhibitors:

A. Beta-Lactam Medications:

• All Natural Penicillins-
  • Penicillin G,
  • Penicillin V
• Semi-synthetic Penicillins-
  • Methicillin (discontinued in the U.S.)
  • Amoxicillin
• Cephalosporins (organized by range of activity)-
  • 1st generation: Cephalothin
  • 2nd generation: Cefaclor
  • 3rd generation: Cefixime & Ceftriaxone (used specifically for Gonorrhea)
  • 4th generation: Cefepime
  • 5th generation: Ceftaroline (newly F.D.A. approved in 2016)

B. NON-Beta-Lactam Cell Wall Inhibitors:

• Vancomycin
• Ethambutol (part of RISE)
• Isoniazid (INH) (part of RISE)

Protein Synthesis Inhibitors:

C. 30S Inhibitors

• Tetracyclines: Tetracycline, Doxycycline
• Aminoglycosides: Streptomycin (part of RISE), Tobramycin, Amikacin

D. 50S Inhibitors

• Macrolides: Erythromycin (oldest version), Azithromycin (Brand: Zithromax or Z-Pak), Clarithromycin

Plasma Membrane:

E. Polymyxins (A, B, C, D, E)

• Type B is the one found in Neosporin (safe for topical use only!)

Nucleic Acid Inhibitors:

F. DNA Inhibitors (inhibit enzyme DNA gyrase):

• Flouroquinolones: Ciprofloxacin (Brand Name: Cipro), Norfloxacin, Levofloxacin, Ofloxacin

G. mRNA Inhibitor:

• Rifampin (name commonly used in the U.S.A.)

Anti-metabolites:

H. “Sulfa” Drugs:

• Sulfamethoxazole (SMX), Sulfisoxazole

I. Trimethoprim (TMP)

J. Sulfamethoxazole/Trimethoprim combination (Brand Name: Bactrim, Septra)

K. All of the above act as “analogs” ACE SAT DNA gyrase = floxacin R-R Clon Xazole 2, bi 4. 5,

Epidemiology

Symbiosis

Normal flora

• Mechanism of protection
  • Occupy spaces pathogens might occupy
  • Production of acids in vaginal tract
  • Production of bacteriocins by E.coli and Lactobacillus
• Specific example (organism & location) E.coli = gut
• Human Microbiome Project purpose
  • To characterize human microbiota then link it to human health and diseases
• How normal flora be disrupted
  • becoming immunosuppressed
  • extended antibiotics
  • microbes move into unusual sites, ex: E.coli entering blood stream
• Connection with weight management
  • Yes, it is believed that a leaner person has more diverse microbiota than heavier person

Robert Koch

• He is one of the founding fathers of Microbiology who hypothesized the Germ Theory of Disease.
• Infectious agents he identified
  • Mycobacterium tuberculosis, Bacillus anthracis, Vibrio cholera

Koch’s Postulates

1. Same pathogen must be present in every case of disease
2. pathogen must be isolated from the disease host and grow in a culture
3. Pathogen from culture must cause the disease when inoculated into healthy susceptible animal
4. pathogen must be reisolated and shown to be the same as original

Experiments to prove his postulates:

1. Isolating the right cause of disease is challenging
2. Finding a susceptible host is another challenge
3. These gents had problems growing the pathogen in the lab, so he ingested it

Issues with his postulates:

• There are definitely challenges with each postulates

Signs vs. Symptoms

• Sign is objective, Symptom is subjective. Sign is measurable like tests, Symptom is what the patient feel like fatigue.

Disease Progression (5 Stages)

1. Incubation period
2. prodromal period
3. period of illness. Acute phase
4. period of decline
5. period of convalescence

Incubation Time

• time between initial infection and first set of signs/symptoms , yes the incubation period depends on the organisms and number of organisms

Disease Reservoirs vs. Source of Infection

• Reservoir and Source can be the same, but not in all case. Reservoir is where a pathogen persists, Source is where it came from

Zoonosis (Zoonotic Diseases)

• When animals are the reservoir and transmits the microbe to humans, e.g., HIV, rabies, Ebola, and Dengue fever, malaria

Link Between Global Warming & Zoonosis

• Earth gets warmer, which favors mosquitoes to breed causing malaria to humans

Disease Transmission Routes

• Direct Transmission: Contact (kissing/sex), droplets (coughing and sneezing), vertical (mom to fetus like HIV or syphilis), and Biological vector (west nile virus and malaria)
• Indirect Transmission: Fomites (door knobs), fecal/oral (food, water), Air (dust, fine particles like TB)

Fomite

• Inanimate objects, door knobs, tables, chair, that can help transmit pathogens

Epidemiology

• Science of disease transmission including microbiology, statistics, sociology etc.

Disease Distribution Terms

1. Endemic: disease that exhibits relatively steady frequency over a long period of time. It won't go away permanently, but cases stay low.
2. Sporadic: occasional cases at irregular intervals
3. Epidemic: when the prevalence of a disease is increasing beyond what is expected
4. Pandemic: epidemic across continents
5. Prevalence: total number of existing case in a population, usually in %
6. Incidence: new cases compared with general healthy population
7. Mortality rate: death rate
8. Morbidity rate: number of people with disease

Lyme Disease Distribution Example

• The occurrence of Lyme disease mainly in areas where certain species of ticks live would define it as a(n) endemic disease.

Disease Causative Agent Table

• The following table will represent many key points regarding disease and causative agents

Skin Infections

Skin Lesion Terms

• Vesicles: small, fluid-filled blister. Not filled with pus. Like chickenpox but just clear fluid

• Abscess: localized collection of pus surrounded by inflammation. Pus is involved

• -itis: means inflammation

• Cellulitis: skin infection due to bacteria; redness or inflammation

• Myositis: inflammation of skeletal muscles. More severe since this involves the muscles

• Necrotizing fasciitis: inflammation & death of tissue surrounding muscles, tissues, and/or skin (fascia). Most severe/worst. Not only inflammation, but also death

  • If the cell/tissue is dead, it can't be reversed

Specific Skin Infections

• Staphylococcus aureus/MRSA; Steptococcus pyogenes, VZV, Pseudomonas aeruginosa
  

Cardiovascular System Infections

|Lyme disease|Spriochete( Borrelia Burgdorferi) | 1-= Erythema migrans( Bulls eye rash) 2- heart irregularties or CNS Symptoms 3- Arthritis=| Tick saliva >deer, antigenic Variation in proteins in outer membrane.| Transmision: Lxoeds tick saliva reservoirs mice and squirrells high risk = farmer, Nymph< adult<|Prevention DDEET , remove quickly, treat first sight w doxy|Antigenetic variation e=immune cannot keep up|
|Toxoplasmosis| Toxoplasma gondii| Mental disability, blindness, stillbirth to the baby Encephalitis to HIV=|Ingests,Cysts persist 1 year even Obligate parasite live hard and brain|Transmission : DIRECT mom to child reservoir cat soil Uncooked meat. causes humans or immune problems | Prevention LIMIT cats Clean litter withou flushing. || | | Schistosomiasis| Species/ Schistosoma-|Fever and Rash , blood inruine, liver and spleen| Cercaia/ larva detects penetrates blood vessels| Vector snails and animals africa and third world| avoid snails and proper waste|| |Gas Gangrene| Perfingens | Swelling and necrosis| breaks down cells causes | soil aquatic humans GI War wounds | prevention and antibotitcs | damages supply|= |Echocardiographic replications|Echolocation-||| | || | # Respiratory Infections | |Streptococcal or strap throaty |Pyrogenes| Red throat fever , swollen lymph nodes| strep throat|Mucus dropletts|Prevention= NoneTreatment: Punician|| TB Active cough weight loss , mycolic acid no toxins, latent= dormancy| Tuberculosis mucus droplet. only human population| Prevention only BGG test 6 months. || Influenza: The Spanish flu. | Influenza Virus , antigenetics shifts| Short. mucus Droplet.|Spikes enter kill cilia mucus| Prevention= flu mist + injectible with an inactive viron|Treat = Anti Viral | Pneumothorax:| C-19| Zoonotic for bats spikes, mucus and stool|. ||TREAT none, Prevention-Live-a-||