unit3

What are the typical sources of clinical specimens?

Blood, urine, feces, abscesses/wounds, throat/nasal swabs, and genital samples.

Medical terms for bacteria in the blood and urine.

Bacteremia (bacteria in blood) and bacteriuria (bacteria in urine).

Differentiate between a selective and a differential medium.

Selective Medium inhibits the growth of certain bacteria. Differential Medium allows for the visualization of certain biochemical pathways/products.

Name the three common methods to test antibiotic sensitivity.

1. Broth Dilution Method (to find MIC). 2. Disk Diffusion Assay (Kirby-Bauer test). 3. Etest.

Define serology and an antibody titer.

Serology is the use of antigen-antibody reactions for diagnostic tests. Antibody Titer is the lowest concentration of serum at which an antibody-antigen reaction is observed.

What is an epitope, and how does it relate to an antigen?

An Epitope (antigenic determinant) is a small region of a molecule to which an antibody binds. The large molecule it is found on is the Antigen.

Name the two antigens used for serotyping E. coli.

The O antigen (from LPS) and the H antigen (from the flagella protein).

Differentiate Direct and Indirect EIA (ELISA).

Direct EIA uses immobilized antibody to detect antigen from the patient. Indirect EIA uses immobilized antigen to detect antibodies from the patient.

Which EIA type determines a current vs. past infection?

Direct EIA detects current infection (detects antigen). Indirect EIA detects past infection (measures patient's antibody titer).

How are PCR and qPCR used for pathogen detection?

PCR detects pathogen DNA in a sample using specific primers. qPCR is used to quantify the amount of pathogen DNA by monitoring fluorescence as dsDNA product is made.

Why is 16S rRNA gene sequencing limited for outbreak investigation, and what techniques are preferred?

16S rRNA gene sequences are often identical among different serotypes/strains of the same species. PFGE (DNA fingerprinting) and whole genome sequencing are preferred because they detect differences in genome rearrangements and mobile genetic elements.

Define toxic dose and therapeutic dose.

Toxic Dose: The level at which the drug becomes toxic to the host. Therapeutic Dose: The concentration required for effective clinical treatment.

What is the mode of action of isoniazid?

A prodrug that is metabolized to its active form (by KatG) and acts as a growth factor analog, blocking the synthesis of mycolic acids in Mycobacterium.

What is the mode of action of quinolones?

They inhibit DNA gyrase , which is necessary for DNA supercoiling, thereby blocking bacterial cell division.

What bacterial enzyme is inhibited by β-lactam antibiotics?

Transpeptidase (also known as penicillin-binding protein or PBP).

Name three classes of antibiotics that bind to bacterial ribosomes, with an example of each.

1. Aminoglycosides (e.g., Kanamycin, Streptomycin). 2. Macrolides (e.g., Erythromycin). 3. Tetracyclines.

How does the ionophore antibiotic daptomycin kill bacteria?

It inserts into the cytoplasmic membrane to create pores , resulting in a de-energized membrane and loss of the Proton Motive Force.

Define selective pressure in the context of antibiotic resistance.

The exposure of bacteria to antibiotics, which favors the survival and growth of the few naturally drug-resistant organisms, increasing their prevalence.

What are the mechanisms of resistance provided by MecA and NDM-1?

MecA encodes a transpeptidase that is resistant to β-lactam antibiotics (e.g., Methicillin), leading to MRSA. NDM-1 is a Metallo-β-lactamase enzyme that inactivates carbapenem antibiotics, found in CRE.

Give examples of innate resistance mechanisms.

Physical (skin barrier, cilia, tight epithelial junctions ). Chemical (stomach acidity, lysozyme ). Microbiological (normal flora competing with pathogens ).

List the three main functions of adaptive immunity.

1. Recognize a pathogen and its toxins. 2. Discriminate between a pathogen and normal body cells. 3. Eliminate the pathogen and/or toxin.

How do phagocytes recognize pathogens at the molecular level?

They recognize PAMPs (Pathogen-Associated Molecular Patterns) (e.g., LPS, peptidoglycan) using Pattern Recognition Receptors (PRR) on their surface.

Describe the process of antigen presentation.

Phagocytes ingest and degrade a pathogen into molecular pieces (antigens). These antigens are attached to MHC proteins and presented on the cell surface to T cells.

What are the functions of TH​1, TH​2, and TC​ cells?

TH​1 cells release cytokines that induce inflammation. TH​2 cells stimulate B cells to proliferate and produce antibodies. TC​ (cytotoxic) cells kill infected host cells (e.g., viral).

What part of an antibody binds to antigens?

The Antigen-binding site, located at the end of the variable regions (VH​ and VL​) of the heavy and light chains.

Distinguish between artificial active and passive immunity.

Artificial Active Immunity uses vaccination to induce an immune response. Artificial Passive Immunity is the individual receiving antibodies (e.g., antiserum); no immune response is involved.

Name the three types of traditional vaccines discussed.

1. Toxoid (inactivated exotoxins). 2. Inactivated Pathogen (killed pathogens). 3. Live Attenuated Pathogen (mutated, non-virulent variant).

Define pathogenesis and list the steps involved.

Pathogenesis is the process by which microorganisms cause disease. Steps: Exposure, Adherence, Invasion, Infection/Growth, Toxicity/Invasiveness, Tissue Damage/Disease.

Define virulence and explain how it is quantified.

Virulence is a measure of pathogenicity. It is quantified using the ID50​ (Infectious Dose) or LD50​ (Lethal Dose) tests in animal models.

How do virulence factors impact ID50​ and LD50​?

Virulence factors increase virulence. Highly virulent microbes have a low LD50​ (fewer cells needed to kill host). Loss of a virulence factor increases the LD50​.

Contrast bacteremia and septicemia.

Bacteremia is the presence of bacteria in the blood. Septicemia is inflammation in the blood (sepsis), often resulting from the infection.

Describe the difference between endotoxin and exotoxin.

Exotoxins are secreted proteins. Endotoxins are LPS of Gram-negative bacteria, released upon cell lysis. Exotoxins are generally much more toxic.

Define enterotoxin and list the three types of exotoxins.

Enterotoxin is an exotoxin that affects the small intestine. Three types: Cytolytic Toxins , AB Toxins , and Superantigens.

What is the mechanism of action for diphtheria toxin?

An AB toxin that blocks protein translation by catalyzing the modification of elongation factor EF-2, killing the host cell.

What is the mechanism of action for tetanus toxin?

An AB toxin that binds to inhibitory interneurons, preventing neurotransmitter release and causing constant muscle stimulation, leading to spastic paralysis.

What is the mechanism of action for botulism toxin?

An AB toxin that blocks the release of acetylcholine from nerve cells, inhibiting muscle contraction and leading to flaccid paralysis.

What is the mechanism of action for cholera toxin?

An AB toxin where the A subunit stimulates the formation of cyclic AMP in intestinal cells, altering ion movement and causing massive water loss (diarrhea) due to osmosis.

Medical uses of Type A botulism toxin.

The Type A botulism toxin is commonly used medically as Botox.

Where does Streptococcus pyogenes (GAS) infect and what is its primary disease?

It mainly infects the upper respiratory tract. The primary disease is streptococcal pharyngitis (strep throat).

What are the sequelae of S. pyogenes (GAS) infections?

Scarlet fever , Rheumatic fever , and Invasive infections (e.g., Necrotizing fasciitis).

What diseases are caused by Group A Strep (GAS) and Group B Strep (GBS)?

GAS (S. pyogenes): Strep throat, Scarlet fever, Rheumatic fever, Necrotizing fasciitis. GBS (S. agalactiae): Sepsis and meningitis in newborn babies.

What diseases does Streptococcus pneumoniae commonly cause?

Community acquired pneumonia and meningitis (especially in children and the elderly).

What virulence factors aid adherence of Bordetella pertussis?

Pertactin, Filamentous Hemagglutinin (FHA), and fimbriae (Type 2 & 3).

List the B. pertussis virulence factors that are vaccine components.

Pertussis toxin, Pertactin, Filamentous Hemagglutinin (FHA), and fimbriae (Type 2 & 3).

Define post exposure prophylaxis (PEP).

Recommendation of a treatment (e.g., antibiotics) for family members and others who have had contact with an active pertussis individual.

What is the pathogen for tuberculosis and what host cells does it infect?

Pathogen: Mycobacterium tuberculosis. It is an intracellular parasite that lives inside macrophage cells.

How are tubercules formed in tuberculosis?

A hypersensitivity immune response forms around the infection sites in the lung, creating nodules called tubercles. These can later calcify and become visible as a granuloma.

List the antibiotic-resistant forms of M. tuberculosis.

Multidrug resistant (MDR-TB) and Extensively Drug Resistant (XDR-TB).

What are the two most common bacterial pathogens for meningitis?

Neisseria meningitidis (meningococcus) and Streptococcus pneumoniae.

Why can a bacterial meningitis infection lead to death quickly?

Meningitis is an inflammation of the meninges (lining of the brain and spinal cord). The onset of symptoms can progress to coma and death in a matter of hours.

Define zoonotic, enzootic, and epizootic diseases.

Zoonotic: Disease found primarily in animals but transmissible to humans. Enzootic: Present endemically (regularly) in a certain animal population. Epizootic: An epidemic/outbreak throughout an animal population.

What is a dead-end host?

A host (often human) in which the pathogen cannot be transmitted further to another host.

Pathogen and vector for Rocky Mountain Spotted Fever and Lyme disease.

RMSF: Rickettsia rickettsii (Pathogen) , Tick (Vector). Lyme Disease: Borrelia burgdorferi (Pathogen) , Deer tick (Vector).

Pathogen and vector for Typhus.

Pathogen: Rickettsia prowazekii. Vector: Head lice (for human-to-human transmission).

What is the major reservoir of Clostridium tetani and how does it cause disease?

Reservoir: Soil. Disease Cause: Spores germinate in the anoxic conditions of deep puncture wounds, leading to growth and production of tetanus toxin.

How does plague get transmitted from wild rodents to humans?

The flea vector becomes infected from a wild rodent reservoir (e.g., rats) and then transmits the pathogen (Yersinia pestis) to a human through a bite.

What are the three forms of human plague?

1. Bubonic plague (lymph nodes). 2. Pneumonic plague (lungs). 3. Septicemic plague (bloodstream).

Define food infection and food poisoning.

Food Infection: Disease results from consuming the organism (live pathogen). Food Poisoning: Disease results from consuming a pre-formed toxin.

How is cholera transmitted?

Through fecal-contaminated water.

How is Legionnaire’s disease transmitted?

By aerosols (breathing in mist) from contaminated water sources (e.g., hot water tanks, cooling towers); it is not spread person-to-person.

Define naked and enveloped virions and their stability.

Naked virions lack an envelope, are more stable in the environment, and exit by lysis/exocytosis. Enveloped virions have an outer lipid envelope, are less stable, and exit by budding.

Why do viruses often carry their own polymerases?

They are carried if the host cell cannot perform the necessary replication or transcription step, such as RNA-dependent RNA polymerase (for RNA viruses) or Reverse Transcriptase (for retroviruses).

HPV: Genome, structure, and cell type infected.

Genome: Circular dsDNA. Virion: Naked. Infected Cell: Basal epithelial cells.

HPV: How does it cause cancer?

Viral early proteins E6 (degrades p53) and E7 (binds Rb) interfere with cell cycle arrest and apoptosis, inducing abnormal cell proliferation.

Name two ways HPV-mediated cancer can be prevented.

1. Use a condom. 2. Get vaccinated.

Influenza Virus: Genome, structure, and major antigens.

Genome: Segmented ss (−) RNA. Virion: Enveloped. Antigens: Hemagglutinin (HA) (attachment) and Neuraminidase (NA) (release).

Distinguish between antigenic shift and antigenic drift.

Antigenic Drift is subtle change due to random mutation. Antigenic Shift is a major change due to genetic reassortment (shuffling of RNA segments).

Explain the role of animals in influenza pandemics.

Animals (e.g., pigs and birds) act as reassortment hosts. When one host cell is co-infected by human and bird viral subtypes, the segments can reassort to form a new, highly virulent strain that can infect humans.

HIV: Genome, structure, and replication factor related to latency.

Genome: ss (+) RNA. Virion: Enveloped Retrovirus. Latency: The virus carries a Reverse Transcriptase which converts its RNA to dsDNA that integrates into the host genome, which can then be silent (latent).

Predict antiviral mechanisms based on HIV features.

Antivirals (HAART) target unique steps: Reverse Transcriptase inhibition , Integrase inhibition , Protease inhibition , and gp120 Entry inhibition.

How does HIV's immune deficiency affect disease progression?

HIV infects and kills CD4+T cells, leading to severe T cell depletion. This results in Systemic immune deficiency , causing susceptibility to opportunistic infections (e.g., Pneumocystis carinii pneumonia) and malignancy.

Coronavirus: Basic virion/genome structure and assembly.

Virion: Enveloped. Genome: ss (+) RNA. Assembly: Occurs at the Endoplasmic Reticulum (ER).

How does SARS-CoV-2 replication relate to its unique genome?

Since it is ss(+)RNA, the genome is structurally similar to mRNA and can be directly translated by host ribosomes immediately upon entry to produce replicase proteins.