Para-Clinical Microbiology Syllabus

Name the four phases of a bacterial growth curve in a closed batch culture, in order.

1) Lag phase, 2) Log (exponential) phase, 3) Stationary phase, 4) Death (decline) phase.

Define generation (doubling) time and give the formula relating it to the number of generations over time.

Generation time is the time required for a population to double. $$g = \frac{t}{n}$$ where $g$ is generation time, $t$ is elapsed time, and $n$ is the number of generations.

Compare exotoxins and endotoxins in bacteria.

Exotoxins: secreted proteins from Gram-positive or Gram-negative bacteria, highly potent, often toxoid-convertible, specific effects. Endotoxin: lipid A of LPS from Gram-negative outer membrane, released on lysis, causes fever/shock, heat-stable, not converted to toxoid.

Which pathogen causes tuberculosis, what staining property does it show, and why?

Mycobacterium tuberculosis. It is acid-fast (retains carbol fuchsin after acid-alcohol in the Ziehl-Neelsen stain) because of the high mycolic acid content of its waxy cell wall.

Name the causative organisms of cholera and tetanus and their characteristic toxins.

Cholera: Vibrio cholerae, producing cholera toxin (activates adenylate cyclase, causing watery diarrhea). Tetanus: Clostridium tetani, producing tetanospasmin (blocks inhibitory neurotransmitters, causing spastic paralysis).

Distinguish the mechanisms of horizontal gene transfer in bacteria: transformation, transduction, and conjugation.

Transformation: uptake of free naked DNA from the environment. Transduction: transfer of DNA by a bacteriophage. Conjugation: direct cell-to-cell transfer of plasmid/DNA via a sex pilus.

What is a nosocomial infection, and name two common nosocomial pathogens.

A nosocomial (healthcare-associated) infection is acquired in a hospital/healthcare setting. Common examples: methicillin-resistant Staphylococcus aureus (MRSA) and Clostridioides difficile; also Pseudomonas aeruginosa.

Define the basic reproduction number $R_{0}$ in infectious disease epidemiology.

$R_{0}$ is the average number of secondary infections produced by one infectious individual in a fully susceptible population. If $R_{0} > 1$ an outbreak can spread; if $R_{0} < 1$ it dies out.

Describe the general structure of a virus and define the terms capsid, capsomere, and nucleocapsid.

A virus consists of a nucleic acid genome (DNA or RNA) enclosed in a protein coat (capsid) made of subunits called capsomeres. The genome plus capsid is the nucleocapsid; some viruses add a lipid envelope.

Compare enveloped and non-enveloped (naked) viruses in terms of structure and environmental resistance.

Enveloped viruses have a host-derived lipid bilayer with glycoprotein spikes; they are more susceptible to drying, heat, detergents, and disinfectants. Naked viruses lack an envelope and are generally more stable/resistant in the environment.

Name the three main types of capsid symmetry in viruses.

Helical, icosahedral (cubic), and complex (e.g., bacteriophages with icosahedral heads and helical tails).

State the Baltimore classification system's basis and list its seven groups by genome type.

Baltimore classification groups viruses by genome type and mRNA production route: I) dsDNA, II) ssDNA, III) dsRNA, IV) (+)ssRNA, V) (−)ssRNA, VI) ssRNA-RT (retroviruses), VII) dsDNA-RT.

List the general stages of the viral replication cycle in order.

1) Attachment (adsorption), 2) Penetration (entry), 3) Uncoating, 4) Synthesis (replication of genome and proteins), 5) Assembly (maturation), 6) Release (lysis or budding).

Contrast the lytic and lysogenic cycles of a bacteriophage.

Lytic cycle: the phage replicates and lyses the host cell, releasing progeny. Lysogenic cycle: the phage genome integrates into the host chromosome as a prophage and replicates passively with the host until induced into the lytic cycle.

What enzyme is unique to retroviruses, what does it do, and name a key example virus?

Reverse transcriptase, an RNA-dependent DNA polymerase that transcribes the viral RNA genome into DNA for integration into the host genome. Key example: Human Immunodeficiency Virus (HIV).

Which cells does HIV primarily infect, via which receptor and co-receptor, and what disease results?

HIV infects CD4+ T-helper lymphocytes (and macrophages) by binding the CD4 receptor plus a co-receptor (CCR5 or CXCR4). Progressive CD4 depletion causes acquired immunodeficiency syndrome (AIDS).

Distinguish antigenic drift from antigenic shift in influenza virus.

Antigenic drift: gradual point mutations in hemagglutinin/neuraminidase genes causing minor changes (seasonal flu). Antigenic shift: sudden reassortment of genome segments between strains producing a novel subtype, capable of causing pandemics.

Name the causative virus and hallmark features of hepatitis B, and its transmission routes.

Hepatitis B virus (HBV), an enveloped dsDNA (partially) hepadnavirus. It causes acute/chronic hepatitis and predisposes to cirrhosis and hepatocellular carcinoma. Transmission: blood, sexual contact, and perinatal (vertical).

Which virus causes chickenpox and shingles, and by what mechanism does shingles occur?

Varicella-zoster virus (VZV, HHV-3). Primary infection causes chickenpox (varicella); the virus becomes latent in dorsal root ganglia and reactivates later as shingles (herpes zoster).

Differentiate the two morphological forms of fungi and define a dimorphic fungus.

Yeasts are unicellular and reproduce by budding; molds are multicellular filaments (hyphae) forming a mycelium. A dimorphic fungus exists as a mold at ambient temperature (~25°C) and as a yeast at body temperature (~37°C), e.g., Histoplasma.

Distinguish septate from coenocytic (aseptate) hyphae.

Septate hyphae have cross-walls (septa) dividing the filament into cells. Coenocytic (aseptate) hyphae lack septa, forming a continuous multinucleate cytoplasm (e.g., in Mucor/Rhizopus).

What are the main components of the fungal cell wall and cell membrane, and why is the membrane a drug target?

The fungal cell wall contains chitin, glucans, and mannans. The cell membrane contains ergosterol (rather than cholesterol). Ergosterol is targeted by azoles (block synthesis) and polyenes like amphotericin B (bind ergosterol).

Compare sexual and asexual reproduction in fungi, naming an example spore of each.

Asexual reproduction produces mitospores such as conidia or sporangiospores (also budding in yeasts). Sexual reproduction produces meiospores such as ascospores, basidiospores, or zygospores after fusion of compatible mating types.

Classify medically important fungi into their major phyla based on sexual spores.

Zygomycota (zygospores, coenocytic hyphae; e.g., Rhizopus), Ascomycota (ascospores; e.g., Aspergillus, Candida), Basidiomycota (basidiospores; e.g., Cryptococcus). Some are grouped as Deuteromycota (fungi imperfecti) with no known sexual stage.

Which fungus causes cryptococcal meningitis, what is its key virulence factor, and how is it detected microscopically?

Cryptococcus neoformans. Its key virulence factor is a thick polysaccharide capsule (antiphagocytic). It is visualized as a halo around the yeast using India ink negative staining of cerebrospinal fluid.

Name the fungus responsible for most cases of oral/vaginal thrush and its typical predisposing factors.

Candida albicans. Predisposing factors include antibiotic use (disrupting normal flora), diabetes, immunosuppression, corticosteroids, and pregnancy.

What are dermatophytes, which three genera are involved, and what tissue do they infect?

Dermatophytes are fungi that infect keratinized tissue (skin, hair, nails), causing tinea (ringworm). The three genera are Trichophyton, Microsporum, and Epidermophyton.

Define an opportunistic mycosis and give two examples of opportunistic fungal pathogens.

An opportunistic mycosis is a fungal infection that occurs mainly in immunocompromised or debilitated hosts. Examples: Aspergillus fumigatus (invasive aspergillosis) and Pneumocystis jirovecii (pneumonia in AIDS patients); also Candida and Mucor.

Classify the medically important protozoa into their four major groups by mode of motility, with an example of each.

Amoebae/Sarcodina (pseudopodia; Entamoeba histolytica), Flagellates/Mastigophora (flagella; Giardia lamblia, Trypanosoma), Ciliates (cilia; Balantidium coli), and Apicomplexa/Sporozoa (non-motile adults; Plasmodium, Toxoplasma).

Which protozoan causes malaria, what is the vector, and name the species causing the most severe disease.

Plasmodium species cause malaria, transmitted by the bite of the female Anopheles mosquito. Plasmodium falciparum causes the most severe, potentially fatal disease (cerebral malaria).

Distinguish the trophozoite and cyst stages of intestinal protozoa such as Entamoeba histolytica.

The trophozoite is the active, motile, feeding, and dividing form found in tissues/lumen. The cyst is the dormant, resistant, infective form passed in feces that survives outside the host and transmits infection via the fecal-oral route.

Classify parasitic helminths into their major groups, with a defining feature and example of each.

Nematodes (roundworms): unsegmented, cylindrical, separate sexes; e.g., Ascaris lumbricoides. Cestodes (tapeworms): flat, segmented (proglottids), scolex; e.g., Taenia. Trematodes (flukes): flat, leaf-shaped, unsegmented; e.g., Schistosoma.

Which helminth causes schistosomiasis, what is the intermediate host, and how do humans become infected?

Schistosoma species (blood flukes). The intermediate host is a freshwater snail. Humans are infected when free-swimming cercariae penetrate the skin during contact with contaminated water.

Define an ectoparasite and give three medically important examples that act as disease vectors.

An ectoparasite lives on the external surface of its host. Examples: mosquitoes (malaria, dengue), fleas (plague, murine typhus), ticks (Lyme disease, rickettsial fevers), lice (epidemic typhus), and mites (scabies).

Which ectoparasite causes scabies, and what characteristic lesion does it produce?

The mite Sarcoptes scabiei. The female burrows into the epidermis, producing characteristic serpentine burrows and intense itching (especially at night) with papular lesions in web spaces, wrists, and skin folds.