Microbiology Study Guide PDF - Bacteria, Viruses, Fungi, and Parasites

Micro Review (Bacteria/Virus/Fungi/Parasites) Bacteria Differentiate between prokaryotes, eukaryotes, and viruses Prokaryotes: lack a nuclear membrane and membrane-bound organelles Eukaryotes: possess a nuclear membrane and membrane-bounded organelles Vir...

Micro Review (Bacteria/Virus/Fungi/Parasites) Bacteria Differentiate between prokaryotes, eukaryotes, and viruses Prokaryotes: lack a nuclear membrane and membrane-bound organelles Eukaryotes: possess a nuclear membrane and membrane-bounded organelles Viruses: Acellular, completely parasitic particles composed of a nucleic acid and protein; sometimes with lipids List and Explain the major ways in which bacteria can be classified Describe the structure and function of the bacterial flagellum Flagella: “H Antigen”; function in motility of cell through environment; rotates 360 degrees (tumble/clockwise/unorganized, and run/counterclockwise/organized); recognized by TLR5 in innate immune response (“true antigenic structure”) 3 parts: Filament (of flagellin), hook, and basal body. Recognized by TLR5 of innate immune response Monotrichous (single flagellum at one end), lophotrichous (small bunches emerging from same site), amphitrichous (flagella at both ends), peritrichous (flagella dispersed over surface of cell; slowest) Explain the mechanism of chemotaxis in motile bacteria Chemotaxis: tumble and run; movement of organism in response to chemical stimulus (gradient) Differentiate between a normal bacterial flagellum and a periplasmic flagellum Periplasmic Flagella: internal flagella, enclosed in space between outer sheath and cell wall peptidocglycan; produce cell motility by contracting and imparting twisting or flexing motion; important for virulence in those bacteria that possess them (spirochetes) Describe the structure, function, and significance of fimbriae Fimbriae: fine, proteinaceous, hair-like bristles emerging from cell surface; predominantly found in gram-; function in adhesion to other cells and surfaces; can aid in immune evasion Describe the structure, function, and significance of pili Pili: rigid, tubular structure made of pilin protein; found only in gram- cells; function to join bacterial cells for partial DNA transfer (conjugation); important in transfer of antibiotic resistance Explain how bacterial conjugation works Conjugation: process by which one bacterium trasnsfers genetic material to another through direct contact; one bacterium is donor, and one is recipient; donor carries DNA sequence called fertility factor (F-factor) Mechanism: step 1 (contact), step 2 (activation of DNA for transfer), step 3 (plasmid transfer), step 4 (synthesis of functional plasmid) Donor F+ cell transfers F plasmid to F- cell through pili.  Differentiate between the two types of glycocalyx Glycocalyx: coating of molecules external to the cell wall, made of sugars and/or proteins; composed mostly of polysaccharides Slime Layer: loosely organized and attached Capsule: highly organized, tightly attached (K antigen); both gram+ and gram – can make capsules Explain the function of the glycocalyx Glycocalyx Functions: protect cells from dehydration and nutrient loss; inhibit phagocytosis by WBCs contributing to pathogenicity, inhibit complement, attachment (formation of biofilms); related to quorum sensing Explain the role of biofilms in bacterial pathogenesis Biofilms: found on solid substrates; consist of many species of bacteria and archaea living as a community; glycocalyx holds the cells together; bacteria living in a biofil can have significantly diff properties from free-floating bacteria; bacteria in biofilms are protected from outside world (increased resistsnce to detergents, resistantce to antibiotics and host defenses); major factor in quorum sensing Quorum Sensing: regulation of gene expression in response to fluctuations in cell-population density; bacteria produce and release chemical signal molecules (autoinducers) that increase in concentration as function of cell density Cell Wall Shenanigans Gram+: have cell membrane; thick layer of peptidoglycan; Lipotechoic acid, techoic acid Gram-: have cell membrane; thin layer of peptidoglycan; another outer membrane (3 layers); more protective; selective of what goes through (porin proteins); very drug resistant Nontypical Cell Walls: some bacterial groups lack typical cell wall structure (Mycobacterium/Nocardia) Gram+ cell wall with lipid mycolic acid (cord factor): pathogenicity and high degree of resistance to certain chemicals and dyes; basis for acid-fast stain used for diagnosis of infections caused by these microorganisms; most familiar species are M. tuberculosis and M. leprae No cell wall: Mycoplasma; cell wall stabilized by sterols incorporated from host; pleomorphic; smallest cells, minimal genome; obligate parasites (mostly); anti-cell wall drugs will not work; most familiar species are M. pneumoniae, M. genitalium, Ureaplasma urealyticum New Stuff Gut Flora: digestion of food, vitamin production; immune stimulation; colonization resistance or microbial antagonism (occupy attachment sites, modify pH, produce bacteriocins); disruption of normal flora almost always leads to problems Opportunistic Infections: cause disease when habitat is changed; may occur due to weakened immune system Trauma: introduce flora to sterile site Immunosuppression: chemotherapy Other Manipulations: by medical personnel; that enable normal flora to cause disease (surgery, catheters, antibiotics) Virulence: quantitative measure of pathogenicity; relative ability of a microorganism to cause disease; 50% lethal dose (LD50) and 50% infectious dose (ID50); highly virulent pathogens are paradoxically often less successful Virulence Factors: traits that determine pathogenicity and virulence (capsules, toxins, adhesive fimbriae); often encoded on pathogenicity islands Toxins Endotoxin: lipopolysaccharide (LPS) toxin that is not secreted; integral part of gram- cell wall (lipid A component) Exotoxin: polypeptide toxin molecule that is secreted; produced by certain species of some gram+ and gram- bacteria; strong specificity of target cell; good antigens (can be used to induce antitoxins); types A-B toxins, cytotoxins, superantigens Viruses EVERYTHING Virus/Virion: obligate/dependent intracellular parasites (unstable outside of host cell); cannot synthesize proteins without host; genome can be DNA or RNA (single or double stranded); host machinery responsible for viral assembly; non-living Structure: nucleic acid core (DNA/RNA, single/double strand); capsid (protects core and mediates viral absorption, composed of capsomeres), envelope (made of host plasma membrane, acquired during exocytosis, either naked or enveloped) dsDNA: goes to nucleus for transcription ssDNA: same as above; recognized by polymerase (+)ssRNA: polymerase recognizes protein (but there will be some diff steps) (-)ssRNA: NEED TO PACK THEIR OWN POLYERMASE dsRNA: polymerase recognizes it (no problem) Size: generally smaller than cells (20-150 nm) Viral Symmetry: helical (gives rod-like appearance), icosahedral (nucleic acid surrounded by capsomeres arranged in icosahedrons; most are naked) Envelope: consists of lipid bilayers from host cell membrane and virally encoded glycoproteins; acquired during late stages of replication as virus undergoes budding; susceptible to denaturation, as desiccation and detergents can destroy Naked Virus: lacks bilayer lipid membrane; heat-resistant Enveloped Virus: enclosed within lipid membrane; sensitive to heat Viral Life Cycle: 1) Adsorption, 2) Penetration, 3) Uncoated, 4) Synthesis (replication and protein prod.), 5) Assembly, 6) Release  Viral Replication: 1) Recognition of/attachment to a target host cell, 2) Internalization (penetration) and uncoating of virus, 3) Macromolecular synthesis (early phase, replication of viral genome, late phase), 4) Virus assembly, 5) Release of virions, 6) Viral maturation (in some viruses) DNA Virus Replication: 1) Early period (nonstructural proteins; transcription is initiated; only part of genome transcribed/translated; regulatory proteins, polymerases, matrix proteins); 2) Late period (progeny nucleic acid; late proteins, capsid protein, envelope, glycoproteins) dsDNA Replication: DNA polymerase enzymes copy both the + and – DNA strands producing dsDNA viral genome; then use mRNA polymerase enzymes (mRNA); then translation ssDNA Replication: Parvovirus; DNA polymerase copy + strand of genome producing dsDNA intermediate; DNA polymerase then copies – DNA strand into ss+ DNA genomes; RNA polymerase enzymes copy – DNA strand into + viral mRNA; + viral mRNA then translated +RNA Virus Replication: CORONAVIRUS; directly translated by cellular polyribosomes into large proteins; RNA polymerase, protease; endocytosis -RNA Virus Replication: Filovirus; need to be transcribed into +RNA strands before synthesized (doesn’t have RNA- dependent RNA polymerase, so virus packs its own polymerases) Retrovirus Replication: reverse transcription, transport, integration, transcription, assembly and release Host Specificity: viruses can infect only certain species of hosts and only certain cells within that host; viral receptor must be found on host cell surface for virus to attach; some have broad range (rabies), some narrow (bacteriophages) Antigenic Shift: mix of 2 diff strains of virus in which new surface proteins (or combination of proteins) are expressed; “leads to new sub-type; a little more dramatic; can lead to pandemic” Virus A + Virus B → Virus C Antigenic Drift: mutations occur in proteins that bind to Abs (antigenic drift is one of main reasons why vaccine development is hard); “only have small mutations; easier to contain” Virus A → Virus B Fungi EVERYTHING Fungi: 2 forms (unicellular/yeast or multicellular/mold/hyphae); cell walls have chitin and glucan; cell membranes have ergosterol; Cryptococcus is only encapsulated fungus (highly diagnostic); mostly aerobic; dimorphic fungi Fungal Disease: skin infections (superficial, cutaneous, subcutaneous), pneumonias and general, disseminated mycoses (typically from pneumonias), opportunistic infections Superficial Skin Infections: cosmetic effects; easily treatment; Tinea versicolor (Malassezia furfur, “spaghetti and meatballs”); dimorphic, normal flora; humidity, poor hygiene contribute to pathology) Cutaneous Skin Infections: dermatophytes (Tineas, Ringworm); molds only (no yeast form); named for body site affected; generally restricted to keratinized layers of skin (keratinolytic); Microsporum, Trichophyton, Epidermophyton; topical treatment 10-20% KOH Wet Mount: of skin scraping; dissolves human cells and leaves fungal cells; can be stained in same prep with various fungal stains Subcutaneous Skin Infections: require trauma to allow entry to deeper layers of skin; Sporothrix Schenckii (“rose- gardener’s disease); dimorphic with cigar-shaped yeast form; lesion at site of entry with travel along lymphatics; dissemination to visceral organs in immunocompromised patients Pneumonias/General Infections: begin in lungs; dissemination to other body sites (often involve granulomas); respiratory exposure to spores or other fungal repro structures that become airborne (no person-to-person spread); dimorphic fungi; geography and soil characteristics become much more important with these clinical presentations Histoplasmosis: MS and OH River valleys (moist soils with guano); “histo hides”; often found inside macrophage Blastomycosis: Eastern/Central US; “broad-based budding yeast”; disseminates to skin, mimics squamous cell carcinoma Coccidioidomycosis: SW US (arid soils are best); spherules filled with spores; dissemination to skin and bones; erythema nodosum Paracoccidioidomycosis: Latin America; “Captain’s Wheel” or “Mariner’s Wheel”; presents similarly to blastomycosis  Opportunistic Infections Pneumocystis Jiroveci: PCP; immunosuppression leads to severe disease Candida Albicans: superficial (oral, GU) or systemic (bloodstream) infections Aspergillus Fumigatus: NOT dimorphic (hyphae only); aspergillomas in existing cavities Cryptococcus Neoformans: NO dimorphic (yeast only); encapsulated; hematogenous spread from lungs to meninges Mucor/Rhizopus: NOT dimorphic (hyphae only); invasion of sinuses and brain in patients with predisposing conditions Parasites EVERYTHING Parasites: “Protozoa and Helminths”; Protozoa: single-celled eukaryotes; trophozoite vs cyst forms; motility can be characteristic; can have multiple hosts (intermediate/asexual vs. definitive/sexual vs. dead-end/accidental hosts); can have unique methods of cell repro (schizogony, conjugation, etc.) Protozoan Disease: GI, CNS, blood, other (cutaneous, systemic, STI) GI Infections: fecal-oral contaminationi Giardia: giardiasis; fatty, foul-smelling diarrhea Entamoeba: amebiasis; dysentery, liver abscess Cryptosporidium: severe diarrhea in immune patients; mild otherwise CNS Infections Toxoplasma: contaminated meat, cat feces; crosses placenta; reactivation in immune patients; brain abscess Naegleria: warm freshwater habitate; enters via cribriform plate; rapidly fatal meningoencephalitis African Sleeping Sickness: “Trypanosoma brucei”; tsetse fly transmission; fever, somnolence, coma Blood Infections: both of these highly diagnostic in blood smears; both highly geographic Plasmodium: malaria, transmitted by Anopheles; fevers and chills (cyclical), headache, anemia, splenomegaly Babesia: tick-borne (Ixodes tick); fever and hemolytic anemia; “Maltese Cross” Other Infections Chagas Disease: “Trypanosoma cruzi”; unilateral periorbital swelling; cardiomyopathy; predominantly South America; “kissing bug” vector Leishmaniasis: cutaneous and visceral (kala-azar forms); Sandfly vector Trichomonas: sexually transmitted (no cyst form); vaginitis with foul smelling discharge Helminths: parasitic worms and flatworms; major target is GI tract, followed by skin and bloodstream; various modes of transmission including insects Ingested: “You’ll get sick if you EATT these” Enterobius, Ascaris, Toxocara, Tichinella, Trichuris Enterobius: pinworms; perianal itching in children; “scotch tape test” Ascaris: intestinal roundworms; travel through lungs can cause resp symptoms Toxocara: dog roundworm; visceral larva migrans (targets liver, eyes, CNS, heart) Trichinella: pork tapeworm; larvae encyst in striated muscle Trichuris: whipworm; heavy infestations cause anemia and rectal prolapse in children  Cutaneous: “These get into your feet from the SANd” Strongyloides, Ancylostoma, Necator Strongyloids: threadworm; larvae in soil penetrate skin; can cause pulmonary, GI, cutaneous symptoms Ancylostoma/Necator: hookworks (old world and new); larvae in soil penetrate skin; causue microcytic anemia in children; cutaneous larva migrans cused by dog and cat hookworms Bites: “Law LOW to avoid getting bitten” Loa loa, Onchocerca volvulus, Wuchereria bancrofti Loa Loa: “African Eye Worm”; deer flies and horse flies; skin swelling and invasion of sclera of eye Onchocerca: black flies; river blindness and “lizard skin” Wuchereria: mosquitoes; lymphatic filariasis (elephantiasis)