Virology, Bacteriology, and Mycology

• This module focuses on virology, bacteriology, and mycology and their clinical implications for humans.

Viruses Overview

• Viruses are subcellular parasites that rely on a host for energy and raw materials.
• To replicate, viruses infect a host cell and take over its replication machinery.
• A virion is a complete virus particle with a capsid, and the viral genome (RNA or DNA).
• Viruses are considered non-living as they require a host's ribosomes and replication machinery.
• Viruses lack true cell membranes but may have membrane-like structures from a previous host.

Viral Components and Shapes

• In addition to the genome (RNA or DNA) and capsid, viral components include:
• Envelope: A membrane shell surrounding some viruses, obtained from a host cell membrane after budding.
• Viral receptors: Proteins on the envelope or capsid recognize a target cell, aiding attachment/entry.
• Common virus shapes: helical, spherical, polyhedral

Viral Life Cycle

• Attachment and Entry: A virus penetrates a host cell, "uncoats," and releases its DNA genome into the host nucleus.
• Transcription: Viral genes in dsDNA are transcribed into mRNA in the nucleus.
• Viral RNAs are translated into proteins in the host cell cytoplasm.
• Viral DNA replicates in the nucleus, aided by produced viral proteins.
• RNA copies and proteins assemble into new virions, which mature, bud, and are released.
• DNA may integrate into the host's DNA as a side effect of the infection.
• RNA viruses replicate, and RNA translates into proteins via host ribosome RNA that does not need entry into the host cell nucleus.
• DNA viruses must enter the host cell nucleus to be transcribed into RNA, then leave for translation into proteins by the host ribosome.
• Retroviruses (e.g., HIV) with RNA genomes use reverse transcription (RNA to DNA) to create copies processed into mRNA and proteins.
• Latency occurs when some viruses remain dormant after infection. This can cause a later reactivation (e.g., herpesvirus causing chickenpox then shingles)

Classification of Viruses

• Categorized by genome type: RNA or DNA.
• Genomes may be linear, circular, single-stranded, or double-stranded.
• RNA and DNA viruses are further grouped into:
• Double or single-stranded DNA viruses, double-stranded RNA viruses and single-stranded RNA viruses
• Positive single-stranded RNA viruses directly translate into proteins (e.g., SARS-CoV-2).
• Negative single-stranded RNA viruses require synthesis of a complementary RNA strand before translation.

Viral Targets

• Antiviral drugs target key stages of the viral life cycle.
• Common therapies target RNA or DNA replication (reverse transcriptase or polymerase inhibitors), viral protein processing (protease inhibitors), or virus entry/attachment (attachment inhibitors).
• Variants and resistance can relies on host cells for replication, variants may develop during replication, particularly in RNA viruses due to mutation.
• The nucleus has proofreading for DNA viruses.

Bacteria Overview

• Binary fission is a method of replication.

Cell Structure and Components of bacteria

• The cell wall of gram-positive bacteria has a thick, homogenous peptidoglycan sheath, along with acidic polysaccharides.
• Gram-negative bacteria possess an outer membrane with porins and a thin peptidoglycan shell.
• Gram- bacteria have specialized lipopolysaccharides/lipoproteins.
• A similar cell membrane exists in both types of bacteria.
• The flexible lipid bilayer with embedded proteins is a site for energy reactions, nutrient processing, and metabolic acitivites
• Transport regulation in the main function of the membrane

Implications of cell envelope structure

• Staining reactions
• The outer membrane in gram-negative bacteria provides an extra barrier that is more impermeable to antimicrobial dyes/disinfectants, making it harder to kill.

Morphology (shape)

• There are 7 classic gram-positive organisms that may cause disease in humans:
• Four bacilli groups: Bacillus, Clostridium, Corynebacterium, Listeria
• Three cocci groups: Streptococcus, Enterococcus, Staphylococcus
• Of the identified gram-negative organisms: One group of gram-negative cocci (Neisseria)
• A group of spiral-shaped organisms: Spirochetes (e.g., Treponema pallidum)
• The remaining gram-negative organisms are rods or pleomorphic

Oxygen Spectrum

• Bacteria need catalyse, hydrogen peroxidase and superoxidase dimutase to break down harmful oxygen products.
• Those containing enzymes need oxygen for survival while other specturm bacteria cannot live in the presence of oxygen

Types of Bacterial Growth vary

• Obligate aerobes use oxygen and contain enzymes to break down toxic oxygen byproducts (e.g., Mycobacterium tuberculosis)
• Obligate anaerobes lack the enzyme system for using oxygen (e.g., Clostridium species)
• Facultative anaerobes do not require oxygen but can switch to fermentation in its absence (e.g., Escherichia coli, Klebsiella, Proteus)

Gram Staining

• Is performed due to colorless and invisible bacteria using light microscopy
• Separates bacteria into gram-negative and gram-positive by making them more visible in infectious specimens
• Gram-positive absorb crystal violet appearing BLUE and gram-negative washed off and absorb safranin and appear RED

Mycobacteria Cell Walls comprised of Mycolic Acid

• Cell walls are thick and waxy for resistance to chemicals and dyes
• Identified with acid-fast stain
• Hot carbon fuschin attached to the cell to avoid dye removal
• High concentration of lipids
• Mycobacterium tuberculosi, Mycobacterium leprae

Major targets on bacterial cells

• Many antibiotics target 70S ribosome for protein translation due to its unique size compared to human 80S ribosomes
• Selectively shuts down synthesis
• Fluoroquinolones target DNA Gyrase/Topoisomerase, blocking DNA replication
• Penicillin, Beta Lactams as antibotics can block Penicillin binding and transpeptidases and prevent cell wall formation
• Trimethoprim as antibacterial and DHFR, target DHPS
• Glycopeptides such as vancomycin bind to peptidoglycan precursors to prevent cell wall formation

Resistance Mechanisms

• Resistance describes the inability of antibiotics to treat bacterial infections, a major issue
• Bacteria transfer genes, modify the target, inacativate enzymatic drugs (beta lactamases), and employ elfflux mechanisms for resistance

Diagnosis

• Dependent on skill and experience of the technician, microscopy can distinguish between colonization and identifying leukocytes
• Performed vis gram-stain, acid-fast stain, fluorescent stains and india ink stains
• Culture on media with increased numbers of organisms to simplify the identification
• Obtain collections from various sites and test indwelling catherters
• Immunologic tests consist of antigen and antibody, complement fixation and enzyme immunoassays
• Quantitative, semi-quantitative, and nucleic acid-based testing

Fungi overview

• Fungi are eukaryotic non-motile cells that possess a rigid membrane
• Fungi cells may be unicellular or complex multicellular organism, most are beneficial to mankind and breakdown and recycle organic material
• Aerboes that are obligate and facultative require oxygen and chemotrophic growth produced outside of the organism
• Fungi secrete enzymes to break down material and absorb nutrients

Classification and Morphology

• Forms of molds and yeasts Molds are multicellular, thread like, classified as:
• septate: divided by transvers walls
• coenocytic: multinucleate

Yeasts are unicellular, spherical, paste-like cell cultures that have rigid membranes and reproduce by budding

Unique Cell Components

• These include glucose cell walls, fibrous proteins, and sterol components
• May be targerted by antifungal drugs by targeting the synthesis of ergosterol

Normal Human Flora includes Bacteria, Fungi and Protozoa

• Sterile and microbe-free sites:
• All organs (heart, liver, kidneys and bladder, brain and spinal cord, muscles, bones, ovaries/testes, glands, sinuses, internal eye, middle and inner ear)
• Blood, CSF
• Urine in kidney, ureters and bladder
• Saliva prior to entering oral cavity
• Amniotic fluid, pleural fluid, pericardial fluid.
• Sites that harbor normal flora:
• Skin and mucous membranes, Upper respiratory tract, Gastrointestinal tract, Outer opening of urethra, External genitalia
• Vagina, External ear and canal, and External eye (lids, lash follicles)
• Skin include staphylococcus and streptococcus and corynebacterium and Propionibacterium acnes and staphylococcus aureus in the nose.
• mouth harbors Candida albicans, Staphylococcus epidermidis and Viridans streptococci
• Haemophilus and Viridans streptococci. others reside inside the Nasopharynx

Throat: Viridans streptococci Colon: Lactobacillus, Escherichia coli (E. coli), Bacteroides, Candida albicans, Corynebacterium,Gardnerella vaginalis Vagina: Gardnerella vaginalis, Lactobacillus, Candida albicans,Bacteroides, CorynebacteriumE. coli,, Staphylococcus epidermidis Urethra: E. coli , Staphylococcus epidermidis.

• Gram-positive cocci include Pneumonia, skin and soft tissue infections
• Gram Positive bacilli includes anthrax, botulism, membrane colitis
• Gram-negative cocci has strains of meningitis and gonorrhea. and in gram negative bacilli
• Aeruginosa, Proteus and Klebiella include Infectious Diarrhea