Study sheet: Microbiology Foundations and Diagnosis

📋 Course Outline

1. Microbial Taxonomy and Naming
2. Prokaryotic and Eukaryotic Cells
3. Normal Microbiota and Flora
4. Modes of Infectious Transmission
5. Bacterial Growth and Cultivation
6. Pathogenicity and Virulence
7. Bacterial Infection Diagnosis
8. Virus Structure and Properties
9. Viral Replication Cycle
10. Bacteriophages and Viral Diagnosis
11. Direct Viral Detection
12. Molecular and Culture Methods

📖 1. Microbial Taxonomy and Naming

🔑 Key Concepts & Definitions

• Taxonomy : the orderly classification and naming of organisms according to their relationships

★ Must-know

• The three components of taxonomy are:

  • classification
  • nomenclature
  • identification

• The taxonomic hierarchy is:

  • Domain
  • Kingdom
  • Phylum
  • Class
  • Order
  • Family
  • Genus
  • Species

📌 Scientific names are binomial, consisting of a capitalized genus followed by a lowercase species name, usually written in italics; after first mention, Escherichia coli may be abbreviated as E. coli.

Further detail

• Bergey's Manual of Systematic Bacteriology was first published in 1923 and organizes bacterial information using characteristics including Gram reaction, metabolism, and morphology.

📌 Biovars differ in biochemical or physiological properties, morphovars differ in morphology, and serovars differ in antigenic or serological properties.

💡 Memory Hook

CNI: classify, name, identify

📖 2. Prokaryotic and Eukaryotic Cells

🔑 Key Concepts & Definitions

• Prokaryotic cell : lacks a true membrane-bound nucleus and includes bacteria and archaea
• Eukaryotic cell : contains a true nucleus surrounded by a nuclear membrane and includes protozoa, fungi, plants, and animals
• Nucleoid : the region containing the bacterial chromosome and is not surrounded by a nuclear membrane
• Plasmid : a small, usually circular DNA molecule separate from the bacterial chromosome that can carry genes such as antimicrobial-resistance genes

★ Must-know

📌 Prokaryotes usually have one circular DNA molecule, 70S ribosomes, no membrane-bound organelles, and binary fission, whereas eukaryotes have multiple linear chromosomes, 80S cytoplasmic ribosomes, membrane-bound organelles, and mitosis or meiosis.

Further detail

• Flagella primarily provide motility, while some pili participate in genetic-material exchange during conjugation.

💡 Memory Hook

Prokaryotes lack a true nucleus; eukaryotes possess one

📖 3. Normal Microbiota and Flora

🔑 Key Concepts & Definitions

• Normal flora : microorganisms that normally inhabit the skin and mucous membranes of healthy individuals, while internal organs and tissues are normally sterile

★ Must-know

📌 Resident flora normally survive and multiply at a body site, whereas transient flora remain temporarily, usually cannot multiply effectively there, and eventually disappear.

📌 Escherichia coli is normal in the gastrointestinal tract but can indicate infection when present in the bloodstream, abdominal cavity, or another normally sterile site.

• Normal flora helps prevent pathogen colonization, synthesize vitamin K, biotin, pantothenic acid, pyridoxine, and riboflavin, contribute to digestion, and produce inhibitory substances such as colicins.

Further detail

• Examples of normal skin flora include:

  • Staphylococcus epidermidis
  • Staphylococcus aureus
  • Cutibacterium or Propionibacterium acnes
  • yeasts
  • Candida albicans

• Reduction of intestinal flora by antibiotics can permit Clostridioides difficile to overgrow and cause disease.

💡 Memory Hook

Resident flora persists and multiplies; transient flora merely passes through

📖 4. Modes of Infectious Transmission

🔑 Key Concepts & Definitions

• Reservoir : the natural habitat where an infectious agent normally lives and multiplies
• Transmission : the movement of an infectious agent from a source or reservoir to a susceptible host
• Common vehicle transmission : Common vehicle transmission occurs through contaminated food, water, blood, air, medication, or another material and can infect many people from one source.

★ Must-know

📌 Direct contact transmission occurs through physical contact without an intermediate object, whereas indirect contact transmission occurs through a contaminated object called a fomite.

📌 Droplet transmission involves relatively large respiratory droplets traveling a short distance, whereas airborne transmission involves small particles or droplet nuclei that remain suspended and travel farther.

Further detail

📌 A mechanical vector carries an infectious agent without allowing its development, whereas a biological vector permits part of the pathogen's life cycle or multiplication.

💡 Memory Hook

Droplets fall nearby; airborne particles remain suspended

📖 5. Bacterial Growth and Cultivation

★ Must-know

• Bacteria primarily reproduce by binary fission, in which one cell divides into two daughter cells and the population increases exponentially under favorable conditions.

• 🔄 The bacterial growth curve proceeds through:

  1. lag phase
  2. log phase
  3. stationary phase
  4. death phase

📌 During the lag phase cells adapt and synthesize cellular components without significant population increase, whereas during the log phase cells divide rapidly and the population increases exponentially.

📌 In the stationary phase, the growth rate equals the death rate because nutrients are depleted and waste accumulates, whereas in the death phase the death rate exceeds the growth rate.

Further detail

📌 A batch culture receives a fixed amount of nutrient medium at the beginning, whereas a continuous culture receives fresh medium continuously while culture material exits.

• Generation time is the time required for a bacterial population to double; it is approximately 20 minutes for E. coli and 18 hours for Mycobacterium tuberculosis.

💡 Memory Hook

Lag → log → stationary → death

📖 6. Pathogenicity and Virulence

🔑 Key Concepts & Definitions

• Pathogenicity : the qualitative ability of an organism to cause disease
• Virulence : the quantitative degree or extent of pathogenicity and reflects how severely an organism affects its host
• Virulence factors : Virulence factors are microbial characteristics that help an organism enter the host, attach to cells, invade tissues, evade defenses, obtain nutrients, damage tissue, or spread.

📝 Essential Points

• Examples of virulence factors include:

  • toxins
  • enzymes
  • adhesins
  • capsules

• Streptokinase, produced by many hemolytic streptococci, activates a plasma proteolytic system that dissolves fibrin clots and can facilitate bacterial spread through tissues.

💡 Memory Hook

Pathogenicity asks whether disease is possible; virulence asks how severe it is

📖 7. Bacterial Infection Diagnosis

🔑 Key Concepts & Definitions

• Streak plate : a technique for isolating individual colonies from a mixed or bacterial culture by repeatedly diluting inoculum across an agar surface
• Colony : a visible mass of microorganisms arising from multiplication of one cell or a small group of cells

★ Must-know

• 🔄 The general diagnostic approach involves:

  1. specimen collection
  2. transport
  3. direct examination
  4. culture
  5. identification
  6. antimicrobial susceptibility testing

• Repeated streaking progressively separates cells across agar until an isolated cell can multiply into a visible colony.

Further detail

• Colonies can be examined for:
  • size
  • shape
  • color
  • margin
  • elevation
  • texture
  • hemolysis

💡 Memory Hook

Collect → transport → examine → culture → identify → test susceptibility

📖 8. Virus Structure and Properties

🔑 Key Concepts & Definitions

• Virus : an acellular obligate intracellular parasite composed mainly of genetic material and a protein coat that can replicate only inside living cells
• Capsid : the protein coat surrounding a viral genome, and its protein subunits are called capsomeres

★ Must-know

• Viruses are approximately 20–300 nm in size and lack cytoplasm, mitochondria, Golgi apparatus, lysosomes, ribosomes, and typical cellular organization.

📌 A viral genome contains either DNA or RNA, not both, and may be single- or double-stranded, linear or circular, and segmented or non-segmented.

📌 The nucleocapsid consists of the viral genome and capsid, whereas a virion is the complete assembled infectious virus particle.

• The major viral symmetry types and examples are:
  • helical—tobacco mosaic virus
  • icosahedral—adenovirus and poliovirus
  • complex—poxviruses and bacteriophages

Further detail

📌 Enveloped viruses possess a lipid envelope and are generally more fragile and sensitive to drying, temperature, pH, and chemicals than naked viruses.

📌 Prions are infectious abnormal proteins lacking nucleic acid, whereas viroids are small infectious RNA molecules associated particularly with plant diseases and do not encode proteins.

💡 Memory Hook

Nucleocapsid is genome plus capsid; virion is the complete infectious particle

📖 9. Viral Replication Cycle

★ Must-know

• 🔄 The viral replication sequence is: attachment, entry, targeting, uncoating, nucleic-acid replication and protein synthesis, maturation, release, shedding, transmission

• Viral attachment to specific host-cell receptors determines tissue or cell tropism; HIV uses gp120 to interact with CD4 on helper T cells.

• Positive-sense RNA can function directly as mRNA, whereas negative-sense RNA requires a viral RNA-dependent RNA polymerase to produce complementary mRNA.

• During release, cell lysis destroys the host cell, whereas budding releases the virus through the cell membrane and gives it an envelope.

Further detail

📌 Viruses enter cells by direct penetration, membrane fusion, or endocytosis, with membrane fusion requiring an enveloped virus.

📌 Many DNA viruses replicate in the nucleus and many RNA viruses replicate in the cytoplasm, although important exceptions occur.

💡 Memory Hook

Attach → enter → target → uncoat → replicate → assemble → release → shed → transmit

📖 10. Bacteriophages and Viral Diagnosis

🔑 Key Concepts & Definitions

• Bacteriophage : a virus that infects bacteria, attaches to bacterial cells, injects its genome, and replicates inside them

★ Must-know

• The three broad approaches to viral diagnosis are:
  • direct detection
  • virus isolation
  • serology

📌 Viral specimens should be collected aseptically in sterile containers, transported appropriately, and collected early because viral shedding is often greatest early in infection.

Further detail

• Viral transport medium prevents drying, preserves infectivity, and reduces bacterial or fungal overgrowth; it may contain buffered isotonic solution, protein, and appropriate antimicrobials.

📌 When immediate processing is impossible, 4°C is preferred for transport, routine storage at −20°C is discouraged because ice crystals can damage specimens, and −70°C may be used for longer delays.

💡 Memory Hook

Bacteriophages infect bacteria; viruses require living cells for replication

📖 11. Direct Viral Detection

🔑 Key Concepts & Definitions

• Cytopathic effect : the visible cellular change produced by viral infection, including cell rounding, cell fusion, and inclusion bodies
• Syncytium : a large multinucleated cell formed when infected cells fuse with neighboring cells, as can occur with RSV in HEp-2 cells

★ Must-know

• Negri bodies are cytoplasmic inclusion bodies found in infected nerve cells during rabies infection.

Further detail

• In immunofluorescence, fixed patient cells or specimens are exposed to fluorescently labeled antibodies, and fluorescence indicates binding to a viral antigen.

• Electron microscopy can visualize viruses at approximately 50,000–400,000× magnification but is expensive, labor intensive, relatively insensitive, and requires a high virus concentration.

💡 Memory Hook

CPE describes cellular change; an inclusion body is a specific intracellular structure

📖 12. Molecular and Culture Methods

🔑 Key Concepts & Definitions

• PCR : or polymerase chain reaction, detects and amplifies specific DNA or RNA sequences and is useful when culture is difficult
• ELISA : or enzyme-linked immunosorbent assay, uses enzyme-linked reagents to detect antigens or antibodies through a measurable signal

★ Must-know

📌 Viruses require living cells for replication and can be cultivated in laboratory animals, embryonated eggs, or cell culture, whereas bacteria can grow on nonliving culture media.

Further detail

• Cell culture can use susceptible living cells such as monkey kidney cells, but culture may be slow or insensitive and can be affected by poor specimens, bacterial contamination, or toxic substances.

📌 PCR generally provides rapid, sensitive, and specific nucleic-acid detection, whereas culture requires viable organisms and may be slower or difficult for viruses.

💡 Memory Hook

PCR detects nucleic acid; ELISA detects antigen or antibody

📊 Synthesis Tables

Major Microbiology Distinctions

Comparison	First notion	Second notion
Cell organization	Prokaryote: no true nucleus, 70S ribosomes	Eukaryote: membrane-bound nucleus, 80S ribosomes
Flora	Resident: persists and multiplies	Transient: temporary and limited multiplication
Transmission	Droplet: larger, short-range particles	Airborne: small suspended particles
Disease potential	Pathogenicity: ability to cause disease	Virulence: degree of disease severity
Virus structure	Nucleocapsid: genome plus capsid	Virion: complete infectious particle