Basics of Infection, Immunity and Neoplasia Module

Module Information

• Department: Anesthesia
• Module title: Basics of infection, immunity and neoplasia module
• Module ECTS: 3 ECTS
• Module code: BioMM - 2321

Introduction to Microbiology

• Microbiology is the science that studies living organisms too small to be seen with the naked eye.
• It investigates the minute, microscopic forms of life and their relationships to humans and other organisms.
• Branches of microbiology include medical microbiology, industrial microbiology, food microbiology, soil microbiology, agricultural microbiology, and water microbiology.

Scopes of Microbiology

• Microbiology studies include cell structure, metabolism, genetics and growth control.
• These subjects create career opportunities in various fields like healthcare, biotechnology, research, environmental science, and agriculture.

Medical Microbiology

• This branch focuses on microorganisms related to humans.
• It investigates etiologic agents, epidemiology, diagnosis, treatment, and prevention of pathogenic microorganisms.
• It also explores the body's defenses against these pathogens.
• Some microbes are pathogenic, while others are non-pathogenic or part of the normal flora.

Subdivisions of Microbiology

• Bacteriology: the study of bacteria
• Mycology: the study of fungi
• Phycology: the study of algae
• Protozoology: the study of protozoa
• Virology: the study of viruses

Historical Background of Microbiology

• Throughout history, humans have faced diseases, initially attributed to divine punishment.

• Early Greeks proposed abiogenesis (living from non-living matter), and the notion that life could come from stones.

• Aristotle believed that life could spontaneously arise from dissimilar organisms or from soil.

• Hippocrates suggested that diseases had natural causes, observing links between illness and factors like air, wind, water, climate, food, and environmental conditions.

• Antony van Leeuwenhoek, the "father of microbiology," discovered the first microscope and observed "animalcules" in water samples, including bacteria.

• He accurately described the different shapes of bacteria.

• Two major theories were formulated: Theory of Abiogenesis and Theory of Biogenesis.

• Abiogenesis stated that living things arise from non-living matter.

• Biogenesis stated that living things arise from pre-existing living things.

• Francesco Redi disproved spontaneous generation of maggots from decaying meat.

• Lazzaro Spallanzani repeated Needham's experiments, but with improved sterilization techniques, to disprove spontaneous generation for microorganisms.

• Louis Pasteur further disproved spontaneous generation by demonstrating that microorganisms exist in the air and can contaminate sterile mediums.

• Louis Pasteur's swan-neck flask experiment provided significant evidence against the ideas of spontaneous generation by proving that access to outside particles is required for the growth in a given medium.

• The germ theory of disease, proposed by Pasteur and Robert Koch, posited that specific diseases are caused by specific microorganisms.

• Robert Koch developed Koch's postulates: an experimental procedure to establish a cause-and-effect relationship between a microbe and a disease.

• Koch's postulates include specific steps, such as isolating the microorganism and reproducing the disease in an experimental animal.

• Several exceptions to Koch's postulates exist since some pathogens are difficult to cultivate in a laboratory setting.

• Major achievements of Robert Koch included introducing solid medium culture, identifying the causative agents of diseases, and furthering development of bacteria studies.

• Scientific progress in microbiology continued into the 20th century.

• The establishment and flourishing of microbiology occurred in America in the early 1900s.

Types of Microorganisms

• Microorganisms are categorized as prokaryotes (simpler cells) or eukaryotes (more complex).
• Eukaryotes include algae (excluding blue-green algae), protozoa, fungi, and slime molds.
• Prokaryotes include bacteria, blue-green algae (cyanobacteria), and archaebacteria.
• Prokaryotes are generally simpler than eukaryotes, except for their complex cell wall.

Bacterial Classification and Nomenclature

• Bacteriology is the study of bacteria.
• There's no official bacterial classification system. Methods used for classifications of bacterial taxonomy include phenotyping (microscopic, macroscopic morphology, biochemical activities), analytical, and genotypic (nucleic acid hybridization, plasmid analysis, and ribotyping).
• Bacteria are categorized in Bergey's Manual of Determinative Bacteriology (1974), using criteria including morphology (shape), staining (Gram stain), motility, growth characteristics, nutritional requirements, biochemical activities, and pathogenicity.

Morphology

• Bacteria show varied sizes and shapes (cocci, bacilli, spirals).
• Different bacteria also present with arrangements/forms (streptococci, staphylococci, diplobacilli).

Bacterial Nomenclature (Binomial System)

• The binomial system, developed in the 18th century, gives each organism two names: genus and species.
• Genus name is capitalized; species name is lower case.
• Example, Escherichia coli or E. coli.

Basic Features of Bacterial Cells

• Bacteria are typical prokaryotic cells, contain DNA and RNA, often grown in artificial media, replicate via binary fission, and possess a rigid cell wall.

Structure of Bacteria

• Bacteria have characteristic size, shape, consistency, texture, and color. -Their structure is generally divided into the cell envelope, intracellular components, and external cell structures.

Cell Envelope

•   A key structural component composed of a capsule, cell wall, and a plasma (cytoplasmic) membrane.
• Cell Wall: provides shape and structural strength and made up of peptidoglycan.
•  Cell wall structure is either Gram-positive (thick peptidoglycan layer) or Gram-negative (thin peptidoglycan layer with an outer membrane).

Chemical Composition of Cell Wall

• The main component of the bacterial cell wall is peptidoglycan (PG), a polymer of disaccharides cross-linked by peptides.
• Peptidoglycan is made up of N-acetyl muramic acid and N-acetyl glucosamine.

Types of Cell Walls

• Gram-positive bacteria have a thick peptidoglycan layer.
• Gram-negative bacteria have a thin peptidoglycan layer with an outer membrane.

Capsule

• A gelatinous layer often present external to the cell wall.
• The composition varies amongst prokaryotes.
• It protects the cell from phagocytosis and aids in tissue attachment.

Cytoplasmic (Plasma) Membrane

• A barrier between the interior and exterior of the cell.
• It exhibits selective permeability for the transport of materials.
• It plays important roles in enzyme synthesis, excretion, and bacterial transport systems (e.g., oxidative phosphorylation).

Other Intracellular Components

• Mesosomes: invaginations of the cytoplasmic membrane. They are involved in DNA segregation during cell division, protein secretion, and active transport.
• Ribosomes: sites of protein synthesis. Prokaryotic ribosomes are smaller (70S) than eukaryotic ribosomes (80S).
• Cytoplasmic Inclusions: reserve materials including glycogen, polyhydroxybutyrate, or sulfur granules.
• Nuclear Material (Nucleoid): concentrated DNA, often a single circular chromosome, without an enclosing membrane. Plasmids are extra-chromosomal genetic material.

External Cellular Elements (Appendages)

• Flagellum: a locomotory appendage composed of flagellin. It exhibits different arrangements: monotrichous, lophotrichous, amphitrichous, and peritrichous.
• Pili: short, hair-like appendages that attach bacteria to surfaces or in the process of genetic material transfer (sex pili).

Bacterial Spores

• Specialized resistant structures formed by some bacteria (e.g., Bacillus, Clostridium).
• They are highly dehydrated and resistant to various harsh conditions (heat, drying, freezing, and chemicals).

Bacterial Metabolism and Growth

• Metabolism: comprises all the cellular processes required for survival and replication.
• Two major categories of metabolic reactions are catabolism (energy production) and anabolism (building of cellular components).
• Bacteria require water, energy, carbon, nitrogen, and various inorganic salts for optimal growth.
• Environmental factors like oxygen, pH, temperature, and light affect bacterial growth rates.
• Diverse nutritional categories for bacteria exist (autotrophs & heterotrophs).
• Autotrophs gain their required carbon from inorganic sources like carbon dioxide, while heterotrophs obtain carbon from organic sources.
• Temperature requirements for bacterial growth vary; they are often categorized into psychrophiles, mesophiles, thermophiles, and hyperthermophiles.

Bacterial Growth Curve

• Bacterial growth has four major phases: lag phase, log phase, stationary phase, and death phase.
• The lag phase, characterized by no increase in cell number, is a time of bacterial adaptation.
• The log phase shows exponential increase in cell number.
• The stationary phase represents a balance between cell division and death rate.
•   The death phase occurs due to nutrient exhaustion and toxic product build-up.
• These four phases compose the bacterial growth curve.

Continuous Culture

• Techniques for maintaining bacterial populations in a continuous exponential growth state, which involves constant addition of fresh medium while the total volume remains constant through an overflow tube.

Host-Parasite Relationship

• Bacterial infectivity emerges from an imbalance between bacterial virulence factors (factors that help bacteria invade the host, cause disease, evade host defenses) and the host's resistance mechanisms.
  • Host factors that protect from infection: numerous chemical and physical defenses (antibacterial secretions on mucosal surfaces, rapid replacement of skin/mucosal epithelial cells and a virtually devoid iron environment)
• Host susceptibility to infection: resistance to bacterial infections can be enhanced by phagocytic cells and an intact immune system.

Bacterial Infectivity

• Bacterial infectivity arises from a disturbance in the balance between bacterial virulence factors and host resistance responses.

Normal Flora

•   Normal microbial flora comprises the microorganisms inhabiting the skin and mucous membranes of healthy individuals. These are divided into resident flora and transient flora.
• Resident flora are relatively constant and significant to host health.
• Transient flora are non-pathogenic or potentially pathogenic organisms that don't establish residency and are often temporary.
• Some of the roles of the normal flora are preventing or competing with pathogenic microbes, or contributing to the health by synthesizing vitamin K & B vitamins.

Bacterial Staining

• Staining is used to add color to microorganisms for visual identification and differentiation using a microscope.
• Key staining methods include Gram stain, Ziehl-Neelsen (acid-fast) stain, and others.
• Gram staining differentiates bacteria based on their cell wall structure (Gram-positive & Gram-negative), while acid-fast staining differentiates specific groups of bacteria that are resistant to the decolorization step.

Culture Media

•   These contain the required nutrients for growth of a given microbial organism.
• Different culture media types include basic, enriched, selective, and differential, each designed for a specific purpose or use based on requirements.

Biochemical Tests

• Biochemical tests aid in precise categorization and identification of different bacteria based on the products or byproducts of chemical reactions of different bacteria.