Bacteriology

Introduction

• Bacteria:
  • Thought to be among 1st life forms on Earth
  • Inhabit almost every environment on Earth 
  • Live symbiotically with plants Plants Cell Types: Eukaryotic versus Prokaryotic and animals Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, animalia was one of the kingdoms. Under the modern three domain model, animalia represents one of the many groups in the domain eukaryota. Cell Types: Eukaryotic versus Prokaryotic 
  • Most bacteria have not been characterized.
• Basic features:
  • Unicellular Unicellular Cell Types: Eukaryotic versus Prokaryotic
  • Prokaryotes: lack envelope-enclosed nucleus Nucleus Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (cell nucleolus). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the endoplasmic reticulum. A cell may contain more than one nucleus. The Cell: Organelles
• Identification Identification Defense Mechanisms:
  • Starts with Gram staining using microscopy
  • Cell culture is helpful in exact identification Identification Defense Mechanisms.
  • Sensitivities are considered to determine treatment options.

Structure

• Prokaryote cell organization:
  • Lack enveloped nucleus Nucleus Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (cell nucleolus). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the endoplasmic reticulum. A cell may contain more than one nucleus. The Cell: Organelles
  • DNA DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure compressed into nucleoid Nucleoid The complete genetic complement contained in a DNA or RNA molecule in a virus. Virology
  • Lack membrane-bound organelles Organelles A cell is a complex unit that performs several complex functions. An organelle is a specialized subunit within a cell that fulfills a specific role or function. Organelles are enclosed within their own lipid bilayers or are unbound by membranes. The Cell: Organelles
  • Metabolism occurs in the cytoplasm.
• Cell wall Cell wall The outermost layer of a cell in most plants; bacteria; fungi; and algae. The cell wall is usually a rigid structure that lies external to the cell membrane, and provides a protective barrier against physical or chemical agents. Cell Types: Eukaryotic versus Prokaryotic:
  • Provides mechanical stability 
  • Allows for the exchange of nutrients and waste
  • Peptidoglycan Peptidoglycan Penicillins murein:
    • Sugar and amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids polymer that forms the basis of cell wall Cell wall The outermost layer of a cell in most plants; bacteria; fungi; and algae. The cell wall is usually a rigid structure that lies external to the cell membrane, and provides a protective barrier against physical or chemical agents. Cell Types: Eukaryotic versus Prokaryotic
    • N-acetyl glucosamine and N-acetylmuramic acid N-Acetylmuramic Acid Penicillins crosslinked with oligopeptides
    • Component of almost all bacterial walls (exception: mycoplasmas)
  • Thickness of cell wall Cell wall The outermost layer of a cell in most plants; bacteria; fungi; and algae. The cell wall is usually a rigid structure that lies external to the cell membrane, and provides a protective barrier against physical or chemical agents. Cell Types: Eukaryotic versus Prokaryotic determines Gram staining.
• Plasma membrane Plasma membrane A cell membrane (also known as the plasma membrane or plasmalemma) is a biological membrane that separates the cell contents from the outside environment. A cell membrane is composed of a phospholipid bilayer and proteins that function to protect cellular DNA and mediate the exchange of ions and molecules. The Cell: Cell Membrane:
  • Analogous to prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic membranes
  • Composed of proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis and phospholipids Phospholipids Lipids containing one or more phosphate groups, particularly those derived from either glycerol (phosphoglycerides) or sphingosine (sphingolipids). They are polar lipids that are of great importance for the structure and function of cell membranes and are the most abundant of membrane lipids, although not stored in large amounts in the system. Lipid Metabolism 
  • Unlike eukaryotic Eukaryotic Eukaryotes can be single-celled or multicellular organisms and include plants, animals, fungi, and protozoa. Eukaryotic cells contain a well-organized nucleus contained by a membrane, along with other membrane-bound organelles. Cell Types: Eukaryotic versus Prokaryotic organisms, lacks sterols Sterols Steroids with a hydroxyl group at c-3 and most of the skeleton of cholestane. Additional carbon atoms may be present in the side chain. Fatty Acids and Lipids
  • Envelops the cytoplasm of cells
• Flagella Flagella A whiplike motility appendage present on the surface cells. Prokaryote flagella are composed of a protein called flagellin. Bacteria can have a single flagellum, a tuft at one pole, or multiple flagella covering the entire surface. In eukaryotes, flagella are threadlike protoplasmic extensions used to propel flagellates and sperm. Flagella have the same basic structure as cilia but are longer in proportion to the cell bearing them and present in much smaller numbers. Helicobacter:
  • Approximately 50% of prokaryotes move with help of flagella Flagella A whiplike motility appendage present on the surface cells. Prokaryote flagella are composed of a protein called flagellin. Bacteria can have a single flagellum, a tuft at one pole, or multiple flagella covering the entire surface. In eukaryotes, flagella are threadlike protoplasmic extensions used to propel flagellates and sperm. Flagella have the same basic structure as cilia but are longer in proportion to the cell bearing them and present in much smaller numbers. Helicobacter:
    • Monotrichic: 1 flagellum 
    • Polytrichic: > 1 flagellum
  • Consist of the protein, flagellin, and are not covered by cell membrane Cell Membrane A cell membrane (also known as the plasma membrane or plasmalemma) is a biological membrane that separates the cell contents from the outside environment. A cell membrane is composed of a phospholipid bilayer and proteins that function to protect cellular DNA and mediate the exchange of ions and molecules. The Cell: Cell Membrane
  • Placement: monopolar, bipolar Bipolar Nervous System: Histology, or peritrich
• Pili Pili Filamentous or elongated proteinaceous structures which extend from the cell surface in gram-negative bacteria that contain certain types of conjugative plasmid. These pili are the organs associated with genetic transfer and have essential roles in conjugation. Normally, only one or a few pili occur on a given donor cell. This preferred use of ‘pili’ refers to the sexual appendage, to be distinguished from bacterial fimbriae, also known as common pili, which are usually concerned with adhesion. Salmonella ( fimbriae Fimbriae Thin, hairlike appendages, 1 to 20 microns in length and often occurring in large numbers, present on the cells of gram-negative bacteria, particularly enterobacteriaceae and Neisseria. Unlike flagella, they do not possess motility, but being protein (pilin) in nature, they possess antigenic and hemagglutinating properties. They are of medical importance because some fimbriae mediate the attachment of bacteria to cells via adhesins. Bacterial fimbriae refer to common pili, to be distinguished from the preferred use of ‘pili’. Escherichia coli):
  • Structurally similar to flagella Flagella A whiplike motility appendage present on the surface cells. Prokaryote flagella are composed of a protein called flagellin. Bacteria can have a single flagellum, a tuft at one pole, or multiple flagella covering the entire surface. In eukaryotes, flagella are threadlike protoplasmic extensions used to propel flagellates and sperm. Flagella have the same basic structure as cilia but are longer in proportion to the cell bearing them and present in much smaller numbers. Helicobacter, but much smaller
  • Aid in adherence to host/other bacteria = virulence Virulence The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its virulence factors. Proteus factor
  • Used to exchange genetic information during conjugation
• Nucleoid Nucleoid The complete genetic complement contained in a DNA or RNA molecule in a virus. Virology:
  • Functional equivalent of prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic nucleus Nucleus Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (cell nucleolus). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the endoplasmic reticulum. A cell may contain more than one nucleus. The Cell: Organelles
  • Lacks membrane
  • Contains genetic material:
    • Usually 1 chromosome Chromosome In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. Basic Terms of Genetics
    • May have additional plasmids Plasmids Extrachromosomal, usually circular DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in genetic engineering as cloning vectors. DNA Types and Structure
• Inclusions and vesicles Vesicles Female Genitourinary Examination:
  • Gas vesicles Vesicles Female Genitourinary Examination allow photosynthetic bacteria to float in water.
  • Organelles Organelles A cell is a complex unit that performs several complex functions. An organelle is a specialized subunit within a cell that fulfills a specific role or function. Organelles are enclosed within their own lipid bilayers or are unbound by membranes. The Cell: Organelles for photosynthesis and chemosynthesis
  • Carboxysomes contain key enzyme for fixing CO₂.
  • Storage granules (e.g., sulfur, phosphate Phosphate Inorganic salts of phosphoric acid. Electrolytes, calcium Calcium A basic element found in nearly all tissues. It is a member of the alkaline earth family of metals with the atomic symbol ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes. Electrolytes, glycogen)

Classification

Gram staining

Gram staining is a technique named after the bacteriologist Hans Christian Joachim Gram, and is used to differentiate between groups of bacteria based on the differences in the constituents of their cell walls. 

Gram staining helps distinguish between gram-positive Gram-Positive Penicillins and gram-negative bacteria by staining cells red or violet.

Process of Gram staining:

• Bacteria treated with crystal violet dye 
• Stain is washed with alcohol.
• Cells are counterstained with red safranin stain Safranin Stain Cystoisospora/Cystoisosporiasis and Cyclospora/Cyclosporiasis.

Staining of gram-positive Gram-Positive Penicillins bacteria: 

• Cell wall Cell wall The outermost layer of a cell in most plants; bacteria; fungi; and algae. The cell wall is usually a rigid structure that lies external to the cell membrane, and provides a protective barrier against physical or chemical agents. Cell Types: Eukaryotic versus Prokaryotic contains a thick layer of peptidoglycan Peptidoglycan Penicillins (murein).
• Retain crystal violet stain and are not affected by safranin counterstain
• Appear purple-blue

Staining of gram-negative bacteria: 

• Cell wall Cell wall The outermost layer of a cell in most plants; bacteria; fungi; and algae. The cell wall is usually a rigid structure that lies external to the cell membrane, and provides a protective barrier against physical or chemical agents. Cell Types: Eukaryotic versus Prokaryotic has a thin layer of peptidoglycan Peptidoglycan Penicillins (murein).
• Do not retain crystal violet stain, but retain safranin counterstain
• Appear pink-red

Staining plays important role in diagnostics/pathology: 

• Gram-positive Gram-Positive Penicillins bacteria:
  • More common commensal
  • Often found on the skin Skin The skin, also referred to as the integumentary system, is the largest organ of the body. The skin is primarily composed of the epidermis (outer layer) and dermis (deep layer). The epidermis is primarily composed of keratinocytes that undergo rapid turnover, while the dermis contains dense layers of connective tissue. Skin: Structure and Functions of healthy individuals
• Gram-negative bacteria:
  • Less sensitive to penicillin Penicillin Rheumatic Fever owing to additional lipid bilayer membrane
  • Contain 2nd membrane in the form of a lipid bilayer
  • Upon degradation, lipopolysaccharides Lipopolysaccharides Lipid-containing polysaccharides which are endotoxins and important group-specific antigens. They are often derived from the cell wall of gram-negative bacteria and induce immunoglobulin secretion. The lipopolysaccharide molecule consists of three parts: lipid a, core polysaccharide, and o-specific chains (o antigens). When derived from Escherichia coli, lipopolysaccharides serve as polyclonal b-cell mitogens commonly used in laboratory immunology. Diarrheagenic E. coli of the 2nd membrane layer can be released as endotoxins.
  • Endotoxins are pyrogens Pyrogens Substances capable of increasing body temperature and cause fever and may be used for fever therapy. They may be of microbial origin, often polysaccharides, and may contaminate distilled water. Fever that cause high fever Fever Fever is defined as a measured body temperature of at least 38°C (100.4°F). Fever is caused by circulating endogenous and/or exogenous pyrogens that increase levels of prostaglandin E2 in the hypothalamus. Fever is commonly associated with chills, rigors, sweating, and flushing of the skin. Fever and chills Chills The sudden sensation of being cold. It may be accompanied by shivering. Fever

Morphology

• Bacteria display a wide diversity of shapes and sizes.
• Most common morphologies are cocci and bacilli Bacilli Shigella, which can occur in many arrangements
• Arrangement:
  • Pairs
  • Tetrads
  • Clusters
  • Chains
  • Palisades

Classification overview

Toxins

Endotoxins

• Generated during the breakdown of bacterial cell wall Cell wall The outermost layer of a cell in most plants; bacteria; fungi; and algae. The cell wall is usually a rigid structure that lies external to the cell membrane, and provides a protective barrier against physical or chemical agents. Cell Types: Eukaryotic versus Prokaryotic when bacteria die
• Activate host complement and coagulation cascades 
• Cause septic shock Septic shock Sepsis associated with hypotension or hypoperfusion despite adequate fluid resuscitation. Perfusion abnormalities may include, but are not limited to lactic acidosis; oliguria; or acute alteration in mental status. Sepsis and Septic Shock
• Non-disease-specific symptoms:
  • Fever Fever Fever is defined as a measured body temperature of at least 38°C (100.4°F). Fever is caused by circulating endogenous and/or exogenous pyrogens that increase levels of prostaglandin E2 in the hypothalamus. Fever is commonly associated with chills, rigors, sweating, and flushing of the skin. Fever
  • Pain Pain An unpleasant sensation induced by noxious stimuli which are detected by nerve endings of nociceptive neurons. Pain: Types and Pathways
  • Shock Shock Shock is a life-threatening condition associated with impaired circulation that results in tissue hypoxia. The different types of shock are based on the underlying cause: distributive (↑ cardiac output (CO), ↓ systemic vascular resistance (SVR)), cardiogenic (↓ CO, ↑ SVR), hypovolemic (↓ CO, ↑ SVR), obstructive (↓ CO), and mixed. Types of Shock
  • Fatigue Fatigue The state of weariness following a period of exertion, mental or physical, characterized by a decreased capacity for work and reduced efficiency to respond to stimuli. Fibromyalgia
  • Discomfort

Exotoxins

• Produced and secreted
• Can result in severe, disease-specific symptoms
• 3 main categories:
  • Enterotoxins
  • Neurotoxins
  • Cytotoxins Cytotoxins Substances that are toxic to cells; they may be involved in immunity or may be contained in venoms. These are distinguished from cytostatic agents in degree of effect. Some of them are used as cytotoxic antibiotics. The mechanism of action of many of these are as alkylating agents or mitosis modulators. Helicobacter
• Examples:
  • Cholera Cholera An acute diarrheal disease endemic in india and southeast Asia whose causative agent is Vibrio cholerae. This condition can lead to severe dehydration in a matter of hours unless quickly treated. Vibrio
  • Botulinum
  • Diphtheria Diphtheria Diphtheria is an infectious disease caused by Corynebacterium diphtheriae that most often results in respiratory disease with membranous inflammation of the pharynx, sore throat, fever, swollen glands, and weakness. The hallmark sign is a sheet of thick, gray material covering the back of the throat. Diphtheria
  • Tetanus Tetanus Tetanus is a bacterial infection caused by Clostridium tetani, a gram-positive obligate anaerobic bacterium commonly found in soil that enters the body through a contaminated wound. C. tetani produces a neurotoxin that blocks the release of inhibitory neurotransmitters and causes prolonged tonic muscle contractions. Tetanus toxins

Metabolism

Bacteria are heterotrophic organisms that need organic substances to survive.

Classified based on oxygen requirements:

• Obligate aerobes (aerophilic): Oxygen is needed to maintain metabolism.
• Obligate anaerobes Anaerobes Lincosamides: 
  • No respiratory enzymes Enzymes Enzymes are complex protein biocatalysts that accelerate chemical reactions without being consumed by them. Due to the body’s constant metabolic needs, the absence of enzymes would make life unsustainable, as reactions would occur too slowly without these molecules. Basics of Enzymes present
  • Energy is generated via anaerobic glycolysis Glycolysis Glycolysis is a central metabolic pathway responsible for the breakdown of glucose and plays a vital role in generating free energy for the cell and metabolites for further oxidative degradation. Glucose primarily becomes available in the blood as a result of glycogen breakdown or from its synthesis from noncarbohydrate precursors (gluconeogenesis) and is imported into cells by specific transport proteins. Glycolysis.
  • Oxygen is toxic.
• Microaerophiles:
  • Oxygen needed for growth
  • If level is too high, growth stops
• Facultative anaerobes Facultative anaerobes Yersinia spp./Yersiniosis: can grow in the presence or absence of oxygen

Reproduction

Bacteria can exchange genetic material:

• Can integrate foreign DNA DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure into their genome Genome The complete genetic complement contained in the DNA of a set of chromosomes in a human. The length of the human genome is about 3 billion base pairs. Basic Terms of Genetics
• Can recombine in the existing gene Gene A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. Basic Terms of Genetics pool
• Can transfer genetic traits between each other:
  • Conjugation: parasexual transfer through contact via pili Pili Filamentous or elongated proteinaceous structures which extend from the cell surface in gram-negative bacteria that contain certain types of conjugative plasmid. These pili are the organs associated with genetic transfer and have essential roles in conjugation. Normally, only one or a few pili occur on a given donor cell. This preferred use of ‘pili’ refers to the sexual appendage, to be distinguished from bacterial fimbriae, also known as common pili, which are usually concerned with adhesion. Salmonella
  • Transduction: through bacteriophages Bacteriophages Viruses whose hosts are bacterial cells. Virology ( viruses Viruses Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. Virology that infect bacteria)
  • Transformation: introduction of free, isolated, foreign DNA DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure into genome Genome The complete genetic complement contained in the DNA of a set of chromosomes in a human. The length of the human genome is about 3 billion base pairs. Basic Terms of Genetics

Virulence Factors

Virulence Virulence The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its virulence factors. Proteus is the degree to which an organism can infect a host and cause disease. Virulence factors Virulence factors Those components of an organism that determine its capacity to cause disease but are not required for its viability per se. Two classes have been characterized: toxins, biological and surface adhesion molecules that affect the ability of the microorganism to invade and colonize a host. Haemophilus are molecules that assist the bacterium in infecting the host and can be either secretory, membrane associated, or cytosolic in nature.