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.

The process of laboratory diagnosis (2) — Process of laboratory identification:
Identification of bacterial pathogens follows a stepwise process that usually begins with Gram staining and is followed by growth in isolated culture.
Image by Lecturio.

Structure

Average prokaryote cell — Structure of a prokaryote cell:
The cell envelope comprises a plasma membrane (green layer) and a thick, peptidoglycan-containing cell wall (yellow layer). No outer lipid membrane is present (as seen in gram-negative bacteria). The capsule (red layer) is distinct from the cell envelope.
Image by Lecturio.

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 Plasma The residual portion of blood that is left after removal of blood cells by centrifugation without prior blood coagulation. Transfusion Products 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)

**Table: Structures of the bacterial cell with their chemical composition and functions**
Structure	Chemical composition	Function
Appendages
Flagellum	Protein	Motility Motility The motor activity of the gastrointestinal tract. Gastrointestinal Motility
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	Glycoprotein	Adherence to cell surface
Specialized structures
Spore Spore The reproductive elements of lower organisms, such as bacteria; fungi; and cryptogamic plants. Microsporidia/Microsporidiosis	Keratin-like coat Dipicolinic acid Peptidoglycan Peptidoglycan Penicillins 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	Gram+ only Resists dehydration Dehydration The condition that results from excessive loss of water from a living organism. Volume Depletion and Dehydration, heat Heat Inflammation, and chemicals
Cell envelope Envelope Bilayer lipid membrane acquired by viral particles during viral morphogenesis. Although the lipids of the viral envelope are host derived, various virus-encoded integral membrane proteins, i.e. Viral envelope proteins are incorporated there. Virology
Capsule Capsule An envelope of loose gel surrounding a bacterial cell which is associated with the virulence of pathogenic bacteria. Some capsules have a well-defined border, whereas others form a slime layer that trails off into the medium. Most capsules consist of relatively simple polysaccharides but there are some bacteria whose capsules are made of polypeptides. Bacteroides	Organized polysaccharide layer	Protects against phagocytosis Phagocytosis The engulfing and degradation of microorganisms; other cells that are dead, dying, or pathogenic; and foreign particles by phagocytic cells (phagocytes). Innate Immunity: Phagocytes and Antigen Presentation
Slime layer	Loose network of polysaccharides Polysaccharides Basics of Carbohydrates	Mediates adherence to surfaces
Outer membrane	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 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	Gram- only Endotoxin Endotoxin Toxins closely associated with the living cytoplasm or cell wall of certain microorganisms, which do not readily diffuse into the culture medium, but are released upon lysis of the cells. Proteus: Lipid A induces TNF TNF Tumor necrosis factor (TNF) is a major cytokine, released primarily by macrophages in response to stimuli. The presence of microbial products and dead cells and injury are among the stimulating factors. This protein belongs to the TNF superfamily, a group of ligands and receptors performing functions in inflammatory response, morphogenesis, and cell proliferation. Tumor Necrosis Factor (TNF) and IL-1.
Periplasm	Peptidoglycan Peptidoglycan Penicillins in middle	Accumulate components exiting gram- cells
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	Peptidoglycan Peptidoglycan Penicillins in sugar backbone	Net-like structure gives rigid support.
Cytoplasmic membrane	Phospholipid bilayer sac	Site of oxidative and transport 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 Lipoteichoic acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance induce TNF-α and IL-1.

TNF: tumor necrosis factor
IL-1: interleukin-1

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.

Differences between gram-positive and gram-negative bacteria cell — Differences between the cell membranes of gram-positive and gram-negative bacteria:
While both gram-positive and gram-negative bacterial cell walls contain peptidoglycan layers, the layer in gram-negative bacteria is much thinner. Gram-negative bacteria make up for this deficit by having another membrane layer outside the peptidoglycan layer.
Image by Lecturio.

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

**Table: Morphology and arrangement of bacteria**
Morphology	Arrangements
Cocci	Spherical Immobile Single or paired (Diplococci) Twisted chains (Streptococci) Clusters (Staphylococci)
Bacilli Bacilli Shigella	Round-ended cylinders Rods
Spirilla	Helical Helical Computed tomography where there is continuous x-ray exposure to the patient while being transported in a spiral or helical pattern through the beam of irradiation. This provides improved three-dimensional contrast and spatial resolution compared to conventional computed tomography, where data is obtained and computed from individual sequential exposures. Computed Tomography (CT) Twisted
Spirochetes Spirochetes An order of slender, flexuous, helically coiled bacteria, with one or more complete turns in the helix. Treponema	Helical Helical Computed tomography where there is continuous x-ray exposure to the patient while being transported in a spiral or helical pattern through the beam of irradiation. This provides improved three-dimensional contrast and spatial resolution compared to conventional computed tomography, where data is obtained and computed from individual sequential exposures. Computed Tomography (CT) Long, flagella-like filaments Corkscrew-like movements Subgroup: Treponema Treponema Treponema is a gram-negative, microaerophilic spirochete. Owing to its very thin structure, it is not easily seen on Gram stain, but can be visualized using dark-field microscopy. This spirochete contains endoflagella, which allow for a characteristic corkscrew movement. Treponema
Genus Selenomonas	Cylinders curved in a plane
Genus Haloquadratum	Unusual morphologies Square, flat box-shaped
Vibrions	Round, comma-shaped bacteria Flagellated

Bacterial cells with various morphologies and arrangements:
Bacteria exist in a wide variety of morphologies and arrangements. Cocci and bacilli in pairs and clusters are among the most common.
Image by Lecturio.

Classification overview

Microbiology flowchart gram-positive bacteria classification — Gram-positive bacteria:
Most bacteria can be classified according to a lab procedure called Gram staining.
Bacteria with cell walls that have a thick layer of peptidoglycan retain the crystal violet stain utilized in Gram staining but are not affected by the safranin counterstain. These bacteria appear as purple-blue on the stain, indicating that they are gram positive. The bacteria can be further classified according to morphology (branching filaments, bacilli, and cocci in clusters or chains) and their ability to grow in the presence of oxygen (aerobic versus anaerobic). The cocci can also be further identified. Staphylococci can be narrowed down on the basis of the presence of the enzyme coagulase and on their sensitivity to the antibiotic novobiocin. Streptococci are grown on blood agar and classified on the basis of which form of hemolysis they employ (α, β, or γ). Streptococci are further narrowed on the basis of their response to the pyrrolidonyl-β-naphthylamide (PYR) test, their sensitivity to specific antimicrobials (optochin and bacitracin), and their ability to grow on sodium chloride (NaCl) media.
Image by Lecturio. License: CC BY-NC-SA 4.0

Gram negative bacteria classification flowchart — Gram-negative bacteria:
Most bacteria can be classified based on a lab procedure called Gram staining.
Bacterial cell walls having a thin layer of peptidoglycan do not retain the crystal violet stain used for Gram staining. However, gram-negative bacteria retain the safranin counterstain and appear pinkish-red. These bacteria can be further classified according to morphology (diplococci, curved rods, bacilli, and coccobacilli) and their ability to grow in the presence of oxygen (aerobic versus anaerobic). Gram-negative bacteria can be accurately identified by culturing on specific media (triple sugar iron (TSI) agar), where their enzymes can be identified (urease, oxidase) and their ability to ferment lactose can be determined.
* Stains poorly on Gram stain
** Pleomorphic rod/coccobacillus
*** Require special transport media
Image by Lecturio.

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 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
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

Bacterial types of genetic transmission — Schematic of types of genetic transmission in bacteria
Image by Lecturio.

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 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 factors are molecules that assist the bacterium in infecting the host and can be either secretory, membrane associated, or cytosolic in nature.

Table: Mechanism of 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, 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 factors, and function
Mechanism	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 factors	Function
Colonization	Teichoic acid (primarily in gram-positive Gram-Positive Penicillins organisms) Adhesins Adhesins Cell-surface components or appendages of bacteria that facilitate adhesion (bacterial adhesion) to other cells or to inanimate surfaces. Most fimbriae of gram-negative bacteria function as adhesins, but in many cases it is a minor subunit protein at the tip of the fimbriae that is the actual adhesin. In gram-positive bacteria, a protein or polysaccharide surface layer serves as the specific adhesin. What is sometimes called polymeric adhesin (biofilms) is distinct from protein adhesin. Diarrheagenic E. coli Biofilms Biofilms Encrustations formed from microbes (bacteria, algae, fungi, plankton, or protozoa) embedded in an extracellular polymeric substance matrix that is secreted by the microbes. They occur on body surfaces such as teeth (dental deposits); inanimate objects, and bodies of water. Biofilms are prevented from forming by treating surfaces with dentifrices; disinfectants; anti-infective agents; and anti-fouling agents. Proteus 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	Allows attachment to and invasion of host cell surfaces Biofilms Biofilms Encrustations formed from microbes (bacteria, algae, fungi, plankton, or protozoa) embedded in an extracellular polymeric substance matrix that is secreted by the microbes. They occur on body surfaces such as teeth (dental deposits); inanimate objects, and bodies of water. Biofilms are prevented from forming by treating surfaces with dentifrices; disinfectants; anti-infective agents; and anti-fouling agents. Proteus protect from antibiotic penetrance Penetrance The percent frequency with which a dominant or homozygous recessive gene or gene combination manifests itself in the phenotype of the carriers. Familial Juvenile Polyposis Motility Motility The motor activity of the gastrointestinal tract. Gastrointestinal Motility
Avoiding the immune system Immune system The body’s defense mechanism against foreign organisms or substances and deviant native cells. It includes the humoral immune response and the cell-mediated response and consists of a complex of interrelated cellular, molecular, and genetic components. Primary Lymphatic Organs	Capsule Capsule An envelope of loose gel surrounding a bacterial cell which is associated with the virulence of pathogenic bacteria. Some capsules have a well-defined border, whereas others form a slime layer that trails off into the medium. Most capsules consist of relatively simple polysaccharides but there are some bacteria whose capsules are made of polypeptides. Bacteroides IgA IgA Represents 15-20% of the human serum immunoglobulins, mostly as the 4-chain polymer in humans or dimer in other mammals. Secretory iga is the main immunoglobulin in secretions. Immunoglobulins: Types and Functions protease Protease Enzyme of the human immunodeficiency virus that is required for post-translational cleavage of gag and gag-pol precursor polyproteins into functional products needed for viral assembly. HIV protease is an aspartic protease encoded by the amino terminus of the pol gene. HIV Infection and AIDS Protein A	Creates physical barrier blocking opsonization and phagocytosis Phagocytosis The engulfing and degradation of microorganisms; other cells that are dead, dying, or pathogenic; and foreign particles by phagocytic cells (phagocytes). Innate Immunity: Phagocytes and Antigen Presentation
Bacterial nutrition	Siderophores Siderophores Low-molecular-weight compounds produced by microorganisms that aid in the transport and sequestration of ferric iron. Klebsiella	Chelate iron Iron A metallic element with atomic symbol fe, atomic number 26, and atomic weight 55. 85. It is an essential constituent of hemoglobins; cytochromes; and iron-binding proteins. It plays a role in cellular redox reactions and in the transport of oxygen. Trace Elements Iron Iron A metallic element with atomic symbol fe, atomic number 26, and atomic weight 55. 85. It is an essential constituent of hemoglobins; cytochromes; and iron-binding proteins. It plays a role in cellular redox reactions and in the transport of oxygen. Trace Elements absorption Absorption Absorption involves the uptake of nutrient molecules and their transfer from the lumen of the GI tract across the enterocytes and into the interstitial space, where they can be taken up in the venous or lymphatic circulation. Digestion and Absorption
Antigenic variation	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 Capsule Capsule An envelope of loose gel surrounding a bacterial cell which is associated with the virulence of pathogenic bacteria. Some capsules have a well-defined border, whereas others form a slime layer that trails off into the medium. Most capsules consist of relatively simple polysaccharides but there are some bacteria whose capsules are made of polypeptides. Bacteroides and 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 expression Antigenic drift Antigenic drift Influenza Viruses/Influenza	Camouflage of surface molecular markers that allow evasion of the immune system Immune system The body’s defense mechanism against foreign organisms or substances and deviant native cells. It includes the humoral immune response and the cell-mediated response and consists of a complex of interrelated cellular, molecular, and genetic components. Primary Lymphatic Organs
Intracellular survival	Inhibition of phagosome-lysosome fusion Exiting phagosomes before fusion occurs Invasins	Prevents intracellular destruction of the bacteria
Type III secretion system Type III secretion system Multiprotein transmembrane complexes in gram-negative bacteria involved in either the secretion of effector proteins from the bacterial cytoplasm into host cells, or the secretion and assembly of flagellar components. The major component of the t3sss is called the injectosome or needle complex. Yersinia spp./Yersiniosis	Injectisome	Allows bacteria to inject toxins into host cells
Inflammatory response	Bacteria-specific antibodies Antibodies Immunoglobulins (Igs), also known as antibodies, are glycoprotein molecules produced by plasma cells that act in immune responses by recognizing and binding particular antigens. The various Ig classes are IgG (the most abundant), IgM, IgE, IgD, and IgA, which differ in their biologic features, structure, target specificity, and distribution. Immunoglobulins: Types and Functions Immune complexes Immune complexes The complex formed by the binding of antigen and antibody molecules. The deposition of large antigen-antibody complexes leading to tissue damage causes immune complex diseases. C3 Deficiency Peptidoglycan Peptidoglycan Penicillins and teichoic acid	Mimic host cells (e.g., group A Streptococcus Streptococcus Streptococcus is one of the two medically important genera of gram-positive cocci, the other being Staphylococcus. Streptococci are identified as different species on blood agar on the basis of their hemolytic pattern and sensitivity to optochin and bacitracin. There are many pathogenic species of streptococci, including S. pyogenes, S. agalactiae, S. pneumoniae, and the viridans streptococci. Streptococcus) Delayed hypersensitivity reactions Granuloma formation

References

Baron, S., Editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Introduction to Bacteriology.
Woese, C.R., Fox, G.E. November 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90.
Cabeen, M.T., Jacobs-Wagner C. August 2005. Bacterial cell shape. Nature Reviews. Microbiology. 3 (8): 601–10.

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