1. Pharmaceutical Microbiology
Part2

2. Pathogenesis of infectious diseases
Microorganism is an organism that is too small to be seen by the unaided eye.
How is it possible for such tiny organisms to cause disease in plants and animals, which are gigantic in comparison to microbes?
The prefix "path" refers to disease.
Examples of words containing this prefix are pathogen (a microorganism capable of causing disease).

3. Pathogenesis of infectious diseases
Pathology is the study of the structural and functional manifestations of disease.
Pathologist is a physician who has specialized in pathology.
Pathogenicity is the ability to cause disease.,
Pathogenesis is the steps or mechanisms involved in the development of a disease.

4. Why infection doesn't always occur
Many people who are exposed to pathogens do not get sick.
Many reasons could explain why infection does not always occur:
1. The microbe may "land" at an anatomical site where it is unable to multiply.
For example, when a respiratory pathogen lands on the skin, it may be unable to grow there because the skin lacks the necessary warmth, moisture, and nutrients required for growth of that particular microorganism.
Additionally, the low pH and presence of fatty acids make the skin a hostile environment for certain organisms.

5. Why infection doesn't always occur
2. Many pathogens must attach to specific receptor sites before they are able to multiply and cause damage.
If they land at a site where such receptors are absent, they are unable to cause disease.
3. Presence of antibacterial factors that destroy or inhibit the growth of microbes (e.g., the lysozyme that is present in tears, saliva, and perspiration) may be present at the site where a pathogen lands.
4. The indigenous microflora of that site (e.g., the mouth, vagina, or intestine) may inhibit growth of the foreign microbe by occupying space and using up the available nutrients.

6. Why infection doesn't always occur
5. The indigenous microflora at the site may produce antibacterial factors (proteins called bacteriocins) that destroy the newly arrived pathogen.
6. The individual's nutritional and overall health status often influences the outcome of the pathogen/host encounter.
A person who is in good health, with no underlying medical problems, would be less likely to become infected than a person who is malnourished and/or in poor health.

7. Why infection doesn't always occur
7. The person may be immune to that particular pathogen, perhaps as a result of prior infection with that pathogen or having been vaccinated against that pathogen.
8. Phagocytic white blood cells (phagocytes) present in the blood and other tissues may engulf and destroy the pathogen before it has an opportunity to multiply, invade, and cause disease.

8. FOUR PERIODS OR PHASES IN THE COURSE OF AN INFECTIOUS DISEASE
Once a pathogen has gained entrance to the body, the course of an infectious disease has four periods or phases.
1. The incubation period which is the time that elapses between arrival of the pathogen and the onset of symptoms.
The length of the incubation period is influenced by many factors, including:
The overall health and nutritional status of the host
The immune status of the host (i.e., whether the host is immunocompetent or immunosuppressed)
The virulence of the pathogen
The number of pathogens that enter the body.

9. FOUR PERIODS OR PHASES IN THE COURSE OF AN INFECTIOUS DISEASE
2. The prodromal period which is the time during which the patient feels "out of sorts" but is not yet experiencing actual symptoms of the disease.
Patients may feel like they are "coming down with something" but are not yet sure what it is.
3. The period of illness which is the time during which the patient experiences the typical symptoms associated with that particular disease (e.g., sore throat, headache, sinus congestion).

10. FOUR PERIODS OR PHASES IN THE COURSE OF AN INFECTIOUS DISEASE
4. The convalescent period which is the time during which the patient recovers.
For certain infectious diseases, especially viral respiratory diseases, the convalescent period can be quite long.
Although the patient may recover from the illness itself, permanent damage may be caused by destruction of tissues in the affected area.
For example, brain damage may follow encephalitis or meningitis, paralysis may follow poliomyelitis, and deafness may follow ear infections.

11. FOUR PERIODS OR PHASES IN THE COURSE OF AN INFECTIOUS DISEASE
An acute disease has a rapid onset, followed by a relatively rapid recovery; measles, mumps, and influenza are example.
A chronic disease has an insidious (slow) onset and lasts a long time; examples are tuberculosis, leprosy (Hansen disease) and syphilis.
Subacute diseases, some diseases such as bacterial endocarditis, come on more suddenly than a chronic disease but less suddenly than an acute disease; they are referred to as subacute disease.

12. SYMPTOMS OF A DISEASE VERSUS SIGNS OF A DISEASE
A symptom of a disease is defined as some evidence of a disease that is experienced or perceived by the patient.
Examples of symptoms include any type of ache or pain, a ringing in the ears (tinnitus), blurred vision, nausea, dizziness, itching, and chills.
Diseases, including infectious diseases, may be either symptomatic or asymptomatic.
A symptomatic disease (or clinical disease) is a disease in which the patient is experiencing symptoms.
An asymptomatic disease (or subclinical disease) is a disease that the patient is unaware of because he or she is not experiencing any symptoms.

13. SYMPTOMS OF A DISEASE VERSUS SIGNS OF A DISEASE
Gonorrhea, at early stages, is usually symptomatic in male patients (who develop a urethral discharge and experience pain while urinating) but asymptomatic in female patients.
Only after several months, during which the organism has caused extensive damage to women reproductive organs, is pain experienced by the infected woman.
Trichomoniasis (caused by the protozoan, Trichomonas vaginalis), is symptomatic in Infected females who are usually (experiencing vaginitis), while asymptomatic in infected males are usually.
tri-kə-mə-ˈnī-ə-səs

14. STEPS IN THE PATHOGENESIS OF INFECTIOUS DISEASES
In general, the pathogenesis of infectious diseases often follows this sequence:
1. Entry of the pathogen into the body which involves
Portals of entry include penetration of skin or mucous membranes by the pathogen.
Inoculation of the pathogen into bodily tissues by an arthropod.
Inhalation (the respiratory tract).
Ingestion (the gastrointestinal tract).
Introduction of the pathogen into the genitourinary tract.
Introduction of the pathogen directly into the blood (e.g., via blood transfusion or the use of shared needles by intravenous drug abusers).

15. STEPS IN THE PATHOGENESIS OF INFECTIOUS DISEASES
2. Attachment of the pathogen to some tissue(s) within the body.
3. Multiplication of the pathogen.
The pathogen may multiply in one location of the body, resulting in a localized infection (e.g., an abscess), or it may multiply throughout the body resulting in systemic infection.
4. Invasion/spread of the pathogen.
5. Evasion of host defenses.
6. Damage to host tissue(s).
The damage may be so extensive as to cause the death of the patient.

16. VIRULENCE
The words virulent and virulence tend to be confusing because they are used in several different ways .
Sometimes virulent is used as a synonym for pathogenic.
For example, there may be virulent (pathogenic) strains and avirulent (nonpathogenic) strains of a particular species.
The virulent strains are capable of causing disease, whereas the avirulent strains are not.

17. VIRULENCE
Sometimes virulence is used to express a measure or degree of pathogenicity.
Although all pathogens cause disease, some are more virulent than others (i.e., they are better able to cause disease).
For example, it only takes about 10 Shigella cells to cause shigellosis (a diarrheal disease), but it takes between 100 and 1,000 Salmonella cells to cause salmonellosis (another diarrheal disease. Thus, Shigella is considered to be more virulent than Salmonella.

18. VIRULENCE
Sometimes virulence is used in reference to the severity of the infectious diseases that are caused, by the pathogens.
Used in this manner, one pathogen is more virulent than another if it causes a more serious disease.

19. VIRULENCE FACTORS
Virulence factor is physical attributes or properties of pathogens that enable pathogens to attach, escape various host defense mechanisms and cause disease.
Virulence factors are phenotypic characteristics that are dictated by the organism's genotype.
Toxins are obvious virulence factors, but other virulence factors are not so obvious.

20. Some virulence factors are shown in the Figure

21. Attachment
Perhaps you have noticed that certain pathogens infect dogs but not humans, whereas others infect humans but not dogs.
Perhaps you have wondered why certain pathogens cause respiratory infections while others cause gastrointestinal infections.
Part of the explanation has to do with the type or types of cells to which the pathogen is able to attach.
To cause disease, some pathogens must be able to anchor themselves to cells after they have gained access to the body.

22. Receptors
The general terms receptor and integrin are used to describe the molecule on the surface of a host cell that a particular pathogen is able to recognize and attach to.
Often, these receptors are glycoprotein molecules.
A particular pathogen can only attach to cells bearing the appropriate receptor.

23. Receptors and Adhesins
A particular pathogen can only attach to cells bearing the appropriate receptor.
Thus, certain viruses cause respiratory infections because they are able to recognize and attach to certain receptors that are present on cells that line the respiratory tract but the virus is unable to cause gastrointestinal infections because those particular receptors are not present on cells lining the gastrointestinal tract
Certain viruses cause infections in dogs but not in humans, because dog cells possess a receptor that human cells lack.
HIV (the virus that causes AIDS) is able to attach to CD4+ cells which bear a surface receptor called CD4.
A category of lymphocytes called T-helper cells (the primary target cells for HIV) are examples of CD4+ cells.

24. Adhesins
The general terms adhesin and ligand are used to describe the molecule on the surface of a pathogen that is able to recognize and bind to a particular receptor.
For example, the adhesin on the envelope of HIV that recognizes and binds to the CD4 receptor is a glycoprotein molecule designated gp 120.
Adhesins are considered to be virulence factors because they enables certain pathogens to attach to host cells.

25. Bacterial Fimbriae
Bacterial fimbriae are long, thin, hairlike, flexible projections compose primarily of an array of proteins called pilin.
Fimbriae are considered to be virulence factors because they enable bacteria to attach to surfaces, including various tissues within the human body.

26. Bacterial Fimbriae
Fimbriated (piliated) strains of Neisseria gonorrhoeae are able to anchor themselves to the inner walls of the urethra cause urethritis.
Nonfimbriated (nonpiliated) strains of N. gonorrhoeae are thus unable to cause urethritis because they are flushed out via urination.
Fimbriated strains of E. coli that gain access to the urinary bladder are able to anchor themselves to the inner walls of the bladder and cause cystitis

27. Capsules
Bacterial capsules are considered to be virulence factors because they serve an antiphagocytic function (i.e., they protect encapsulated bacteria from being phagocytized by phagocytic white blood cells).
Phagocytes are unable to attach to encapsulated bacteria because they lack surface receptors for the polysaccharide material of which the capsule is made.
If they cannot adhere to the bacteria, they cannot ingest them.
Because encapsulated bacteria that gain access to the bloodstream or tissues are protected from phagocytosis, they are able to multiply, invade, and cause disease.

28. Flagella
Bacterial flagella are considered virulence factors because flagella enable flagellated (motile) bacteria to invade aqueous areas of the body that nonflagelated (nonmotile) bacteria are unable to reach.
Perhaps flagella also enable bacteria to avoid phagocytosis as it is more difficult for phagocytes to catch a moving target.

29. Exoenzymes
The major mechanisms by which pathogens cause disease are the exoenzymes and/or toxins that they produce.
Some pathogens release enzymes (called exoenzymes) that enable them to evade host defense mechanisms, invade, or cause damage to body tissues.
These exoenzymes include necrotizing enzymes, coagulase, kinases, hyaluronidase, collagenase, hemolysins, and lecithinase.
Although pili, capsules, and flagella are considered virulence factors, they really do not explain how bacteria and other pathogens actually cause disease.

30. Necrotizing Enzymes
Necrotizing enzymes are exoenzymes that are produced by many pathogens and resulted in tissues destruction.
Notorious examples include:
The "flesh-eating" strains of Streptococcus pyogenes, which produce proteases and other enzymes that cause very rapid destruction of soft tissue, leading to a disease called necrotizing fasciitis.
The Clostridium species that cause gas gangrene (myonecrosis) produce a variety of necrotizing enzymes, including proteases and lipases.

31. Coagulase
An important identifying feature of Staphylococcus aureus in the laboratory is its ability to produce a protein called coagulase.
Coagulase binds to prothrombin, forming a complex called staphylothrombin.
The protease activity of thrombin is activated in this complex, causing the conversion of fibrinogen to fibrin.
In the body, coagulase may enable S. aureus to clot plasma and thereby to form a sticky coat of fibrin around themselves for protection from phagocytes, antibodies, and other host defense mechanisms.

32. Kinases Kinases (fibrinolysins) have the opposite effect of coagulase.
Sometimes the host will cause a fibrin clot to form around pathogens in an attempt to wall them off and prevent them from invading deeper into body tissues.
Kinases are enzymes that lyse (dissolve) clots; therefore, pathogens that produce kinases are able to escape from clots.
Streptokinase is the name of a kinase produced by streptococci. Staphylokinase is the name of a kinase produced by staphylococci .
Streptokinase has been used to treat patients with coronary thrombosis.

33. Hyaluronidase
The "spreading factor," as hyaluronidase is sometimes called, enables pathogens to spread through connective tissue by breaking down hyaluronic acid, the polysaccharide "cement" that holds tissue cells together.

34. Collagenase
The enzyme collagenase, produced by certain pathogens, breaks down collagen which is the supportive protein found in tendons, cartilage, and bones,.
This enables the pathogens to invade tissues.
Clostridium perfringens, a major cause of gas gangrene, spreads deeply within the body by secreting both collagenase and hyaluronidase.

35. Hemolysins
Hemolysins are enzymes that cause damage to the host's red blood cells (erythrocytes).
Lysis of red blood cells harms the host and provides the pathogens with a source of iron.
In the laboratory, the effect an organism has on the red blood cells in blood agar enables differentiation between alpha-hemolytic (α-hemolytic) and beta-hemolytic (ß-hemolytic) bacteria.

36. Hemolysins
The hemolysins produced by α-hemolytic bacteria convert hemoglobin (which is red) to methemoglobin (which is green), resulting in a green zone around the colonies of α-hemolytic bacteria.
The hemolysins produced by ß-hemolytic bacteria cause complete lysis of the red blood cells, resulting in a clear zone around the colonies of ß-hemolytic bacteria.

37. Hemolysins
Hemolysins are produced by many pathogenic bacteria, but the type of hemolysis produced by an organism is of most importance when attempting to speciate a Streptococcus in the laboratory.

38. Obligate Intracellular Pathogens
Obligate intracellular pathogens (or obligate intracellular parasites) are pathogens that must live within host cells to survive and multiply such as Rickettsia and Chlamydia spp (all of which are Gram-negative bacteria)
obligate intracellular pathogens are propagated using cell cultures, laboratory animals, or embryonated chicken eggs.

39. Obligate Intracellular Pathogens
Rickettsias invade and live within endothelial cells and vascular smooth muscle cells.
Rickettsias are capable of synthesizing proteins, nucleic acids, and adenosine triphosphate (ATP), but are thought to require an intracellular environment because they possess an unusual membrane transport system (they have "leaky" membranes).

40. Obligate Intracellular Pathogens
The different species and serotypes of chlamydias invade different types of cells, including conjunctival epithelial cells, and cells of the respiratory and genital tracts.
Chlamydias lack several metabolic and biosynthetic pathways and depend on the host cell for intermediates, including ATP.

41. Facultative Intracellular Pathogens
Facultative intracellular pathogens (or facultative intracellular parasites), are pathogens that capable of both an intracellular and extracellular existence.
Many facultative intracellular pathogens that can be grown in the laboratory on artificial culture media are also able to survive within phagocytes.

42. Intracellular Survival Mechanisms
Phagocytes play an important role in our defenses against pathogens.
The two most important categories of phagocytes in the human body (referred to as "professional phagocytes") are macrophages and PMNs.
Once phagocytized, most pathogens are destroyed within the phagocytes by hydrolytic enzymes (e.g., lysozyme, proteases, lipases, DNAse, RNAse, myeloperoxidase, hydrogen peroxide, superoxide anions, and other mechanisms.

43. Intracellular Survival Mechanisms
Some pathogens (such as the bacterium, Mycobacterium tuberculosis) have a cell wall composition that resists digestion.
Mycobacterial cell walls contain waxes, and it is thought that these waxes protect the organisms from digestion.
Other pathogens (like the protozoan, Toxoplasma gondii) prevent the fusion of lysosomes (vesicles that contain digestive enzymes) with the phagocytic vacuole (phagosome).
Other pathogens (such as the bacterium, Rickettsia rickettsii) produce phospholipases that destroy the phagosome membrane, thus preventing lysosome-phagosome fusion.