The immune system responds variedly to different microorganisms often determined by the features of the microorganism. These are some different ways in which the immune system acts

Immune Response to Bacteria

Response often depends on the pathogenicity of the bacteria[5]:

• Neutralizing antibodies are synthesized if the bacterial pathogenicity is due to a toxin
• Opsonizing antibodies - produced as they are essential in destroying extracellular bacteria
• The complement system is activated especially by gram-negative bacterial lipid layers
• Phagocytes kill most bacteria utilizing positive chemotaxis, attachment, uptake and finally engulfing the bacteria
•  CD8+ T cells can kill cells infected by bacteria

Immune Response to Fungi [6]

• The innate immunity to fungi includes defensins and phagocytes
•  CD4+ T helper cells are responsible for the adaptive immune response against fungi
• Dendritic cells secrete IL-12 after ingesting fungi, and IL-12 activates the synthesis of gamma interferon which activates the cell-mediated immunity

Immune Response to Viruses [7]

• Interferon, NK cells, and phagocytes prevent the spread of viruses in the early stage
• Specific antibodies and complement proteins participate in viral neutralization and can limit spread and reinfection
• The adaptive immunity is of foremost importance in the protection against viruses - these include CD8+ T cells that kill them and CD4+ T cells as the dominant effector cell population in response to many virus infections

Immune response to parasites[8]:

• Parasitic infection stimulates various mechanisms of immunity due to their complex life cycle
• Both CD4+ and CD8+ Cells protect against parasites
• Macrophages, eosinophils, neutrophils, and platelets can kill protozoa and worms by releasing reactive oxygen radicals and nitric oxide
• Increased eosinophil number and the stimulation of IgE by Th-2 CD4+ T cells are necessary for the killing of intestinal worms
• Inflammatory responses also combat parasitic infections

Despite Immune response(s) generated by intact and functional Immune system we still fall sick, and this is often due to evasive mechanisms employed by these microbes. Here are some of those. 

Strategies of Viruses to Evade the Immune System

Antigenic variation: It is a mutation in proteins that are typically recognized by antibodies and lymphocytes. HIV continually mutates, thus making it difficult for either the immune system to protect against it and also hinders the development of a vaccine.

 By disrupting 2',5'-oligoadenylate synthetase activity or by the production of soluble interferon receptors viruses disrupt the Interferon response.

By several mechanisms, Viruses affects the expression of MHC molecules.   

A virus can infect immune cells: Normal T and B cells are also sites of virus persistence. HIV hides in CD4+T cells and EBV in B cells.

Strategies of Bacteria to Evade the Immune System

Intracellular pathogens may hide in cells: Bacteria can live inside metabolically damaged host leukocytes, and escaping from phagolysosomes (Shigella spp).

Other mechanisms:  

• Production of toxins that inhibit the phagocytosis
• They are preventing killing by encapsulation
• The release of catalase inactivates hydrogen peroxide
• They infect cells and then cause impaired antigenic presentation
• The organism may kill the phagocyte by apoptosis or necrosis

Strategies of Fungi to Evade the Immune System

• Fungi produce a polysaccharide capsule, which inhibits the process of phagocytosis and overcoming opsonization, complement, and antibodies
• Some fungi inhibit the activities of host T cells from delaying cell-mediated killing
• Other organisms (e.g., Histoplasma capsulatum) evade macrophage killing by entering the cells via CR3 and them escape from phagosome formation

Strategies of Parasites to Evade the Immune System  

• Parasites can resist destruction by complement
• Intracellular parasites can avoid being killed by lysosomal enzymes and oxygen metabolites
• Parasites disguise themselves as a protection mechanism
• Antigenic variation (e.g., African trypanosome) is an essential mechanism to evade the immune system
• Parasites release molecules that interfere with immune system normal function

The most important mechanisms of the immune system by which it generates immune response include:

Macrophages produce lysosomal enzymes and reactive oxygen species to eliminate the ingested pathogens. These cells produce cytokines that attract other leukocytes to the site of infection to protect the body. The innate response to viruses includes the synthesis and release of interferons and activation of natural killer cells that recognize and destroys the virus-infected cells. The innate immunity against bacterial consist of the activation of neutrophils that ingest pathogens and the movement of monocytes to the inflamed tissue where it becomes in macrophages. They can engulf, and process the antigen and then present it to a group of specialized cells of the acquired immune response. Eosinophils protect against parasitic infections by releasing the content of their granules.[9][10]

Antibody-dependent cell-mediated cytotoxicity (ADCC): A cytotoxic reaction in which Fc-receptor expressing killer cells recognize target cells via specific antibodies.

Affinity maturation: The increase in average antibody affinity mostly seen during a secondary immune response.

Complement system: It is a molecular cascade of serum proteins involved in the control of inflammation, lytic attack on cell membranes, and activation of phagocytes. The system can undergo activation by interaction with IgG or IgM (classical pathway) or by involving factors B, D, H, P, I, and C3, which interact closely with an activator surface to generate an alternative pathway C3 convertase. 

Anergy: It is the failure to induce an immune response following stimulation with a potential immunogen.

Antigen processing: Conversion of an antigen into a form that can be recognized by lymphocytes. It is the initial stimulus for the generation of an immune response.

Antigen presentation: It is a process in which specific cells of the immune system express antigenic peptides in their cell membrane along with alleles of the major histocompatibility complex (MHC) which is recognizable by lymphocytes.

Apoptosis: Programmed cell death involving nuclear fragmentation and the formation of apoptotic bodies.

Chemotaxis: Migration of cells in response to concentration gradients of chemotactic factors.

Hypersensitivity reaction: A robust immune response that causes tissue damage more considerable than the one caused by an antigen or pathogen that induced the response. For instance, allergic bronchial asthma and systemic lupus erythematosus are an example of type I and type III hypersensitivity reactions respectively.

Inflammation: Certain reactions that attract cells and molecules of the immune system to the site of infection or damage. It featured increased blood supply, vascular permeability and increased transendothelial migration of blood cells (leukocytes).

Opsonization: A process of facilitated phagocytosis by deposition of opsonins (IgG and C3b) on the antigen.

Phagocytosis: The process by which cells (e.g., macrophages and dendritic cells) take up or engulf an antigenic material or microbe and enclose it within a phagosome in the cytoplasm.

Immunological tolerance: A state of specific immunological unresponsiveness.

Hypersensitivity Reactions

They are overreactive immune responses to antigens that would not normally cause an immune reaction.

Type 1 hypersensitivity reactions: Initial exposure to the antigen causes stimulates Th2 cells. They release IL-4 leading the B cells to switch their production of IgM to IgE antibodies which are antigen-specific. The IgE antibodies bind to mast cells and basophils, sensitizing them to the antigen.

When the body is exposed to the allergen again, it cross-links the IgE bound to the sensitized mast cells and basophils, causing the degranulation and release of preformed mediators including histamine, leukotrienes, and prostaglandins. This causes systemic vasodilation, bronchoconstriction, and increased permeability of vascular endothelium.

The reaction can be divided into two stages – 1) Immediate, in which release of preformed mediators cause the immune response, and 2) Late-phase response 8-12 hours later, in which the cytokines released in the immediate stage stimulate basophils, eosinophils, and neutrophils even though the allergen is removed.

Type 2 hypersensitivity reactions (Antibody dependant cytotoxic hypersensitivity): Immune response against the antigens present on the cell surface. Antibodies binding to the cell surface, activate the complement system and cause the degranulation of neutrophils and destruction of the cell. Such reactions can be targeted at self or non-self antigens. ABO blood group incompatibility leading to acute hemolytic transfusion reactions is an example of Type 2 hypersensitivity.

Type 3 hypersensitivity reactions are also mediated by circulating antigen-antibody complex that may be deposited in and damage tissues. Antigens in type 3 relations are soluble as opposed to cell-bound antigens in type 2. 

Type 4 hypersensitivity reactions (delayed-type hypersensitivity reactions): They are mediated by antigen-specific activated T-cells. When the antigen enters the body, it is processed by antigen-presenting cells and presented together with the MHC II to a Th1 cell. If the T-helper cell has already been sensitized to that particular antigen, it will be stimulated to release chemokines to recruit macrophages and cytokines such as interferon-γ to activate them. This causes local tissue damage. The reaction takes longer than all other types, around 24 to 72 hours. 

Transplant Rejection

• Xenografts are grafts between members of different species, triggers the maximal immune response. Rapid rejection.
• Allografts are grafts between members of the same species.
• Autografts are grafts from one part of the body to another. No rejection.
• Isografts are grafts between genetically identical individuals. No rejection.

Hyperacute Rejection: In hyperacute rejection, the transplanted tissue is rejected within minutes to hours because vascularization is rapidly destroyed. Hyperacute rejection is antibody mediated and occurs because the recipient has preexisting antibodies against the graft, which can be due to prior blood transfusions, multiple pregnancies, prior transplantation, or xenografts. Activation of the complement system leads to thrombosis in the vessels peventing the vascularization of the graft. 

Acute Rejection: Develops within weeks to months. Involves the activation of T lymphocytes against donor MHCs. May also involve humoral immune response, which antibodies developing after transplant. It manifests as vasculitis of graft vessels with dense interstitial lymphocytic infiltrate. 

Chronic Rejection: Chronic rejection develops months to years after acute rejection episodes have subsided. Chronic rejections are both antibody- and cell-mediated. The use of immunosuppressive drugs and tissue-typing methods has increased the survival of allografts in the first year, but chronic rejection is not prevented in most cases. It generally presents as fibrosis and scarring. In heart transplants, chronic rejection manifests as accelerated atherosclerosis. In transplanted lungs, it manifests as bronchiolitis obliterans. In liver transplants, it manifests as vanishing bile duct syndrome. In kidney recipients, it manifests as fibrosis and glomerulopathy. 

Graft-versus-host Disease: The onset of the disorder varies. Grafted immunocompetent T cells proliferate in the immunocompromised host and reject host cells which they consider 'nonself' leading to severe organ dysfunction. It is a type 4 hypersensitivity reaction and manifests as maculopapular rash, jaundice, diarrhea, hepatosplenomegaly. Usually occurs in the bone marrow and liver transplants, which are rich in lymphocytes. 

The immunological investigations for the study of innate and adaptive immunity are listed below and include the assessment of immunoglobulins, B and T-lymphocyte counts, lymphocyte stimulation assays, quantification of components of the complement system and phagocytic activity.[11][12][13][14][15]

Quantitative Serum Immunoglobulins

• IgG
• IgM
• IgA
• IgE

IgG Sub-Classes

• IgG1
• IgG2
• IgG3
• IgG4

Antibody Activity 

IgG antibodies (post-immunization)

• Tetanus toxoid
• Diphtheria toxoid
• Pneumococcal polysaccharide
• Polio

IgG antibodies (post-exposure)

• Rubella
• Measles
• Varicella Zoster

Detection of isohemagglutinins (IgM)

• Anti-type A blood
• Anti-type B blood

Other assays

• Test for heterophile antibody
• Anti-streptolysin O titer
• Immunodiagnosis of infectious diseases (HIV, hepatitis B, and C, HTLV and dengue)
• Serum protein electrophoresis

Blood Lymphocyte Subpopulations

• Total lymphocyte count
• T lymphocytes (CD3, CD4, and CD8)
• B lymphocytes (CD19 and CD20)
• CD4/CD8 ratio

Lymphocyte Stimulation Assays

• Phorbol ester and ionophore
• Phytohemagglutinin
• Antiserum to CD3

Phagocytic Function  

Nitroblue tetrazolium (NBT) test (before and after stimulation with endotoxin)

• Unstimulated
• Stimulated

Neutrophil mobility

• In medium alone
• In the presence of chemoattractant

Complement System Evaluation

Measurement of individuals components by immunoprecipitation tests, ELISA, or Western blotting

• C3 serum levels
• C4 serum levels
• Factor B serum levels 
• C1 inhibitor serum levels

Hemolytic assays

• CH50
• CH100
• AH50

Complement system functional studies

• Classical pathway assay (using IgM on a microtiter plate)
• Alternative pathway assay (using LPS on a microtiter plate)
• Mannose pathway assay (using mannose on a microtiter plate)

Measurement of complement-activating agents

• Circulating immune complexes
• Cold agglutinins 

Assays for complement-binding

• C1q autoantibody ELISA
• C1 inhibitor autoantibody ELISA

Others complement assays

• LPS activation assay
• Specific properdin test
• C1 inhibitor activity test

Autoimmunity Studies

• Anti-nuclear antibodies (ANA)
• Detection of specific auto-immune antibodies for systemic disorders (anti-ds DNA, rheumatoid factor, anti-histones, anti-Smith, anti-(SS-A) and anti-(SS-B)
• Detection of anti-RBC, antiplatelet, and anti-neutrophil
• Testing for organ-specific auto-immune antibodies

Microbiological Studies

• Blood (bacterial culture, HIV by PCR, HTLV testing)
• Urine (testing for cytomegalovirus, sepsis, and proteinuria)
• Nasopharyngeal swab (testing for Rhinovirus)
• Stool (testing for viral, bacterial or parasitic infection)
• Sputum (bacterial culture and pneumocystis PCR)
• Cerebrospinal fluid (culture, chemistry, and histopathology)

Coagulation Tests 

• Factor V assay
• Fibrinogen level
• Prothrombin time
• Thrombin time
• Bleeding time

Other Investigations  

• Complete blood cell count    
• Tuberculin test
• Bone marrow biopsy
• Histopathological studies
• Liver function test
• Blood chemistry
• Tumoral markers
• Serum levels of cytokines
• Chest x-ray
• Diagnostic ultrasound
• CT scan
• Fluorescent in situ hybridization (FISH)
• DNA testing (for most congenital disorders)

The immune system protects the body against many diseases including recurrent infections, allergy, tumor, and autoimmunity. The consequences of an altered immunity will manifest in the development of many immunological disorders some of which are listed below:

• X- linked agammaglobulinemia (Bruton disease)
• Selective IgA Deficiency
• Selective IgG deficiency
• Congenital thymic aplasia (DiGeorge Syndrome)
• Chronic mucocutaneous candidiasis
• Hyper-IgM syndrome
• Interleukin-12 receptor deficiency
• Severe combined immunodeficiency disease (SCID)
• ZAP-70 deficiency
• Janus kinase 3 deficiency
• RAG1 and RAG2 deficiency
• Wiskott-Aldrich syndrome
• Immunodeficiency with ataxia-telangiectasia
• MHC deficiency (bare leukocyte syndrome)
• Complement system deficiencies 
• Hereditary angioedema
• Chronic granulomatous disease (CGD)
• Leukocyte adhesion deficiency syndrome
• Job syndrome
• Chediak Higashi syndrome
• Acquired immunodeficiency syndrome
• Anaphylaxis 
• Allergic bronchial asthma  
• Allergic rhinitis
• Allergic conjunctivitis
• Food allergy
• Atopic eczema 
• Drug allergy 
• Immune thrombocytopenia 
• Autoimmune hemolytic anemia  
• Autoimmune neutropenia 
• Systemic lupus erythematosus  
• Rheumatoid arthritis 
• Autoimmune hepatitis  
• Hemolytic disease of the fetus and the newborn (erythroblastosis fetalis) 
• Myasthenia gravis 
• Goodpasture syndrome 
• Pemphigus 
• Tuberculosis 
• Contact dermatitis 
• Leprosy 
• Insulin-dependent diabetes mellitus 
• Schistosomiasis 
• Sarcoidosis 
• Crohn disease
• Autoimmune lymphoproliferative syndrome
• X-linked lymphoproliferative disorder
• Common variable immunodeficiency
• B-cell chronic lymphocytic leukemia
• B-cell prolymphocytic leukemia
• Non-Hodgkin lymphoma (including mantle cell lymphoma) in leukemic phase
• Hairy cell leukemia
• Multiple myeloma
• Splenic lymphoma with villous lymphocytes
• Sezary syndrome
• T-cell prolymphocytic leukemia
• Adult T-cell leukemia-lymphoma
• Large granulated lymphocyte leukemia
• Leukocyte adhesion deficiency syndrome      
• Chronic active hepatitis
• Coccidioidomycosis
• Behcet disease
• Aphthous stomatitis
• Familial keratoacanthoma
• Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy   
• Idiopathic CD4+ lymphocytopenia
• Complement system deficiencies
• ADA-SCID  
• Artemis SCID
• Newly diagnosed non-germinal center B-cell subtype of diffuse large B-cell lymphoma
• Melanoma
• Chagas disease

Highly specific and discriminatory immunity is of utmost importance for survival. The immune system has evolved as a collection of protective mechanisms to defend the host against a long list of potential invaders that would take advantage in immunodeficiency disorders, inflammatory diseases, cancers, and autoimmunity. This system has to be sophisticated enough to recognize "self" from "non-self" and provide help in infections, malignant tumors, organ transplantations, and various other situations the immune system encounters.