Molecular Pa Tho Genesis

Molecular Pathogenesis The MP program is perhaps the broadest of the research programs in the Skirball Institute. It includes a large proportion of NYU's Immunology community, which has a rich tradition, and its members have taken the lead in establishing a new graduate program in immunology and host defense mechanisms. The MP program's immunology laboratories study diverse problems in the areas of lymphocyte signal transduction, immunological synapse formation, leukocyte trafficking, VDJ recombination, and innate immune responses. Immunologists in the MP program also study medically relevant problems such as the mechanisms of HIV pathogenesis, allergic disease, autoimmunity, and lymphomagenesis. Other MP laboratories are investigating telomere maintenance, protein misfolding, bacterial virulence, and genomic instability while striving to understand human afflictions as diverse as diabetes, cholesterol toxicity, cancer, and aging. Close collaborations of the laboratories in the MP program with groups in the other Skirball research programs have been instrumental in studying the genetic basis of the unfolded protein response, the role of lipid phosphatases in vesicular traffic, and the roles of chemokine receptors in morphogenesis of different organ systems. Members of the MP program have appointments in NYU School of Medicine departments of Cell Biology, Medicine, Microbiology, Pathology and Pharmacology. The term pathogenesis means step by step development of a disease and the chain of events leading to that disease due to a series of changes in the structure and /or function of a cell/tissue/organ being caused by a microbial, chemical or physical agent. The pathogenesis of a disease is the mechanism by which an etiological factor causes the disease. The term can also be used to describe the development of the disease, such as acute, chronic and recurrent. The word comes from the Greek pathos, "disease", and genesis, "creation". Types of pathogenesis include microbial infection, inflammation, malignancy and tissue breakdown. Most diseases are caused by multiple pathogenetical processes together. For example, certain cancers arise from dysfunction of the immune system (skin tumors and lymphoma after a renal transplant, which requires immunosuppression). Often, a potential etiology is identified by epidemiological observations before a pathological link can be drawn between the cause and the disease.

In medicine, disease pathogenesis is a term used to refer to the origin and development of a disease. The study of disease pathogenesispathogenesispathogenesis, which is more often referred to simply as pathogenesispathogenesispathogenesis, forms a sub-branch of the wider fields of pathobiology and pathology. While pathobiology and pathology refer to the general biology, development, and progress of a disease, pathogenesispathogenesispathogenesis usually focuses on the factors that lead to the initial origin of the disease. Pathogenesis is the development of disease, from the initial appearance of disease all the way to its end stages. The study of pathogenesis is important for medical professionals, as it helps them identify and treat diseases. It is also part of the work of laboratory sciences who work on cures and treatments for diseases, as each stage of pathogenesis represents a potential possibility for interrupting the progression of the disease. The term “pathogenesis” comes from the Greek words for “disease” and “beginning.” The origins of disease are the first step in pathogenesis, as are the progressive changes which occur in the body as the disease takes hold and begins to act on the body. For example, when someone is cut and the wound is colonized by Staphylococcus bacteria, the bacteria cause inflammation as they start to spread, ultimately leading to infection. Each step from cut to full-blown infection is part of pathogenesis. There are a number of uses for the study of pathogenesis. In the case of individual patients, it allows to a doctor to determine what caused a disease, and how the disease can be treated. Being able to identify the stage which a disease has reached can also be important for a doctor providing medical treatment, as in the case of an oncologist who wants to determine the level of severity of a cancer. Studying pathogenesis can also provide insight to the ways in which diseases spread, and potentially contribute to the development of a program which is designed to slow the spread of disease. In the example of an infected cut above, for example, the infection might have been prevented by regular cleansing of the wound with an antibacterial soap, a procedure which is widely used in homes and hospitals all over the world to reduce the risk of infection. Pathogenesis is also a critical part of the study of new and emerging diseases, as these diseases cannot be effectively fought without understanding where they come from. In the case of many diseases, multiple factors affect the disease pathogenesis. For example, an individual may have a genetic predisposition to a disease, but the disease may not actually occur unless certain environmental factors are also present. Similarly, some kinds of infectious disease are often fought off by an infected individual without any symptoms ever appearing. Such infections might cause disease, for example, only if the bacteria or virus that causes it are present, and at the same time the immunity of the infected person is weakened by malnutrition or a disorder of the immune system. There are many different types of disease pathogenesis. These include invasion of the body by viruses or bacteria, inflammation as a response to chemicals, physical trauma,

the presence of cancerous cells, and many different kinds of genetic disorders. As there are so many possible origins of disease, doctors and researchers who study disease pathogenesis often specialize in one particular field of pathogenesis. Some specialist fields of pathogenesis include hematopathology, clinical microbiology, genetics, and immunopathology. Hematopathology relates to abnormalities of the blood, the bone marrow, and the lymphatic system, and how such abnormalities may lead to disease. In clinical microbiology, the study of pathogenesis includes examining how bacteria and viruses spread and multiply. Genetics has a very important bearing on pathogenesis, as a great number of diseases originate partly, or wholly, as a result of a particular gene, a mutation, or an abnormality in the genetic material of the patient. Immunopathology is of particular importance in the disease pathogenesis of infectious diseases, as it relates to the immune system, including how immunity weaknesses may allow a virus or bacterium to take hold and cause a disease.

Microbial Pathogenesis Definitions: Disease is: 'any deviation from or interruption of the the normal structure and/or function of any part of the body'. A pathogen is: 'a disease causing organism'. Opportunistic pathogens: e.g. Escherichia coli is a normal, 'non-pathogenic' commensal organism in the human gut, but infection of the bladder can result in ascending infection of the ureters & eventually, the kidneys, resulting in renal failure. Most strains of E.coli are inefficient in establishing such infections, but some strains express particular adherence factors which allow them to ascend the ureter & reach the kidney. Obligate pathogens display the most extreme adaptation to their host organisms. What does a pathogen have to do? • • •

Infect (infest) a host Reproduce (replicate) itself Ensure that its progeny are transmitted to another host

Mechanisms of Transmission: • • • •

Aerosols - inhalation of droplets, e.g. Rhinoviruses, the 'Common Cold Virus' or Adenoviruses. Faecal-Oral - e.g. Astroviruses, Caliciviruses; these viruses cause acute gastroenteritis. Vector-borne - e.g. in Arthropods such as mosquitos, ticks, fleas: Arboviruses. Close personal contact - especially exchange of bodily fluids: Sex; Blood, e.g. Herpesviruses.

Sites of virus entry:

Transmission patterns: • •

Horizontal Transmission: Direct person-to-person spread. Vertical Transmission: Relies on PERSISTENCE of the agent to transfer infection from parents to offspring. Several forms of vertical transmission can be distinguished:

Neonatal infection at birth, Infection in utero e.g. syphilis, Germ line infection - via ovum or sperm.

e.g. CMV,

gonorrhorea, Rubella (CRS),

AIDS. AIDS.

The eventual outcome of any virus infection depends on a balance between two processes: PERSISTENCE of the agent vs. CLEARANCE from the host Host Responses Mammals have a variety of defences against infection. Non-specific mechanisms: • • •

Skin Enzymes Fever

Specific mechanisms - the immune response: • • •

Mucosal Immunity Humoral Immunity Cell Mediated Immunity

Bacterial Pathogenesis Aims and Objectives To describe the complex interaction between bacteria and the human host, including the modes of transmission, progression and outcome of infection. After reading this document, you should: 1. Be able to define the terms infection, pathogen, commensal, symbiosis, parasitism, saprophytism, opportunistic infection and nosocomial infection. 2. Be familiar with Koch's postulates and their relevance to bacterial pathogenesis. 3. Be familiar with the transmission cycle, stages of progression and possible outcomes of bacterial infection. 4. Be familiar with the spectrum of virulence mechanisms employed by microorganisms. In examining the mechanisms that bacteria use to cause infections, it is worth pointing out one fact right at the start - it is the fundamental object of both humans and bacteria to survive and prosper! Whilst some bacteria seem to do very well by causing a succession of infections, passing from one susceptible human host to another, the majority of bacteria that we come into contact with exist in a state of equilibrium, either living on us or in us quite peacefully. For this second group, it is only when this happy balance is disturbed for some reason that infection may result. Clearly there are two very important elements that control the interaction between bacteria and humans - the defences, or immunity, employed by the human host and the virulence factors exhibited by the bacteria that enable them to produce infection. We will be concentrating on just one side of the picture in this section, namely the properties of the bacteria, but before doing that we should define a few relevant terms. Infection: This is when an organism enters the body, increases in number and causes damage to the host in the process. A pathogen: This is an organism that is able to evade the various normal defences of the human host to cause infection. Commensalism: Literally `eating at the same table'! This refers to a neutral situation where the host and bacteria live together, but have no effect on each other's life cycle either positive or negative. Some authors broaden the definition to allow benefit to occur to one group through the association, providing no damage is caused to the other. Overall, this is just about the best way to describe the relationship that humans have with most of the normal bacterial flora of the skin and mucus membranes, including the upper respiratory tract, the lower gastrointestinal tract and the vagina. These bacteria are often described as non-pathogenic or commensal.

Symbiosis: This describes a situation where species live together for their mutual benefit, with each receiving a valuable contribution from the other. There is an element of symbiosis in the relationship between the human host and the gut flora; humans provide the bacteria with a warm, moist, protected environment and, in return, the gut flora uses up all the available nutrients and so makes it difficult for more pathogenic species to become established and initiate infection. Parasitism: This describes an unequal relationship where one organism clearly benefits from an association to the detriment of another. To some extent this happens in all infections, but the word is often reserved for situations where the invading pathogen has quite clearly hijacked host processes for its own benefit, such as in viral infections. Saprophytism: This refers to the situation where one organism lives on the dead tissues of another. Fungi often display this ability. Opportunistic infection: This occurs when the normal human defences are so weakened that it allows infection to take place by organisms that would not generally be able to cause infection in a healthy human. Examples of these include the many infections that are seen in AIDS patients, including Pneumocystis carinii pneumonia, Toxoplasma gondii brain abscesses and systemic infections with Candida sp. and atypical Mycobacterium sp. Nosocomial infection: These are infections that are transmitted in hospitals. Some of these may be opportunistic infections mentioned above affecting seriously ill patients, others, for example infections with Methicillin-Resistant Staphylococcus aureus (MRSA), may occur because of the special nature of the hospital environment. Stages of Infection: The time between the exposure to an agent and the first appearance of clinical symptoms is called the incubation period and, although there are no symptoms, the organism may be causing substantial damage during this interval. There may follow a period known as the prodrome, where non-specific signs and symptoms such as headache, fever and lethargy are noted, before the development of a specific symptom complex suggestive of a classical infectious disease such as pneumonia, meningitis or diarrhoea. Once the acute stage has passed, a period of resolution occurs, where the severity of the symptoms gradually decreases, and finally convalescence where the symptoms have largely gone, but the body is still recovering. The time course and severity of the disease depends upon the balance between the virulence of the infecting agent and the success with which the immune system combats the organism. Some infections may occur which are not sufficiently severe to produce clinical symptoms and these are called asymptomatic or subclinical infections. Clinical infection has a number of outcomes covering the spectrum between death and complete recovery. The term chronic infection is self-explanatory, but carriage is a term that has been used rather loosely. In bacteriology, it is often used to describe the situation where a person continues to harbour a pathogenic organism but suffer no ill-effects themselves, examples being Salmonella typhi in the gut and Corynebacterium diphtheriae in the

respiratory tract, but in virology the persistent virus may be associated with low level damage, an example being hepatitis B infection. Latency refers to a situation where an agent persists in a dormant, inactive form without causing damage, but which may reactivate to cause problems at a later date; an example is herpes simplex virus which lies dormant within dorsal root ganglia after the primary infection, but may periodically reactivate to cause cold sores. Studies of Bacterial Pathogenesis: Some of the earliest and most influential work in this area was performed by the German microbiologist, Robert Koch, in the late nineteenth century. In identifying the bacteria responsible for diseases such as anthrax and tuberculosis, he described a number of requirements that must be satisfied before an organism can definitely be regarded as the cause of the disease. These conditions have become known as Koch's postulates and they can be summarised as follows: 1. The organism occurs in every case of the disease and under circumstances which account for the pathological changes and clinical course of the disease. 2. The organism occurs in no other disease as a fortuitous and non-pathogenic finding. 3. After being isolated from the body and grown in pure culture, the organism will repeatedly produce exactly the same clinical disease when inoculated into a new host. These ideas have formed the foundation for all our ideas about infectious diseases, although it is now becoming increasingly clear that they can no longer be applied in all situations. For example, they do not take account of advances in serological diagnosis nor the recent developments in molecular biology looking at agents that cannot be cultured in the laboratory. They also seem less appropriate when considering infections by commensal organisms in immunosuppressed patients, a group that has become much more important as a result of the advances in modern medical care. Our current medical ethics would prevent many of the human challenge studies that were carried out in the past and for many infections there is no acceptable animal model of infection. However, we should not forget that Koch's postulates have been an extremely valuable tool over the years because they have provided a firm scientific basis to studies of bacterial pathogenesis. This work has revealed a number of steps in the development of infection which are still very relevant to all of today's infections. Contact with the Host Transmission: Clearly the commensal flora is already in intimate contact with the host, but these organisms are of low pathogenicity and are usually held in check by the immune mechanisms described below. More pathogenic organisms, that are not normal parts of the commensal flora, have developed numerous strategies that allow them to move from a source or reservoir to the susceptible host in a viable state. The spores that are produced by some bacteria and fungi, and bacteria such as Mycobacterium tuberculosis, are very resistant to the effect of drying in the environment. Gram positive organisms such as Staphylococcus aureus seem to be very well adapted to surviving on

skin surfaces such as the hands and this is a very important route of transmission within hospitals. Gram negative organisms can be adept at surviving in fluids; contaminated water supplies are usually responsible for infection with Vibrio cholerae whilst major outbreaks of infection have occurred in hospitals due to contamination of fluids used in medicine by bacteria such as Klebsiella. Other bacteria, such as Salmonella and Shigella, thrive under conditions of poor hygiene and are transmitted by faecal-oral spread, whilst more fragile organisms, such as Neisseria gonorrhoeae, may require the most intimate contact of all. Protection of External Surfaces: The skin normally represents an impenetrable barrier to micro-organisms and mucosal surfaces, such as those of the respiratory tract and the gut, are protected by a number of factors including the secretion of mucus, powerful proteolytic enzymes, antibodies (particularly IgA) and the high turnover of surface cells. Injections, vascular lines, accidental trauma, surgery and conditions such as eczema, all breakdown the integrity of the skin and increase the chance of infection. Increased risks of infections are also seen when the mucosal defences are disturbed: this includes alterations in mucus distribution in long term smokers; production of specific IgA proteases by bacteria such as Haemophilus influenzae, Neisseria meningitidis and Streptococcus pneumoniae; and the loss of mucosal endothelial integrity as a side effect of modern cytotoxic therapy. Adherence: Many of the body surfaces are washed by fluids, including mucus in the upper respiratory tract and the gut, peristalsis of gut contents throughout the bowel and the movement of urine in the urinary tract. If a bacterium is to multiply and cause infection it must have some way of fixing its position and becoming established. This adherence is produced by bacterial adhesins or ligands that bind specifically to host molecules known as receptors. These adhesins can be proteins found on the bacterial cell wall / membrane or they can be collected together on structures that project from the cell surface, for example fimbriae and pili, which seem to be expressly aimed at increasing the chance of adherence. A huge number of bacterial adhesins and their associated host cell receptors have been described, but one of the most well-studied concerns the ability of certain strains of Escherichia coli to cause urinary tract infection. Studies of E. coli isolates have shown that only a relatively small number of types are found in urinary tract infections, although there are many more types to be found nearby colonising the human gut. The reason seems to be that strains that express the type 1 pilus can attach to the Tamm-Horsfall protein in the mucus of the lower urinary tract and this prevents them being flushed away by the flow of urine; if they do manage to ascend the urethra into the bladder, strains of E. coli that do not express this pilus cannot adhere and are immediately washed out. However, when the isolates from upper urinary tract infections are examined, a different pattern is seen. It appears that these E. coli strains that have swam up against the flow of urine in the ureters may change their cell surface such that they now express P pili that allows them to attach to the P blood group antigen that is found on the cells in the renal pelvis.

Bacteria may also secrete viscous substances onto their surface which increase adherence in a non-specific fashion. This would include alginate capsule production by Pseudomonas aeruginosa in the lungs of cystic fibrosis patients and the production of polysaccharide slime by Staphylococcus epidermidis when it colonises intravenous lines. Entry into Cells and Tissues: Certain agents take the attachment process a stage further by using adhesins as the first step towards promoting their uptake into the host cell. The entry of Listeria monocytogenes into phagocytic cells following its attachment to the complement receptor CR3 is one example of this amongst bacteria, but all viruses need to use this mechanism to produce infection. Human immunodeficiency virus (HIV) uses a protein on its surface called gp120 to target CD4-bearing T lymphocytes and initiate uptake, whilst influenza virus attaches and enters cells using a protein called haemagglutinin as the adhesin and neuraminic acid on the surface of respiratory epithelium as the receptor. Entry into cells may lead to an infection that is limited to that cell type, or it may be a first step towards wider dissemination of the infecting agent throughout the body. As an alternative to bypassing the epithelium through intracellular invasion, some bacteria penetrate this barrier by squeezing through the junctions between adjacent epithelial cells and so reach deeper tissues. Production of Disease: Once a bacterium has entered the body, there are a number of ways in which it can cause disease. It may produce damage to local tissues as well as damage to distant tissues through the action of bacterial toxins, although this distinction may not be clear cut as there is nothing to stop toxins from acting locally too. Bacteria must continue to evade the responses of the immune system and, although it will not be discussed here, it is important to remember that an excessive immune response may itself produce a great deal of damage and be responsible for many of the symptoms of disease. Local Effects: Certain bacteria cause diffuse infections by producing enzymes that enable them to breakdown the cells and intracellular matrices of host tissues. Streptococcus produce the enzyme hyaluronidase which hydrolyses hyaluronic acid, a polysaccharide component responsible for binding cells together. Clostridium produce a similar enzyme called collagenase and many bacteria produce different kinases, lecithinases and proteases with varying effects upon host tissues. On the other hand, some bacteria produce more localised infections with the production of pus in the affected tissues; bacteria that do this are described as pyogenic. Staphylococcus aureus produces an enzyme coagulase which coagulates fribrinogen and abscesses are particularly likely to develop where infections involving Bacteroides fragilis take place. Distant Effects: There are over 220 known bacterial toxins and they can be divided up into two groups. Endotoxin is a component of the cell wall of all gram negative bacteria whilst the exotoxins include a huge number of proteins that are secreted from the bacterial cell and which are mostly, but not exclusively, produced by gram positive bacteria. Endotoxin is the lipid portion of lipopolysaccharide, lipid A, and is a potent inducer of interleukin-1 (IL-1) from macrophages, which resets the hypothalamus to

produce fever, and tumour necrosis factor (TNF) from phagocytes, which induces severe shock. The toxin is effective when it is present within the cell walls of living bacteria, but its greatest effect is usually seen when bacteria are killed, lysed and their products released into the systemic circulation. Exotoxins are often divided up into three main groups, although not every toxin falls neatly into these categories. Cytotoxins destroy host cells and an example of this is the alpha-toxin of Clostridium perfringens. Neurotoxins interfere with neural transmission, famous examples being the toxins of Clostridium tetani and Clostridium botulinum. Enterotoxins affect the cells lining the gastrointestinal tract, and the enterotoxins of Staphylococcus aureus and many of the toxins produced by Escherichia coli are examples of this. Evasion of Host Defences: The host tissue is a hostile environment for bacteria and they need to develop strategies for maintaining their nutrition. The acquisition of iron is particularly important, as its availability is tightly controlled by the host. Most pathogenic organisms have developed a number of secretory proteins, called siderophores, which can steal iron from host carrier-proteins and so make it available to bacteria. Some bacteria, such as Streptococcus pneumoniae, Haemophilus influenzae and Klebsiella pneumoniae, and the fungus Cryptococcus neoformans produce a glycocalyx capsule that inhibits phagocytosis. Mycobacterium tuberculosis accomplishes this by the insertion of waxes into its cell wall and Streptococcus pyogenes has the M protein in its cell wall to decrease phagocytosis. Staphylococcus and Streptococcus use leukocidins to destroy leukocytes and macrophages and haemolysins to disrupt erythrocytes. The parasite Trypanosoma undergoes rapid antigenic variation to evade the host's immune response and some viruses, such as human immunodeficiency virus, actually infect the cells of the immune system themselves. Choosing a New Victim :The final stage in the infection cycle is for the agent to find a new host to infect which usually ties in with how the present host first acquired the disease. Thus bacteria that cause sexually transmitted diseases, such as Chlamydia trachomatis and Neisseria gonorrhoeae, will tend to multiply and produce a discharge from the urethra or endocervix and so maximise their chances of being passed on to the next sexual contact. Bacteria that are spread by the faecal-oral route, such as Salmonella and Shigella, tend to multiply within the gut and produce diarrhoea, which challenges an individual's hygiene and increases their chance of transmission. The many agents that use the respiratory route for infection tend to produce symptoms such as nasal discharge, coughing and sneezing which enhances the production of aerosols and therefore the potential for transfer to new hosts.