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Please, checkout the uploaded file below, where you will find information and instructions. biod_171___module_5_questions..docx Unformatted Attachment Preview BIOD 171 - Essential Microbiology w/Lab Module 5 - Page 1 Assessing Unknown Pathogens Note: The following module will contain images of the various stages of disease brought about by several pathogenic microbes. Viewer discretion is advised. Assessing Unknown Pathogens When an unknown biological sample arrives in the lab for assessment and further characterization, universal precautions must be taken. As defined in an earlier module, the practice of universal precautions means any and all samples, whether known or unknown, are to be treated as potentially hazardous (or pathogenic) materials. Thus, the appropriate personal protective equipment (PPE) should always be used. When assessing an unknown sample, several basic yet essential observations can be made in addition to the differential techniques described in Module 4. During the process of analyzing a microbial sample, a lab researcher would be certain to note (1) the morphological characteristics (size and shape), (2) the presence of any observable motility when viewed under a microscope and (3) if possible, capture images of any of the characteristics described above or at the very least manually draw the aforementioned observations. Once differential testing has concluded, one should also document (4) whether or not the organism was Gram-positive or Gram-negative, (5) the presence of any chemical reactions such as gas production (bubbling), fermentation, etc. and finally (6) any distinct changes in color localized to the organism itself or its surrounding media (e.g.) staph aureus on MSA agar. Properly documenting these observations significantly aids trained professionals to identify the causative agent and select the appropriate treatments against a foreign microbe. In the sections below we will discuss in greater detail the diseases caused by and the pathogenic effects of various microbes, starting with the wellknown bacteria streptococcus and staphylococcus. Please watch this 1st video below as you study the material in this module. https://onedrive.live.com/?authkey=\%21AAy7Gs1xcloYa3o&cid=3DAF964F40D5BF4A&id=3DAF964 F40D5BF4A\%21114&parId=3DAF964F40D5BF4A\%21103&o=OneUp Page 2 Please watch this 2nd video below as you study the material in this module. https://onedrive.live.com/?authkey=\%21ACC0nyr2QZpHlVY&cid=3DAF964F40D5BF4A&id=3DAF96 4F40D5BF4A\%21115&parId=3DAF964F40D5BF4A\%21103&o=OneUp Streptococcus Streptococcus is a Gram positive, round bacteria that tend to link together in chain-like structures. Strep is catalase negative, meaning it cannot breakdown peroxides and is often cultured on blood agar plates (BAP). As there are numerous subtypes of streptococcus, culturing on BAP is perhaps the quickest way to identify and classify a potential streptococcus microbe based on its hemolytic properties. Note: As a reminder, Streptococcus, when grown on blood agar, can be alpha, beta or gammahemolytic. Alpha-hemolysis presents as a greenish-brown discoloration surrounding the bacterial colony, the result of the partial decomposition of hemoglobin found within blood cells. Alpha hemolysis is characteristic of Streptococcus pneumonia and so can be used as a diagnostic feature in the identification of the bacterial strain. Beta-hemolysis is classified as the capacity of a microbe to completely lyse red blood cells. The resulting lysis presents as a distinct zone of clearing around the growing colony. Beta-hemolysis is characteristic of Streptococcus pyogenes and some strains of Staphylococcus aureus. Gamma-hemolysis designates the absence or lack of hemolytic activity and the resulting colonies are often white/tan in color growing on the red background color of the unaffected blood agar plate. Gamma hemolysis is a characteristic of Enterococcus faecalis. Beta-hemolytic Streptococcus can be divided into antigenic groups known as Lancefield groupings. While all bacteria within this system are catalase-negative and coagulase-negative, the distinction lies in the carbohydrate composition of bacterial antigens located in the cell wall. Grouped based on similarities, each grouping is designated by a single letter (i.e.) Group A, Group B, Group C, etc. Notably, Streptococcus pyogenes, which belongs to Group A, is the causative agent behind >90\% of human streptococcal infections resulting in pharyngitis, scarlet fever or rheumatic fever. As such, the genus Streptococcus contains numerous disease-causing species and some of the most common are described below. Streptococcal pharyngitis (strep throat) is a Group A disease characterized by fever, enlargement of lymph nodes in the neck and a reddening within the lining of the throat surface tissue causing soreness and discomfort. Step throat can also lead to additional complications within the ear, lung or sinus cavities. If left untreated, strep throat can progress to rheumatic fever. Figure 5.1. Streptococcus. (A) Staining of a step + sample, notice the characteristic formation of chains of cocci. (B) Patient presents with swelling within the throat, red patches at the site of inflammation and is associated with soreness and discomfort. Rheumatic fever occurs in approximately 3\% of untreated cases of streptococcal pharyngitis, presenting approximately 2-3 weeks post-infection. Rheumatic fever presents with an inflammation of the joints, involuntary jerking movements, the development of pea-sized nodules beneath the skin, and reddened areas with raised edges over the surface of the skin. The most serious development is the damage to heart valves as the bacteria targets this organ. Treatment with penicillin is essential to combat this infection, but treatment must occur promptly at the onset of symptoms. Inflammation of the heart tissues occurs due to the similarities between antigens found within heart tissue and those belonging to Streptococcus. As such, antibodies meant to destroy the microbe have the potential to (undesirably) cross-react with the heart tissue, causing further inflammation and damage. Streptococcal septicemia (blood poisoning) is caused by a Group B streptococcus infection of the blood but can also secondarily infect other surrounding tissues. In actuality, the host response (fever, increased heart rate, etc) to the infectious foreign agent and not just the foreign microbe alone can be equally damaging to the body. Septicemia is a serious, life-threatening infection that worsens quickly due to its systemic nature. It can arise from infections in the lungs, abdomen, or urinary tract and may precede or accompany meningitis or endocarditis. Septicemia often presents with fever, chills, rapid breathing and an increased heart rate. Symptoms rapidly progress to shock (with fever or hypothermia) and a decrease in blood pressure. Treatment often involves antibiotics, IV fluids and oxygen. It should also be noted that septicemia is not limited to just Streptococcus but can also be caused by other foreign microbes including species of E. coli, Pseudomonas and Klebsiella. Page 3 Staphylococcus Staphylococcus is a Gram positive, round bacteria that tend to form grape-like clusters. Staph is both catalase and coagulase-positive and is a facultative anaerobe meaning it is capable of growth both aerobically and anaerobically. Staphylococcus can be differentially screened, as all species are capable of growth in the presence of bile salts. Under most circumstances, staphylococcus can be found in ~30\% of the human population where it remains non-symptomatic. Staphylococcus is considered a commensal bacterium, meaning it neither harms nor benefits the host from which it obtains nutrients. However, under the correct circumstances (compromised immunity being the most common) the population of the colonized staphylococcus can rapidly expand and cause severe illnesses. Staphylococcus is the causative agent of the following diseases: Folliculitis (Staph aureus) affects the hair follicles causing the formation of lesions called pustules. However, the lesions are not restricted solely to hair follicles. Larger pus-filled skin lesions (boils and carbuncles) can also develop anywhere on the surface of the skin (Figure 5.2). Figure 5.2. Staphylococcus. (A) Gram-staining shows clusters of positive cocci. (B) Folliculitis localized to the upper regions of the trunk and shoulder, which, if left untreated, can also spread systemically to regions such as the torso shown in (C). Scalded skin syndrome (Staph aureus) is most often seen in young children and infants due to an infection by Staph aureus. The infection causes pustules to rupture yielding a ‘scalded’ appearance due to the peeling of the skin. Staph infections can be successfully treated with Penicillin or erythromycin antibiotics. Impetigo (Staph aureus) is a contagious childhood skin disease and presents as fluid-filled red sores near the mouth and/or nose. When ruptured, scratched or rubbed the infection can be spread to other parts of the body or to anyone who comes into direct contact with the fluid. The sores may cause mild discomfort and are often itchy. Impetigo can be successfully treated with Penicillin antibiotics (Figure 5.3). Figure 5.3. Impetigo. (A) The hallmark red sores of impetigo localized to the nose. If the fluid-filled sores are opened (scratched) the infection can then spread to other parts of the body, such as the forearm (B). Please watch this 3rd video below as you study the material in this module. https://onedrive.live.com/?authkey=\%21AHk6n\%2D83tWTU9PQ&cid=3DAF964F40D5BF4A&id=3D AF964F40D5BF4A\%21116&parId=3DAF964F40D5BF4A\%21103&o=OneUp Conjunctivitis is an infection of the conjunctiva, the thin transparent layer of tissue that covers the white part of the eye (sclera) as well as the inner surface of the eyelid. Commonly referred to as ‘pink eye,’ conjunctivitis can actually be caused by either a bacterial or viral infection. While Staphylococcus is the most common causative agent, infection by streptococcus bacteria will yield similar results. Viral conjunctivitis is most often associated with signs and symptoms of the common cold virus: upper respiratory infection, sore throat, cough, etc. In either case, symptoms include the trademark red/pink color in either one or both eyes often associated with a painful, burning or itching sensation. Those infected may find their eyelids are ‘stuck shut’ in the morning due to an increase in tear production. The best precaution against conjunctivitis is proper and consistent hand washing, as the infection is most often established by rubbing your eyes with contaminated hands. Pink eye is common in children and can be rapidly spread if proper precautions are not taken. While conjunctivitis is usually a minor eye infection, sometimes it can develop into a more serious problem (Figure 5.4). Ophthalmia Neonatorum is a severe form of bacterial conjunctivitis that occurs in newborn babies that could lead to permanent eye damage unless it is treated immediately. Ophthalmia neonatorum occurs when an infant is exposed to Chlamydia or gonorrhea bacterium while passing through the birth canal. For this reason, an antibiotic ointment containing Neomycin is often applied to newborns eyes to prevent potential infections and permanent eye damage. Figure 5.4. Conjunctivitis. Bacterial conjunctivitis (staph infection) displays the hallmark reddening of the sclera, inflamed linings of the eyelid and tear ducts. Discoloration and even yellowing fluid may be present. Page 4 Mycobacterium Please watch this 4th video below as you study the material in this module. https://onedrive.live.com/?authkey=\%21AJe545d\%5FtQcC5Ms&cid=3DAF964F40D5BF4A&id=3DA F964F40D5BF4A\%21117&parId=3DAF964F40D5BF4A\%21103&o=OneUp Tuberculosis (also known simply as ‘TB’) Mycobacterium tuberculosis is a small, aerobic, non-motile, rod-shaped bacterium. As discussed in previous modules, TB shows a poor Gram stain (weakly positive at best) phenotype and is best visualized via an acid-fast stain. TB is spread from person to person through the air via mucosal emissions, (i.e.) cough, sneeze, spit, etc., and must be inhaled in order to be infectious. People most effectively spread TB when residing in close quarters to one another. Important to note, as per the Center for Disease Control guidelines, simply shaking someone’s hand, sharing a drink or even kissing cannot spread TB. The bacterium must be inhaled. While TB is primarily considered a respiratory infection, once it fully colonizes the lungs, TB can move through the blood to other areas including the brain, spine and kidneys. However, when located outside of the lung, TB tends to be non-infectious. If infected, a patient will usually exhibit the following primary symptoms: a bad cough for > 3 weeks, pain located in the chest, coughing up blood or heavy sputum (mucus). Secondary symptoms include weakness, fatigue, weight loss, and fever/chills. Exposure to TB can be tested either by a skin test, where a small fluid sample of tuberculin—a purified protein extract of tubercle bacillus—is placed under the skin of your arm or via a direct blood test. If previously exposed to TB, the skin test will reveal a raised, red bump at the site of injection. This indicates the body already has some level of immunity (antibodies) against the TB bacteria and additional tests will need to be performed in order to determine the level of disease progression. Current treatment strategies include a combination of the drugs isoniazid (INH), rifampin (RIF), ethambutol (EMB) and pyrazinamide (PZA). Treatment can last 6 to 9 months and it is imperative patients take the medications precisely as prescribed. If meds are stopped too soon, the levels of TB bacteria may re-emerge in the patient. If the meds are taken inconsistently or improperly, the surviving TB bacteria may develop drug resistance. Leprosy (also known as Hansen’s disease) is caused by Mycobacterium leprae, a small rodshaped, acid-fast bacterium. Infections usually remain asymptomatic and can remain this way for 3 or even up to 20 years. Similar to TB, leprosy is spread from person to person via airborne fluid droplets from the nose and/or mouth but is surprisingly not as infectious. Leprosy mainly affects the skin, nerves, upper respiratory tract and eyes of infected individuals (Figure 5.5). Left untreated, severe nerve damage commonly results in further physical injuries due to the lack of sensation and feedback signals. Leprosy is completely curable using a multiple-drug therapy regimen consisting of various combinations of the drugs dapsone, rifampin and clofazimine. Amazingly, all drug treatments for leprosy are provided free of charge by the World Health Organization (WHO). Figure 5.5. Leprosy. (A) Acid-fast staining of the pathogen Mycobacterium leprae (red). (B) Skin lesions found on the upper thigh of an infected individual. (C) In rare cases where leprosy goes untreated, the ski lesion can spread, covering the face and even the ears. Page 5 Clostridium Please watch this 5th video below as you study the material in this module. https://onedrive.live.com/?authkey=\%21AN9u05TfVcAgkL8&cid=3DAF964F40D5BF4A&id=3DAF96 4F40D5BF4A\%21118&parId=3DAF964F40D5BF4A\%21103&o=OneUp Botulism is caused by Clostridium botulinum, a Gram-positive, anaerobic, spore forming, bacillus bacterium. When exposed to anaerobic conditions C. botulinum releases a paralytic toxin that affects motor neurons. As such, botulism is a serious illness and medical treatment should be sought out immediately. Although the bacteria/spores can be found in the soil and water, they remain harmless until anaerobic conditions become available and the bacteria become metabolically active. Three main conditions are often the cause of toxin production. First, foodborne botulism is often the result of improperly canned, contaminated, low-acidic foods such as green beans, corn and beets. Within this low-oxygen environment the production of the botulin toxin is stimulated, and if later eaten can cause severe illness. When consumed, muscle weakness or even paralysis is observed. Second, infant botulism occurs when children, usually under the age of 6 months consume foods containing the bacteria. A potential source of infant botulism is honey (which is why pediatricians recommend avoiding feeding honey to infants) but can also be found in common places such as soil. Due to infants still maturing intestinal tract and lack of an adult microbiota, the bacteria are able to colonize and produce the associated toxin. In adults, only the direct ingestion of the pre-formed toxin causes disease—ingestion of C. botulinum or the associated spores do not cause illness as a mature intestinal microbiota sufficiently prevents bacterial germination and growth. Third, wound botulism occurs when C. botulinum bacteria colonize a deep wound (Figure 5.6). Potential contaminations may occur in deep puncture wounds (especially if in an open, dirty environment) but are most often observed in individuals who inject street drugs such as heroin. As contaminated needles are injected through the skin, spores enter the body and, in the absence of oxygen, release the toxin. Note: Although botulism can cause severe, life-threatening illnesses, researchers have also found a way to harness the paralytic effects of the botulin toxin in the form of Botox. Although most commonly used cosmetically to prevent wrinkles (the paralytic toxin prevents the skin from moving and wrinkling) certified physicians are also able to inject small doses of the toxin in precise areas to prevent cranial muscle spasms in patients with severe migraine headaches. Figure 5.6. Botulism. (A) Gram-positive staining of the bacillus C. botulinum. (B and C) A puncture wound in the arm of a 14 yr. old male patient resulting in wound botulism. Although fully wake, the paralytic effects of the microbe cause ‘sleepy eyes.’ Additionally, his pupils are fixed and dilated despite being exposed to bright light. Tetanus is caused by Clostridium tetani, a Gram-positive, anaerobic, spore forming, bacillus bacterium often found in soil, dust and animal feces. Similar to C. botulinum, it is the tetanospasmin toxin produced by C. tetani (also under anaerobic conditions) that causes illness, not the bacteria itself. The toxin acts on inhibitory neurons causing systemic muscle stiffness and spasms, most often seen initially in the masseter muscle of the jaw. For this reason, tetanus was also known by its pseudo name: ‘lockjaw’. Left untreated, the toxin-induced muscle tightening can lead to respiratory failure as the muscles associated with breathing no longer function properly. Currently, there is no cure for tetanus. Instead, medical intervention depends on managing the complications associated until the effects of the toxin resolve. However, tetanus is entirely preventable through vaccination. As reported by the World Health Organization (WHO), nearly all cases of tetanus occur in unvaccinated individuals or in those who have not received a booster vaccination every 10 years. Gas gangrene is caused by Clostridium perfringens, a Gram-positive, anaerobic, spore forming, bacillus bacterium that can be found nearly anywhere in nature. Similar to botulism and tetanus, C. perfringes produces an alpha-toxin, perfringolysin, under anaerobic conditions most often established from deep puncture wounds. As the naming suggests, perfringolysin acts by forming pores in the plasma membrane of host cells (effectively perforating the membrane) resulting in uncontrolled ion fluxes and eventually cell lysis and death. Perfringolysin induced toxicity is characterized by muscle necrosis, swelling of infected areas, fever and intense gas production—the byproduct of robust carbohydrate fermentation under anaerobic conditions. Gas production leads to further cell damage (necrosis) and in turn further invasion of the pathogenic bacteria. Treatment enta ... Purchase answer to see full attachment