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Sunday, November 27, 2016

Clinical Microbiology HW#14



Chapter 24
1. The patient is suffocating because of an inflamed epiglottis. What is the etiology of the symptoms?
Haemophilus

2. The patient has a sore throat. What is the etiology of the symptoms?
The answer cannot be determined based on the information provided

3. It is common for a normal, healthy individual to carry potentially pathogenic organisms in their upper respiratory tract.
TRUE

4. Which of the following diseases has a cutaneous form, especially in individuals over 30 years of age?
Diphtheria

5. The patient is suffocating because of the accumulation of dead tissue and fibrin in her throat. What is the etiology of the symptoms?
Corynebacterium

6. A patient has a paroxysmal cough and mucus accumulation. What is the etiology of the symptoms?
Bordetella

7. All of the following are true of the common cold EXCEPT
early treatment will drastically reduce the disease symptoms

Concept Map: Tuberculosis
1. Tuberculosis is the name of the ___________ caused by the _________ Mycobacterium tuberculosis.
Disease; bacterium

2. What can you deduce from the treatment strategy for M. tuberculosis infection?
The organism has some innate resistance to antibiotics.
**It is rare that you have to treat an infection with multiple antibiotics for such a long period of time.

3. Which of the following could be true of tuberculosis of the kidney?
All of the above could be true
**TRUE:
The disease could be subsequent to a normal primary infection.
The disease could be subsequent to a reactivated latent infection.
The patient would likely be infected with MDR TB or XDR TB.
The patient would likely have a positive skin test.

Chapter 24
1. Which of the following is mismatched?
Mycoplasma – gram-positive pleomorphic rod

2. Which of the following statements regarding tuberculosis is FALSE?
Nearly 1/3 of the worlds population shows symptoms of tuberculosis

3. A patient has fever, difficulty breathing, chest pains, fluid in the alveoli, and a positive tuberculin skin test. Gram-positive cocci are isolated from the sputum. The patient most likely has
pneumococcal pneumonia

4. Which one of the following produces small "fried-egg" colonies on medium containing horse serum and yeast extract?
Mycoplasma

5. The most common causative agent of bacterial pneumonia is Streptococcus pneumoniae.
TRUE

6. A positive tuberculosis skin test indicates that the patient has active tuberculosis.
FALSE

7. The primary victims of the influenza pandemic of 1918-1919 were
young adults

8. Vaccination with the influenza vaccine confers lifelong immunity to influenza virus.
FALSE

9. Microscopic examination of a lung biopsy shows thick-walled cysts. What is the etiology of the symptoms?
Pneumocystis

10. Which statement regarding influenza (flu) is true?
Antigenic shift can occur because the genome is in several pieces.

Diseases in Focus Chapter 24 – Male, age 78

MEDICAL HISTORY (Hx)
The patient is a male, age 78. He was admitted to the hospital for fever, chills, chest pain, and a productive cough. He lives in Houston, Texas, and is an aspiring author and retired investment banker. He spends much of his retired life golfing, or working on his novel. He is sexually active, and in a non-monogamous relationship. He and his partners are consistent with their use of birth control. He lives in a loft apartment by himself, and owns a dog. He is allergic to peanuts, but does not have any special concerns that would affect your ability to treat him. His family history does not suggest any factors associated with genetic disease. He smokes regularly (1 pack/day), and reports drinking alcohol (5+ drinks) 3 times a week, on average. He does not use drugs of abuse. Two weeks ago, he traveled to Seattle for two days to meet with his editors. Within the last five days he began to feel unusually tired with a persistent dry cough. As time passed, his cough worsened, and he developed a fever and chest pains. He also had several bouts of loose, watery diarrhea. Upon admission to the hospital, he seems clumsy and uncoordinated, with a fever of 40.8C.

Differential Diagnoses
Differential diagnosis is the process of identifying a disease from a list of possible diseases that fit the information derived from examining a patient. Your job will be to synthesize information from a patient whose main presenting symptoms are consistent with a microbial disease of the respiratory system. Use the "Diseases in Focus" 24.1, 24.2, and 24.3 tables and your knowledge about microbial diseases of the respiratory system to identify the patient's risk factors and symptoms, evaluate diagnostic evidence, formulate and test a diagnosis about the pathogen responsible for the patient's woes, and suggest a course of treatment.

1. Identify relevant information
Review the patient's medical history, and then identify risks and concerns that could be relevant to your diagnosis (and the patient's treatment).
Relevant:
Age-related risk of disease
Risk of sexually transmitted infection
Risk of vector-borne disease
Risk of travel-related disease exposure
Not Relevant:
Occupational risk of disease
Risk of drug-related disease exposure
Risk of genetic/familial disease
Special concerns for treatment
Risk of immunocompromised
**You have reviewed your patient's medical history, and you recognize several factors that could be relevant to your diagnostic process. His age, sexual habits, travel history, and pet dog all could increase his exposure to diseases, pathogens, or vector organisms.
Your first concern however, is that your patient's symptoms seem to include changes in his mental state. He is clumsy and uncoordinated, which could potentially signal a serious or life-threatening condition. He also has a high fever, a productive cough, and occasional diarrhea. These latter symptoms are general enough that they could apply to several different types of respiratory disease, but your patient's fever and possible cerebral involvement up the ante enough that you would like to begin treating him as soon as possible. You take a blood sample and a nasal swab from your patient, and order smear preps from the samples for Gram-staining and other diagnostics. While you wait for your results, you order a chest x-ray for your patient.

X-ray results
Your patient's x-ray is shown here. You observe bilateral (both sides of the body) basal (lower) pulmonary congestion, as well as pleural effusion, indicating excess fluid between the two pleural layers. These results are compatible with a diagnosis of pneumonia.
 
2. Interpret your results
Now that you have considered the evidence at hand, you should start to build a hypothesis about what disease your patient has. In the beginning of your diagnostic process you should try and think broadly to help you consider any and all reasonable possibilities. You can then narrow down these possibilities by performing diagnostics that can support or refute your hypothesis.
A form of bacterial pneumonia
Melioidosis
Viral pneumonia, RSV
Coccidioidomycosis
**You have narrowed down the diseases you suspect are responsible for your patient's condition to a form of bacterial or viral pneumonia, melioidosis, influenza, or coccidioidomycosis. Now you must wait for your initial diagnostics to return from the lab.

3. Interpret your results
After a day, you receive the following results:

What does this tell you?
Your patient's samples show the presence of a Gram-negative bacteria.
**Your initial results are positive for the presence of a Gram-negative bacterium. You believe your patient has a form of bacterial pneumonia!

4. Refine your hypothesis
Based upon these results, which of the following could your patient have?
Haemophilus influenzae pneumonia
Legionellosis
Melioidosis
**Your patient's Gram-stained sample does not show clear evidence for a Gram-positive pathogen, or for one with an obligate intracellular habit. Thus, you suspect your patient has Haemophilus influenzae pneumonia, legionellosis, or meliodosis.

5. Select a diagnostic
You would now like to try and culture your pathogen. Shown are three different types of media: A. Blood agar with gentamicin
B. Buffered charcoal-yeast extract agar
C. Chocolate agar with X and V factors
            Blood agar with gentamicin – Burkholderia pseudomallei
            Buffered charcoal-yeast extract agar – Legionella pneumophila
            Chocolate agar with X and V factors – Haemophilus influenza
After a five days, you observe the following:

 

6. Diagnose the disease
What diseases could result from the organism you cultured?
legionellosis
Pontiac fever
** Legionella pneumophila can cause both Pontiac fever and legionellosis

7. Fill in the disease that best fits your patient's symptoms.
Of the two diseases caused by the pathogen you isolated,  legionellosis fits your patient's symptoms the best.

8. Treat the disease
How will you treat this disease?
Erythromycin
** You start your patient on a course of erythromycin

9. Legionelllosis is a nationally reportable disease, and you must notify the authorities of your finding. Before you call in your diagnosis however, you want to try and identify how your patient first contracted it. You decide to question your patient about his possible exposure history in the ten days before his illness. You ask him if he has been in, around, or used:
a decorative fountain
any form of respiratory therapy equipment (e.g. sleep apnea, asthma devices)
a mall or other large enclosed shopping venue
long-term care, senior, or assisted living facility (e.g. nursing home, rehab facility)
a hospital (besides his current stay)
a shower (away from home)
construction or projects affecting, plumbing and/or water lines
a hotel
a pool, hot tub, jacuzzi or whirlpool spa
a doctor's or dentist's office
a steam room or sauna
grocery stores with misters for fruit and vegetables
recreational misters
a humidifier
** Legionellosis can be transmitted by almost any situation involving water conditions where the bacteria can grow, particularly if they are able to form a highly resistant biofilm. Legionella already exists in most water systems; however the frequency of outbreaks still remains relatively low.

10. As you read off the above questions to your patient, you start to get a feeling for the ubiquity of Legionella pneumophila in water sources. If Legionella is so common, then why doesn't everyone get sick? Generally, the risk of contracting legionellosis is low for an immunocompetent person; however there are some factors that seem to increase the likelihood of contracting the disease. Which of the following factors specific to your patient do you think played a role in whether or not he got sick once exposed to the bacterium?
His age
His cigarette and alcohol consumption
His travel history
** Men over the age of 50 are the most likely to contract legionellosis, especially if they are heavy smokers or drinkers.

Conclusion
Your patient answers your questions one by one. In Seattle, he stayed at a hotel with a decorative fountain in the lobby. He swam in the hotel's pool once, and spent roughly thirty minutes each night (for two nights) in the hotel's jacuzzi. He also took a shower in his room's bathroom. Subsequent analysis of the water sources throughout the hotel and his room were negative for Legionella.
Once back at home, your patient recalls going shopping at a local grocery store that uses misters to keep vegetables fresh. He also brought his dog to a grooming salon, where he opted to bathe the animal himself. He spent an hour bathing the dog, and was often splashed by the water from the grooming sink. Lastly, he visited the dentist for to get a filling replaced shortly before he took ill.
Water sources and lines were analyzed at every location he visited. The water at the grocery store and the dentist's was negative for Legionella; however the water at the dog grooming salon tested positive! The salon was immediately shut down, and all recent clients were contacted regarding a possible outbreak.
Your patient makes a full recovery on your course of erythromycin, and further spread of the disease was prevented by your speedy diagnosis!

Influenza: From the Great War to Today
It was the spring of 1918, and the world was at war. In Haskell County, Kansas, an epidemic of influenza was underway. Public health officials in Washington, D.C. were notified; however, no investigators were sent. Meanwhile, soldiers from all across Kansas were reporting to Camp Funston in training for the war. In hindsight, it appears that a soldier from Haskell County brought influenza with him to Camp Funston. By the middle of March, there was an epidemic in the camp. Ultimately, about 1100 soldiers were infected and 38 died during the outbreak. Unfortunately, the reporting methods at that time were not particularly good. The epidemic at Camp Funston essentially went unnoticed by public health officials. Within only a few months, the country would be caught in an epidemic that no one could ignore.
During the initial epidemic at Camp Funston, the infection was characterized by several of the typical symptoms of influenza infection.

1. Which of the following are symptoms of influenza infection?
Headache; fever; muscle pain
** After the person is exposed to the flu virus, there is a short incubation period—only about one day—before symptoms of infection appear. Influenza infection commonly causes muscle aches and headache. These are most likely due to the fever that is part of the normal immune response to infection. As fever raises the body temperature, cellular demand for water will increase. At the same time, the person’s appetite and thirst are typically depressed, leading to decreased consumption of water. These two factors contribute to dehydration and an electrolyte balance, which typically manifest as general malaise and headache.

The structure of the influenza virus is central to its ability to cause disease in susceptible hosts. The structure of the virus is relatively simple (compared to that of a prokaryotic or eukaryotic cell); however, each component has an important role to play in the infectious cycle of influenza.

2. Drag each one of the labels onto the figure to identify the function of each structure.
 
** During infection, the structure of influenza plays a vital role. Hemagglutinin (HA) mediates attachment to the host cells, after which the lipid envelope fuses with the host cell membrane. This allows the virus to be internalized, followed by release of the RNA genome from the capsid. Viral proteins will be produced, assembled, and released from the host cell. Release is mediated by neuraminidase (NA), and as the viral particles leave, they take part of the host membrane, thereby creating their envelope.

During the spring and summer of 1918, cases of influenza began to emerge throughout Europe. Soldiers on both sides of the front were struck down by this invisible pathogen. In contrast to the cases seen at Camp Funston, these infections were much more severe, with symptoms resembling those of pneumonia. As the months went on, the death toll continued to rise.

3. The successful infection of a host, and subsequent spread to another, results from a specific sequence of events known as the replication cycle. Each of the statements below describes an important step in the replication cycle of influenza.
Arrange the following statements in the order that best describes the sequence of events involved in the replication of influenza.
1. Hemagglutinin (HA) spikes attach to host cells.
2. Influenza enters the host cell.
3. Nucleic acid enters the host cytoplasm.
4. Influenza proteins are synthesized.
5. Influenza nucleic acid is packaged in capsid.
6. Influenza particles bud from the cell, releasing the virus into the surrounding environment.
** After gaining entry to the host respiratory system, influenza adheres to host cells. The virus then enters the cells and begins the process of hijacking host machinery in order to produce new viral particles. After all the components are synthesized, they are assembled, and the virus leaves via budding. The newly released particles then infect neighboring cells, perpetuating the infection.

It is thought that in Europe, the influenza virus changed in such a way to make it more virulent in the human population, resulting in increased severity of disease and increased mortality. What changes could have led to the differences in pathology observed in Camp Funston and in Europe? Research in recent years has led to our understanding that these changes were due to the process known as antigenic shift.

4. Which of the following statements regarding antigenic shift are true?
Viral strains resulting from antigenic shift contain RNA segments from different species.
Little immunity to virus strains resulting from antigenic shift exists in the population.
Antigenic shift results in a major change in the genetic composition of the virus.
** Genetic analysis of the 1918 flu revealed that it contained genetic material that was both avian and mammalian in origin. This reassortment led to a deadly combination—a virus that was both highly virulent and transmissible. These factors, coupled with the lack of immunity in any population, led to the pandemic that impacted the entire world.

Research conducted in recent years on the 1918 flu indicated that the high mortality rate and the severe pathology associated with the disease were likely due to a cytokine storm that was stimulated during infection. Recall that when they are released, cytokines stimulate the production of more cytokines (positive feedback). Sometimes, this feedback spins out of control, leading to an overproduction of cytokines known as a cytokine storm.

5. Predict which of the following are reasonable outcomes of the cytokine storm during the 1918 flu pandemic.
an excessive inflammatory response leading to extensive tissue damage
increased fluid in the lungs and labored breathing
** The cytokine storm during infection with the 1918 influenza was extremely destructive. The massive release of cytokines in the lungs led to an uncontrolled inflammatory response. As cells moved into the lung tissue, the tissue was destroyed. Fluid entered the lungs, and patients struggled to breathe. Furthermore, the ability to deliver oxygen to the body was severely compromised, giving many patients a blue appearance.

As soldiers returned home to the United States in the fall of 1918, they brought the deadly flu with them. The first cases were noted in August of 1918. By September of that year, influenza epidemics were reported in California, Texas, North Dakota, and Florida. The disease would continue to spread throughout the fall and winter of 1918 and into the spring of 1919. It is estimated that the 1918–1919 influenza pandemic resulted in approximately 675,000 deaths in the United States and more than 20 million worldwide. Today, approximately 30,000 to 50,000 people die each year from influenza infection. Several factors play a role in this relatively low mortality rate. One factor is the availability of an influenza vaccine. But although the vaccine does offer protection, its design and production are not without their challenges.

6. What are some of the current challenges to production of the influenza vaccine?
In order to yield a vaccine, the virus must be produced in eggs.
The virus undergoes antigenic changes on a regular basis.
** A vaccine for influenza has been available since about 1945. The current vaccine generates protection against the three strains most likely to cause infection during the flu season. The vaccine is currently available in two forms: a nasal spray (made from live, attenuated virus) and an injection (made from inactivated virus). Although both offer protection, the effect is relatively short-lived and is specific only for the three strains contained in the vaccine.

In addition to the vaccine, several antiviral drugs are available to treat influenza infection. One of the most prescribed treatments for influenza is Tamiflu (osteltamivir). Tamiflu works by inhibiting the action of neuraminidase (NA).

7. Predict which of the following would be outcomes of treatment with Tamiflu.
overall decrease in the replication rate of influenza
an increase in the ability of the immune system to combat the infection
a decrease in the release of viral particles from the cell
** If taken within 30 hours of the appearance of symptoms, Tamiflu is quite effective at inhibiting viral replication. Because NA has been inhibited, the viral particles are unable to bud from the infected cells. As a result, the infection isn’t perpetuated. This slowing in the replication cycle gives the body enough time to mount an effective immune response and eventually eliminate the infection.

Big Picture Coaching Activity: Pertussis
Megan woke up this morning with a feeling of dread. School was about to start, and Megan was due for her fifth DTaP, her second MMR, and her second Varicella vaccinations. Her physician explained that the DTaP vaccine would give her protection against diphtheria, tetanus, and whooping cough. He also said that the MMR would protect her against measles, mumps, and rubella, while the varicella shot would help protect against the chicken pox.

1. Causative Agent of Whooping Cough
Bordetella pertussis
** Whooping cough is caused by Bordetella pertussis, a small, obligately aerobic, gram-negative coccobacillus.

2. Pathogens of the Bacterium
Lower respiratory system infections, such as whooping cough, can lead to bronchitis or pneumonia due to the inhibition of normal protective responses. Which of the following explains how the pathogen overcomes normal protective responses of the respiratory system?
The bacteria attach to the ciliated cells of the trachea, thus preventing mucus from being cleared.
** Bordetella pertussis attaches to the ciliated epithelial cells of the trachea, which impedes the movement of the cilia. Without being able to move, the cilia cannot clear the mucus from the respiratory system and excess amounts accumulate.

While Megan was waiting for the administration of her vaccines, she was looking at all of the posters on the wall in the exam room. One of the posters was an information sheet on whooping cough. This poster listed the characteristics of the organism, signs and symptoms, the progression of infection, and finally the various vaccine options for this organism.

3. Progression of infection
Megan learned from the poster that there were three main stages of whooping cough. Place the following in order of how they would occur during progression of the infection.
Catarrhal; Paroxysmal; Convalescence
** Catarrhal refers to the initial stage of whooping cough that closely resembles a common cold. This may lead to misdiagnosis or delay in treatment. Paroxysmal refers to the second stage of disease progression when the patient, usually a child, suffers prolonged sieges of coughing. This excessive coughing is a result of the body trying to clear the mucus that has accumulated after the cilia were destroyed in the trachea. The final stage of whooping cough is the convalescence stage and can last several months.

4. Vaccine Effectiveness
The exam room poster for whooping cough also listed the various vaccines that could be given. The three possible vaccines were the DTP, the DTaP, and the Tdap. The DTP was made with heat-killed whole cells of the bacterium B. pertussis, while the DTaP and the Tdap were made with acellular pertussis components. Which of the following statements regarding the vaccines explains why the DTP vaccine is no longer used?
Bordetella pertussis was not killed during the heating process used on the DTP vaccine and could cause an active infection
** Bordetella pertussis whole cells used in the vaccine were heat-killed before being included in the vaccine. If the heating process was not done properly, the cells were not killed. When this happened to an entire batch of the vaccine, an epidemic of whooping cough resulted. It was determined that the bacteria in the vaccines were living and capable of causing infection. This led the health officials to determine that a safer vaccine was necessary.

The DTaP vaccine mentioned in the previous question was created as a safer vaccine than the DTP. After this vaccine was transitioned into use, epidemiologists were surprised to find that whooping cough infection rates were still increasing, rather than decreasing.

5. Immune Response
Many possible explanations were given as to why the numbers of pertussis infections were increasing, but the most likely explanation was that the DTaP vaccine was not as effective as the DTP at protecting children long-term. Which of the following best describes why this is the case??
The DTaP vaccine is not made with cellular components that would stimulate the immune system as effectively as the DTP vaccine.
** Cellular components are more effective at stimulating the immune response than non-cellular or acellular components. The reason that the number of cases most likely rose after the switch to the DTaP is that it did not offer the same long-term effectiveness because it lacked cellular components. As a result, an additional booster called the Tdap vaccine helps to provide protection after the memory has worn off from the DTaP vaccine, but it is not recommended for teenagers and expectant moms.