UNKNOWN #5071
Patient History
The 7-years old boy, B, is suffering from common symptoms of gastrointestinal (GIT)
infection as the symptoms are related to GIT. He is feeling uneasiness in his stomach and
abdomen, along with vomiting. He also has loose motions, but the stool is non-bloody. He has
severe pain in his abdominal region. Based on the data from Healthline, this seems to be a GIT
infection. GIT infections are very common among children. “It affects 2,195 children every day
— more than AIDS, malaria, and measles combined” (Frothingham, 2018). As seen that the
white blood cell count of the patient is within the normal range, it suggests that there is no
serious infection.
However, the article also suggests that the common causes of GIT infections are either
bacterial, viral, or parasitic. Based on the symptoms, it looks like bacterial. The main two
bacteria responsible for such infections are Escherichia coli iand Salmonella. The fever is not too
high (less than 101°F), representing one of the symptoms of a bacterial infection. But as the
patient was in contact with a pet baby chicken, there are chances of spreading from the chicken
to the patient. There are some references to the fact presented by The Center for Disease Control
(CDC, 2022).
Results
For a proper differential diagnosis, the patient’s stool sample was sent to the lab for
further testing. The tests performed on the sample were as follows. The table presents the results
of the tests and their identification (obtained with the help of the dichotomous key and the results
from PDF data).
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Test /
Information provided by the test
The physical appearance
Test
Media
Metabolic properties tested
of the media/Test
results
(positive /
negative)
Oxidase
It focuses on the isolation of the cells
It doesn’t appear to be
that can produce the enzyme
violent in colour.
Negative
cytochrome oxidase.
It provides information if the
microorganism is aerobic.
MacConkey It is a selective agar for gramnegative bacteria.
There were isolated
Positive
colonies to be seen with a
It tests for the fermentation of lactose. reddish colour.
Lysine
The test is for determining if the
The result showed purple
microorganism can produce
colour.
Positive
decarboxylase or deaminate.
SIM Indole
The test determines the ability of the
There is a red ring in the
organism to reduce sulfur, produce
tube.
Positive
indole and swim through the agar. It
differentiates members of
Enterobacteriaceae.
Gram Stain
The test allows observing the
The colour of bacteria is
chemical composition of the
pink.
organism’s cell wall.
Negative
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In the case of the oxidase test, the test was negative because of the absence of the
cytochrome oxidase enzyme. Some of the oxidase-positive bacteria are Pseudomonas or
Neisseria, while E. coli belongs to the negative oxidase group. In the MacConkey Agar, the
reddish colour is present due to the production of acid with the change of the colour of the dye
when the pH of the agar medium goes below 6.8. The next test is SIM, which stands for sulphur,
indole, and motility, which is a differential media. The result was positive, which shows that the
production of HS is used to diagnose enteric bacteria. The picture below shows that it is E. coli,
indole positive.
Figure 1: Results of SIM Media (UWYO, 2021).
Discussion
As explained in the case study, the patient has the symptoms caused by E. coli that appear
between 3 and 8 days after infection. These are abdominal pain and diarrhea, which can progress
to bloody forms (hemorrhagic colitis), but the patient’s stool is currently without blood. The
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other symptoms include vomiting and nausea. The tests do show that the diagnosed
microorganism is E. coli. The oxidase test is negative, and all other results prove that it is
Escherichia coli (Shields and Cathcart, 2010).
Escherichia coli or “Colibacillus” is a very common mammalian intestinal bacterium in
humans. In 1885, Theodore Escherich discovered a fecal coliform generally commensal, nonpathogenic, living on the skin and mucous membranes without harming the host which harbors
it. Over 95% of E. coli strains are harmless, and we need them to live. Escherichia coli (E. coli)
is a bacterium that resides in the digestive tract of humans and warm-blooded animals. Most E.
coli strains are harmless; only a few are pathogenic for humans. These cause bloody diarrhea and
produce a powerful toxin that causes hemolytic uremic syndrome (HUS). Regularly, strains of E.
coli are the cause of food poisoning through the consumption of animal products (meat or dairy
products) that are poorly cooked or eaten raw.
This bacterium can become pathogenic if the host’s defenses are weakened or if it
acquires specific virulence factors. Each year, a strain of this bacterium (enterotoxigenic
Escherichia coli or ETEC) infects 200 million people and causes the death of 380,000 people in
developing countries (Allocati et al., 2013).
The normal habitat of E. coli is the intestine. The bacteria can cause serious food
poisoning. The infections for which they are responsible have become more varied in their
locations and manifestations. They now play a major role in nosocomial infections and infectious
pathologies (urinary tract infections, intestinal infections, neonatal infections). E. coli is,
therefore, a model species for studying the continuum between commensal bacteria and
pathogenic bacteria (Gomes et al., 2016).
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Some strains of the bacteria live in the digestive tract of healthy people, while some
strains acquire genes that cause infections. They can be transferred from one organism to another
via several methods. The most spread infections via E. coli are UTIs or digestive tract infections.
It is one of the most common causes of bladder infections. Some of the strains of the bacteria
produce toxins that cause diarrheas. Based on the research, “E. coli have many virulenceassociated factors, including adhesins, toxins, iron acquisition factors, lipopolysaccharides,
polysaccharide capsules, and invasions, which are usually encoded on pathogenicity islands
(PAIs), plasmids, and another mobile genetic element” (Sarowska et al., 2019).
Most antibiotics are not recommended for treating E. coli infections. Destroying the
bacteria leads to the release of Shiga-toxins in the body, aggravating HUS. However, treatments
based on certain antibiotics, such as azithromycin, which do not lead to the release of these
toxins, are currently being evaluated. While waiting for their results, the therapeutic strategy of
the HUS consists of compensating for the deficiencies caused by Shiga-toxins (fall in red blood
cells, platelets, kidney damage) by transfusion, dialysis, and plasma exchanges (Suojala,
Kaartinen, & Pyörälä, 2013). Diarrheal episodes are treated symptomatically: patients are
rehydrated but do not take antidiarrheals to allow the elimination of the bacteria and its toxins in
the stool. There is a recommendation that the patient must keep themselves hydrated, and there
must be replenishment of minerals (Wassenaar, 2018).
Current knowledge does not make it possible to reduce EHEC incidence within cattle
farms. On the other hand, it is possible to determine whether an animal is a carrier of the bacteria
through tests. If necessary, the meat can undergo a bactericidal treatment which consists of
heating or irradiating it. These techniques, although effective, do not systematically guarantee
the absence of E. coli in food. To effectively protect against these infections, it is necessary to
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respect the application of strict hygiene practices throughout the food chain, from producer to
consumer.
References
Allocati, N., Masulli, M., Alexeyev, M. F., & Di Ilio, C. (2013). Escherichia coli in Europe: an
overview. International journal of environmental research and public health, 10(12),
6235-6254.
CDC, (2022). Backyard Poultry. Center for Disease Control.
https://www.cdc.gov/healthypets/pets/farm-animals/backyard-poultry.html
Frothingham. S., (2018). Gastrointestinal Infection: Symptoms, Causes, and Treatment.
Healthline. https://www.healthline.com/health/gastrointestinal-infection
Gomes, T. A., Elias, W. P., Scaletsky, I. C., Guth, B. E., Rodrigues, J. F., Piazza, R. M., … &
Martinez, M. B. (2016). Diarrheagenic Escherichia coli. Brazilian journal of
microbiology, 47, 3-30.
Shields. P., and Cathcart. L., (2010). Oxidase Test Protocol. American Society for Microbiology.
https://asm.org/getattachment/00ce8639-8e76-4acb-8591-0f7b22a347c6/oxidase-testprotocol-3229.pdf
Sarowska, J., Futoma-Koloch, B., Jama-Kmiecik, A., Frej-Madrzak, M., Ksiazczyk, M., BuglaPloskonska, G., & Choroszy-Krol, I. (2019). Recent reports include virulence factors,
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prevalence, and potential transmission of extraintestinal pathogenic Escherichia coli
isolated from different sources. Gut pathogens, 11(1), 1-16.
Suojala, L., Kaartinen, L., & Pyörälä, S. (2013). Treatment for bovine Escherichia coli mastitis–
an evidence‐based approach. Journal of veterinary pharmacology and therapeutics, 36(6),
521-531.
Wassenaar, T. M. (2018). E. coli and colorectal cancer: a complex relationship that deserves a
critical mindset. Critical reviews in microbiology, 44(5), 619-632.
UNKNOWN #507
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Unknown Project Report Draft
Grading Rubric
20 pts
☒ Report submitted on time – 5 points deducted per day if assignment submitted late.
Plagiarism (copying from source material) – Academic dishonesty is a serious offense. Copying
the work of a reference or another student will result in a grade of 0 and be referred to the Dean
of Students.
– Check that your entire report is written in your own words. This does not mean
changing a few words here and there – it means presenting the idea/information in a
new way.
– All information you got from another source should be cited – both in-text (Author,
year) and with a full reference at the end of the paper.
o You do not need to cite info from the Modules. We consider this ‘common
knowledge’ for students of BIOS 351.
– You cannot use quotes, even if they are cited. Rephrase the info in your own
words.
Patient History (4 pts)
Your
Score
1
2
1
Possible
Target
Points
1
Infection type is identified and correct (UTI, wound infection, etc)
Section explains which symptoms suggest which infection is present, and
2
information is supported with reliable references
Section summarizes relevant information from patient case (without
1
copy/pasting the case itself)
Results (4 points)
Your
Score
0.5
1
0.5
Possible
Target
Points
Source of unknown (body fluid/location sample was taken from) and
1
isolation media is included from the clinical case
All tests used in dichotomous key are explained. Tests are presented in the
2
logical order performed in key. Whether test is +/- and how trait was
identified (observations) is included.
One figure and one table are present and labeled with a caption.
1
Dichotomous key and table of data should be referenced in the text.
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Discussion (9 points)
Your
Score
1
2
2
1
2
Possible
Target
Points
There is a brief transition at beginning, summarizing patient symptoms,
1
infection type, and unknown identified
Biology of the unknown section – a comprehensive summary of the
normal habitats, important features of the microbe are presented. 1-2
2.5
paragraphs with minimum of 3 high quality references – may be websites
or peer reviewed journal articles.
Infection biology of the unknown section – a comprehensive summary of
what is known about this organism in relation to the infection type
2.5
(virulence factors, diseases, etc) is presented. 1-2 paragraphs and
minimum of 4 high quality references – peer reviewed journal articles.
Treatment section – a brief conclusion where specific antibiotics,
resistance, recommendations for patient are made. Avoid vague
1
recommendations – mention specific antibiotics if appropriate. 1
paragraph with minimum of 1 high quality reference.
Overall writing quality – ideas are supported by references. References are
2
integrated into a narrative (not a random collection of facts). Writing is
overall grammatically correct and free of typos.
References (3 points)
Your
Score
0.5
1
1
Possible
Target
Points
1
Student used in-text citations correctly throughout paper (Author, year).
1
Student provided a list of full references for all in-text citations mentioned.
Formatting of references is appropriate with only minor deviations from
1
APA style.
Examples:
Schaefer, N. K., & Shapiro, B. (2019, September 6). New middle chapter in the story of human
evolution. Science, 365(6457), 981-982. https://doi.org/10.1126/science.aay3550
Example in-text citation: (Schaefer & Shapiro, 2019)
Toner, K. (2020, September 24). When Covid-19 hit, he turned his newspaper route into a
lifeline for senior citizens. CNN. https://www.cnn.com/2020/06/04/us/coronavirus-newspaperdeliveryman-groceries-senior-citizens-cnnheroes-trnd/index.html
Example in-text citation: (Toner, 2020)
World Health Organization. (n.d.). The top 10 causes of death. https://www.who.int/newsroom/fact-sheets/detail/the-top-10-causes-of-death
Example in-text citation: (World Health Organization, n.d.)
Unknown Project Report
For this assignment you will prepare a written report analyzing a clinical case of the
unknown microbe.
Module 9
Prepare a Gram positive
dichotomous key.
Prepare a Gram negative
dichotomous key.
Describe how to interpret each
test used in your keys.
Interpreting Media Skills Assessment
You are assigned Gram stain results and media
test results for an Unknown.
Use the Gram + or Gram – key you constructed in
Module 8 to identify the Unknown.
Unknown Project Report
Research the biology of your Unknown, your (mock) patients’ case history, and prepare a written
report analyzing your identification.
You may use passages you have previously written for Modules 9 in the report. You
should revise your work and correct mistakes as needed following your TA’s feedback.
Important dates and deadlines:
Sunday April 3 11:59pm – Report Draft due (20 points)
Sunday April 10 11:59pm – Deadline to receive your TA’s feedback on Report
Draft
Sunday April 17 11:59pm – Final Report due (40 points)
A late penalty of 5 points per day will be deducted for reports submitted late.
Instructions
1. Check your dichotomous key with your TA.
2. Use your dichotomous key and the data set assigned to you to identify your unknown
in Interpreting Media Skills Assessment.
3. Read the patient case study for your unknown.
4. Identify the type of infection your patient has.
5. Research whether your unknown typically causes this type of infection. Is your
identification surprising?
6. Continue researching your unknown. What is interesting or important to know about
it?
7. Prepare your report with the following sections:
Patient History (1-2 paragraphs)
Read the case study. Explain how any relevant parts of the patient’s history or
symptoms contributed to your final diagnosis as to the type of infectious disease
seen here. Search reliable medically oriented Internet sources to support this. Reliable
sources you might consider include:
Medscape https://www.medscape.com
Medline Plus https://medlineplus.gov
Mayo Clinic https://www.mayoclinic.org
Healthline https://www.healthline.com
Other sources from universities, hospitals, or sites ending in .gov, .edu, .org
The patient’s history and symptoms should suggest a general type of infectious
disease that is present. The infection type will be one of the following: urinary tract
infection, wound infection, gastroenteritis, pharyngitis, pneumonia, or septicemia. Use
at least one reference to support your diagnosis of the type of infectious disease
seen here.
This paragraph should summarize the most important and relevant parts of the case
study. Do not copy/paste the entire case information. Only discuss the information that
contributed to your diagnosis of the infection type. Look up and explain any technical
terms in the case history that are unfamiliar to you. For example, if the case history says
the patient has “dyspnea”, you might write this as “difficulty breathing” in this paragraph.
Results (1 figure, 1 table & 2-3 paragraphs)
Describe the results of the biochemical tests that led to your identification of the
unknown. The section you prepared for Module 9 will be helpful here. Describe how
you used your dichotomous key to identify the Unknown.
•
•
•
•
Describe the source of the unknown (from the patient case) – what type of
sample was the unknown isolated from, and what media was first used to grow
it?
Include the tests that you interpreted, in order.
Explain whether each test was positive or negative, and how you could tell. What
did you observe?
Explain what trait the test identifies.
Include a copy of your dichotomous key as Figure 1. You should revise your key if you
made mistakes in Modules 9. Prepare a figure legend as shown below.
Figure 1. Dichotomous key for identifying Gram negative unknowns.
Include a data table with the name of tests and observed results that you used in
identifying your unknown. Include a title below the table as shown below:
Test
Result
Gram stain
Gram + cocci
Starch hydrolysis
+
Casein hydrolysis
Hemolysis (blood agar)
alpha
Table 1. Staining and biochemical test results in identification of Unknown #111.
Finally, state what you believe the identity of the unknown is.
Discussion (1-2 pages)
Begin your discussion by quickly summarizing the most important patient symptoms,
your diagnosis of infection type, and the organism responsible for the infection in 1-2
sentences. Then describe the biology of the microbe that was identified. The
paragraphs you wrote in Module 9 can be used as a starting point here – you may want
to expand on this section further. A strong paper would include at least 3-4
references for this section. You should address most of the following:
o What is the species normal habitat? Is it commonly found in/on the human
body? If so, where?
o Are there any diseases/illnesses caused by infection with this species?
What are they?
o Are there any important virulence factors we should know about? Does
this species produce a capsule, toxins, adhesins, hemolysins, etc?
o Share some interesting facts about this microbe. What makes it
unique/interesting?
Next, research whether your organism typically causes the type of infection that has
been diagnosed. You may find that this species is often involved in these infections. Or,
you may find that this patient’s case is quite rare. In 1-2 paragraphs, discuss what is
known about your unknown and this type of infection. Information that is relevant to the
treatment or severity of the infection would be particularly helpful. You should use
reputable sources including journal articles here. A strong paper will incorporate 4-5
different journal articles in this section. Two resources are:
PubMed https://www.ncbi.nlm.nih.gov/pmc/
UIC Library https://library.uic.edu
Finally, propose a treatment plan that may work for the patient. You can write in general
terms here – we do not expect that you will know the best treatment, dose, or course of
treatment. Use the resources in the preceding paragraph to propose some antibiotics
that may be used. Is antibiotic resistance a problem for this species? If so, mention it
here. If there are any behavioral changes you recommend for the patient or their care
team, discuss them here. For example, if your patient has a history of food poisoning,
recommending practicing better hygiene during food preparation and storage would be
appropriate.
References
Provide a full list of all references you used in the paper in APA format. You can read
more about APA format here: https://apastyle.apa.org
You do not need to cite information that came from Blackboard or any of our course
modules.
Examples:
Grady, J. S., Her, M., Moreno, G., Perez, C., & Yelinek, J. (2019). Emotions in
storybooks: A comparison of storybooks that represent ethnic and racial groups in the
United States. Psychology of Popular Media Culture, 8(3), 207217. https://doi.org/10.1037/ppm0000185
Schaefer, N. K., & Shapiro, B. (2019, September 6). New middle chapter in the story of
human evolution. Science, 365(6457), 981982. https://doi.org/10.1126/science.aay3550
Toner, K. (2020, September 24). When Covid-19 hit, he turned his newspaper route into
a lifeline for senior citizens. CNN. https://www.cnn.com/2020/06/04/us/coronavirusnewspaper-deliveryman-groceries-senior-citizens-cnnheroes-trnd/index.html
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