ONPS1045 Assignment 1 – Case Study Report
This assignment is worth 15% of the final assessment.
Due Date:
Friday April 13,2018 midnight
Length – 2500 words +/- 10%
(Word count does not include references and tables).
Assignment:
Each student will be allocated patient case notes and a sputum sample on day 1.
The task is to perform an identification and sensitivity testing within 72 hours (practical
days 1-3) using a workflow similar to a standard diagnostic lab. This will require you to:
1. Identify the organism involved using appropriate media, workflow, biochemical tests,
and anti- microbial sensitivity testing.
2. Write a brief clinical report to the physician on your findings. A reporting template
will be provided.
3. Write a report on your case study and identification. You are required to describe
the method, workflow and results of your identifications, and to discuss your
findings, and the anti microbial sensitivity findings. In addition, you will research the
symptoms, pathogenesis and treatment of the pathogen you identify.
Format
The following headings should be used for your Case Study report:
• Cover sheet
• Introduction
• Materials and Methods
• Results
• Laboratory Report
• Discussion
• References (Vancouver format).
• Laboratory Notes- attach a scanned copy of the notes from your laboratory
notebook.
Further details on what to include under these headings are given below.
Please note correct formatting and referencing are part of the assessment criteria
and marks will be deducted if format is not correct.
Cover sheet.
Please include a cover sheet with your name, student number, practical group and
demonstrator, the name of your practical partner, and the identification code of your
unknown organism.
Note: The methods section of your report will probably be very similar so other
students- this is not a problem.
Introduction
The introduction should include general background information including: the
significance infections of the particular body system being studied, reasons for
performing microbiological investigations on these patients, and expected outcome
or benefit from such investigations.
The introduction should end with a brief statement that summarises the aim of the
exercise and nature of the case that was investigated.
Materials and Methods
The protocol used in your own investigations should be explained and justified, this
should be written in the past tense. e.g. “To identify Salmonella spp. to the level of
serotype, the following tests were performed. . .”.
Methods section should be written so that the work could be repeated by another
student.
For this type of report, you do not need to list materials used as these are standard
and may be found in any microbiology laboratory. Any test procedures described in
detail in the RMIT Techniques Manual, or other such as the Manual of Clinical
microbiology, or Melbourne University Techniques Manual should be simply
referenced by giving the source and page number (Vancouver style, include a
page number in references to Technical manuals). The only specific materials you
need to report are kits or commercial test kits that were used, these should be
named and the manufacturer should be stated.
The simplest way to present this information is in a simple paragraph, or dot- point
format for example:
Eg. The following tests were used to identify organisms in this study. Methods were
as described in the RMIT Techniques Manual (1) or the Manual of Clinical
Microbiology (2) as indicated.
For organism A the following tests were used A:
• Catalase test (1)p24
• DNAse test (1)p56
• Hippurate test (2)p 27
Note: Many students have used the online GERMM database at RMIT in previous
classes. These methods are a great reference in the lab, but this is not an
appropriate reference for these reports because it is not easily accessible, and
because web links are not an appropriate reference for this type of report. The test
descriptions in the RMIT technical manual are almost identical to those in the
GERMM. You are required to refer to an easily accessible source with page
numbers. Students are advised to use a copy of the RMIT techniques manual.
Copies are available for use in class and/ or you can purchase your own at low cost
from the microbiology prep room staff.
Results
Your results should be organised and presented as clearly as possible, avoiding
repetition. Tables and diagrams are usually preferable to long descriptions of positive
and negative test results. Tables should have clear headings and any abbreviations
should be explained below the table.
You should note the gram stain result and any growth conditions, (eg. O2 or AnO2) or
growth on any specialist or selective media, if relevant. You do not need to describe the
colour change or appearance of the tests, simply record wether the results was positive
or negative, or gas production etc.
For example:.
Summary of test results for Case 12.
Test Result
Growth in air +
Growth on MCA +
Lactose fermentation on MCA –
Growth on HBA +
Haemolysis on HBA α
Optochin R
If tables are used, the key points in the table should also be briefly summarised in
the text in a manner that explains the workflow, e.g. Under your results table write a
short paragraph : “The organism in Case 12 was identified to species level using
four biochemical tests. Using the gram stain appearance, and the growth on MCA, it
was possible to identify the organism as member of the Streptococci (Table 1, (ref
3)). Then the presence of alpha haemolysis, susceptibility to Optochin permitted
identification of Streptococus pneumoniae (Table 4 (3)).”
You may wish to make a flow diagram to illustrate the workflow and process of
identification. It is best not to include results in the flow diagram, test results should
be recorded in a table. Remember that all charts need a descriptive figure legend.
Make sure that your results section includes a statement of the identity of the
organism/s!
Laboratory Report to Requesting Physician
Use the template provided to complete the 1 page laboratory report on your sputum
(download template from the Practical classes page on Canvas site). This report
should only contain the information that would be reported back to the clinician.
Refer to the example reports provide in class. You will also be writing your own
reports in the weeks before starting this assignment to get experience with the
correct terminology.
In the laboratory report, state the relevant patient and specimen details and present
your results clearly and concisely. Methods used to obtain those results are the
responsibility of the laboratory and are not included in the report. Do not list
antimicrobials used for identification purposes only. Students are advised to discuss
the report with their demonstrators.
Note: if patient details such as name and address are not provided for the cases you are
writing, you can make up this information to complete the form.
Discussion
The Discussion section should provide an interpretation of the results, including any
unusual findings or difficulties in the identification. It should not contain extensive
repetition of the results or of information in the introduction. A good way to discuss the
results is to point out the critical tests that made it possible to identify the organism to
genus and species level for example. If you had any unexpected results you should
provide explanation, and discuss how it could have been done better.
Make sure you discuss your findings in the context of the case notes you received. How
does the organism you identified fit with the patient type, symptoms etc.
The discussion section must also include a short discussion of the significance of the
pathogens that were isolated in the case study under investigation, with appropriate
reference to the scientific literature (approx. 3-10 references in Vancouver style). Your
discussion should address the following points for each pathogen you isolated:
• Symptoms, duration and possible complications of infection
• Discussion of how the pathogenesis of infection leads to the symptoms
• Usual treatment recommendations, and any considerations for anti microbial
susceptibility testing for the organism you isolated.
Laboratory notes
Attach a scanned copy of the original laboratory notes to your report. We will review
your lab notes when marking your reports to ensure that the conclusions are consistent
with your lab results.
References :
The Vancouver reference format must be used.
In the course of preparing your report, it is expected that you will have read some of
the scientific literature on the subject. This might include a textbook, but should
also include peer-reviewed journal articles, and/or a clinical laboratory
manual. Web links from non- peer reviewed sources are NOT appropriate for a
scientific report. Please see the reference list for my document below for examples.
The best way to prepare a reference list is to use referencing software like Endnote
™. You can download this free if you are an RMIT student. The RMIT library can also
provide help and training tutorials.
As a rule the in formation on web sites are not peer-reviewed and are therefore not
acceptable as references for a university report. Government health department web
sites (eg. CDC, WHO) may be acceptable if necessary, for example for quoting
health statistics.
Submitting your Case Study Report
• Please combine all parts of your assignment into one word or PDF document and
submit using the Turnitn link .
FAQ on Turnitin scores:
All students will be using similar methods so some parts of your report are likely to
be similar to other students. As a guide we would expect Turnitin scores to be
<15% similarity for this type of report. If your score is higher than this, you should
review which sections are similar and make changes. If the only similarity is in the
materials and methods, or references section then a little over 15% is OK. It is
important that your Introduction and discussion are in your own words. Remember
that we can see the Turnitin reports when we mark and are able to judge. Scores
over 20% are NOT acceptable. You will need to revise your report and resubmit.
Remember that a Turnitin report can take about 24 hours when the deadlines get
close so don’t leave it to the last moment. If you cannot get a Turnitin score back in
time to check you are under 15% by the closing time then just submit your
assignment anyway. The scores will be usually available the next day. You do not
need to send emails to explain. If any discrepancies are found during marking we
will contact you to work them out.
General formatting requirements for scientific reports:
• Organism names are always italicised.
• The first time an organism is mentioned by name, the name must be written out in
full. Afterwards, the shortened version is used, for example, Escherichia
coli then coli.
• The same applies to other abbreviations, for example calibrated dichotomous
sensitivity first then CDS. You should use an abbreviation such as CDS only if it
comes up at least five times in the text; otherwise write out in full.
• The American Society for Microbiology (ASM) website has a list of abbreviations that
can be used without definition. These include PCR and MIC. All microbiologists
know what these mean and they do not need explanation.
• Be careful with the use of capitals. The only words that are capitalised mid sentence
are names of people, places or companies (Proper nouns). Incorrect usage; …. were
plated onto Horse Blood Agar (HBA)’ correct usage …. The organisms were plated
onto horse blood agar (HBA).
References for these guidelines. These are in Vancouver format!!
1. Williams H, Walduck AK, Deighton M, Lawrie A. RMIT Microbiology Techniques
Manual 2013, 2nd Ed. RMIT University; 2013.
2. Jorgensen JH, Pfaller MA. Manual of Clinical Microbiology. Pfaller MA, Richter SS,
Funke G, Jorgensen JH, Landry ML, Carroll KC, et al., editors. Amer Society for
Microbiology; 2015. 1 p.
3. RMIT University. RMIT Identification Tables for Bacteria. 2009.
NOTE: Appropriate reference for websites eg. CDC documents is below. URL is in
this case actually part of the reference.
1. Author Surname Author Initial. Title [Internet]. Year Published [cited Date Accessed].
Available from: http://Website URL
Marking Rubric.
Students may view the marking rubric for case study reports on the Canvas site, a
copy is also attached to these guidelines.
Marking scheme for assignment (Case Study Report: Respiratory Tract infections)
Criteria Mark
Appropriate structure- and clarity,coversheet with correct info, understanding what
goes into “introduction”, “methods”, “results”, “discussion”sections. 4
Scientific English- including the correct tense, correct use of species names, italics,
correct terms for reporting 3
Materials and Methods- logical description, succinctly described, correctly referenced 3
Organism ID- workflow indicated, use of sufficient tests to accurately identify isolate
to species level, correct results. 5
Results- clear layout, good use of figures and/ or tables 3
Discussion -of results, clear, concise, related back to case notes, points on symptoms,
pathogenesis and treatment addressed 6
Referencing, (present, methods clearly referenced Vancouver format, adequate
reference to peer- reviewed literature), other aspects 3
Laboratory Report (appropriate information, clarity) 4
Original laboratory notes, attached and of good standard 4
Total 35