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Length – 2500 words +/- 10%
(Word count does not include references and tables).
Assignment: In class, work through the Week 3 bacterial infections of the gastrointestinal tract Case studies 1-4. Identify the organisms involved using appropriate media, workflow, biochemical tests, and serology as appropriate.
Write a report on these case studies using the format below. You are required to describe the method, workflow and results of your identifications, and to discuss your findings. In addition, you will research the symptoms, pathogenesis and treatment of these infections.
Format
The following headings should be used for Case Study reports:
- Cover sheet
- Introduction
- Materials and Methods
- Results
- Laboratory Report
- Discussion
- References
- Laboratory Notes- attach your original notes
Further details on what to include under these headings are given below.
Please note correct formatting and referencing are part of the assessment criteria.
Cover sheet.
Please include a cover sheet with your name, student number, practical group and demonstrator and the name of your practical partner.
In addition:
A word count (does not include references and tables) and Turnitin score (preferably a screen shot of your Turnitin receipt and score). Note: The methods section of your report will probably be very similar so other students- this is not a problem.
Case Study Report sections, important points to include:
Introduction
It is preferable to write one introduction encompassing several case histories rather than write a separate introduction for each Case Study.
The introduction should include general background information on the significance infections of the particular body system being studied, reasons for performing microbiological investigations on these patients, the expected outcome or benefit from such investigations.
The introduction should end with a brief statement that summarises the nature of the cases that were 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). You should also note any kits or commercial test kits that were used, including the manufacturer.
The simplest way to present this information is in a table 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)
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 document. You are required to refer to an easily accessible source with page numbers. The test descriptions in the RMIT technical manual are almost identical to those in the GERMM.
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 1,
| Test | Result |
| Growth in air | + |
| Growth on MCA | + |
| Lactose fermentation on MCA | – |
| Growth on HBA | + |
| Haemolysis on HBA | α |
| Lancefield group | D |
| Optochin | R |
If tables are used, the key points in the table should be briefly summarised in manner that explains the workflow, e.g. “Organism A was identified to species level using from 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 pneumonia ( Table 4 (3)).
Alternatively you may wish to make a flow diagram to illustrate the workflow and process of identification. Remember that all charts need a descriptive figure legend.
Example of flow chart.
Make sure that your results section includes a statement of what the organism you identified is!
Laboratory Report to Requesting Physician
Use the template provided to complete the 1 page laboratory report (download template from Case study report folder on Blackboard site). This report should only contain the information that would be reported back to the clinician. You demonstrator can give advice if you are unsure.
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.
Refer to the example report on the following page.
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.
Examples for Laboratory reports
Example 1.
Patient’s name, identification and other details
Faeces
Dates of collection and processing
Culture Shigella sonnei isolated
Campylobacter spp. not isolated
Salmonella. spp. not isolated
Example 2.
Patient’s name, identification and other details
Sputum
Dates of collection and processing
Gram Numerous polymorphs, moderate mixed organisms resembling oral flora and a heavy growth of Gram-positive diplococci resembling S. pneumoniae.
Culture Heavy growth of S. pneumoniae, moderate growth of oral flora.
susceptible to …..