ONPS2118 Assignment 1 – Wound Isolates Report

This assignment is worth 25% of the final assessment.
Due Date:
Check the date for your class
Length – 2200 words +/- 10%
(Word count does not include references and tables).

Assignment:
Each student will be allocated overnight cultures of a wound swab on day 1 of the exercise.
Your task is to perform an identification of the organism/s in the swab you have been allocated over 3 days (practical classes in weeks 5-7) using biochemical tests and appropriate media. This will require you to:

1. Identify the organisms involved using appropriate media, workflow, biochemical tests.
2. Write a brief laboratory 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 methods, workflow and results of the test you used to identify the pathogens, and to discuss your findings. In addition, you will research and discuss the type of wound usually associated with this pathogen, symptoms, pathogenesis and treatment of the pathogens you identify.

Format
Your Wound Isolate Report must have the following structure:
• 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 in each section are given below. These guidelines and the marking rubric can also be downloaded here.

Please note correct formatting and referencing are part of the assessment criteria and marks will be deducted if format is not correct. The marking scheme is shown at the end of this document.

Cover sheet.
Please include a cover sheet with your name, student number, a word count ( you can exclude tables and references), practical group and demonstrator, the name of your practical partner, and the identification code of your unknown organism.
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. eg. “Overnight cultures on HBA were examined and suspicious colonies were picked for identification”
The methods section needs only to be brief, and should be written so that the work could be repeated by another student in the class.
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.
Note: The methods section of your report will probably be very similar so for other students this is not a problem.

Results
Your results section should be organized 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 whether 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 Streptococcus 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
This report is very brief and should only contain the information that would be reported back to the clinician.
Use the Report pus.docx to complete the 1 page laboratory report on your wound swab (download template from the Practical classes page on Canvas site). 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.
After you have decided which type of wound your isolate came from, you can write this as the site in your lab report
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. If no case notes were received, then discuss the type of wound and or patient that is usually associated wth this pathogen. 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 both the pathogens that were isolated in the case study under investigation, with appropriate reference to the scientific literature (approx. 3-10 references each). Your discussion should address the following points for each pathogen you isolated:
• Type of wound and or patient type usually associated with this pathogen

• Symptoms, duration and possible complications of infection
• Brief discussion of how pathogenesis of infection leads to the symptoms
• Usual treatment recommendations

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 general rule, the information on websites is not peer-reviewed and is therefore not acceptable as references for a university report. Government health department websites (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 processor (Word or Pages) or PDF document, and submit using the Turnitin link.
Questions about your Turnitin score? Check the FAQ General formatting requirements for scientific reports:
• Organism names are always italicized.
• The first time an organism is mentioned by name, the name must be written out in full. Afterward, 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 it 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 an explanation.

• Be careful with the use of capitals. The only words that are capitalized midsentence are names of people, places or companies (“Proper nouns”).
• Incorrect usage: “The organism was plated onto Horse Blood Agar (HBA)”.
• Correct usage “The organisms were plated onto horse blood agar (HBA)”.

Reference list for these instructions. These are in Vancouver format!

Williams H, Walduck AK, Deighton M, Lawrie A. RMIT Microbiology Techniques Manual 2013, 2nd Ed. RMIT University; 2013.

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.

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.

Author Surname Author Initial. Title [Internet]. Year Published [cited Date Accessed]. Available from: http://Website URL