Respiratory tract infection

Respiratory tract infection

Respiratory tract infection

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.



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.


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 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 other students- this is not a problem.


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

This report should only contain the information that would be reported back to the clinician.

Use the template provided to complete the 1 page laboratory report on your sputum (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.


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.


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 colithen 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