ONPS1054 Assignment 1 – Wound Isolates Report


ONPS1054 Assignment 1 – Wound Isolates Report

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ONPS1054 Assignment 1 – Wound Isolates Report
This assignment is worth 15% of the final assessment.
Due Date:
Thursday Class Friday May 5, 2018 midnight
Tuesday Class Wednesday May 9, 2018. midnight
Length – 2000 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 other
students- this is not a problem.
Results
Your results section 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 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 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 is very brief and 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 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.
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 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 processor ( Word or
Pages) or PDF document, and submit using the Turnitn link.
Questions about your Turnitin score? Check the FAQ
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: “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!
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 are advised to review the marking scheme below
when preparing their report.
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 ( Accurate, dates,
logical, detailled) 4
Total 35

 

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An unknown mixture A was handed to me by our demonstrator Heather, which was 2 plates : first one was divided in HBA and MCA incubated aerobically with growth of colonies on both.

The second one was HBA incubated anaerobically with growth of colonies on it

 

Mix A

Growth on medium:

O2 , 35°C, 24 h Mac conkey MCA : cream colonies

No lactose fermentation on MCA

 

O2 , 35°C, 24 h horse blood agar HBA: large grey colonies

No haemolysis on HBA

AnO2 , 35°C, 24 h horse blood agar : white colonies

Haemolysis on HBA

Then Heather (our demonstrator) gave us pure AnO2 on schaedler blood agar SBA :

White colonies

2 zones of haemolysis: complete haemolysis and partial haemolysis

 

Identification :

Gram stain((2) p8)

Isolate 1  from aerobic culture : rod gram negative

Isolate 2 from anaerobic culture: rod gram positive square ended

After distinguishing our unknown isolate from the growth on HBA and MCA and using the gram stain appearance we were able to do further test for each isolates.

Table 1.1: Identification test results for isolate 1

Test Result
Growth in air +
Growth on mac conkey +
Oxidase
Catalase +

 

 

 

Isolate 1 is in Family Enterobacteriacae  (table 12, page 53 ) Identification table for bacteria.

 

 

 

 

Table 2.1 : Identification test results for isolate 1 related to family Enterobacteriacae

Test Result
Motility 37°C +
Lactose fermentation on MCA
Xylose
Mannitol +
ONPG
Urease +
H2S production (Kligler)
Indole production +
Ornithine decarboxylase
Citrate utilization +

 

Based on our test results Isolate 1 is Providencia rettgeri (table 13, page 55 and table 15, page 59)

 

Identification for isolate 2 rod gram positive

Table 1.3: Identification test results for isolate 2.

Test Result
Growth in air
Growth anaerobically +
Growth on HBA +
Haemolysis on HBA 2 zones partial and complete haemolysis

 

Based on the results in table 1.3 and our gram stain appearance, our isolate 2 is Clostridium because Eubacacterium have a very irregular shape from coccobacilli to long rods and many species are fastidious ((3) p31).

Table 1.4: Biochemical test results for isolate 2

Test Result
Meat digestion
Litmus milk:

A= acid

C= coagulation of casein

G= gas

D= digestion of casein

AGC

+

+

+

EYA – Lecithinase +
           Lipase

 

Our isolate 2 is Clostridium perfringens((3)p 37)

Materials and Methods :

Medical microbiology 1 semester 2018 (1)

Medical microbiology techniques manual(2)

Identification tables for bacteria (3)

Microbiological technique manua,l February 2000 (4)

Microbiological technique manual (5)

The procedures(1), lab techniques(2) and bacterial identification tables(3) were obtained from our university names cited above

Test for isolate 1: Oxidase test ((2) p 23)    catalase test ((2) p10)  all tests done for isolate 1 are from (2) and identification results from (3).

Test for isolate 2 : meat digestion ((4) p 144)

Litmus milk ((5) p169)

EYA lecithinase ((5) p 59)  EYA lipase ((5) p p55)

 

Word count: 2000 words (+/- 10%) Total word count, (not including references, tables and figures)

Choose one of the scientific journal articles from the list below and write a review of the article with the following sections:

  1. Cover sheet- your name, the article you are reviewing, word count.
  2. Summary and Background
  3. Critical Review

Your critical review should be written in 2 sections:

  1. Summary of background and contents of paper (50% of marks)

Write at 2 or 3 pages on the background and contents of the paper, this should cover the background of the study so that you can put it in context and its importance in microbiology. Then write and a summary of what was done in the study and its outcomes.

You should write a short review of the background of the article to make its context in medical microbiology clear, this should include a short discussion of the other relevant published studies in the area. This is likely to include the studies referenced in the article you are reading, but may also include other studies they don’t mention. In the case of a very novel technique there may be few other published studies, in which case you should focus your discussion of the background of the paper on the problem that it is addressing and its significance.

Your summary of the work done in the paper should cover the introduction, materials and methods, results and discussion sections.  You may either write a section under each of these sections or write an overall “summary” of the contents of the paper, provided all sections are mentioned in your report.  Don’t forget to read any supplementary information that is linked to the paper.

As this paper is written primarily for microbiologists working in medical microbiology, there may be some sections that are not explained in the detail that you need for your own understanding.  In that case, do some research of the scientific literature using a database such as PubMed and fill in the gaps.  Additional references used should be cited using the Vancouver referencing system.

  1. Critical Review. 50% of marks

The aim of this section is to show the examiner that you have understood the purpose, need for and content of the paper- particularly in relation to other published work in the field.

Present a critical review of the article.  The following points will be helpful in the review:  It is not essential that you answer all of these questions (not all will be directly relevant to the article you have chosen), or even that you write your review in the order set out below, but use these points as a guide and check list.

The major focus of the critical review should be the findings of the study, or the experimental approach in relation to other published work in the field.

You can point out typographic and grammatical errors, or state whether you think some parts of the paper are too long, or difficult to understand, but do not devote a large part of your review to these issues.

Questions to consider when critically reviewing an article:

The following guidelines are modified from guidelines for reviewers of the European Journal of Microbiology and Infectious Diseases (EJMID):  Permission was obtained from the journal to reproduce this information.

General:

  • study? How original is this paper? For example, is it simply applying the methods used in another study to a new situation or is the idea completely novel?
  • Are there any published studies on the same topic?
  • What is unique about this study?
  • How important is this study to medical microbiology?
  • Are there any sections of the paper that are too long and could be shortened?
  • Is the writing clear, simple and concise?

Abstract

  • Does the abstract outline the aims of the study, main methods, results and conclusions?

 Introduction

  • Does the introduction state the research question to be addressed?
  • Is sufficient background information provided for readers to understand the question?

 Materials and methods

  • Are the methods appropriate to the research question/s being addressed?
  • Are the methods described in sufficient detail to be repeated by another microbiologist? Is any important information missing? 
  • Have references been provided for all the methods, except new ones developed by the authors?

 Results

  • Are there any results in the text that would be better presented in a table or figure?
  • Is there any material presented in a table or figure that would be better presented in the text? Is there any repetition of results in text AND a table or figure?

Discussion

  • Do you agree with the author’s interpretation of results? And the significance of the study? (You are free to agree or disagree- you need to justify your statements with explanations and or reference to relevant scientific literature)
  • Have the authors clearly distinguished between their own results and the results of others?
  • Are there any negative findings in the results that could be important but have not been discussed?
  • Have the authors adequately discussed their results and conclusions in relation to the results of other investigators?
  • Are the author’s conclusions acceptable and is there sufficient evidence for the conclusions they have drawn?
  • Do the findings of the study agree with, or contradict other studies? Has this been discussed?
  • Are there any relevant studies on this topic that have not been referred to or discussed by the authors?

 References

  • Check that all statements in the text that require a reference are properly referenced.

Tables and figures

  • Do all tables and figures have complete legends so that they can be understood without reference to the text?
  • Could any of the tables and figures be omitted or simplified?

Ethics and Conflicts of interest:

If relevant-  Were all studies approved by the relevant animal or human ethics committees?

Do you think there could be any conflict of interest regarding the results of the study? Are any conflicts declared? Are there commercial interests in the study?

 

General Requirements for assignment.

Reports in Microbiology are written in scientific format. The purpose of scientific writing is to inform the reader of the procedures and results of an experiment. The introduction section provides the background and context for the reader. The writing should be clear, logical and easy to understand. For this reason scientific writing usually follows a defined format.

The report should be word-processed. Use font 12 or higher and double space the report. Include a computer word count and usually at least one table or figure with results should be included. Pages should be numbered. Please use the Vancouver Referencing style in your report. The easiest way to do this is to use referencing software (eg. Endnote).

Students can access Endnote software through the RMIT library. Please see: http://www1.rmit.edu.au/library.

Please ask for advice on installing and using Endnote at the library or IT. Endnote training sessions are run on a regular basis.

In a scientific report, it is important to write as clearly and precisely as possible. After writing the first draft, read the report and see if you can reduce the word count by using good precise scientific writing. The word limit for any report does not include tables, figures or reference list. This word limit is for the entire report, not for each individual section.

 

To get your Assignment/Homework solutions;

Simply Click ORDER NOW and fill your paper details. Our support team will review the assignment(s) and assign the right expert whose specialization is same to yours to complete it within your deadline. Our Editor(s) will then review the completed paper (to ensure that it is answered accordingly) before we email you a complete paper

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