Overview
In this unit you will build upon the foundational knowledge gained in microbiology and apply it in a clinical context. You will explore the role of commensal flora in maintaining health and the role of bacterial, fungal, viral, protozoal and helminthic pathogens in disease and learn about their detection, identification, treatment and management. You will also consider new and emerging technologies and you will also explore the concept of 'One Health' while considering emerging diseases, pandemics and zoonoses as well as the emergence of antimicrobial resistance.
Details
Pre-requisites or Co-requisites
Pre-requisite: MBIO19012
Important note: Students enrolled in a subsequent unit who failed their pre-requisite unit, should drop the subsequent unit before the census date or within 10 working days of Fail grade notification. Students who do not drop the unit in this timeframe cannot later drop the unit without academic and financial liability. See details in the Assessment Policy and Procedure (Higher Education Coursework).
Offerings For Term 2 - 2025
Attendance Requirements
All on-campus students are expected to attend scheduled classes - in some units, these classes are identified as a mandatory (pass/fail) component and attendance is compulsory. International students, on a student visa, must maintain a full time study load and meet both attendance and academic progress requirements in each study period (satisfactory attendance for International students is defined as maintaining at least an 80% attendance record).
Recommended Student Time Commitment
Each 6-credit Undergraduate unit at CQUniversity requires an overall time commitment of an average of 12.5 hours of study per week, making a total of 150 hours for the unit.
Class Timetable
Assessment Overview
Assessment Grading
This is a graded unit: your overall grade will be calculated from the marks or grades for each assessment task, based on the relative weightings shown in the table above. You must obtain an overall mark for the unit of at least 50%, or an overall grade of 'pass' in order to pass the unit. If any 'pass/fail' tasks are shown in the table above they must also be completed successfully ('pass' grade). You must also meet any minimum mark requirements specified for a particular assessment task, as detailed in the 'assessment task' section (note that in some instances, the minimum mark for a task may be greater than 50%). Consult the University's Grades and Results Policy for more details of interim results and final grades.
All University policies are available on the CQUniversity Policy site.
You may wish to view these policies:
- Grades and Results Policy
- Assessment Policy and Procedure (Higher Education Coursework)
- Review of Grade Procedure
- Student Academic Integrity Policy and Procedure
- Monitoring Academic Progress (MAP) Policy and Procedure - Domestic Students
- Monitoring Academic Progress (MAP) Policy and Procedure - International Students
- Student Refund and Credit Balance Policy and Procedure
- Student Feedback - Compliments and Complaints Policy and Procedure
- Information and Communications Technology Acceptable Use Policy and Procedure
This list is not an exhaustive list of all University policies. The full list of University policies are available on the CQUniversity Policy site.
Feedback, Recommendations and Responses
Every unit is reviewed for enhancement each year. At the most recent review, the following staff and student feedback items were identified and recommendations were made.
Feedback from Student Unit Evaluation.
Some students had difficulty in unpacking requirements for the clinical case studies.
Consider reviewing tutorial content to ensure clarity and provide consistent exemplars of clinical case studies.
Feedback from Staff Reflection
Limited turnaround time between receiving feedback on Assessment 1 and the submission deadline for Assessment 2.
Consider increasing the time between the submission of Assessment 1 and Assessment 2 to allow adequate reflection on feedback and its application to subsequent work.
- Discuss the clinical significance, laboratory detection, treatment and management of commensal flora, pathogens and opportunistic pathogens of each of the human body systems
- Appraise the use of standard and emerging techniques for detecting and identifying bacteria, viruses, fungi and parasites causing human disease
- Evaluate the use of antimicrobial chemotherapeutic agents and vaccines in the treatment and prevention of infectious diseases caused by bacteria, viruses, fungi and parasites
- Discuss the mechanisms of antimicrobial resistance in bacteria, viruses, fungi and parasites
- Compare and contrast emerging infectious diseases, including definitions, factors leading to disease emergence, monitoring and intervention strategies.
- Demonstrate a critical understanding of how artificial intelligence technologies are impacting clinical diagnostic microbiology and healthcare.
Alignment of Assessment Tasks to Learning Outcomes
Assessment Tasks | Learning Outcomes | |||||
---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | |
1 - Group Work - 40% | ||||||
2 - Written Assessment - 10% | ||||||
3 - Laboratory/Practical - 0% | ||||||
4 - Online Test - 50% |
Alignment of Graduate Attributes to Learning Outcomes
Graduate Attributes | Learning Outcomes | |||||
---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | |
1 - Communication | ||||||
2 - Problem Solving | ||||||
3 - Critical Thinking | ||||||
4 - Information Literacy | ||||||
5 - Team Work | ||||||
6 - Information Technology Competence | ||||||
7 - Cross Cultural Competence | ||||||
8 - Ethical practice | ||||||
9 - Social Innovation | ||||||
10 - Aboriginal and Torres Strait Islander Cultures |
Textbooks
Bailey and Scott's Diagnostic Microbiology
15th edition (2021)
Authors: Patricia M Tile
Elsevier
St Louis St Louis , MO , USA
ISBN: 9780323354820
You may have already purchased this text in the previous unit, BMSC12011. Both eBook and paper copies can be purchased from the CQUni Bookshop here: Bookshop
You may have already purchased this text in the previous unit, BMSC12011. Both eBook and paper copies can be purchased from the CQUni Bookshop here: Bookshop
Bench to Bedside: Diagnostic Microbiology for the Clinicians
Edition: 1st (2018)
Authors: Khardori, Nancy
Taylor & Francis Group
ISBN: 9781351643726
Digital version available via the library
Digital version available via the library
IT Resources
- CQUniversity Student Email
- Internet
- Unit Website (Moodle)
- ZOOM
All submissions for this unit must use the referencing styles below:
For further information, see the Assessment Tasks.
m.s.gregory@cqu.edu.au
Module/Topic
Clinical Diagnostic Microbiology Contextualisation and Overview: Introduction, revision of microbial structure, function and taxonomy
Chapter
1 and 2
Events and Submissions/Topic
Tutorial - Assessment Expectations
Module/Topic
Colonisation vs Infection vs Disease
Chapter
3
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 2 content (Colonisation, Infection & Disease)
Module/Topic
Respiratory Infections including Ear, Nose & Throat Infections
Chapter
69
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 3 content (Respiratory Infections including Ear, Nose & Throat Infections)
Module/Topic
Gastrointestinal & Biliary Infections
Chapter
74
Events and Submissions/Topic
BDG Tutorial Groupwork Assessment on Week 4 content (Gastrointestinal & Biliary Infections)
Module/Topic
Urogenital Infections including Sexually Transmitted Infections
Chapter
73
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 5 content (Urogenital Infections including Sexually Transmitted Infections)
Module/Topic
Chapter
Events and Submissions/Topic
Preparing for Assessment 2 submission in Week 6
Module/Topic
Skin, Soft Tissue, Joint & Bone Infections
Chapter
75
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 6 content (Skin, Soft Tissue, Joint & Bone Infections)
Assessment 2: AI Assignment Due 23:59 Thursday 28/8/25
Assessment Task 2: AI and Clinical Diagnostic Microbiology Due: Week 6 Tuesday (26 Aug 2025) 11:59 pm AEST
Module/Topic
Blood Borne Infections including Lymphatics & Sepsis
Chapter
67
Events and Submissions/Topic
ROK Residential School (Wed-Fri)
BDG Tutorial Groupwork Assessment on Week 7 content (Blood Borne Infections including Lymphatics & Sepsis)
Module/Topic
Central Nervous System including Ocular Infections
Chapter
70 and 71
Events and Submissions/Topic
BDG Residential School (Wed-Fri)
ROK Tutorial Groupwork Assessment on Week 7 content (Blood Borne Infections including Lymphatics & Sepsis)
Module/Topic
Zoonoses and "One Health"
Chapter
3
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 8 content (Central Nervous System including Ocular Infections)
Module/Topic
Epidemiology, epidemics & pandemics
Chapter
3
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 9 content (Zoonoses and "One Health")
Module/Topic
Emerging & re-emerging infections and "Exotic Infections"
Chapter
3
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 10 content (Epidemiology, epidemics & pandemics)
Module/Topic
Exam Preparation
Chapter
All unit materials
Events and Submissions/Topic
Tutorial Groupwork Assessment on Week 11 content (Emerging & re-emerging infections and "Exotic Infections")
Module/Topic
Chapter
Events and Submissions/Topic
Online Quiz Monday 13/10/25 11:00 - 13:00
Assessment 4: End-of-Term Online Test Due: Review/Exam Week Monday (13 Oct 2025) 10:00 pm AEST
Your Unit Coordinator for BMSC13021 Clinical Diagnostic Microbiology is Dr Sarah-Jane Gregory.
You can contact me using the forum on the unit Moodle page, alternatively by email (m.s.gregory@cqu.edu.au), on teams or by phone (07 4150 7750). The forum for this unit is regularly monitored and you can expect a response within 48 hours of posting your question.
Each week you will be expected to complete:
- 2-hour pre-recorded lecture
- 2-hour tutorial (compulsory, in-person and assessable Weeks 2-12)
- 3-5 hours of self-directed study
- 3-5 hours of assessment preparation
Online sessions will be facilitated via Zoom with links provided on the unit Moodle page.
Recordings of lectures and tutorials will be made available on the unit Moodle page.
This unit includes a Compulsory Residential School, and your attendance and completion of associated tasks is required to pass the unit.
1 Group Work
Tutorial Classes in Weeks 2-12 will be assessed with a combination of Group and Individual Assessment Tasks.
Level of GenAI use allowed:
AIAS Level 3: You may use AI to assist with specific tasks such as drafting text, refining and evaluating your work. You must critically evaluate and modify any AI-generated content you use.
PRIOR TO CLASS
Each Monday, two tutorial case studies with associated questions will be provided on Moodle.
Students will be expected to prepare their responses for questions 1 & 2 prior to the scheduled tutorial.
DURING CLASS
Part One: Case response development
Students will be allocated randomly to work on one of the two case studies during the tutorial.
They will discuss their responses to questions 1 & 2 with their assigned group and then provide a list of diagnostic test procedures they would like performed for the patient.
The results of these tests will then be provided to the group.
The tutorial group will then spend the remaining first hour developing a group response to questions 3-7. A minimum of two (2) students must work on any given question but the group should be across the entire response.
This response will be documented on the template provided on Moodle.
At the end of this time, each student will submit a copy of their group response to Moodle.
PART 2: Case response presentation (Second hour of tutorial)
Each member of the group will be required to orally present one component of their group response with a 20-minute allocation.
Group responses will be marked in real time and immediate feedback provided where information may be missing, insufficient in depth or incorrect. Written feedback will also be provided on the submitted document.
AFTER CLASS
Each week students will be provided with several prompts to support their integration of knowledge and professional practice. Students will individually write a response applying the CARL critical reflective writing framework.
This reflection will be due 24hrs after the completed tutorial.
Further extensive information and exemplars are available on the unit Moodle site.
There is no 72-hour grace period available for this assessment task.
Groupwork submissions are due at the 1hr mark of tutorials. Individual reflections are due by 5:00pm of the following day. There is no 72-hour grace period available for this assessment task.
Students will receive immediate feedback on their group submission during the 2nd hour of the tutorial. Students will receive written feedback on their group submission and individual components within two (2) weeks of submission.
Extensive assessment criteria will be provided on the unit Moodle site.
The mark for each tutorial (worth 4% of overall unit mark) will be a combination of groupwork submission (70%) and individual reflection (30%).
Group submissions will be marked regarding overall accuracy, demonstration of clinical reasoning and appropriate use of literature.
Individual reflections will be marked on depth of critical reflection, demonstrated insights and application of framework.
- Evaluate the use of antimicrobial chemotherapeutic agents and vaccines in the treatment and prevention of infectious diseases caused by bacteria, viruses, fungi and parasites
- Discuss the mechanisms of antimicrobial resistance in bacteria, viruses, fungi and parasites
- Compare and contrast emerging infectious diseases, including definitions, factors leading to disease emergence, monitoring and intervention strategies.
- Demonstrate a critical understanding of how artificial intelligence technologies are impacting clinical diagnostic microbiology and healthcare.
2 Written Assessment
Use a Large Language Model of your choice (egs OpenAI – ChatGPT, Anthropic Claude, Google Gemini etc) to curate information and instruct the AI write a 1000-word essay on the use of artificial intelligence technologies in one aspect of clinical diagnostic microbiology that aligns with the content topics of this unit.
Australian English should be used for the summary table and reflections.
Level of GenAI use allowed:
AIAS Level 4: You may use AI extensively throughout your work either as you wish, or as specifically directed in your assessment. Focus on directing AI to achieve your goals while demonstrating your critical thinking. Specifically, you may use it:
· To develop prompts
· To write the essay
· To brainstorm for reflective writing (include prompts and output for comparison to your final reflections)
· For spelling and grammar checking.
Submission will include:
· The name and version of the AI used
· A copy of the prompts used to generate the essay
· A copy of the annotated essay indicating areas of accurate and inaccurate information. Annotation should include verification statements (what sources did you use to verify content provided, citation, word count etc).
· A table summarising the strengths and weaknesses the AI had in generating the essay.
· Two short critical reflections (minimum 200 words each), using the CARL reflective writing. One focusing on what you have learnt about the use of AI-Ts in CDM and the other what you have learnt about using a LLM for research and writing in an educational context.
To support this task, further detailed information, examples of potential prompts and potential unit-aligned topic options will be provided on the unit Moodle site.
Week 6 Tuesday (26 Aug 2025) 11:59 pm AEST
Your assignment must be submitted using the provided template, available on the Moodle Site. Ensure the correct naming convention has been applied to the submitted file. The university 72hr grace period is available for this assessment task. Final submission with this extension in place will be Friday 28th Aug 11:59pm.
Marks will be available to students within two weeks of their submission. Individual and group feedback will be available after all students have submitted the assessment task.
A detailed marking rubric and information to support comprehension of the marking rubric will be provided on the unit Moodle site. Exemplars will also be provided to help set student expectations of marking.
Marked Out of 100 marks
Weighted 10% of total unit mark
Marking Scheme
AI-generated essay annotation (50 marks total)
- Identification of correct/incorrect information (10 marks)
- quality of annotations & comments (10 marks)
- use of reliable sources for verification process (10 marks)
- evaluation of presentation and structure (10 marks)
- depth of demonstrated critical thinking (10 marks)
Strengths Analysis (10 marks)
Weaknesses Analysis (10 marks)
Reflection on AI in Clinical Diagnostic Microbiology (15 marks)
Reflection on Using LLMs for Academic Work (15 marks)
Please refer to the marking rubric for details on how to achieve the different mark allocation.
- Discuss the clinical significance, laboratory detection, treatment and management of commensal flora, pathogens and opportunistic pathogens of each of the human body systems
- Appraise the use of standard and emerging techniques for detecting and identifying bacteria, viruses, fungi and parasites causing human disease
- Demonstrate a critical understanding of how artificial intelligence technologies are impacting clinical diagnostic microbiology and healthcare.
3 Laboratory/Practical
For this task, you will be required to attend a Block Practical where practical laboratory skills will be developed to allow you to better understand how pathogenic organisms may be isolated and identified and how antimicrobial sensitivity testing is performed, and it's use in directing antimicrobial therapy. You will be required to document the results of the tests performed and to draw conclusions on the identification and treatment options for the pathogens isolated.
The final half day of the residential school will involve you developing awareness and competencies associated with the use of artificial intelligence in modern clinical diagnostic microbiological practices.
There are two components to the assessment for residential school:
1. You will be required to complete a laboratory workbook and have your work signed off by an academic across the residential school activities.
2. Critical reflection on both wet lab practices and AI-Ts in Clinical Diagnostic Microbiology
The critical analysis and reflection will be submitted online and due the Monday following residential school. Monday 8/9/2025 11:49pm for ROK students and Monday 15/9/2025 11:49pm for BDG students
Level of GenAI use allowed:
AIAS Level 2 You may use Al for planning, idea development, and research. Your final submission should show how you have developed and refined these ideas. Specifically, you may use it for development of reflections only. Prompt and response information must be included in the submission.
Laboratory manuals will be marked progressively throughout the residential school. Post residential school reflections will be due on the Monday 9:00 AM following residential school ROK 8th August, BDG 15th August. The automated 72hr extension is not available for this assessment task.
Manuals will be returned at the end of the residential school. Reflections will be marked within two weeks of submission due date.
The residential school has a Pass/Fail marking allocation.
You will be assessed through:
(i) confirmation of experimental completion of works in a laboratory manual
(ii) appropriate critical analysis and reflection of competencies completed progressively throughout the residential school.
Further details regarding how to meet each of these requirements is available on the unit Moodle site.
- Appraise the use of standard and emerging techniques for detecting and identifying bacteria, viruses, fungi and parasites causing human disease
- Demonstrate a critical understanding of how artificial intelligence technologies are impacting clinical diagnostic microbiology and healthcare.
4 Online Test
For this task, you will be required to complete an online open book test that will be conducted in Week 12.
Level of GenAI use allowed:
AIAS Level 2: You may use AI for planning, idea development, and research. Your final submission should show how you have developed and refined these ideas. As this is not an invigilated examination, it is not possible to prohibit the use of AI. Should you choose to use AI it will affect your ability to successfully complete the assessment task in the time required so we recommend not relying on this strategy.
The test will consist of three (3) parts:
Part A: 30 multiple choice questions (1 mark per question, total of 30 marks)
Part B: 20 short answer style questions (1.5 marks per question, total of 30 marks)
Part C: Choose two (2) out of a total of four (4) clinical case study style questions where you are presented with a brief patient history. You are required to suggest a provisional and differential diagnosis and answer questions about the case or condition (20 marks per question, total of 40 marks)
The online test will be available to commence between 07:00 and 19:00 on Monday 13/10/25 (Week 13 Study period). Once commenced, you will have a total of three (3) hours to complete the test. You will not be permitted to exit and return to the quiz. After three (3) hours the quiz will automatically close. You are only permitted a single attempt.
The 72-hour grace period does not apply to this assessment.
Review/Exam Week Monday (13 Oct 2025) 10:00 pm AEST
All submissions are due on this day but submission time will be variable dependent on when students choose to commence the quiz. The 72-hour grace period does not apply for this assessment task.
Questions will align with all of the Unit Learning Outcomes:
1 - Discuss the clinical significance, laboratory detection, treatment and management of commensal flora, pathogens and opportunistic pathogens of each of the human body systems.
2 - Appraise the use of standard and emerging techniques for detecting and identifying bacteria, viruses, fungi and parasites causing human disease.
3 - Evaluate the use of antimicrobial chemotherapeutic agents and vaccines in the treatment and prevention of infectious diseases caused by bacteria, viruses, fungi and parasites.
4 - Discuss the mechanisms of antimicrobial resistance in bacteria, viruses, fungi and parasites.
5 - Compare and contrast emerging infectious diseases, including definitions, factors leading to disease emergence, monitoring and intervention strategies.
Mark allocation will be accordingly:
Part A: 30 questions; 1 mark per question, total of 30 marks
Part B: 20 questions; 1.5 marks per question, total of 30 marks
Part C: 2 questions; 20 marks per question, total of 40 marks
The online quiz will cover questions relating to the causative organisms of infectious diseases, their pathophysiology, isolation and identification, treatment, management and prevention. You will also explore the emergence of new pathogens and antimicrobial resistance. This will require you to demonstrate your knowledge of risk factors, clinical manifestations and pathophysiology of various diseases as well as the isolation and identification of specific pathogens. The test will be designed to incorporate questions from the wide variety of content covered throughout the entire term, enabling you to demonstrate your depth of understanding of the content. The use of case studies will also provide contextualisation and authenticity to the test.
This test utilises a combination of recognised techniques such as question banks, clinical scenarios, randomisation and automated submission to reduce the potential for academic misconduct.
- Discuss the clinical significance, laboratory detection, treatment and management of commensal flora, pathogens and opportunistic pathogens of each of the human body systems
- Appraise the use of standard and emerging techniques for detecting and identifying bacteria, viruses, fungi and parasites causing human disease
- Evaluate the use of antimicrobial chemotherapeutic agents and vaccines in the treatment and prevention of infectious diseases caused by bacteria, viruses, fungi and parasites
- Discuss the mechanisms of antimicrobial resistance in bacteria, viruses, fungi and parasites
- Compare and contrast emerging infectious diseases, including definitions, factors leading to disease emergence, monitoring and intervention strategies.
As a CQUniversity student you are expected to act honestly in all aspects of your academic work.
Any assessable work undertaken or submitted for review or assessment must be your own work. Assessable work is any type of work you do to meet the assessment requirements in the unit, including draft work submitted for review and feedback and final work to be assessed.
When you use the ideas, words or data of others in your assessment, you must thoroughly and clearly acknowledge the source of this information by using the correct referencing style for your unit. Using others’ work without proper acknowledgement may be considered a form of intellectual dishonesty.
Participating honestly, respectfully, responsibly, and fairly in your university study ensures the CQUniversity qualification you earn will be valued as a true indication of your individual academic achievement and will continue to receive the respect and recognition it deserves.
As a student, you are responsible for reading and following CQUniversity’s policies, including the Student Academic Integrity Policy and Procedure. This policy sets out CQUniversity’s expectations of you to act with integrity, examples of academic integrity breaches to avoid, the processes used to address alleged breaches of academic integrity, and potential penalties.
What is a breach of academic integrity?
A breach of academic integrity includes but is not limited to plagiarism, self-plagiarism, collusion, cheating, contract cheating, and academic misconduct. The Student Academic Integrity Policy and Procedure defines what these terms mean and gives examples.
Why is academic integrity important?
A breach of academic integrity may result in one or more penalties, including suspension or even expulsion from the University. It can also have negative implications for student visas and future enrolment at CQUniversity or elsewhere. Students who engage in contract cheating also risk being blackmailed by contract cheating services.
Where can I get assistance?
For academic advice and guidance, the Academic Learning Centre (ALC) can support you in becoming confident in completing assessments with integrity and of high standard.
What can you do to act with integrity?
