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 - 2026
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 - First Nations Knowledges | ||||||
| 11 - 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
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
IT Resources
- CQUniversity Student Email
- Internet
- Unit Website (Moodle)
All submissions for this unit must use the referencing styles below:
For further information, see the Assessment Tasks.
m.s.gregory@cqu.edu.au
Week 1
Begin Date: 13 Jul 2026Module/Topic
Phase 1: Reactivation & Clinical Framing
W1: Clinical Microbiology Foundations
Chapter
1 and 2
Events and Submissions/Topic
Tutorial - Assessment Expectations and Using AI
Week 2
Begin Date: 20 Jul 2026Module/Topic
Phase 1: Reactivation & Clinical Framing
W2: Diagnostic Anchor Framework (Signs/Symptoms → Test → Diagnosis→ Treatment)
Chapter
3
Events and Submissions/Topic
AT1: W2 Tutorial groupwork + individual reflection
Week 3
Begin Date: 27 Jul 2026Module/Topic
Phase 2: System-based Learning
W3: Respiratory & ENT Diagnosis
Chapter
69
Events and Submissions/Topic
AT1: W3 Tutorial groupwork + individual reflection
Week 4
Begin Date: 03 Aug 2026Module/Topic
Phase 2: System-based Learning
W4: GIT & Hepatobiliary Diagnosis
Chapter
74
Events and Submissions/Topic
AT1: W4 Tutorial groupwork + individual reflection
Week 5
Begin Date: 10 Aug 2026Module/Topic
Phase 2: System-based Learning
W5: Urogenital & STI Diagnosis
Chapter
73
Events and Submissions/Topic
AT1: W5 Tutorial groupwork + individual reflection
AT2a: AI Essay Critique due
Week 6
Begin Date: 17 Aug 2026Module/Topic
Phase 2: System-based Learning
W6: Skin, Soft Tissue, Joint & Bone Diagnosis
Chapter
75
Events and Submissions/Topic
AT1: W6 Tutorial groupwork + individual reflection
AT2b: AI Essay Critique - Peer Review with Feedback Fruits
Vacation Week
Begin Date: 24 Aug 2026Module/Topic
Chapter
Events and Submissions/Topic
AT3: ROK Residential School (Wed-Fri)
Week 7
Begin Date: 31 Aug 2026Module/Topic
Phase 3: High Complexity
W7: CNS & Ocular Diagnosis
Chapter
70 and 71
Events and Submissions/Topic
AT1: W7 Tutorial groupwork + individual reflection
AT2c: AI Essay Critique Feedback Reflection
Week 8
Begin Date: 07 Sep 2026Module/Topic
Phase 3: High Complexity
W8: Bloodborne Infections & Sepsis
Chapter
67
Events and Submissions/Topic
NO TUTORIAL THIS WEEK
AT3: BDG Residential School (Wed-Fri)
Week 9
Begin Date: 14 Sep 2026Module/Topic
Phase 4: Systems Thinking & Public Health
W9: Zoonoses & 'One Health'
Chapter
3
Events and Submissions/Topic
AT1: W8 Tutorial groupwork + individual reflection
Week 10
Begin Date: 21 Sep 2026Module/Topic
Phase 4: Systems Thinking & Public Health
W10: Epidemiology
Chapter
3
Events and Submissions/Topic
AT1: W9 Tutorial groupwork + individual reflection
Week 11
Begin Date: 28 Sep 2026Module/Topic
Phase 4: Systems Thinking & Public Health
W11: Emerging & Exotic Infections
Chapter
3
Events and Submissions/Topic
AT1: W10 Tutorial groupwork + individual reflection
Week 12
Begin Date: 05 Oct 2026Module/Topic
Exam Preparation
Chapter
All unit materials
Events and Submissions/Topic
AT1: W11 Tutorial groupwork + individual reflection
Exam Week
Begin Date: 12 Oct 2026Module/Topic
Chapter
Events and Submissions/Topic
AT3: End of Term Online Test
Assessment 4: End-of-Term Online Test Due: Exam Week Tuesday (13 Oct 2026) 10:00 am AEST
Vacation/Exam Week
Begin Date: 19 Oct 2026Module/Topic
Chapter
Events and Submissions/Topic
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). 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 materials
2-hour tutorial (compulsory, in-person and assessable Weeks 2-12)
3-5 hours of self-directed study
3-5 hours of assessment preparation
Recordings of lectures 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.
Assessment Security Level - Medium
GenAI permitted under controlled conditions with mandatory real-time verification. 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 with appropriate citations provided.
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 maximum 1 page response applying the 'What? So What? Now What? 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 demonstrate use of appropriate 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
This assessment develops the real-world skills of working ethically and strategically with Generative AI (GenAI) in clinical diagnostic microbiology. Students will navigate a three-stage process to evaluate the accuracy of AI-generated medical information and participate in professional peer-to-peer feedback.
The task consists of three steps:
(a) Drafting & Technical Evaluation (Due: Thursday 6 Aug 11:59pm, Week 4): Students instruct a Large Language Model (LLM) of choice to generate a 500-word academic essay on an application where AI has been used to support clinical microbiology diagnostic processes. Students then annotate the essay to verify the accuracy of claims using reliable clinical sources and provide a summation of identified strengths and weaknesses relative to their specific essay.
(b) Peer Review (Due: Thursday 19th Aug 11:59pm, Week 6): Using Feedback Fruits, students will be randomly allocated two peer submissions to review. Students evaluate the quality of their peers' annotations and the rigor of their technical factchecking.
(c) Final Submission & Reflection (Due: Thurs 3rd Sept 11:59pm, Week 7): Students will write a single consolidated reflection using the 'What? So What? What now?' framework.
To support this task, further detailed information, examples of potential prompts, potential topic options and marking criteria will be provided on the unit Moodle site.
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 each component of the task with last date for submission for Part (a) 9/8/2026, Part (b) 23/8/2026 and Part (c) 6/9/2026.
Marks will be available to students within two weeks of their Part (c) 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 critique (40 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 strucutue, clarity, and scientific communication (10 marks)
Technical Analysis of AI Output (20 marks total)
- insights into strengths and weaknesses of AI-generated content (10 marks)
- depth of critical evaluation of accuracy, bias, and limitations (10 marks)
Quality of Peer Review (15 marks)
- constructiveness and specificity of feedback
- demonstrated engagement with peer work
- ability to evaluate annotation quality and verification rigor
Integrated reflection on AI, LLM use and peer review (25 marks total)
- Integration of learning (10 marks)
- Depth of critical reflection (10 marks)
- Application to future practice (5 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
The 3-day residential school is a compulsory requirement. It provides an authentic, high-stakes clinical laboratory environment where you will apply technical diagnostic skills in a PC2 facility. To successfully complete this requirement, you must demonstrate professional practice, technical competency, and clinical reasoning through four integrated components.
The Four Components of Completion
1. Pre-laboratory Test (Engagement & Safety) Due Fri 9:00am ROK 20th Aug, BDG 3rd Sept. Prior to attending the first laboratory session, you must complete an online pre-laboratory test on Moodle. This test verifies your independent mastery of foundational laboratory protocols, PC2 safety requirements, and the technical procedures outlined in the residential school manual. You must gain 100% but may have as many attempts as required.
2. Clinical Laboratory Workbook (Technical Competency) Throughout the residential school, you will maintain a comprehensive laboratory workbook documenting your diagnostic investigations of clinical isolates.
3. Ward-Style Oral Presentation (Clinical Reasoning) In the final session, as part of a group, you will deliver a professional, ward-style oral presentation of one "wet-lab" case you investigated during the residential school.
4. Critical Integration Reflection (Reflective Practice) Due Monday 9:00am after residential school ROK Aug 31st BDG Sept 4th. Following the conclusion of the residential school, you will submit a single critical reflection using the 'What? So What? Now What?' framework, that synthesises your learnings from both the wet-lab and AI components of the residential school.
Assessment Security Level: Medium
AI Guidance Level 2: GenAI may be used to brainstorm for reflective writing and refine the structure of the oral presentation, provided human judgement and process documentation are evidenced.
Pre-lab test will be due Friday 9:00am prior to the week of residential school. For ROK 21st Aug & BDG 4th Sept. Laboratory manuals will be marked progressively throughout the residential school. Oral presentation during the Friday of residential school. Post residential school reflections will be due on the Monday 9:00 AM following residential school ROK 30th August, BDG 14th Sept. The automated 72hr extension is not available for this assessment task.
Pre-lab test will available before 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) Successful completion of all pre-test questions accurately.
(ii) Confirmation of experimental completion of works in a laboratory manual
(iii) Satisfactory-level presentation of a component of the ward-round presentation
(iv) 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
This comprehensive online test assesses your ability to synthesise the clinical diagnostic microbiology (CDM) technical content covered throughout the entire term (Weeks 1–12). You will be required to apply clinical reasoning to complex infectious disease scenarios, moving from initial symptoms to definitive diagnosis and basic management.
Format and Structure: The test consists of 5 mandatory integrated clinical case studies, each worth 20 marks (100 marks total).
Each case study mirrors the "Diagnostic Anchor Framework" used in tutorials and includes a combination of multiple-choice (MCQ), short-answer (SAQ), and extended-response questions.
Across the 5 cases, you will be assessed on all 11 unit topics.
The test utilises sequential navigation in Moodle. You must submit your answers for the clinical presentation stage (e.g., provisional diagnosis) before the system discloses subsequent laboratory data.
Timing: You will have a total of three (3) hours to complete the test once commenced.
Availability: The test will open at 10:00am on Monday 12th October, 2026 and will close at 10:00am on Tuesday 13th of October, 2026.
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.
Assessment Security Level: Medium
Exam Week Tuesday (13 Oct 2026) 10:00 am 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 are aligned with Unit Learning Outcomes 1–5.
Marks are awarded based on:
1. Accuracy of provisional and definitive identifications.
2. Rigor of technical justifications for specimen collection and test selection.
3. Depth of pathophysiology and virulence factor analysis.
4. Appropriateness of management strategies and public health reporting.
To support this task, further detailed information, including technical guides for sequential navigation and case study exemplars, will be provided on the unit Moodle site.
- 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?
