Outline

Overview

This unit is designed to further develop an interest in, and understanding of, medical microbiology from the introduction in Intermediate Microbiology. Through an examination of microbial structure, virulence, body defences and pathogenesis, the process of acquisition and establishment of disease is covered. The unit is divided into three themes: 1. Clinical Microbiology: host defences, infections, virulence mechanisms; 2. Public health microbiology: epidemiology, international public health, transmission, water and food borne outbreaks; 3. Emerging and re-emerging diseases: the impact of societal change with respect to triggering new diseases and causing the re-emergence of past problems, which are illustrated using case studies. The practical component is designed to enhance students' practical skills and to complement the lecture series. In these practical sessions experience will be gained handling live, potentially pathogenic microbes. Clinical tutorial sessions underpin and investigate the application of the material covered in the practical classes.

Unit details and rules

Unit code	MICR3011
Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prohibitions ?	MICR3911
Prerequisites ?	[6cp from (BIOL1XX7 or MBLGXXXX or GEGE2X01 or GENE2002) and 6cp from (MEDS2004 or MICR2X22 or MIMI2X02)] OR [BMED2401 and BMED2404]
Corequisites ?	None
Assumed knowledge ?	MICR2X21 or MICR2024 or MICR2X31
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Helen Agus, helen.agus@sydney.edu.au
Laboratory supervisor(s)	Aidan Kane, aidan.kane@sydney.edu.au
Lecturer(s)	Timothy Newsome, timothy.newsome@sydney.edu.au
	Peter Reeves, peter.reeves@sydney.edu.au
	Dee Carter, dee.carter@sydney.edu.au
	Christopher Harmer, christopher.harmer@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam	Online examination Written exam: 40 multiple choice (50%); short answer style (50%)	60%	Formal exam period	2 hours
Outcomes assessed:
Online task	Compulsory compliance quiz Online quiz	0%	Week 02	No restriction
Outcomes assessed:
Assignment	Unknown case study: group worksheet 2 plan Answer questions in Worksheet	3%	Week 04	No limit
Outcomes assessed:
Tutorial quiz	Quiz 1 Online quiz	0%	Week 06	30 minutes
Outcomes assessed:
Online task	Canvas eLearning quizzes wk8 Online quiz	0%	Week 08	No restriction, multiple attempts
Outcomes assessed:
Tutorial quiz	Quiz 2 Online quiz	10%	Week 10	30 minutes
Outcomes assessed:
Presentation	Unknown case study: presentation Online Zoom presentation of case study process and findings	5%	Week 11	10 minutes
Outcomes assessed:
Online task	Canvas elearning quizzes wk13 Online quiz, multiple choice	0%	Week 13	No restriction, multiple attempts
Outcomes assessed:
In-semester test	Online theory of practical exam Canvas timed test: Multiple-choice questions	15%	Week 13 Due date: 29 May 2020 at 16:00	60 minutes plus 10 minutes reading time
Outcomes assessed:
Skills-based evaluation	Unknown case study: labarchives online work Labarchives notebook assessment of activity, entries and group interaction	7%	Weekly	Collaborative across 6 prac sessions
Outcomes assessed:
= hurdle task ? = group assignment ?

Assessment summary

Compulsory compliance quiz: Online quiz in Canvas MICR30X11 website.
Quiz 1: Online formative multiple choice answer questions.
Quiz 2: Online quiz in Canvas MICR3X11 website: multiple choice answer questions.
Unknown case study - group worksheet 2 plan: The case study is a group activity that is designed to allow you to apply the logic, analytical process and methodology that you will learn in the formal exercises in the rest of the practical classes to the isolation, identification and reporting of a specific case of infection that has been caused by an 'unknown' pathogen.
Unknown case study - group work: Investigate the cause of a scenario-based infection, designed to allow you to apply the logic, analytical process and methodology that you have learned in the formal exercises in the rest of the practical classes to the isolation, identification and reporting of a specific case of infection that has been caused by an 'unknown' pathogen. Various group self-directed practical activities spanning 6 weeks of semester, culminating in a group presentation of findings.
Unknown case study - group presentation: Oral presentation by group with full member participation.
Final practical exam: Assessment of practical skills in the timetabled slot in week 13: theory of prac and interpretive skills.
Canvas eLearning quizzes wk 8: 48 multiple choice answer question formative online quiz on lecture material covered to end of week 8.
Canvas eLearning quizzes wk 13: 48 multiple choice answer question formative online quiz on lecture material covered to end of week 13.

Detailed information for each assessment can be found on the Canvas MICR3X11 site.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name	Mark range	Description
High distinction	85 - 100	Complete mastery of topics showing extensive assimilation; treatment of tasks show an advanced synthesis of ideas; demonstration of initiative, complex understanding and analysis; work is well presented; all criteria addressed and learning outcomes achieved to a high level
Distinction	75 - 84	Excellent achievement, consistent evidence of deep understanding and application of knowledge; treatment of tasks show advanced understanding of topics; demonstration of initiative, complex understanding and analysis; work is well-presented; all criteria addressed and learning outcomes achieved strongly
Credit	65 - 74	Confident in explaining microbial processes, with evidence of solid understanding and achievement; occasional lapses indicative of unresolved issues; treatment of tasks show a good understanding of topic; work is well-presented with a minimum of errors; all criteria addressed and learning outcomes achieved clearly
Pass	50 - 64	Satisfactory level of engagement with and understanding of topic; some inconsistencies in understanding and knowledge of microbes in infection; work is adequately presented, with some errors or omissions, most criteria addressed and learning outcomes achieved adequately
Fail	0 - 49	When you don’t meet the learning outcomes of the unit to a satisfactory standard.

For more information see sydney.edu.au/students/guide-to-grades.

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

Deduction of 5% of the maximum mark for each calendar day after the due date.
After ten calendar days late, a mark of zero will be awarded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

You may only use artificial intelligence and writing assistance tools in assessment tasks if you are permitted to by your unit coordinator, and if you do use them, you must also acknowledge this in your work, either in a footnote or an acknowledgement section.

Studiosity is permitted for postgraduate units unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission.

Learning support

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

Weekly schedule

WK	Topic	Learning activity
Multiple weeks	Theme 1: Clinical Microbiology	Lecture (7 hr)
	Module 2: Skin, burns and wound infections	Practical (9 hr)
	Theme 2: Public health microbiology	Lecture (7 hr)
	Module 3: Respiratory tract infections; Module 4: Sterile body fluids	Practical (9 hr)
	Theme 3: Emerging and re-emerging diseases	Lecture (9 hr)
	Module 5: Urinary tract infections; Module 6: Gastrointestinal tract infections	Practical (12 hr)
Week 01	Introduction	Lecture (1 hr)
Week 01	Introduction to practical sessions; Module 1: Laboratory safety - compulsory biosafety induction	Practical (4 hr)
Week 04	Clinical tutorial 1: Skin, wounds and burn infections	Practical (2 hr)
Week 07	Clinical tutorial 2: Infections of respiratory tract, blood & CSF	Practical (2 hr)
Week 08	Excursion to Institute of Clinical Pathology and Medical Research at Westmead Hospital (optional)	Field trip (3 hr)
Week 12	Clinical tutorial 3: Infections of urinary and gastrointestinal tracts	Practical (2 hr)
Week 12	Revision tutorial	Practical (1 hr)
Week 13	Revision, exam skills and review	Lecture (2 hr)

Attendance and class requirements

Due to the exceptional circumstances caused by the COVID-19 pandemic, attendance requirements for this unit of study have been amended. Where online tutorials/workshops/virtual laboratories have been scheduled, students should make every effort to attend and participate at the scheduled time. Penalties will not be applied if technical issues, etc. prevent attendance at a specific online class. In that case, students should discuss the problem with the coordinator, and attend another session, if available.

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Required readings

All readings for this unit can be accessed on the Library eReserve link available on Canvas.

Recommended textbook: Medical Microbiology by Murray, PR, Rosenthal, KS & Pfaller, MA, 8th ed., 2016 (available as an ebook at: http://site.ebrary.com/lib/usyd/docDetail.action?docID=10618082)
Recommended textbook: Willey JM, Sherwood LM & Woolverton CJ: Prescott’s Microbiology. 11th or 10th ed., McGrawHill (2020, 2017)

Learning outcomes

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

Outcomes
Graduate qualities

At the completion of this unit, you should be able to:

LO1. have a detailed knowledge of bacterial virulence mechanisms and their role in invasion, establishment and progression of infection in the human host
LO2. explain the relationship between these mechanisms and the development of symptoms associated with the disease at particular sites of the body
LO3. have developed a practical dexterity in and detailed knowledge and understanding of laboratory diagnostic processes to be able to formulate and execute diagnostic plans for the identification and successful treatment of bacterial infections
LO4. interpret medical microbiology laboratory results and reports effectively
LO5. explain the various contexts and infrastructure of public health microbiology, specifically, the main mechanisms required to achieve and maintain good public health
LO6. explain the ways in which important microbial pathogens pose a challenge for public health
LO7. explain, using specific illustrative examples, how microbial disease might emerge or re-emerge to impact on human health
LO8. critically evaluate the research literature dealing with pathogenic processes of microbial infection in the human body.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1	Depth of disciplinary expertise Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.
GQ2	Critical thinking and problem solving Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.
GQ3	Oral and written communication Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.
GQ4	Information and digital literacy Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.
GQ5	Inventiveness Generating novel ideas and solutions.
GQ6	Cultural competence Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.
GQ7	Interdisciplinary effectiveness Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.
GQ8	Integrated professional, ethical, and personal identity An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.
GQ9	Influence Engaging others in a process, idea or vision.

Outcome map

Learning outcomes	Graduate qualities
Learning outcomes

Responding to student feedback

This section outlines changes made to this unit following staff and student reviews.

Many students provided feedback and really enjoyed this unit. The overall USS score was one of the highest in our School. Students said that they appreciated the link between the prac and lecture content and that the material was relevant to their interests. Recently, the functionality of LabArchives, as the practical course platform, has been improved to make flow improvements and the major case study has been improved with extra support for the assessments. The interaction between demonstrators and students is now better framed, making time for demonstrators to provide feedback on students’ pre- and post-practical class answers and notes. One of the highlights of this unit is a voluntary excursion to Westmead Institute of Clinical Pathology and Medical Research. Feedback from students is that this is really valuable because it allows them to experience the real-world context of medical microbiology. This visit significantly underpins the major case study work in this unit.

Additional information

More information can be found on Canvas and in the associated LabArchives notebook.

Site visit guidelines

Full detailed requirements for the optional excursion to the Institute of Clinical Pathology and Medical Research at Westmead Hospital will be published on the Canvas unit site and in the LabArchives practical notebook closer to the date. In principle: • Access: All student visitors to CIDMLS must be registered on the visitor list and stay in their allocated group. • PPE is required: gowns (provided by CIDMLS), safety glasses (provided by University) and closed-toe and heel footwear (provided by student). Long hair must be tied back to avoid injury. • General: * Smoking is prohibited in all areas (buildings and grounds) of Westmead Hospital. * Food and drink (including drinking from water bottles) must not be consumed in laboratories. * At the end of the visit, students must wash their hands thoroughly with disinfectant hand wash before exiting and after removing their laboratory gown and safety glasses. * Any injury or accident during the visit must be reported to CIDMLS safety officer without delay.

Work, health and safety

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General Laboratory Safety Rules

No eating or drinking is allowed in any laboratory under any circumstances
A laboratory coat, safety goggles, gloves and closed-toe shoes are mandatory
Follow safety instructions in your LabArchives notebook, notified by staff and posted in laboratories
In case of fire, follow instructions posted outside the laboratory door
First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory
You must remove your laboratory gown, goggles and gloves and then wash your hands with disinfectant soap, before leaving the laboratory
As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au/

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Site visit guidelines

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

MICR3011: Microbes in Infection

Semester 1, 2020 [Normal day] - Camperdown/Darlington, Sydney

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Site visit guidelines

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect