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Unit of study_

MICR3911: Microbes in Infection (Advanced)

Semester 1, 2021 [Normal day] - Remote

This unit is available to students who have performed well in Intermediate Microbiology. 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 unique aspect of this advanced unit that differentiates it from the mainstream unit is six tutorial style sessions that replace six mainstream lectures in the theme 'Emerging and re-emerging diseases'. These dedicated research-led interactive advanced sessions support self-directed learning and involve discussion around specific topics that will vary from year to year. Nominated research papers and reviews in the topic area will be explored with supported discussion of the relevance to and impact of the work on current thinking around emergence of microbial disease. The focus will be on microbial change that lies critically at the centre of understanding the reasons for the emergence of new diseases and challenges in an era of significant scientific ability to diagnose and treat infection. The practical component is identical to the mainstream unit and is designed to enhance students' practical skills and to complement the lectures. 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 MICR3911
Academic unit Life and Environmental Sciences Academic Operations
Credit points 6
Prohibitions
? 
MICR3011
Prerequisites
? 
[6cp from (BIOL1XX7 or MBLGXXXX or GEGE2X01 or GENE2002) and a mark of 70 or above in (MEDS2004 or MICR2X22 or MIMI2X02)] OR [BMED2401 and a mark of 70 or above in BMED2404]
Corequisites
? 
None
Assumed knowledge
? 

MICR2X21 or MICR2024 or MICR2X31

Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Dee Carter, dee.carter@sydney.edu.au
Laboratory supervisor(s) Aidan Kane, aidan.kane@sydney.edu.au
Lecturer(s) Dee Carter, dee.carter@sydney.edu.au
Andrew Holmes, andrew.holmes@sydney.edu.au
Peter Reeves, peter.reeves@sydney.edu.au
Christopher Harmer, christopher.harmer@sydney.edu.au
Helen Agus, helen.agus@sydney.edu.au
Timothy Newsome, timothy.newsome@sydney.edu.au
Type Description Weight Due Length
Final exam (Record+) Type B final exam Canvas exam
Written exam: multiple choice, short answer and extended response questions
45% Formal exam period 1.5 hours
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8
Skills-based evaluation Genotyping Labarchives Online work
Labarchives notebook assessment of activity, entries and analysis of result
7% Please select a valid week from the list below
Due date: 14 May 2021 at 23:59

Closing date: 09 Feb 2021
Continuous assessment pracs 6-10
Outcomes assessed: LO1 LO8 LO7 LO6 LO5 LO4 LO3 LO2
Tutorial quiz hurdle task Compulsory compliance quiz
Online quiz
0% Week 02 No restriction
Outcomes assessed: LO3
Presentation Advanced presentation
Presentation of topic literature review
0% Week 05 5 minutes
Outcomes assessed: LO1 LO8 LO7 LO6
Online task Quiz 1
Online quiz
0% Week 06 30 minutes
Outcomes assessed: LO1 LO6 LO5 LO4 LO3 LO2
Assignment Genotyping literature analysis
Read assigned papers and answer questions in LabArchives
3% Week 07
Due date: 19 Apr 2021 at 23:59

Closing date: 09 Feb 2021
Submitted in LabArchives
Outcomes assessed: LO3 LO4
Tutorial quiz Quiz 2
Online quiz
10% Week 10 30 minutes
Outcomes assessed: LO1 LO6 LO5 LO4 LO3
Assignment Advanced assignment
Literature review (10%), graphical abstract (5%)
15% Week 11 1500 words
Outcomes assessed: LO1 LO6 LO7 LO8
Assignment group assignment Genotyping presentation
Online Zoom presentation of genotyping paper
5% Week 12 10 minutes
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8
Online task Bioinformatics quiz
Short answer and extended response questions
15% Week 13
Due date: 02 Jun 2021 at 14:00

Closing date: 02 Jun 2021
2 hours
Outcomes assessed: LO1 LO6 LO5 LO4 LO3 LO2
hurdle task = hurdle task ?
group assignment = group assignment ?
Type B final exam = Type B final exam ?

Assessment summary

  • Compulsory compliance quiz: Online quiz in Canvas MICR30X11 website.
  • Quiz 1: Online formative multiple choice and short answer questions.
  • Quiz 2: Online multiple choice and short answer questions.
  • Genotyping prac: Interpretation of literature You will read provided literature and answer a series of questions based on your reading.
  • Genotyping – LabArchives work: Investigate the cause of an outbreak, designed to allow you to apply the genotyping methodology. Various group self-directed activities spanning 4 weeks of semester, culminating in a short report of your findings.
  • Genotyping - group presentation: Oral presentation by zoom on a genotyping paper of your choice in pairs with full member participation.
  • Bioinformatics exam: Assessment of bioinformatic skills in the Tuesday lab slot in week 13: analytical and interpretive skills.
  • Final exam: Assessment of your knowledge of the material presented in this Unit of Study

 

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.

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.

WK Topic Learning activity Learning outcomes
Multiple weeks Theme 1: Clinical Microbiology Lecture (6 hr) LO1 LO2 LO5 LO6 LO7 LO8
Advanced sessions Workshop (6 hr) LO1 LO2 LO4 LO5 LO6 LO7 LO8
Module 2: Clinical microbiology Practical (9 hr) LO3 LO4 LO5 LO6 LO7
Theme 2: Public health microbiology Lecture (9 hr) LO1 LO2 LO5 LO6 LO7 LO8
Module 3: Analysis of an outbreak by genotyping Practical (9 hr) LO3 LO4 LO5 LO6 LO7
Theme 3: Emerging and re-emerging diseases Lecture (6 hr) LO1 LO2 LO5 LO6 LO7 LO8
Module 4:Bioinformatic analysis of virulence and resistance genes Practical (12 hr) LO3 LO4 LO5 LO6 LO7
Week 01 Introduction Lecture (1 hr) LO5 LO6 LO7
Introduction to practical sessions; Module 1: Laboratory safety - compulsory biosafety induction Practical (4 hr) LO3 LO4
Week 13 Revision, exam skills and review Lecture (1 hr) LO1 LO2 LO5 LO6 LO7 LO8

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 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 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.

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 bioinformatic analysis 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
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

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

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.

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

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.