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Unit of study_

INIM5013: Clinical Mycology and Parasitology

Semester 1, 2020 [Normal day] - Westmead, Sydney

This unit aims to equip science and medical graduates with an in-depth knowledge of medical mycology and parasitology that will enable them to work effectively as laboratory personnel, clincians and medical scientists in relevant hospital laboratories, clinics or research institutions. The course will allow students to develop skills in recognising fungal and parasitic infections, interpret laboraroty reports on identification clincial epidmeiology of the mycotic and parasitic disease agents, molecular typing of clincial isolates, and evaluation of scientific literature, in problem-solving and in scientific communication that will enable graduates to develop careers as microbiologists, clinicians and administrators or policy-makers in hospitals, health care organizations or government bodies. The course structure involves lectures on diseases caused by fungal, protozoan and helminthic agents, laboratory classes on identification of fungal and parasitic infections (classical methods, such as morphology and biochemistry, molecular methods, including: sanger and next generation sequencing, whole genome sequencing, a number of PCR based techniques and MALDI-TOF), molecular typing techniques used to investigate potential disease outbreaks, techniques used in research investigations and specific tutorials (e.g. clinical cases, investigation of outbreaks of disease and prevention strategies). Specific lectures will be given by expert clinicans in infectious diseases, basic microbiology, mycology, and parasitology scientists and leading diagnostic specialists in the field. Seminars consisting of presentations of specified topics researched by individual students will complement the course. The course takes place at the new Westmead Institute for Medical Research, in the Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Emerging infectious Diseases and Biosecurity, Faculty of Medicine and Health, at the Westmead Campus, Westmead Clinical School.

Unit details and rules

Unit code INIM5013
Academic unit Infectious Diseases and Immunology
Credit points 6
Prohibitions
? 
None
Prerequisites
? 
None
Corequisites
? 
None
Assumed knowledge
? 

Knowledge in general microbiology and molecular biology.

Available to study abroad and exchange students

No

Teaching staff

Coordinator Wieland Meyer, wieland.meyer@sydney.edu.au
Lecturer(s) Rogan Lee, rogan.lee@sydney.edu.au
Type Description Weight Due Length
Final exam Final exam
Written exam
55% Formal exam period 2 hours
Outcomes assessed: LO1 LO5 LO4 LO3 LO2
Assignment Mycology written protocol
Written assignment
15% Multiple weeks To be added by the unit coordinator
Outcomes assessed: LO1 LO2 LO3 LO4 LO5
Assignment Parasitology written protocol
Written assignment
15% Multiple weeks To be added by the unit coordinator
Outcomes assessed: LO1 LO2 LO3 LO4 LO5
Online task Academic honesty
Academic honesty
0% Week 04 n/a
Outcomes assessed: LO1
Presentation Presentation
Presentation
15% Week 12 20 minutes
Outcomes assessed: LO5

Assessment summary

Detailed information for each assessment can be found on Canvas.

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

Student has submitted all practical report completed with all sections in a comprehensive matter on the subject. 

Distinction

75 - 84

Student has submitted more than 80% of the practical report completed with all sections in a comprehensive matter on the subject. 

Credit

65 - 74

Student has submitted more than 80% of the practical report completed with all sections in parcial understanding of the matter of the subjetc.

Pass

50 - 64

Student has submitted less than 80% of the practical report completed with all sections in parcial understanding of the matter of the subjetc.

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
Week 01 1. WIMR Building enrolment; 2. WIMR orientation / PC2 Training; 3. Introduction to mycology; 4. Classical fungal ID: morphology and semi automated fungal identification Lecture (3 hr) LO1 LO3
Mycology Practical 1: Classical Fungal ID Practical (3 hr) LO1 LO2 LO3
Week 02 1. Introduction to parasitology - Helminths - cestodes; 2. Parasitic arthropods; Lecture (2.5 hr) LO1 LO2 LO3
Parsasitology practical 1: VIEWING LABORATORY SPECIMENS Practical (3 hr) LO3
Case studies Tutorial (1 hr) LO1 LO4
Week 03 1. Molecualr fungal ID; 2. MALDI-TOF for fungal ID Lecture (2 hr) LO1 LO2 LO3 LO4
Mycology practical 2: Fungal species ID via ITS amplification Practical (5.5 hr) LO3 LO4
Week 04 1. Parasitology - Helminths - Nematodes Lecture (1.5 hr) LO1 LO2 LO4
1. Parasitology practical 2: viewing laboratory specimens Practical (3 hr) LO1 LO4
Case studies Tutorial (1.5 hr) LO1 LO4
Week 05 1. Molecular epidemiology of fungal infections; 2. Systemic mycoses due to dimorphic fungi; 3. Opportunistic mycoses due to yeasts Lecture (3 hr) LO1 LO2 LO3 LO4
Mycology practical 3: Fungal species ID via RFLP analysis of the ITS region (discussion of the ITS amplification results and setup of restriction digestion of the provided PCR products) Practical (4.5 hr) LO3
Week 06 1. Enteric protozoa (Entamoeba, Cryptosporidia/Cyclospora, Giardia, Dientamoeba); 2. Genotyping of Cryptosporidium and Giardia from clinical samples Lecture (2.5 hr) LO1 LO2 LO3 LO4
Parasitology practical 3: viewing laboratory specimens Practical (2 hr) LO2 LO3
1. Entamoeba histolytica; 2. Microsporidia - the new fungus on the block Tutorial (2 hr) LO1 LO2 LO3 LO4
Week 07 1. Sequence based fungal ID; 2. Impact of the changes in fungal nomenclature on fungal ID; 3. Endemic mycoses Lecture (3 hr) LO1 LO2 LO3 LO4
Mycology practical 4: sequence based fungal ID Practical (2 hr) LO3
Week 08 Malaria - life cycle, epidemiology, pathology, treatment Lecture (1 hr) LO1 LO2 LO3 LO4
Parasitology practical 4: Malaria detection by PCR Practical (5 hr) LO3
Laboratory diagnosis of malaria Tutorial (1 hr) LO3
Week 09 1. Antifungal susceptibility testing; 2. Superficial mycoses (Dermatophytosis, Pityriasis, Versicolor, Tinea Nigra etc.) Lecture (2 hr) LO1 LO2 LO3 LO4
Mycology practical 5: Dermatophyte Morphology/Antifungal susceptibility testing Practical (3 hr) LO3 LO4
Week 10 Helminths - trematodes (Schistosomes, Paragonimus, Fasciola, Clonorchis/Opisthorchis, Fasciolopsis) Lecture (1.5 hr) LO1 LO2 LO3 LO4
Parasitology practical 5: viewing laboratory specimens Practical (1 hr) LO3
1. Parasitology; 2. Case studies on human trematode infections Tutorial (2 hr) LO1 LO2 LO3 LO4
Week 11 1. Pneumocystis jirovecii - a novel fungus and its implementations in nosocomial outbreaks; 2. Opportunistic mycoses due to filamentous fungi (Aspergillosis, Zygomycosis, Scedosporiosis etc.) Lecture (2 hr) LO1 LO2 LO3 LO4
Mycology practical 6: Molecular techniques for strain typing - PCR-fingerprinting Practical (5 hr) LO2 LO3
Week 12 Student presentations on mycological and parasitological topics Tutorial (7 hr) LO1 LO2 LO3 LO4 LO5
Week 13 Tissue protozoans (Leishmania, African Trypanosoma, Chagas, Toxoplasma, Trichomonas, Acanthamoeba) Lecture (1.5 hr) LO1 LO2 LO3 LO4
Parasitology practical 6: viewing laboratory specimens Practical (2.5 hr) LO3
1. Parasitology; 2. Case studies Tutorial (2 hr) LO1 LO2 LO3 LO4

Attendance and class requirements

Attendance will be recorded from students' arrival date on campus or from March 31st, whichever is the earliest. From February 24 (week 1), students enrolled in this unit should engage with and study all online content, as directed in the Canvas site, including the submission of any required formative tasks and completion of any asynchronous activities.

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.

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. demonstrate a thorough understanding of the scientific basis and clinical applications of medical mycology and parasitology
  • LO2. demonstrate basic knowledge of the main human pathogenic fungi and parasites and their epidemiology
  • LO3. demonstrate an understanding of laboratory techniques used to diagnose infections caused by fungi and parasites
  • LO4. demonstrate an understanding of clinical pictures of disease in connection with the laboratory findings to generate appropriate treatment responses
  • LO5. demonstrate developed skills in evaluation of scientific literature, in problem-solving and in scientific communication that will enable you to develop careers as laboratory personal, administrators or policy-makers in hospitals, health care organisations or government bodies.

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.

No specific critics have been received. More hands on exerience has been added.

Work, health and safety

Closed shoes need to be worn all times.

Lab coats need to be worn all times.

safety glasses need to be worn all times.

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.