University of Technology Sydney

91559 Bacterial Pathogenesis

Warning: The information on this page is indicative. The subject outline for a particular session, location and mode of offering is the authoritative source of all information about the subject for that offering. Required texts, recommended texts and references in particular are likely to change. Students will be provided with a subject outline once they enrol in the subject.

Subject handbook information prior to 2020 is available in the Archives.

UTS: Science: Life Sciences
Credit points: 6 cp
Result type: Grade and marks

There are course requisites for this subject. See access conditions.


This subject exposes students to a range of novel technologies that are playing a pivotal role in the advancement of infectious diseases diagnosis and therapy. The subject covers diagnostic technologies like biomarker development, sequencing technologies, microbiome analysis, therapeutic technologies like genome editing, as well as new approaches to understanding antimicrobial resistance and an integrated overview of these topics from the ‘One Health’ perspective. Upon successful completion of this subject, the students should have not only an understanding of the science behind these technologies, but also an appreciation of the fast-evolving nature of this field and the challenges the world faces with the advent of new biotechnology.

Subject learning objectives (SLOs)

Upon successful completion of this subject students should be able to:

1. Demonstrate knowledge of the foundation of molecular biology methods relevant to the development of new technologies to tackle important public health issues caused by infectious diseases.
2. Demonstrate knowledge of how new biotechnologies are developed and applied to solve medical problems related to infectious diseases.
3. Communicate results from an experiment in the format of a journal article/scientific poster, including the formulation of background/justification, interpretation of results, discussion and conclusion.
4. Develop critical thinking by providing personal insights on the possible future technologies and what this means for the healthcare industry.
5. Work professionally in a team environment to generate research data.
6. Be able to provide well-reasoned opinions on the future of biotechnology as it relates to infectious diseases.

Contribution to the development of graduate attributes

1. Disciplinary knowledge and its appropriate application

Your disciplinary knowledge will be provided with online material for you to review and come prepared to discuss during the workshops. This material will give you the basic foundation for the workshops, and it will be assessed in the format of 4 quizzes. The workshops are designed to be dynamic. You will learn from academics who regularly conduct research that contribute to the development of new technologies. Because these academics have different experiences and research backgrounds, they will give you diverse insights, perspectives, and perceived challenges in the field.

You will conduct lab experiments: extracting nucleic acid and identifying biomarkers, which will give you an understanding of how knowledge is generated. Through computer labs, you will have the opportunity to learn another important aspect of this process, which is data analysis. You will also need to communicate your results in a journal format, and a scientific poster format.

2. Research, inquiry and critical thinking

During the pracs and computer labs, you will learn how experimental design and data analysis is applied to answer research questions. The workshops will allow you to understand how these research questions arise based on previous knowledge, how the scientific process is carried out. The information provided online, as well as the material presented during the workshops, will help you with different assessments in which you will have to apply critical thinking: Assessment 2: journal-style prac lab report, specifically in the interpretation of results and discussion section. In assessment 3: scientific poster, you will have to apply your understanding of the results and relevance of the findings to present the poster to your peers.

3. Professional, ethical and social responsibility

You will have an opportunity to develop professional-level competency in basic hands-on experimental methods and data analysis. Also, technical and creative skills will be developed to investigate, analyse and synthesise complex information, problems, concepts and theories. You will then apply these skills to examine and critique established theories. Finally, you will practice the integration of these concepts and lab exercises within the broader scope of the healthcare industry.

You will have an opportunity to develop skills in the management of the work-load required for scientific-based practice and professional work. Time management will be developed through strictly time-limited practical and tutorial sessions.

4. Reflection, Innovation, Creativity
You will be encouraged to participate and engage in dynamic discussions with different academic experts in their field. These engagements will guide the students to understand how new knowledge is generated and how this is translated to biotechnology and clinical applications to solve infectious diseases problems.

5. Communication

You will be able to go through the process of data generation during pracs, and data analysis through computer labs. You will be able to interpret and communicate these results by a written group assignment in a journal format, by a visual/oral method in a poster presentation.

Teaching and learning strategies

This subject is delivered by way of online material, workshops, practical laboratories, computer laboratories. Attendance at workshops and practical classes is compulsory. You will need to complete revising at least 10 videos with content that is crucial for understanding the workshops that will be evaluated with online quizzes. Throughout the session, you will have 18 hours of face-to-face workshops and up to 9 hours of hands on wet lab, and 9 hours of hands-on computer lab.

Online videos

The purpose of the online content is to give the students a foundation and basic concepts in molecular biology and background for specific workshop topics.


The workshops are delivered by academics that are currently researching on: biomarkers, genetic epidemiology, antimicrobial resistance, spores, gene editing, microbiome, and health. The workshops will be delivered interactively, so the students can discuss the research and applied technologies.


The students will be working in groups and guided by a demonstrator to conduct hands-on activities. During prac 1 the students will be presented with a scenario for which a sample has to be processed to solve an outbreak source study, that involves the topic of antimicrobial resistance and genetic analysis. The student will have to conduct the steps specified in the prac lab to complete the task presented. In prac 2, (divided in two different weeks) the students will be presented with a problem in which they will have to give a diagnosis to a sample based on biomarkers profiles.

Computer labs

There will be 3 computer labs. In computer lab 1 the students will need to solve sources of transmission or outbreaks based on genetic sequencing of pathogens using phylogenetic methods. In computer lab 2, a continuation of Prac 1, in which the students will have to analyse the sequence data from a microorganism to determine their resistance profiles. Computer lab 3 will be dedicated to data analysis of biomarker data using R software.


To ensure that you have every opportunity to understand the subject material, feedback will be constantly available to you. Teaching staff will be available in practical classes and workshops for you to ask questions and expand your knowledge of the subject. While answering questions, the teaching staff will be asking you to apply logic and knowledge for you to answer your questions and thus gain understanding. For your written submissions, especially assessment tasks 2, draft copies can be submitted to the teaching staff (subject coordinator) for comment and feedback before the due date. The teaching staff are available during face-to-face contact time and via email. Also, forums on Canvas will be used for group discussions and general feedback. The poster presentation (assessment 3), will be a follow-up presentation of assessment 2, for which you will get feedback from, and you will be able to apply it for developing scientific posters.

You are expected to monitor Canvas on a regular basis for information or changes to scheduling, assessment tasks, lectures and tutorial times and locations.

You will get feedback from your peers using the SPARK mid-session online assessment as scores for your work from your peers; and at the end of the session as assessment marks. You also get feedback after your assignmenttalk, brief and pamphlet) in the form of a marked rubric, which will be available in UTS Online at the conclusion of each assignment task.

Content (topics)

Infectious diseases are a major health problem around the world. Form something as simple as the common cold
and flu to devastating and fatal diseases like HIV and Ebola every part of the globe is affected. The morbidity and
mortality associated with both acute and chronic infectious diseases not only creates an economic burden but also
causes a lot of social and psychological issues. This can turn into a vicious circle, making it difficult for the patient to
return to normal life even after being cured.

Biotechnology can help prevent as well as eliminate some of these problems. You just need the right tools.
Biotechnology plays a major role in the prevention, diagnosis and treatment of these diseases. Throughout this
course, you will be introduced to multiple novel biotechnologies that have or will solve the problem of infectious

In this subject, you are going to be shown either through the practical classes that you attend, the computer labs you
work through or the workshops that you participate in several biotechnologies. This subject will teach you to think
about all the possibilities of the technologies out there and how they are being used to combat infectious diseases.
Through the assessment tasks, you will learn how to communicate the results of your research work that is carried
out in the practical classes both in the form of a journal article and through a poster presentation.


Assessment task 1: Quiz


This task assesses the following graduate attributes

  1. Disciplinary Knowledge and its appropriate application
  2. Research enquiry and critical thinking

Task – This is a completely online component of the course. This assessment will be undertaken in the form of 4 short quizzes throughout the semester.

There will be a short (5 questions each) multiple choice quizzes posted online every 2 weeks (4 in total) and questions will be based on the content that has been covered in resources (videos, articles etc.) provided online. The quizzes will be timed, and students will be expected to complete the quiz in the allotted time. They can be completed off campus. At the end of the quiz, marks will be provided along with the explanation for the answers.

Type: Quiz/test
Groupwork: Individual
Weight: 20%

Automated marking online based on the correctness of the answer.

Assessment task 2: Report- Journal style


Intent: This task assesses the following graduate attributes

  1. Disciplinary knowledge and its appropriate application
  2. Research inquiry and critical thinking
  3. Professional skills, ethics and social responsibility
  4. Communication skills

This report is based on the practical on DNA extraction and related computer laboratory on genetic analysis of a bacterial genome focused in antimicrobial resistance.

Students will be expected to write a report in the format of a journal article (1500 words max. excluding references and figure and table legends). This will be based on the results of the first practical and computer lab: DNA extraction and sequencing of a microbial genome. This topic will also be presented in workshops on weeks 3 and 4. The report should include the following sections: Introduction, Material and Methods, Results, Discussion, Conclusion, References. While the data for the report will be generate in class through groupwork, each student must submit an original, individual report for which they will be given an individual grade. Submission will be through Turnitin to ensure that each student’s work is substantially different from that of their peers.

Type: Report
Groupwork: Group, individually assessed
Weight: 50%

A marking rubric is provided in UTS online. The report will be marked by demonstrators. Assessment criteria are as follows:

  • Thorough literature review providing background outlining the research gap
  • Clearly articulated methods which would allow someone else to replicate the study.
  • Data analysis is well written and visually clear
  • Accurate interpretation of results
  • Discussion of results and future directions for research

Assessment task 3: Poster presentation


Intent: This task assesses the following graduate attributes,

  1. Disciplinary knowledge and its appropriate application
  2. Research inquiry and critical thinking
  3. Professional skills, ethics and social responsibility
  4. Reflection, creativity and innovation
  5. Communication skills

Task – This assessment will be based on the prac report (assessment 2- sequencing and antimicrobial resistance) from which students will get feedback to develop a scientific poster.

The students will be provided with results of sequencing from their second practical and will be expected to use the data mining and bioinformatics techniques they have learnt in the computer practical session/tutorial to analyse their results and provide the reasons for their conclusion. The task will be assessed in the form of a poster presentation session at a conference where academics will be invited to review the posters and grade the student’s ability to explain their results. The students will be assessed on two aspects:

  1. The physical appearance and communication clarity of the poster and its content, and
  2. Their oral delivery of the content and understanding of the research.

Students will conduct both aspects as a group and receive one mark per group. Peer feedback of individual team member’s contributions to the group work will be conducted by students through Sparkplus.

Type: Presentation
Groupwork: Group, group assessed
Weight: 30%

Criteria: A marking rubric is provided on UTS online. At least 2 academics will grade each poster.

Poster Criteria: (10%)

  • Quality of the poster content, ability to summarise the highlights.
  • Graphical presentation of results.
  • The visual composition of the poster (layout)
  • Data analysis well written and visually clear.

Presentation criteria: (10%)

  • Oral presentation is clear
  • Student displays a thorough understanding of the research
  • Ability to answer questions of the research experiment (especially its impact as a biotechnology application in the healthcare industry, and the impact in ‘one health’).

Minimum requirements

  • Any assessment task worth 40% or more requires the student to gain at least 40% of the mark for that task. If 40% is not reached, an X grade may be awarded for the subject irrespective of an overall mark greater than 50.
  • In order to pass this subject, students must obtain at least 50% of the total combined mark available for the assessment tasks.
  • Tutorial and laboratory pracs attendance is compulsory (failing to attend will result in a X grade).