Course Title

Advanced Microbial Pathogenesis

Course Code


Offered Study Year 3, Semester 2
Course Coordinator Kimberly Kline (Assoc Prof) 6316 2800
Pre-requisites BS2002, BS2007
No of AUs 3
Contact hours Lectures: 26, Tutorials: 13, Laboratories: 6
Approved for delivery from AY 2018/19, semester 1
Last revised 19 Oct 2018, 09:25

Course Aims

This course aims to give you a background to the molecular and structural mechanisms by which microbial pathogens cause disease. You will understand and appreciate the path of scientific advancement in the field of microbial pathogenesis, from historical observations to the most recent discoveries. You will be able to read, think critically, and discuss primary scientific literature about bacterial pathogens. This course provides important background for those interested in fields of pharmaceuticals, biotechnology, academic research and health care.

Intended Learning Outcomes

Upon successfully completing this course, you should be able to:

  1. Critically analyse and interpret experiments in pathogenesis
  2. Design experiments to test hypotheses
  3. Communicate scientific discoveries in a precise manner
  4. Use protein modelling software to predict protein functions

Course Content

Immune Responses to Infection

Microbial Immune Evasion and Survival Strategies

Microbial Genetics, Regulation, and Evolution

Microbial Virulence Factors

Opportunistic Pathogens


Component Course ILOs tested SBS Graduate Attributes tested Weighting Team / Individual Assessment Rubrics
Continuous Assessment
Written Report 4 1. b, c
2. c
3. b
5. c
7. a, b
20 individual See Appendix for rubric
Multiple Choice Questions 1, 2 1. a, b, c, d
2. a, b, d, f
3. e, g
20 both
Presentation 1, 3 2. a, b, d, f, h
3. a, b, c, d, e, f, g
5. a, b, c, d
6. a
7. a, c
30 both See Appendix for rubric
Short Answer Questions 1, 2 1. a, b, d
2. a, b, d, f
3. e, g
5. c
6. a, b
30 individual See Appendix for rubric
Total 100%

These are the relevant SBS Graduate Attributes.

1. Recognize the relationship and complexity between structure and function of all forms of life, resulting from an academically rigorous in-depth understanding of biological concepts

a. Possess a conceptual framework that identifies the relationships between the major domains in the field of biology.

b. Explain the relationship between structure and function of all forms of life at the molecular level

c. Explain the relationship between structure and function of all forms of life at the cellular level

d. Explain the relationship between structure and function of all forms of life at the organism level

2. Critically evaluate and analyze biological information by applying the knowledge, scientific methods and technical skills associated with the discipline

a. Identify the assumptions behind scientific problems and issues

b. Create and evaluate hypotheses

c. Create abstract models of data

d. Design experiments relevant to authentic problems and their models

f. Evaluate results in primary biological literature

h. Identify unintended results as opportunities for discovery

3. Develop and communicate biological ideas and concepts relevant in everyday life for the benefit of society

a. Simplify and explain scientific concepts and results of experiments to a non-biologist (avoiding jargon)

b. Display and explain scientific results clearly and persuasively to peers both verbally and in writing (includes the ability to graph data appropriately and accurately).

c. Demonstrate an understanding of the recursive nature of science, where new results continually modify previous knowledge

d. Explain the role of peer review in science as a quality control mechanism

e. Discuss current critical questions in the field of biology

f. Demonstrate an understanding of the social and natural context of knowledge (role of science in society, influence of society on science)

g. Demonstrate an understanding of the history of ideas and development of the major fields of biology

5. Develop communication, creative and critical thinking skills for life-long learning

a. Learn independently and then share that knowledge with others

b. Learn collaboratively and be willing to share expertise with peers

c. Demonstrate critical thinking skills such as analysis, discrimination, logical reasoning, prediction and transforming knowledge

d. Question the assumptions, sources, and contexts of scientific investigation

6. Develop codes of social responsibility and scientific ethics, particularly in relation to biological advancement and applications

a. Debate the ethical implications of scientific processes and results

b. Design human or animal experiments that do not cause harm

7. Demonstrate information literacy and technological fluency

a. Locate and evaluate information needed to make decisions, solve problems, design experiments, and understand scientific data

b. Work effectively with common technologies in biology

c. Evaluate and use biological databases (literature and public datasets)

Formative Feedback

After each weekly quiz (consisting of multiple choice and short answer questions), the ideal answer(s) are posted online. During the next lecture session, quiz questions and/or topics that were most troublesome for the students will be reviewed. This feedback is designed to reinforce fundamental concepts as they apply to the critical analysis and interpretation of experiments, as well as to the design of experiments to test hypotheses.

During each tutorial session, which are entirely focused on group presentations, students will get real-time feedback in the form of question/answer and discussion with peers, the TAs, and the professor. This format is designed to improve clarity and precision in communicating scientific discoveries. For the final, graded group presentation, the students will receive anonymous written feedback from their peers, as well as written feedback from the professor and TAs.

Laboratory reports, based on interpretation of results derived from protein modelling software, will be returned to students with comments.

Learning and Teaching Approach

(26 hours)

The lectures provide important conceptual background regarding the main topics of the course, thus addressing outcomes 1,2,3,4.

Topical problem solving exercises will be performed in group settings during lecture.

(13 hours)

You will complete a weekly quiz that involves MCQ an short answer questions based on both lecture and tutorial material. Quizzes are taken in both individual and via a Team-based Learning approach, in which you will sometimes be given the opportunity to answer some quiz questions as a group. The topics in the quizzes address learning outcomes 1,2,3,4.

Group presentations during tutorials addressing learning outcomes 1 and 3 will occur weekly in informal (ungraded) and formal (graded) formats. These tutorials are run as a "flipped" classroom, in which the students present and teach one another the key concepts in the assigned primary literature.

(6 hours)

During the laboratories, you will learn to apply computer software for protein modeling. You will model a protein that is involved in Bacterial Pathogenesis and then you will write a report based on your structural analysis of that protein and how it relates to the protein function.

Reading and References

Bacterial Pathogenesis: A Molecular Approach, ASM Press (current edition), electronic or print version 2011; ISBN : 9781555814182.

For each of the lecture topics, the following chapters are recommended reading:

Innate responses to infection - Ch 2-3
Adaptive responses to infection & vaccines - Ch 4&17
Mechanisms of genetic modification & exchange - Ch 7
Identification of virulence factors - Ch 8-10
Mechanisms of survival in the host - Ch 11
Regulation of virulence factors - Ch 14
Delivery of virulence factors - Ch 13

One article from the primary literature will be required reading for each week's tutorial. All tutorial papers will be posted at the beginning of the term.

The following textbook is recommended for background reading for preparation of laboratory reports. Antibiotics: Actions, Origins, Resistance by Christopher Walsh, ASM Press (current edition 2003); ISBN-13: 978-1555818937

Toxins Ch 12
Antimicrobials and resistance I Ch 15-16
Development of next-generation antibacterials review article TBD
Opportunistic pathogens Ch 18-19
Microbiome and infection Ch 5

Course Policies and Student Responsibilities

Assessment comes in the form of weekly quizzes, given promptly at the beginning of the lecture period each week. Quizzes will cover the previous week's lecture and tutorial material, and will be in the form of MCQ and short answer. If you arrive late for the quiz, you will not be given extra time. The lowest two quiz grades of the term will be dropped from the final grade. The first two doctor-approved medical leave, or SBS-approved absences, will be counted toward the two dropped grades. After two excused absences, make-up quizzes will be scheduled. The makeup will be different from the quiz given during class.

You should come tutorial prepared to take part in class discussion, which includes reading and studying the paper for discussion ahead of time. Graded group presentations occur at the end of the term. All group members must participate in the group presentation.

The laboratory report must be submitted on time. No late reports will be accepted.

Academic Integrity

Good academic work depends on honesty and ethical behaviour. The quality of your work as a student relies on adhering to the principles of academic integrity and to the NTU Honour Code, a set of values shared by the whole university community. Truth, Trust and Justice are at the core of NTU’s shared values.

As a student, it is important that you recognize your responsibilities in understanding and applying the principles of academic integrity in all the work you do at NTU. Not knowing what is involved in maintaining academic integrity does not excuse academic dishonesty. You need to actively equip yourself with strategies to avoid all forms of academic dishonesty, including plagiarism, academic fraud, collusion and cheating. If you are uncertain of the definitions of any of these terms, you should go to the Academic Integrity website for more information. Consult your instructor(s) if you need any clarification about the requirements of academic integrity in the course.

Course Instructors

Instructor Office Location Phone Email
Kimberly Kline (Assoc Prof) SBS-B1n-27 6316 2800

Planned Weekly Schedule

Week Topic Course ILO Readings/ Activities

Innate responses to infection

1, 2, 3

Ch 2-3
article from primary literature - tbd


Adaptive responses to infection & vaccines

1, 2, 3

Ch 4&17
article from primary literature - tbd


Mechanisms of genetic modification & exchange

1, 2, 3

Ch 11
article from primary literature - tbd


Regulation of virulence factors

1, 2, 3

Ch 14
article from primary literature - tbd


Delivery of virulence factors

1, 2, 3

Ch 13
article from primary literature - tbd



1, 2, 3

Ch 14
article from primary literature - tbd


Antimicrobials and resistance

1, 4

Ch 12
article from primary literature - tbd


Development of next-generation antibacterials

1, 2, 3

Ch 15-16
article from primary literature - tbd


Opportunistic pathogens

1, 2, 3

Ch 18-19'
article from primary literature - tbd


Microbiome and infection

1, 3

article from primary literature - tbd


Identification of virulence factors

1, 3

Ch 8-10
article from primary literature - tbd

Appendix 1: Assessment Rubrics

Rubric for Laboratories: Written Report (20%)


This performance assessment is intended to evaluate a formal computer lab report about two projects, conducted during the lab components of the course.

The student’s evaluation on this performance assessment will be based on students’ ability to give rationale for, to interpret, and to discuss the data that they generate during the computer labs.

Below is a summary of the process in which students will participate:

1 Students will be introduced to toxins and antibiotics/antibiotic resistance.

2 Students will be given examples for each topic.

3 During the comp prac, students will work in pairs conducting a set of analysis using graphics software and research articles related to the task.

4 Students will be asked to analyze the data provided.

5 Each student will report findings in a formal lab report in which rationale for the project will beexplained,collected data will be summarized, the study will be presented and the results ofthe analysis will be interpreted.

6 The formal lab report will be handed in near the end of the semester for evaluation by the instructor.


After completion of the computer labs and lab report, students should be able todemonstrate the following:

#1 Understand and explain the rationale of related questions to comp prac and experiments, and accurately interpret related data

#2 Interpret resistance data

#3 Design simple experiments for further hypothesis testing


All of the following criteria will be applied to each formal lab report. The scale used for assessing thecriteriawill be as follows:

3 Advanced

2 Intermediate

1 Novice

0 Not addressed/Below novice

1 Demonstrates a clear understanding of the rationale for experiments conducted: how does this lab project address the problem being studied?

3 The writer provides a clear sense of the data/paper provided during prac.

2The writer provides some relevant context.

1 The writer provides vague or generic context for the problem.

0 This is not addressed or missing.

Scoring out of 100

76‐100 Advanced

51‐75 Intermediate

26‐50 Novice

0‐25 Below novice

Rubric for Tutorials: Presentation (30%)






5 pts

Student presents information in logical, interesting, and informative manner which audience can follow .All parts of the presentation (intro, hypothesis, approach, results, conclusions, caveats, future directions) are thoroughly addressed.

3.5 pts

Student presents information in logical sequence which audience can follow. Most parts of the presentation (intro, hypothesis, approach, results, conclusions, caveats, future directions) are thoroughly addressed.

2 pts

Audience has difficulty following presentation because students jump around. Some parts of the presentation (intro, hypothesis, approach, results, conclusions, caveats, future directions) are thoroughly addressed.

1 pt

Audience cannot understand presentation because there is no sequence of information. Few parts of the presentation (intro, hypothesis, approach, results, conclusions, caveats, future directions) are thoroughly addressed.



20 pts

Students demonstrate full knowledge (more than required) by incorporating information beyond the paper and beyond lecture, and answering all questions with explanations and elaboration. Students will demonstrate the ability to critically analyze and interpret experiments presented in the paper.

15 pts

Students are at ease with information and expected answers to all questions, but fail to elaborate.

7.5 pts

Students are uncomfortable with information and are able to answer onlyrudimentary questions.

2.5 pts

Students do not have grasp of information; students cannot answer questions about subject.



5 pts

Great use of time, got through all of the information, unique, interactive, and exciting presentation. Language is precise yet comfortable, practiced yet not stilted.

3.5 pts

Good use of time, got through more than half of each article, presentation was unique, and interactive. Most language is precise, most speakers are practiced and comfortable.

2 pts

Adequate use of time, got through one complete article, presentation was not interactive. Some language lacked precision. Some speakers recite memorized text, sounding robotic and uncomfortable.

1 pt

Poor use of time, was unable to get through the necessary information, presentation was boring or script was read.

Rubric for Tutorials: Short Answer Questions (30%)

For each short answer question, the point assignment will be described within the question.

Some question that have only one correct answer, no partial credit will be given. Some questions require design, analysis, and/or interpretation of experiments. For these questions, full credit will be given for answers showing a complete understanding of the experimental system in question.

Appendix 2: Intended Affective Outcomes

As a result of this course, it is expected you will develop the following "big picture" attributes:

An ethical approach to designing animal experients

An awareness of societal responsibilities regarding antibiotic use, drug treatments, vaccines

A critical approach to popular press articles about science

A willingness to work in a group to develop a presentation