Agents of Disease - AVBS3001 Notes

General Course Information

1.1 Introduction to Agents of Disease

  • Infectious diseases are caused by a variety of biological agents:
    • Arthropods
    • Protozoans
    • Helminths (worms)
    • Bacteria
    • Viruses
    • Fungi
    • Algae
    • Prions
  • These agents can negatively impact animal health and production, leading to economic losses and reduced wild animal populations.
  • Zoonotic agents (those causing disease in both animals and humans) present significant public health concerns.
  • Detailed knowledge of the structure, morphology, and properties of infectious agents is crucial for understanding how they cause disease.
  • The relationship between the animal, infectious agents, and the environment is a key focus.
  • Understanding the host-pathogen-environment interaction (HPEI) allows for prediction of disease outbreaks and identification of at-risk animals and organ systems.
  • Management strategies can be developed to favor the animals and facilitate optimal animal health and production.
  • A thorough understanding is therefore required:
    • Nature of the infectious agents
    • Pathogenesis of the diseases they manifest
    • Methods for diagnosing infectious diseases
    • Means of treatment, control, and prevention
  • Practical knowledge enables active participation in investigating animal health problems and developing new means of protecting animals from infectious agents.
  • This unit is designed to provide knowledge and understanding of infectious agents of local and worldwide significance to primarily production and wild animals.
  • A systematic taxonomic approach will be used to study significant animal pathogens using real world examples and industry activities to develop understanding and expertise.
  • The knowledge obtained in this unit will give a solid foundation to build upon in later units within the Animal Health, Disease and Welfare major and Bachelor of Advanced Studies within the AVBS stream.

1.2 Learning Aims and Outcomes

  • Aims:
    • Build upon epidemiological, pathological, and immunological knowledge from AVBS 2001.
    • Examine the physical, chemical and genetic charateristics of infectious disease causing agents.
    • Cover significant pathogens of local and global significance to domestic and wild animals
    • Examine and relate the concepts and principles of host-pathogen-environmental interactions
    • Procedures for accurate identification and recognition of agents and the diagnosis of infectious diseases in animals will be examined
    • The unit will also introduce issues related to zoonoses, chemical treatment and food safety that affect the handling and treatments of infectious diseases in animals.
    • Students will obtain practical knowledge of significant animal infectious agents & understand how the agents’ interaction with animals and their environments ultimately dictate animal health and production outcomes.
    • Encourage students to discuss, critically evaluate and conceptually formulate methods for effective infectious disease control and prevention in animal population.
    • Provide a solid foundation of knowledge in infectious disease-causing agents for later units, such as AVBS 3888, AVBS 3005, and AVBS 4020.
  • Learning Outcomes: By the end of this Unit of Study, students will be able to:
    1. Recognise, describe and name the common infectious disease causing agents that impact the animal/veterinary industry.
    2. Understand the significance and interplay of the host-pathogen-environment interaction (HPEI) in disease manifestation and animal production outcomes.
    3. Recognise the behavioural, pathological and productivity signs associated with given agents of disease.
    4. Know and perform the methods, tests and sampling strategies (including sampling and transport) which underpin the diagnosis of an infectious disease.
    5. Demonstrate an understanding of HPEI as it underscores strategic disease control and prevention.
    6. Appreciate the various issues related to zoonoses, chemical treatment and food safety that affect handling and treatments for infectious agents.
    7. Use the most recent information from literature to evaluate and describe new diagnostic techniques, therapeutics and management strategies to combat infectious disease in farmed and wild animal populations.

1.3 Graduate Qualities

  • Depth of disciplinary expertise
    • BSc graduates undertaking this unit will identify infectious agents of disease that cause disease in various domesticated and wild animals.
  • Critical thinking and problem solving
    • BSc graduates undertaking this unit will be able to understand how the interaction between animal-pathogens-environment influence disease risk in population and the development of pathology through the pathogenesis process.
    • Through understanding these interactions students can appreciate the capacity to influence disease risk and health outcomes at the population and individual animal level. The unit will enable students to evaluate these interactions and suggest strategies to influence these interactions in order to optimize animal health and prevent and control disease.
  • Oral and written communication
    • BSc graduates undertaking this unit will undertake written assessment task that will enable students to develop their scientific literacy and expand their expertise in the topic by review recent discoveries related to the pathogens that affect animals.
    • Students will develop skills in writing to their scientific peers as well as to a lay audience educating the public about animal disease issues and emergencies.
  • Information and digital literacy
    • BSc graduates undertaking this unit will resource the most recent information from various appropriate scientific databases to explore and discuss cutting edge scientific knowledge related to pathogens of animals and epidemiology of infectious disease of animals.
    • Students will create informative material in assessment tasks that will convey information to their peers and provide instructional and informative material to the lay public or government bodies to influence and educate on animal disease issues.
  • Inventiveness
    • BSc graduates undertaking this unit will be encourage to generate novel ideas and solution to case based animal disease scenarios through the application of their knowledge of HPEI.
  • Cultural competence
    • BSc graduates undertaking this unit will be encourage to appreciate the religious, social, and traditional and race issues that can influence the risk of animal disease in various community settings.
    • Students will also appreciate the cultural roles animals play in communities worldwide, especially the roles of domestic and wild animals in aboriginal and Torrs Strait Islander cultures.
    • Students undertaking group assignments in these unit will be asked to appreciate cultural diversity in their groups and address cultural issues that may be important to consist in any problem solving strategies suggested to manage animal diseases.
  • Interdisciplinary effectiveness
    • BSc graduates undertaking this unit will appreciate the interdisciplinary nature of animal health and the multifactorial of disease risk. Students will also gain an understanding of how animal disease outbreaks can influence public health and local and international economies and industries.
    • Students will appreciate that managing animals and specifically effectively managing infectious disease risk involves an interdisciplinary approach to be successful.
  • Integrated professional, ethical and personal identity
    • BSc graduates undertaking this unit will hold personal beliefs and values consistent with their role as responsible members of local, national, international and professional communities.
    • Graduates will provide advice in animal health management and recognize when an appropriate professional should be consulted regarding specialist animal infectious disease issues.
    • Graduates will ensure the sustainability of animal industries and the natural environment through practice that considers the economic, social and ecological needs of the environment, various animal industries and society within Australia and worldwide.
  • Influence
    • BSc graduates undertaking this unit will learn communication skills that will enable them to engage colleagues and the public about pathogens which affect animals. Through justified and science based responses to assessed problems in this unit, students will gain skills that will engage teams in disease management strategies with a vision of optimizing animal health and eliminating highly infectious and deleterious diseases of wild and domestic animals.

1.4 Your Facilitators

  • Details of facilitators, their research interests, contact information (Dr. Gary Muscatello, Assoc Prof Tim Newsome, Prof Jan Slapeta, Dr. Katharine Muscat, Dr. Carola Venturini, Dr. Emily Francis, and Dr. Mark Westman).

1.5 Unit of Study Program

  • Weekly learning activities consist of 3 lectures + one 1–2.5-hour tutorial or practical class each Friday afternoon.
  • Minimum of 6 hours per week outside of class for studying weekly content is recommended.
  • Week 1: Introduction to Agents of Disease
    • Lectures (GM): Unit introduction, curriculum outline, overview of microbial structure and function, principles of microbial pathogenesis.
    • Tutorial (GM): Assignment workshop, outline of assessment tasks, expectations.
  • Week 2: Virology
    • Lectures (GM): Examine RNA viruses.
    • Tutorial (GM): RNA virus case studies
  • Week 3: Virology
    • Lectures (TN & GM): Examine virological techniques and DNA viruses.
    • Tutorial (GM): DNA virus case studies and virological techniques discussion.
  • Week 4: Virology
    • Lectures (TN, MW & KM): Examine virological techniques, DNA viruses, and Retrovirus.
    • Tutorial (KM): Herpesvirus and Retrovirus case studies and virological techniques discussion.
  • Week 5: Virology and Parasitology
    • Lectures (KM & EF): Examine Herpesviruses and ectoparasites.
    • Practical (EF & JS): Examination and identification of ectoparasites, discussion of control and prevention strategies.
  • Week 6: Parasitology
    • Lectures (EF): Examine nematodes, helminths and integrated pest management.
    • Practical (EF & JS): Methods for examining and identifying nematodes, sheep faecal egg counts, anthelminthic discussion.
  • Week 7: Parasitology
    • Lectures (EF & JS): Examine protozoa.
    • Practical (JS & EF): Protozoal culture and test sensitivity, protozoal ecology/life-cycle discussion.
  • Week 8: Parasitology and Bacteriology
    • Lectures (JS and GM): Examine exotic parasitic zoonosis, Gram-positive cocci.
  • Week 9: Bacteriology and Mycology
    • Lectures (GM): Examine Gram-positive rods.
    • Tutorial/Quiz (GM/JS/EF): MCQ and summary tutorial covering the curriculum to date.
  • Week 10: Bacteriology and Mycology
    • Lectures (GM & CV): Gram-positive rods and Gram-negative, oxidase-negative rods.
    • Practical (GM): Bacteriological Diagnostics (Part 1) - case study introduction, clinical samples, Gram staining, streak plate agar cultures, initial steps for identifying bacterial agents.
  • Week 11: Bacteriology and Mycology
    • Lectures (GM): Gram-negative rods.
    • Practical (GM): Bacteriological Diagnostics (Part 2) - description of plate agar colony morphology, use of determinative keys, primary and secondary tests.
  • Week 12: Bacteriology and Mycology
    • Lectures (GM): Gram-positive spore formers, special bacteria, Gram-negative curved rods, spirochaetes, mollicutes and Coxiella.
    • Practical (GM): Bacteriological Diagnostics (Part 3) - tertiary tests and subcultures, antimicrobial sensitivity assays, bacteriological diagnosis, case tutorial summation.
  • Week 13: Bacteriology and Mycology
    • Lectures (GM): Examine fungal pathogens.
    • Tutorial (JS and GM): Student-driven course review and examination preparation session.
  • Occupational Health and Safety (OHS) requirements in laboratory classes must be obeyed, including wearing specified personal protective equipment (PPE).
  • Students should attend/view 90% of lectures. It is a requirement to attend the following: 2 of 3 virology tutorials, 2 of 3 parasitology practicals, and 2 of 3 bacteriology practicals.
  • Attendance at lectures, tutorials, and practicals will be monitored.

1.6 Textbooks and References

  • Recommended textbooks:
    1. Veterinary Microbiology (2nd edition), Hirsh DC, MacLachlan NJ, Walker RL, Blackwell, Iowa (2004)
    2. Veterinary Microbiology: Bacteria and Fungal Agents of Animal Disease, Songer JG, Post KW, Saunders, St. Louis (2005)
    3. Veterinary Microbiology and Microbial Disease (2nd edition), Quinn PJ, Markey BK, Leonard FC, Fitzpatrick ES, Fanning S, Hartigan PJ, Wiley-Blackwell, Iowa (2011)
    4. Pathogenesis of Bacterial Infections in Animals (5th edition), Prescott JF, MacInnes JI, Van Immerseel F, Boyce JD, Rycroft AN, Vazquez-Boland JA, Wiley-Blackwell, Iowa (2023)
    5. Australasian Animal parasites- Inside and Out. Available at http://parasite.org.au/publications/australasian-animal-parasites-inside-and-out/ for free download.
  • A veterinary dictionary - Saunders Comprehensive Veterinary Dictionary (5thedition), Studdert VP, CC Gay, Hinchcliff KW, Saunders Ltd (2020).
  • Scientific journals include:
    1. Trends in Parasitology https://www.cell.com/trends/parasitology/home
    2. Veterinary Microbiology https://www.sciencedirect.com/journal/veterinary-microbiology
    3. Applied and Environmental Microbiology http://aem.asm.org/
    4. Infection and Immunity http://iai.asm.org/
    5. Emerging Infectious disease https://wwwnc.cdc.gov/eid/
    6. The Journal of Virology http://jvi.asm.org/
    7. Journal of Clinical Microbiology http://jcm.asm.org/
  • Websites:
    • PubMed http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed
    • ProMed https://promedmail.org/
    • World Health Organisation http://www.who.int/zoonoses/diseases/en/
    • Veterinary bacteriology: Information about important bacteria https://www.vetbact.org/

1.7 Library and Online Resources

  • University Library Services http://sydney.edu.au/library
    • Scitech and Camden Libraries are the specialist libraries for veterinary science.
  • Other services for students include:
    • Free access to the library’s print and online resources including books, journals, videos, and research databases, with free transfer of books and articles between campus libraries.
    • Librarians are here to help you: Ask for help at any library, using the Ask a Librarian links (usyd.libanswers.com) or contact our Faculty liaison librarian
    • Your Student Card is your library card. Use it to borrow books, print, photocopy and more.
    • Classes, tours, online tutorials, computing facilities and wireless access.
  • An online subject guide. Your School Liaison Librarian is: Monica Cooper Tel: 9351 5317 Email: monica.cooper@sydney.edu.au
  • Online Learning The Unit of Study you are currently enrolled in has some elements available online (CANVAS).

1.8 Assessment

  • Various assessment tasks to evaluate knowledge and practical understanding of the material.
  • Assessment tasks, weightings, and due dates are listed below:
    • Individual scientific review (1500 words, 25%, due 16/4/25)
    • Mid-semester quiz (individual, 60 minutes, 10%, due 2/5/25)
    • Group assignment (1000 words, 15%, due 14/5/25)
    • Final exam (individual, 2 hours, 50%, date TBA)
  • Mid-Sem Quiz (10%)
    • Multi-choice questions (MCQs) covering the first 8 weeks of lectured material (parasitology and virology).
  • Individual scientific literature review (25%)
    • Recently published (2024) scientific paper on an aspect of the pathogenesis or epidemiology of a specific viral pathogen plus 2 other original scientific papers (NOT REVIEW ARTICLES!!!) published in journals within the last 5 years (2020-2025).
    • Produce a 1500-word literature review based on the 3 papers exploring a specific theme of relevance and importance in our current understanding of a given viral animal pathogen.
    • Restricted use of Artificial Intelligence (AI) is permitted in this task to help you review your grammatical writing, structure and flow of the reviewed theme.
  • Group case/scenario report (15%)
    • Small groups (maximum of 5) work on a specific metazoan parasite, protozoa, viral or prion infectious disease scenario to inform and educate stakeholders.
      • Report (one per group) must be submitted via the CANVAS.
    • Restricted use of AI is permitted in this task to help you review your grammatical writing and structure of the written aspect of this report and the generation of images within the flow diagram.
  • Written examination (50%)
    • In-person invigilated examination of 2 hours duration.
    • Multi-choice questions, short answer questions, and short essay case based questions.

1.9 University and Faculty Policies & Guidelines

  • Student code of conduct
  • Academic Honesty in Coursework
  • Artificial Intelligent tools can be used in your learning but need to be used with caution
    https://www.sydney.edu.au/students/academic-integrity/new-policy.html
  • Academic Dishonesty and Plagiarism
  • Special Consideration Applications
  • Student Appeals Against Academic Decisions
  • University Learning Hub

1.10 University Learning Hub

  • The Learning Hub offers a range of workshops and other activities for students to help develop your learning and language skills for academic studies.

2 Practical Classes

2.1 Laboratory Classes
  • The practical component of Agents of Disease (AVBS 3001) will consist of 6 laboratory sessions, in 2 blocks of 3 weekly sessions covering parasitology (weeks 5-8) and bacteriology (weeks 10-12).
  • In weeks, 2-4, the virology component of the unit will be explored in greater detail through small group tutorial activities.
  • Students need to obey the PC2 lab rules for the bacteriology lab classes, undergo a PC2 lab induction during week 10, and sign off on a document indicating that they understand the occupational health and safety (OH&S) requirement for laboratory exercises in the unit of study.
2.2 Laboratory Rules
  • Rules for LabA, Gunn Building
    1. A buttoned up laboratory coat must be worn at all times in the laboratory.
    2. Closed footwear must be worn.
    3. Bring your own saftey glasses or googles.
    4. Long hair must be tied back.
    5. Handle potentially infectious material with extreme care.
    6. Do not, eat, drink or smoke in the laboratory and NEVER place pencils, pens or other materials that you use in laboratory in your mouth.
    7. Samples are never to be taken from the laboratory
    8. Samples must be properly labelled
    9. Do not sit on benches.
    10. Any personal accident must be reported to a practical facilitator immediately.
    11. Any spillage of sample material must be reported to a practical facilitator immediately.
    12. At the beginning of each session, the work area must be wiped down with disinfectant.
    13. At the end of the session leave the bench clean and disinfected and wash your hands with a skin disinfectant provided before leaving the laboratory.
    14. Ensure that you know where the nearest emergency exit is and leave these exits free from obstruction.
      Failure to comply with all laboratory rules may result in you being asked to withdrawal from laboratory classes and a FAILURE of the unit of study.
  • Rules for PC2 teaching lab Rm 403 LEES1
    1. Carefully follow the instructions of your practical facilitator.
    2. A laboratory gown must be worn at all times in the laboratory.
    3. Closed footwear must be worn.
    4. Long hair must be tied back.
    5. When handle potentially infectious material in a PC2 laboratory you must wear gloves.
    6. You must wear safety glasses or goggles at all times in the laboratory.
    7. Do not, eat, drink or smoke in the laboratory and do not bring in any written material or writing materials.
    8. Preferable do not use your mobile phone in the laboratory.
    9. DO NOT bring personal tablets or laptop computers into the laboratory.
    10. Store bags, coats, umbrellas, mobile phones etc. in lockers outside the Lab.
    11. Cultures and samples are never to be taken from the laboratory.
    12. Cultures and samples must be properly labelled with your name (or initial), date and when appropriate the nature of the sample.
    13. Do not sit on benches.
    14. Any personal accident must be reported to a practical facilitator immediately.
    15. Any spillage of culture or sample material must be reported to a practical facilitator immediately.
    16. At the beginning of each session, the work area must be wiped down with disinfectant (i.e. 80% (v/v) alcohol) to minimise contamination.
    17. At the end of the session leave the bench clean and disinfected (i.e. 80% (v/v) alcohol) and wash your hands with a skin disinfectant provided after de-gowning removing safety glasses and de-gloving before leaving the laboratory.
    18. During the classes you may be required to use a biosafety cabinet to minimize the risk of aerosol contamination.
    19. Ensure that you know where the nearest emergency exit is and leave these exits free from obstruction.
      Failure to comply with all laboratory rules will be noted and you may be asked to withdrawal from the laboratory class. Repeated failure to comply with these rules may result in a ban from laboratory classes and FAILURE of this unit.

3 Lecture Guide

  • Recommend to supplement these notes with the knowledge gained from the reference material and to produce your own personal notes.
  • Additional material associated with these lectures, including PowerPoint lecture presentations and pre- recorded lectures will be made available on Sydney eLearning (CANVAS) during the course of this unit.

3.1 Introduction to Agents of Disease

L1 Introduction to agents of disease
  • Aim: To introduce students to key issues and topics, infectious disease significance, and underlying factors for infectious disease control.
  • Learning Outcomes: By the end of this lecture, you should be able to:
    1. Understand the meaning of infection and disease.
    2. Recognise the animal and public health importance associated with infectious disease-causing agents.
    3. Recognise the various groups of infectious agents that affect animals.
    4. Identify factors that contribute to infectious disease development and manifestation in the animal.
    5. Understand the concept of causation.
    6. Recognise your role as an animal and veterinary bioscience graduate in diagnosing and managing animal infectious disease agents.
  • What is disease, what causes it and why does it occur?
    • Disease: A change in the state of health of host leading to inability to carry out normal functions, often due to structural and/or biochemical damage to tissues.
    • Clinical vs. Subclinical Disease
      • Causative Agents:
        1. Physical Agents: heat, cold, radiation, trauma
        2. Genetics: inherited causes
        3. Chemical Agents: toxins, poisons, drugs, metabolites, free radicals
        4. Infectious Agents: metazoan and protozoan parasites, bacteria, viruses, fungi, algae and prions/infectious proteins
  • Disease occurs because of interactions of factors (environmental, host and pathogen, these three are often referred to as the disease triad) that all contribute to the final disease or health outcome. It is usually not enough just to know the factor rather; it is the interactions of the factors that are critical.
  • When these interactions favour the pathogen and pathological responses in the host, disease is often the result.
  • The resulting disease manifestation can give us a clue about the identity of the causative agent
  • Infection and Disease
    • Infection: presence of an infectious agent within or on the animal, with or without signs of disease.