MEDICAL MICROBIOLOGY 332

Transcription

1 MEDICAL MICROBIOLOGY 332 UNIT OUTLINE Associate Professor Martin Finn July, 2012 School of Biomedical Sciences

2 Medical Microbiology 332 Semester 2, 2012 Unit Index No: Credit points: v1 25 points Unit availability: 2012, study period: Semester 2. location: Bentley only. Pre-requisite Units: Medical Microbiology 331 Unit Coordinator: Address: Assoc Professor Martin Finn School of Biomedical Sciences Curtin University of Technology GPO Box U1987 PERTH WA 6845 Phone: (08) Fax: (08) Online category: Supplemental Prerequisites All students in this unit will have completed the prerequisite units in Medical Microbiology or their equivalent and it is assumed that you have knowledge and skills to this level. Despite this previous study there is a significant degree of reinforcement in the material covered in this unit. However if your study of microbiology occurred some time ago and you feel that your understanding might be inadequate you should revise material covered in the second year and first semester third year units. Students will be expected to display practical skills and understanding, particularly with respect to safe practice and asepsis commensurate with their level of microbiology background. Students who do not show satisfactory laboratory competence will have this reflected in Laboratory grades. Aims The aim of this unit is to further extend students understanding of the infectious agents causing human disease, their pathogenesis and control especially through chemotherapy. A particular emphasis will be made of the role of the microbiology laboratory in the diagnosis and treatment of infection caused by specific organisms. Unit Outcomes This unit is designed to introduce you to both theoretical and practical aspects of Medical Microbiology, particularly as undertaken for the diagnosis of infectious disease but also for research in associated fields. On successful completion of this unit a student will be able to: 2

3 1. Recognise the role of specific viruses in human disease and describe the characteristics of selected viral pathogens. Explain and describe the laboratory methods used in the diagnosis of specific virus infectious diseases. 2. Briefly describe common infectious diseases affecting various body sites and discuss the choice and application of the laboratory methods needed to investigate these diseases and identify their causative organisms. 3. Discuss the role of Parasites in human infectious disease and apply parasite diagnostic methods in the laboratory. 4. Describe fungal pathogens of humans and describe and apply methods for their laboratory recognition. 5. Choose, describe, perform and interpret the laboratory methods for "in vitro" detection of bacterial resistance to antibiotics. 6. Select, perform and interpret laboratory investigations required to examine specimens in diagnostic microbiology. Effectively communicate results of these laboratory investigations. 7. Show an awareness of recent developments and research in medical microbiology. Professional Skill Outcomes Students will be expected to bring forward and further develop the following skills from the first semester prerequisite unit in Medical Microbiology: o display a sound understanding and application of aseptic methods in the handling of infectious materials including laboratory cultures. o plate out a mixture of bacterial organisms and successfully separate the organisms. o successfully pick and subculture bacterial isolates from single colonies. o Understand and practice suitable labelling of laboratory cultures. o prepare and microscopically exam stained smears stained by Gram s, Acidfast and other simple staining methods. o perform and interpret primary identifying tests for bacterial cultures including: catalase, coagulase, oxidase, OF(glucose), motility. o know the culture requirements for the isolation of bacterial pathogens studied during the laboratory sessions. o recognise the growth characteristics of common pathogens and know how to proceed to identify these isolates o recognise common fungal pathogens in culture and apply methods needed for the identification of genera and species including stained wet mounts, slide cultures and identification tests. o show a working knowledge of methods used for the identification of viruses in clinical samples. o know the requirements for the successful culture of cells in vitro. o prepare materials for microscopy to find and identify common parasite forms in clinical material 3

4 As a result of completing the laboratory exercises in this unit students will develop the following skills and be able to: o perform direct microscopy on clinical specimens as appropriate and choose and inoculate suitable culture media for the isolation of common pathogens from clinical samples o recognise the presence of pathogens in cultures from clinical specimens and successfully isolate and identify pathogens as possible with the methods available. o understand the effects of antibiotics on bacteria and the methods used for susceptibility testing and detection of bacterial resistance. Perform susceptibility test methods as appropriate for pathogens isolated from clinical specimens. o report the results from laboratory examination of clinical samples in a meaningful and concise fashion consistent with diagnostic laboratory practise. o further specific outcomes are shown with the individual laboratory exercises. These outcomes will be assessed in practical exercises, assessment exercises and end of semester examinations. 4

5 Syllabus Virology Nature of a virus: Viral components - capsids, envelopes, nucleic acids. Classification of viruses. Laboratory methods used in the diagnosis of virus infections Viral culture: cell cultures, animals, detection of infection, cytopathic effects, haemadsorption, immunofluorescence, neutralization. Serological tests for virus infection. Direct demonstration; immunofluorescence, electron microscopy, EIA, PCR. Human Papilloma Virus and Human Immunodeficiency Virus contrast replication and impact. clinical Hepatitis B & Picorna viruses. Additional viral pathogens comparison of DNA and RNA viruses. Viral Haemorrhagic fevers Prions infectious proteins once thought to be viruses. Anti-viral therapy chemotherapy and vaccination. Antimicrobial Chemotherapy: Antimicrobial Chemotherapy - Basic Principles. Antibiotic groups review.. Bacterial susceptibility testing and resistance detection review principles and methods Parasites Causing Human disease: Revision and consolidation of the following: laboratory methods in parasitology, the lifecycles and diagnostic forms of trematodes, cestodes, nematodes and protozoa encountered in Australia. Extend knowledge of protozoa to include Entamoeba, Cryptosporidium, Isospora, Pneumocystis and Balantidium Recognition of faecal protozoa that are generally regarded as non-pathogenic e.g. Entamoeba coli, Entamoeba hartmanni, Endolimax nana and Iodamoeba bütschlii. Introduce some of the more exotic parasites not commonly seen in Australia, their detection and diagnosis. Blood nematodes e.g. Wuchereria bancrofti, Brugia malayi, Brugia timori, Loa loa, Mansonella sp. Microfilaria worms found in tissue and skin e.g. Onchocerca volvulus, Mansonella streptocerca, Dracunculus medinensis. Trypanosomiasis, Leishmaniasis. Molecular diagnostic methods. Principles of nucleic-acid detection methods. Polymerase chain reaction, principles and application to infection diagnosis. Skin and soft tissue infection a review of bacterial pyoderma and impetigo, cellulitis, wound infections. MYCOLOGY Revision of fungal structure and terminology Superficial Mycoses Definition, diseases and causal fungi Cutaneous Mycoses Definition, dermatophytes, clinical types, epidemiology classification, morphology, laboratory identification Subcutaneous Mycoses General characteristics, causal fungi, etiological characteristics and laboratory identification Systemic Mycoses Diseases which occur in Australia, causal fungi and their characteristics Urinary tract infection and urinalysis review of laboratory examination of urine including microscopy and culture methods. Genital tract infection. Sites and types of infections in males and females. STI's their laboratory diagnosis. Review of Upper and Lower respiratory tract infections including Pneumonias Typical and Atypical forms. Chronic infections - tuberculosis CNS infections: meningitis; causes clinical presentation, laboratory examination of CSF.. Cardiovascular infections. Blood culture; methods and requirements. Diseases; Gram-negative septic shock, endocarditis, other bacteraemia. 5

6 Unit Materials Lecture notes See below. Laboratory notes Laboratory notes will be provided online at the Blackboard site for this unit this semester. Textbooks and References The following book is the recommended text for this unit to supplement lecture and laboratory notes it is the same as the recommended text for Medical Microbiology 331. Winn, Washington. C. et al. (2005). Koneman s Colour Atlas and Textbook of Diagnostic Microbiology. Sixth Edition. Lippincott, Williams and Wilkins. This books does not necessarily cover all areas and reading from other sources including books from the list below is recommended although students need not purchase these books - copies are available in the Curtin library. Mahon, C.R. and G. Manuselis. (2011) Textbook of Diagnostic Microbiology. 4th Ed W B Saunders. OTHER SUGGESTED READING AND REFERENCES TEXTS Copies of some of these books may be held in closed reserve in level 2 of the library. Brooks, G.F., Butel, J.S. (2004) Jawetz, Melnick&Adelberg s Medical Microbiology 23 rd Ed. McGraw Hill Collier L & J Oxford. (2003) Human virology 2 nd Ed. Oxford University Press Mims, C., Dockrell, H.M.. et al (2004) Medical Microbiology. 3rd Ed. Mosby. Versalovic, J et al. (2011) Manual of Clinical Microbiology, 10th Ed. ASM Press Murray, M. R. et al. (2007) Manual of Clinical Microbiology, 9th Ed. ASM Press Wagner E & M J Hewlett Basic Virology (2004) Blackwell Science 6

7 Web-Based Resources and Lecture notes Lecture notes in the form of PowerPoint presentations and other information will be made available on the Internet through Flexible Learning for Curtin Students (FLECS-Blackboard) site. You can access Blackboard vis the OASIS portal at lms.curtin.edu.au/webapps/portal/frameset The Home Page has a FLECS-Blackboard tour for Students that introduces how to use the different facilities offered by Blackboard. This information is available to all users. However, the Medical Microbiology 331 section of the site will be password-protected. To use Blackboard, you will need to use your username and password. You will be advised of these at the login point. (a) Contact Details The unit coordinator for this unit is: A/Prof Martin Finn, Deputy Head, School of Biomedical Sciences at Curtin. Office m.finn@curtin.edu.au Phone (08) Fax (08) The phone is connected to a Voice Answering system that will prompt you to leave a message if I m unable to take your call. If you do so, please clearly state your name, why you are calling, a contact number (slowly) and suggested time to ring. (b) Delivery of Unit This unit has up to 3 lectures and 4 hours of laboratory time scheduled/week. In some weeks there will be 3 lectures but in other weeks there may be a tutorial session incorporated into the laboratory times and one lecture may be omitted. For some tropics the lectures for this unit will be those scheduled for Medical microbiology 432 students should attend these lectures when scheduled. IMPORTANT NOTE During this semester you will be working with specimens from hospital patients and reagents prepared from blood, blood products or body fluids. These materials may be capable of transmitting disease. For this reason, all specimens and reagents must be handled as if they were infectious. Students should review laboratory rules provided in Semester 1. 7

8 (c) Assessment Details Assessment Task Applies to. Marks Completion of Practical exercises and selected laboratory reports. Practicals 10% Theory Test (1 mid Semester week 7, 50 minutes duration, held in lecture time) Theory content 20% Final Practical Examination (week 13-14). This will consist of spot questions and laboratory exercises. Practicals 20% Final Theory Examination (Exam period) format to be advised. Lectures 50% TOTAL 100% In accordance with Curtin policy, students are advised that this unit is a SIGNIFICANT UNIT in which failure twice may lead to termination of a student s course. Students should note that a mark of 50% or more in both the theoretical and practical component of the unit is required in order to secure a pass, and that failure in any one area may result in an overall failure in this unit regardless of the total marks accrued. That is, a pass in the practical component but failure in the theory component (or vice versa) may lead to a fail grade for the unit, even though the student's total mark may exceed 50%. Plagiarism Policy It is not acceptable to simply copy the words of other students or authors when completing the weekly exercises and assignments in this unit. This action constitutes plagiarism and is regarded as academic malpractice. The penalties for plagiarism can be severe and may include termination from your course of study. All direct quotes must be correctly attributed to the author and should be kept to a minimum. Also, you should include a list of references to acknowledge the source(s) of information used to produce any written work. Useful examples and explanations of plagiarism may be seen at the Academic Integrity page of the Curtin website integrity.curtin.edu.au/studentbook.html Students are encouraged to read and understand the University s policy on plagiarism. 8

9 (d) Supplementary Examinations Supplementary examinations are awarded only at the discretion of the Board of Examiners. The aim of a supplementary examination is to allow the student to correct minor problems /deficiencies in the initial assessment to the satisfaction of the unit examiner. Supplementaries are not granted to give extra study time or correct major problems. The number of supplementary examinations awarded to a student will be kept to a minimum for this course of study University guidelines stipulate a maximum of two Supplementary assessments for a student in a semester and only where the semester mark is over 45%. You should not presume that if you fail a unit you will be granted a supplementary examination. NB. Supplementary examinations are not automatically awarded. The Board of Examiners will carefully review individual cases. No written application for supplementary examination will be considered. Supplementary examinations, if awarded, will be indicated on the official Curtin examination result statement posted to all students through Oasis. It is your responsibility to check your status. Students should note that supplementary examinations for units conducted in the School will be held during semester breaks on dates to be advised. A student who does not sit for a scheduled supplementary examination has no claim to a further examination. If you are awarded a supplementary examination it is imperative that you confirm the time and venue for the exam and ensure you are available at that time. (e) Deferred Assessment Deferment of an examination is not automatic. Students may be permitted by the relevant Board of Examiners to defer an examination or other assessment where circumstances outside their control have arisen. However, a student's overall performance may be taken into account in granting permission to defer an examination. Applications for deferment on health grounds or as a result of extenuating circumstances must be submitted not later than seven (7) days after the end of the relevant examination period or assessment date during the semester. Detailed medical certificates should be attached to the application where appropriate. The prescribed application form may be obtained either from Faculty Student Services Office (building 400) or downloaded from the Curtin website. Completed forms should be submitted to the School or the FSSO before prescribed deadlines. 9

10 Proposed Timetable for Medical Microbiology 332 Semester 2, 2012 WEEK commencing LECTURE Mon 8 am LECTURE Mon 9 am Lecture/Tutorial Fri 11 am PRACTICAL Wed-Fri July Virology July Virology July Virology August Virology 7 Virology 2 Virology 4 Virology 6 Virology 8 No lecture Antibiotics 1 (MPF) Susceptibility 2 testing (MPF) Molecular Diagnostics (IK) No Practical Practical 1 Virology cell culture Practical 2. Virology /Bacteriology Practical 3 Virology 5 13 August Parasitology (MPF) Parasitology (MPF) Skin & soft tissue infection (MPF) 6 20 August Mid Semester test: Virology wks 1-4 Urinary tract infection 1(MPF) NO LAB Practical 4 Parasitology/Bacteri ology 7 27 August Week free of classes 8 3 September Parasitology (MF) Parasitology (MF) Genital tract infections (MPF) 9 10 September Parasitology (PC) Parasitology (PC) CNS infection (MF) Practical 5. Parasitology/Bacteri ology Practical 6. Urine /Genital Infection revision September Mycology 1 Tuberculosis and other mycobacterial infections (PC) September Mycology 2 Atypical pneumonia(pc) Respiratory Infections (MF) Cardiovascular infection (MF) Practical 7. Mycology Practical 8 Mycology 13 1 October Mycology 3 HACEK organisms(pc) Case studies Recent developments 14 8 October Mycology 4 Mycology 5 Revision Practical 9. Mycology Thurs: Prac Assessment Practical 10: Wed: Mycology Thursday: Prac Assessment October Study week Unit lecturers: : Dr Brian Brestovac; MPF: Assoc Prof Martin Finn ; IK: Ian Kay ; PC: Dr Paul Costantino Please not changes to this lecture schedule may have to be made if unforseen changes in lecturer availability occur. 10