Antimicrobial resistance - theory and methods (Coursera)

Antimicrobial resistance - theory and methods (Coursera)
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Antimicrobial resistance - theory and methods (Coursera)
The course will cover the topics related to antimicrobial resistance with basic definitions and overview on antimicrobials their use and the emergence and spread of resistance. The course will guide you through the concepts and the importance of resistance spread and dissemination and how that happens. It will show you how bacteria become resistant and which mechanisms they might use for this. And as part of the course you will also receive some training in methods for antimicrobial susceptibility testing (AST) and detection of specific resistance in the microbiological laboratories with the basic methods available and with focus on the obtention of good quality results which can be interpreted and used for different purposes.

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Additionally, it will show you how to use genomic analysis tools to analyze whole genome sequencing data to detect resistance genes (and or other genes of interest) in a simple and easy way using online tools freely available.

After this course you should be able to:

1. Describe the most important families of antimicrobials and mode of action

2. Understand the basic concepts of antimicrobial resistance from several perspectives (clinical, research and microbiological)

3. Enumerate and describe how bacteria can become resistant and the mechanisms that may be involved in that process

4. Describe how antimicrobial resistance emerges and spreads around the world including concepts of antimicrobial resistance transfer, selection and dissemination

5. Enumerate the methods used for antimicrobial susceptibility testing (AST)

6. Compare dilution and diffusion methods and know the basic techniques of agar disk diffusion, broth dilution and agar dilution methods

7. Have detailed theoretical knowledge on how to perform the main methods in a laboratory

8. Know the basic concepts about analysis and interpretation of results of AST, including different breakpoints, cut-off setting and their applications.

9. Understand the importance and related concepts related to quality management and quality assurance method standardization, applied to AST

10. Relate the information obtained in this course with real cases of resistant bacteria spreading in patients, the community, animals or the environment

11. Relate the phenotypical results with results from genotyping using molecular techniques for detection of resistance mechanisms

12. Understand the concept and be able to apply genomic analysis tools used to detect resistance genes and other relevant genes from Whole Genome Sequencing (WGS) data (with demonstration of selected online tools)


Syllabus


WEEK 1

Welcome to the course

This module is basically a welcome to the course were you can find information on the Course structure, the contents you will be learning in the next modules, the grading, and introduction to the instructors and to the teaching material.

Module A- Antimicrobial and antimicrobial action

Antimicrobials and antimicrobial action ( includes two lectures and one quiz). Here you will learn a lot about antibiotics/ antimicrobials and you will know more about:what they are, where do they come from, what are the major groups and how can we classify them, how do they have an effect, how do they act on the bacterial cells


WEEK 2

Module B - Antimicrobials and resistance

This module containd information about antimicrobials and the development of resistance in bacteria including causes for resistance and their mechanisms, as well as an insight in how resistance disseminates and how it can be selected.


WEEK 3

Module C- Antimicrobial susceptibility testing

This module deals with antimicrobial susceptibility testing in the laboratory: its importance and use, descriptions of the methods and their applications and detailed descriptions of the procedures applied for the main methods.


WEEK 4

Module D- Interpretation

This module gives practical insight on how to interpret antimicrobial susceptibility results.

Module E- Quality assurance

This module is dedicated to Quality management and Quality assurance (QA/ Quality control (QC) procedures and use of QC strains to assure the qulaity of results of antimicrobial susceptibility testing: importance, elements and principles.


WEEK 5

Module F- Alternatives to AST- Genome analysis tools

As alternative to the phenotypical methods, the researcher might decide to use genotypically based methods to identify genes of interest. in the lectures of this module we present the Resfinder tool which may be used to find resistance mechanisms ( genes and in the future versions also specific point mutations)from Whole genome sequences of bacteria of interest. The second Lecture is a demonstration of the My DB Finder which can be used to identify genes of interest defined by the user from Whole genome sequence data.

Module G- specific resistances



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