Course: Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis

How to learn on this course You are going to learn by watching videos, reading articles, completing exercises where you apply some of the knowledge you acquire on this course, …

In this video, this week’s educator and the lead educator for this course Conor, is talking about your learning opportunities in week 1 of the course Antimicrobial resistance (AMR) and …

In this interview, you will hear from Rolf Summer Kass, Senior Researcher from the National Food Institute in Denmark, talking about how the ResFinder data base started and how it …

Watch this week’s educator Jane telling you about the learning opportunity in this part of the course Before you continue, take a moment to reflect on your learning so far:

Each database we covered in step 2.3 has a specific tool to access that database and return predicted AMR patterns. AMRFinderPlus: https://www.nature.com/articles/s41598-021-91456-0 CARD/RGI: https://pubmed.ncbi.nlm.nih.gov/36263822/ ResFinder: https://academic.oup.com/jac/article/75/12/3491/5890997 Each of the tools …

We have just covered a range of databases that contain bacterial AMR mechanisms and you have heard about their strengths and weaknesses. In this section we are going to cover …

Let’s look at the input data types the databases and tools described so far require, as well as at the output reports they generate Input data Many of the databases …

The following table compares and contracts the three databases. You can use the databases with their associated tools (which are also listed in the table).   NCBI CARD ResFinder URL …

In this course, we have focused on the three main tools used to access the three main AMR databases. However, there are more than 18 open-source AMR detection tools currently …

Mycobacterium tuberculosis and drug resistance M. tuberculosis causes approximately 10 million infections in humans each year, causing the disease tuberculosis. Around 0.5M of these are due to drug-resistant strains. Only …

Quality control in antimicrobial susceptibility testing (AST) The validity, reproducibility, and accuracy of Antimicrobial Susceptibility Testing (AST) results depend on testing alongside fully characterized strains provided by the American Type …

In the next three steps, we will focus on different phenotypic data approaches The first type of phenotypic testing is qualitative approaches. Here we look for the binary resistant/sensitive readout. …

Quantitative methods look beyond the binary R/S and estimate the minimum inhibitory concentration (MIC) Quantitative methods can be tested on liquid medium (broth) or solid agar Broth dilution method (macrodilution …

Acknowledgments Many thanks to all those who were involved in making of the course Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis Course Lead Educator Dr Conor Meehan Course …

Examples of different gene-drug pairings for AMR detection For a set of strains, three different genes were sequenced and compared to phenotypic data for various drugs. In scenario A) a …