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Skip to 0 minutes and 8 seconds Hello, everyone. In this section of the tutorial, we will learn how we can detect antimicrobial resistance genes from the contigs that we assembled in the previous section. A number of bioinformatic tools exist that can be used to achieve this. These tools are either available online or offline. The online tools are advantageous because they require less bioinformatics expertise and resources when compared to offline methods. Here we will be using Pathogenwatch which is an online tool to developed by Centre for Genomic Epidemiology based at Wellcome Sanger Institute. The tool allows us to upload the contigs and detect antimicrobial resistance genes in them. So let’s get started. In the new tab, copy the link for Pathogenwatch and paste in the address bar.

Skip to 1 minute and 6 seconds This takes us to the homepage of Pathogenwatch. Click on Upload. Remember, each user has to sign up to use this tool. Once you are signed up, you will see a page like this. Then the next step is, go into the folder where you have downloaded the contigs, drag and drop the contigs onto the Pathogenwatch page. And now you can see the process. Click on the View Genomes page, and here you can see the contigs the name of the file that you uploaded which is contigs the organism that has been detected, which is Salmonella typhi. Click on the Contigs button. So it performs a number of operations other than detecting antimicrobial resistance genes.

Skip to 1 minute and 58 seconds First, it identifies the genus and the species, which is Salmonella typhi in our case. Then it presents the information of MLST, sequence type one, in our case, all the links that are present, and then serotype and genotype information. And then if you scroll down, in the antimicrobial resistance section you can see a table of drugs and the corresponding genes that has been identified in the contigs. So this table is most important for us if we are looking for antimicrobial resistance genes, where we have now identified the genes and the drugs that this organism is resistant to. So this is how we take in contigs and detect the antimicrobial resistance genes.

Detection of resistance using Pathogenwatch

In this video, you can see how the Pathogenwatch tool can be used to detect antimicrobial resistance

Link to downloadable fasta file (Important - in order to download data from the Sanger ftp site, you will need to copy and paste the link in your internet browser, rather than just click on it):

ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/AMR/contigs.fasta

Link to ResFinder tool: https://cge.cbs.dtu.dk/services/ResFinder/

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This video is from the free online course:

Bacterial Genomes: Antimicrobial Resistance in Bacterial Pathogens

Wellcome Genome Campus Advanced Courses and Scientific Conferences