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

AMR analysis is a broad, sprawling and ever-growing field. Creating and using the databases we covered in week 2 is just the tip of the iceberg. Once we have these …

The most widely used and regularly updated AMR databases (e.g., NCBI, ResFinder, CARD) directly incorporate new AMR data from peer-reviewed literature as well as their own genomic analyses. However, differences …

In this screencast, Kristy is demonstrating ways to download files from a database Kristy also discusses the advantages of using the European Nucleotide Archive (ENA) for downloading FASTQ files and …

Uploading data to these databases is not easy, but well worth the effort. Attached here are some of the Excel forms that are used to capture the data descriptions alongside …

NLM-NCBI now also enables phenotypic AST data to be uploaded, to facilitate the development and population of the National Database of Antibiotic Resistant Organisms (NDARO). This enables the development of …

Depending on what is being uploaded to the public databases, you might need to supply metadata. Metadata can describe data attached to the biosample or data attached to the reads. …

Data within the repositories of INSDC are structured in an interoperable way, with each sharing a general model for how data is captured and stored. In general the structure is …

The most widely shared biological data type is sequence data, either in its raw or processed (e.g. assembled) form. Therefore much effort has been put into ensure this data type …

In this video interview, Silvia Argimón, Senior technical advisor at the World Health Organization (WHO), talks to Conor to discuss her work on antimicrobial resistance (AMR) and genomic surveillance She …

Expanding your skills after the course As mentioned in earlier weeks, there are many options for investigation of AMR mechanisms in bacteria. We covered some of the well known and …

In this video we will touch on some future directions for the AMR databases field. We will speak on why it’s important to have and grow representative datasets. Contribution from …

By now you should have an understanding of the main AMR detection tools and what their inputs and outputs look like. In this exercise, you will download a plasmid sequence …

Check your learning: connecting to databases In this activity we will download and search the NCBI database list to find the blaKPC gene. You can find out more about this …

Not all data is created and shared equally. It is important that when we contribute data to the wider community, we follow some basic principles to ensure it is useable …

Pathogen and AMR epidemiology is not just about tracking strains, it’s also about tracking the spread of the AMR mechanisms. In the previous sections, we discussed the use of core …