Current vs Deprecated AMR Pipelines

Jump to Section:

• Pipeline Features
• AMR Tool Resources

Overview

There are two pipelines used to detect antimicrobial resistant (AMR) genes within CZ ID, namely the current AMR pipeline and the old (referred to as "deprecated") AMR module. Here we summarize differences between these pipelines.

Current vs Deprecated AMR Pipelines

In its simplest form, any pipeline used to identify AMR-related sequences compares input sequences to a reference AMR database and provides results summarizing which AMR-associated sequences are present in a given dataset. CZ ID integrates AMR detection tools that have been already developed and optimized.

Our team improved the CZ ID AMR module in 2022, mainly, by replacing the AMR detection tool and the reference database. The newest AMR detection tool implemented in CZ ID, named Resistance Gene Identifier (RGI), offers several advantages over the tool used in the deprecated version, including:

• Better parameterization for both whole genome sequence (WGS) and metagenomic data.
• Use of a reference database that is routinely updated and curated, namely the Comprehensive Antibiotic Resistance Database (CARD).
• Use of both sequence reads and assembled sequences (contigs) for AMR detection. 
• Pathogen-of-origin prediction by matching query sequences to known pathogen sequences using a k-mer classifier approach.

Below we summarize features for the current and deprecated AMR modules as implemented in CZ ID.

Pipeline Features

Resources for AMR Tools

See the following resources to learn more about the different tools and methods implemented within CZ ID AMR pipelines.

Resources for current AMR module:

• Resistance Gene Identifier (RGI) GitHub page 
• K-mer alignment (KMA) publication
• KMA Bitbucket page
• Comprehensive Antibiotic Resistance Database (CARD) webpage 

Resources for deprecated AMR module:

• Short Read Sequencing Typing (SRST2) publication
• SRST2 GitHub page
• ARG-ANNOT publication
• Bowtie2 GitHub page