Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform.

ABSTRACT:

Background

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next-generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences.

Results

To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and single-isolate whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-r

SUBMITTER: Lu D 

PROVIDER: S-EPMC12057172 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature