This is page is were make available our proposed protocols, developed software and databases, as well as any additional data.

Recommendations and final documents

Tools and Databases

  • MuMaMe – Software for finding resistance mutations in shotgun metagenomic data
  • argNorm – Software for ARG normalization by mapping to the ARO ontology
  • ResFinderFG – Database and online platform for antibiotic resistance determinants identified through functional metagenomics
    Database link
  • GMGC – The Global Microbial Gene Catalog, an integrated, consistently-processed, gene catalog combining metagenomics and high-quality sequenced isolates

Drafts/Work in progress

  • EMBARK Suggested sampling and sample processing protocol
    (Note that this is a work in progress, and that this might not be the final version of the protocol)
  • Suggested antibiotic resistance genes to be targeted for monitoring based on previous qPCR studies. See Abramova et al. (2023) for detailed motivation of this choice of genes
    • intI1
    • sul1
    • blaTEM
    • blaCTX-M
    • qnrS
    • tetA or tetG
    • Additional targets of interest: sul3, vanA, tetH, aadA2, floR, ereA and mexF