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

Recommendations and final documents

• Perspective paper on environmental AMR monitoring: Why to monitor AMR in the environment, how to implement it, and what is needed to succeed.

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