This is the home of the ESGEM-AMR Working Group, which focuses on curating organism-specific rule sets for interpreting AMR genotypes under the AMRrules framework.
The goal of AMRrules is to develop interpretive standards for AMR genotypes, akin to the interpretive standards developed by EUCAST and CLSI for antimicrobial susceptibility phenotyping.
An overview of the AMRrules concept and software is available in here, and version 1 rules curated by ESGEM-AMR are available here.
In 2024 ESGEM, the ESCMID Study Group on Epidemiological Markers, partnered with the AMRrules team to form the ESGEM-AMR Working Group to curate organism-specific rule sets for AMRrules.
The convenors of ESGEM-AMR are Kat Holt (LSHTM), Natacha Couto (ESGEM Chair), and Jane Hawkey (Monash, leading bioinformatics development). We have ~200 members (listed below), structured into:
- Organism-focused subgroups who curate AMRrules for their focus organism (species or genus), and
- Data & Tools subgroup who developed the AMRrules specification and contribute to technical development and interoperability with other tools in the AMR genomics ecosystem.
An initial call for members was launched at the ESGEM General Meeting in April 2024. We have now grown to nearly 200 members (listed below).
ESGEM-AMR members volunteer their time to the working group, which involves attending monthly group-wide calls (slides are publicly available here), as well as subgroup-specific meetings and activities to encode rules. All members agree to the group's Terms of Reference and Code of Ethics.
Additional requests to join ESGEM-AMR will be considered periodically. You may register your interest and let us know what organism/s you have expertise in, using this form. We are particularly interested in hearing from potential new members with expertise in organisms for which there is not yet a subgroup, or with small subgroups (see list below).
We have partnered with EUCAST to ensure alignment of the AMRrules approach with the EUCAST Subcommittee on WGS and Phenotypic AST (including their first report (2017) and ongoing updates), as well as important EUCAST concepts and guidance including Expected Phenotypes, Expert Rules, wildtype distributions and ECOFFS, and Resistance Mechanisms.
ESGEM-AMR members include individuals from allied resources like the Comprehensive Antibiotic Resistance Database (CARD), NCBI Pathogens, the Beta-Lactamase DataBase (BLDB), the Public Health Alliance for Genomic Epidemiology (PHA4GE) and others, which helps ensure our efforts are aligned with the goals of the broader AMR genomics community.
We are keen to partner with other allied organisations and initiatives, please get in touch if you'd like to discuss.
- AMRrules Specification & Syntax - v1.0 [docs]
- AMRrules Technical Guidance - v1.6 [PDF]
- AMRrules Browser [website]
- AMRrules Software pacakge [docs]
- AMRrules Documentation [docs]
- AMRgen R package for analysing matched genotype/phenotype data [AMRgen repo]
- AMRrulemakeR R package for automating rule generation using AMRgen analyses [AMRrulemakeR repo]
- Code and tools for accessing public AMRFinderPlus + AST data [datacuration repo]
- CARD/Antimicrobial Resistance Ontology (ARO): [browser]
- Variant specification: HGVS
- AMRrules syntax: [docs]
- EUCAST: [Breakpoints] [Expected Resistance]
- NCBI AMRFinderPlus: [software]
- NCBI refgene (AMR Gene Catalog): [browser]
- NCBI AMR Reference Gene Hierarchy: [browser] [TXT file download]
- NCBI refseq: [browser]
- NCBI AST data: [browser]
- NCBI AST data submission: [info] [submission format]
- NCBI Taxonomy: [browser]
- Introductory webinar slides: [PDF]
- Kickoff meeting slides: [PDF]
Before submitting rules for review, they should be first checked using the Python rulevalidator.
Data & Tools - Jane Hawkey/Kat Holt, Andrew McArthur, Finlay Maguire, Michael Feldgarden, Brody Duncan, Kristy Horan, Leonid Chindelevitch, Kara Tsang, Amogelang Raphenya, Dag Harmsen, Emily Bordeleau, Mackenzie Wilke, Romain Pogorelcnik, Yu Wan, Zoe Dyson, Bogdan Iorga, Derek Sarovich, John Rossen, Silvia Argimon, Charlene Rodrigues, Rolf Kaas, Nick Duggett, Louise Teixeira Cerdeira, Matthijs Berends, Adrian Egli, João Perdigão, Tiffany Ta, Karyn Mukiri, Chiara Crestani, Jalees Nasir, Arjun Prasad
Enterococcus - Francesc Coll, Thomas Demuyser, Ana R. Freitas, Guido Werner, Precious Osadebamwen, Theo Gouliouris, Fiona Walsh, Valeria Bortolaia, Basil Britto Xavier, Helena Seth-Smith
Staphylococcus - Natacha Couto, Birgitta Duim, Valeria Bortolaia, Sarah Baines, Sandra Reuter, Assaf Rokney, Holly Grace Espiriu, Manal AbuOun, Sankarganesh Jeyaraj, Robert Kozak, Nick Duggett, Birgit Strommenger, Lina Cavaco, Varun Shamanna, Sabrina Di Gregorio, Teresa Ribeiro, Tim Read, Georgina Lewis-Woodhouse, Raphael Sieber
Acinetobacter baumannii - Paul Higgins, Rahul Garg, Mehrad Hamidian, Bogdan Iorga, Priyanka Khopkar-Kale, Margaret Lam, Bruno Silvester Lopes, Ignasi Roca, Varun Shamanna, Clement Tsui, David Wareham, Valeria Bortolaia, Adrian Egli, Lucie Amoureux, Vera Manageiro, Antoine Abou Fayad, Beverly Egyir
Enterobacter - Teresa Coque/Rafael Canton, Paul Higgins, Fernando Lazaro Perona, Po-Yu Liu, Elena Martinez, Rietie Venter, Ana Budimir, Angela Novais, Patrick Harris, Valeria Bortolaia, Val Fernandez, Vera Manageiro, Lorena Lopez Cerero
Pseudomonas aeruginosa - Antonio Oliver, Adriana Cabal Rosel, Alasdair Hubbard, Bogdan Lorga, Xena Li, Carla Lopez Causape, Juliette Severin, David Wareham, Adam Witney, Ørjan Samuelsen, Bela Kocsis, Derek Sarovich, Fernando Lazaro Perona, Valeria Bortolaia, Francesca Saluzzo, Vera Manageiro
Klebsiella pneumoniae - Kat Holt/Kara Tsang, Valeria Bortolaia, Adam Komorowski, Elisenda Miro, Jon Iredell, Ørjan Samuelsen, Sally Partridge, Manal AbuOun, Sandra Reuter, Sankarganesh Jeyaraj, Fernando Lazaro Perona, Richard Goodman, Teresa Coque, Bogdan Iorga, Clement Tsui, Margaret Lam, Priyanka Khopkar-Kale, Varun Shamanna, Adam Witney, Alasdair Hubbard, Nicole Stoesser, Sam Lipworth, Deepali Desai, Ângela Novais, Luis Gustavo Carvalho Pacheco, Iren Høyland Löhr, Daniela M Cirillo, Adrian Egli, Francesca Saluzzo, Nicholas Feasey, João Perdigão, Timothy Walsh, Oliver Pearse, Kelly Wyres, Vera Manageiro +KlebNet Geno/Pheno Consortium
Escherichia coli/Shigella - Ebenezer Foster-Nyarko/Kat Holt Pieter-Jan Ceyssens, Fiona Walsh, Carolina Silva Nodari, Soe Yu Naing, Richard Goodman, Abdurrahman Hassan Jibril, Jelalu Kemal Birmeka, Elena Martinez, Teresa Coque, Ramon Maluping, Ana Vale, Gultekin Unal, Axel Hamprecht, Valeria Bortolaia, Bogdan Lorga, Alasdair Hubbard, Manal AbuOun, Jon Iredell, Sally Partridge, Nicole Stoesser, Sam Lipworth, Etienne Rupée, Gherard Batisti Biffignandi, Kate Baker, Adrian Egli, Timothy Walsh, Vera Manageiro, Leonor Silveira, Benjamin Parcell
Salmonella enterica - Kristy Horan/Pieter-Jan Ceyssans, Anthony Smith, Gültekin Ünal, Abdurrahman Hassan Jibril, Manal AbuOun, Jelalu Kemal Birmeka, Varun Shamanna, Assaf Rokney, Malgorzata Ligowska-Marzeta, Megan Carey, Regina Russanova, Tom Koritnik, Zoe Dyson, Leonor Silveira
Neisseria gonorrhoeae - Leonor Sanchez Buso, Yonatan Grad, Sheeba Manoharan-Basil, Martin McHugh, Tatum Mortimer, Anna Roditscheff, Faina Wehrli, Adam Witney, Raffael Frei, Daniel Golparian, Magnus Unemo
Mycobacterium tuberculosis - Leonid Chindelevitch, Iñaki Comas, Philip Fowler, Kristy Horan, Priyanka Khopkar-Kale, Mariana López, Conor Meehan, Adam Witney, Brian Alcock, Francesca Saluzzo, João Perdigão, Dylan Adlard, Margo Diricks
Streptococcus - Mario Ramirez, Assaf Rokney, Holly Grace Espiriu, Stefanie Desmet, Elita Jauneikaite
Campylobacter - Birgitta Duim, Bruno Silvester Lopes, Malgorzata Ligowska-Marzeta, Monica Oleastro, Tee Keat Teoh, Bogdan Iorga, Diana Costa, Sangeeta Banerji, Alexandra Nunes
Haemophilus influenzae - Assaf Rokney, Charlotte Michel, Priyanka Khopkar-Kale, Derek Sarovich, Margo Diricks, Matthias Merker
Anaerobes - Trefor Morris, Ulrik Stenz Justesen, Marcela Krutova, Linda Veloo, Kathleen Boiten
Stenotrophomonas maltophilia - Jane Hawkey, Derek Sarovich, David Wareham, Fiona Walsh, Rietie Venter, Kat Holt
Serratia - Sandra Reuter, Teresa Coque, Adam Komorowski, Basil Britto Xavier, Brian Forde, João Pedro Furlan
Citrobacter- Teresa Ribeiro, Roberto Sierra, Diego Andrey
Achromobacter xylosoxidans - Charlotte Michel, Lucie Amoureux, Miglė Gabrielaitė, Lisa Påhlman
Aeromonas - Po-Yu Liu, João PedroFurlan, Hsien-Po Huang, Po-Hsiui
Shewanella - Po-Yu Liu, João PedroFurlan, Ting-Kuang Yeh
Bordetella - Laurence Luu, Carla Rodrigues
Brucella - Jelalu Kemal Birmeka
Listeria - Jelalu Kemal Birmeka, Basil Britto Xavier, Marc Lecuit, Alexandra Moura
Edwardsiella - Jelalu Kemal Birmeka
Pasteurella - Jelalu Kemal Birmeka
Burkholderia cepacia complex - Charlotte Michel, David Wareham
Burkholderia pseudomallei - Claire Chewapreecha, Derek Sarovich, Jessica Webb, Chalita Chomkatekaew
Chryseobacterium indologenes - Rietie Venter
Corynebacterium diphtheriae - Sylvain Brisse, Louise Teixeira Cerdeira, Adrian Egli, Teresa Ribeiro
Legionella - Charlotte Michel, Ghislaine Descours, Christophe Ginevra, Stefano De Giorgi, Nancy Flountzi, Sophie Jarraud
Mycoplasma - Mike Beeton, Anna Roditscheff, Sabine Pereyre, Patrick Meyer Sauteur, Nick Duggett, Jørgen Skov Jensen
Neisseria meningitidis - Célia Bettencourt, Leonor Sanchez Buso, Ala-Eddine Deghmane, Wesley Mattheus, Ana Filipa Vale, Alexandra Nunes
Proteus mirabilis - Axel Hamprecht, Janko Sattler, Elisenda Miro, Rémy Bonnin, Stephan Goettig, Shereen Shaban Abdelkareem
Treponema - Brian Alcock
Vibrio - Assaf Rokney
Yersinia - Pieter-Jan Ceyssens, Cyril Savin, Regina Russanova