Antimicrobial resistance is one of the biggest challenges facing modern medicine. Because the management of COVID-19 was increasingly becoming dependent on pharmacological interventions, there is greater risk for accelerating the evolution and spread of antimicrobial resistance [Afshinnekoo et al. 2021]. A study in a tertiary hospital environment revealed concerning colonisation patterns of microbes during extended periods [Chng et al. 2020]. It also highlighted the diversity of antimicrobial resistance gene reservoirs in hospitals that could facilitate the emergence and transmission of new modes of antibiotic resistance and AMR burden in cities in general [Danko et al. 2021]. This year we would like CAMDA Community to look into AMR related challenges.

This challenge consists in developing and testing models for predicting antimicrobial resistance (AMR) in 8 different bacterial pathogens and 2 drugs from the WHO’s Priority Pathogen List. You will be provided with a training dataset taken from public databases, about 6,000 isolates in total, containing both WGS accession numbers for each isolate (for about a quarter of those you get accession numbers for assemblies rather than short reads), as well as the antibiotic susceptibility phenotype. The developed models will then be tested on data from another collection of the same pathogens, over 1500 isolates in total, for which you will be provided with the genotypes, but not the phenotypes.

Each team will be able to submit predictions up to 3 times for accuracy evaluation on the withheld phenotypes, and the final submission from each team will qualify as the CAMDA challenge submission; the teams with the best submissions will be invited to present their methods at CAMDA conference at ISMB.