ASIST is an automated pipeline that can be used for the characterization of clinical isolates in terms of their acquired resistance profile. The acquired resistance profile of isolates can be analyzed using three global standards i.e. determination of susceptibility based on MIC breakpoints provided by EUCAST and CLSI, phenotypic classification criteria developed by CDC/ECDC and standards for assessing quality of whole genome sequence for reporting AST by EUCAST. In this study, public databases and literature were used to obtain AB genomes and their susceptibility patterns. These datasets were then evaluated based on these standards definition. Three standards were tested on 4776 strains of AB. From over four thousand genomes, only 788 (~16%) are associated with metadata that allows for interpretation of AST in globally acceptable standards. Also, in literature more than 70% studies do not reference any of the standards.
Antimicrobial susceptibility testing (AST) is used to determine susceptibility of organisms to antibiotics. Determination of susceptibility is based on MIC breakpoints and are provided by EUCAST and CLSI. Likewise, phenotypic classification criteria is developed by CDC/ECDC and standards for assessing quality of whole genome sequence for reporting AST by EUCAST. In this study, public databases and literature were used to obtain AB genomes and their susceptibility patterns. These datasets were then evaluated based on standards definition. Three standards were tested on 4776 strains of AB in a systematic fashion and an automated pipeline “ASIST” is developed on the basis of these global standards. We converged three global standards including whole genome sequence (WGS) inferred AST on clinical isolates of AB and have designed an automated pipeline that allows for characterization of other clinical isolates based on these standards.
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ASIST (Antimicrobial Susceptibility standards based phenotypes) is developed by ASIST Team »