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Antimicrobial gene detection is based on assembled genomes generated from WGS data. Reads are assembled into large contiguous sequences called contigs and these are interrogated for the presence of resistance genes. abriTAMR reports genes found in full as well as partial matches (Figure 1). Genes are considered to be found in contigs in full if there is > 90% of the target protein identified at greater than 90% identity to a protein in the database. This allows for the detection of alleles that may have mutations either in the form of SNPs (single nucleotide polymorphisms) or small insertions/deletions. Partial recovery of genes from contigs is reported when there is between 50% and 90% of the gene present with >90% identity to a protein in the database. This allows for the detection of genes across contig boundaries, which can occur due to the use of short read technology. abriTAMR will bin genes into drug classes based on NCBI annotations provided in the database and in-house assessment.

Currently, this software tool focuses on detection of a wide range of resistance genes conferring resistance to all antimicrobial classes as distinct from detecting chromosomally-located resistance-conferring mutations. It is also important to note that abriTAMR reports gene presence/absence; it does not infer phenotypic resistance. Many of the resistance genes detected by abriTAMR may not be relevant for clinical management or antimicrobial surveillance.