The easy-to-interpret AMR summary report generated by ARDaP ( Fig.2) represents a major improvement over current AMR software such as AMRFinderPlus, ARIBA, CARD, and ResFinder, which require an intimate understanding of AMR determinants to correctly interpret outputs and to ignore naturally occurring genetic variation. The AMR report produced by ARDaP represents a crucial step towards the incorporation of WGS as a routine tool for guiding best-practice AMR stewardship and personalised treatment regimens in the clinical diagnostic setting, and will help to accelerate the translation of NGS-to-bedside diagnostics.

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phylogeny Use this flag if you would like a whole-genome phylogeny, or an annotated variant matrix file. Note that this may take a long time if you have a large number of isolates. Default=false When creating your own custom database, please use the database templates to ensure ARDaP compatibility. Army Vantage is part of the Army Data and Analytics Platforms (ARDAP) program, which manages a portfolio of systems that enable warfighters through data and analytics. ARDAP modernizes aging, disjointed, and legacy systems through enterprise-scale digital transformation efforts, according to the request for information. Home flea repellants should be used when you are sure or suspect there are fleas in your home, such as clues from your pet or if you are being bitten. There is the analytics layer. So, it is the part of the work that involves developing a data platform working with the specific Army users to ingest unstructured and structured data that’s in legacy systems into a new visualization platform and then developing it in a way that can work. That’s what Vantage does,” Camarillo said.

SNP and indel AMR variants can be added to the 'Data' tab of the 'Variants_SNP_indel' table (as illustrated in Figure 2). Required information includes the AMR gene name, the SnpEff AMR variant annotation (and alternate gene annotation, if applicable), and the antimicrobial/s affected by the variant. For example, in row 3 of Figure 2, a frameshift mutation is present in the P. aeruginosa ampD AMR gene at residue 18 (serine), which confers AMR towards the cephalosporin antibiotics, ceftazidime (CAZ) and cefipime (FEP). Within this table is also a ‘known combination’ column, which should be populated in instances where two or more stepwise mutations are required to confer AMR. If potentially airborne sprays and foggers are not suitable as you or your pet have respiratory issues, a powder could work.AMR software parameters. The default RGI v5.1.0 database parameters of CARD v3.0.9 ( https://card.mcmaster.ca/analyze/rgi; accessed 25Jun20), ARIBA v2.14.5 ( https://github.com/sanger-pathogens/ariba), ResFinder v4.1 ( https://cge.cbs.dtu.dk/services/ResFinder/), and AMRFinderPlus v3.8.28 ( https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/) were examined for performance across the B. pseudomallei genomes. species Use this flag to specify an ARDaP database that contains species-specific AMR determinant information. ARDaP ( Antimicrobial Resistance Detection and Prediction) is a pipeline designed to identify genetic variants (i.e. single-nucleotide polymorphisms [SNPs], insertions/deletions [indels], copy-number variants [CNVs], and gene loss) associated with antimicrobial resistance (AMR) from microbial (meta)genomes or (meta)transcriptomes. Further, ARDaP reports these variants in a user-friendly manner that does not require extensive domain-specific knowledge, and that links AMR genotype to AMR phenotype. The impetus behind developing ARDaP was our frustration with current methodology being unable to detect AMR conferred by "complex" chromosomal alterations, and accurate AMR detection from mixtures, meaning that many tools cannot offer comprehensive AMR determinant detection. Our species of interest, Burkholderia pseudomallei, Pseudomonas aeruginosa*, and Haemophilus influenzae*, can develop AMR in a multiple ways, predominantly through chromosomal gene loss, CNVs, SNPs, and indels; and in B. pseudomallei, gene gain plays no role in conferring AMR, rendering many existing AMR tools entirely ineffective. ARDaP first identifies all genetic variation in a microbial sequence data (either .fasta assemblies or Illumina paired-end data; other data types currently not supported), and then interrogates this information against a user-created database of AMR determinants. The software will then summarise the identified AMR determinants and produce an easy-to-interpret summary report. The Army seeks to continually improve its information readiness and data agility to gain decision advantage. Army Data and Analytics Platforms (ARDAP) contributes to this goal by providing modern data and decision support tools and platforms, harnessing data across defense business systems and modernizing the Army’s training management system.