Package: abritamr
logo by Charlie Higgs (PhD candidate)Taming the AMR beastabriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or  list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia.Acquired resistance mechanims in the form of point mutations (restricted to subset of species)Streamlined output.Presence of virulence factorsInstallCondaabritAMR is best installed withcondaas described below (~2 minutes on laptop)conda create -n abritamr -c bioconda abritamr
conda activate abritamrA note on dependenciesabriTAMR requiresAMRFinder Plus, this can be installed separately withcondaif required.abriTAMR comes packaged with a version of the  AMRFinder DB consistent with current NATA accreditation. If you would like to use another DB please download it usingamrfinder -Uand use the-dflag to point to your database.Current version of AMRFinder Plus compatible with abritAMR 3.10.42 (tested on versions down to 3.10.16)Command-line toolabritamr run --help


optional arguments:
  -h, --help            show this help message and exit
  --contigs CONTIGS, -c CONTIGS
                        Tab-delimited file with sample ID as column 1 and path to assemblies as column 2 OR path to a contig
                        file (used if only doing a single sample - should provide value for -pfx). (default: )
  --prefix PREFIX, -px PREFIX
                        If running on a single sample, please provide a prefix for output directory (default: abritamr)
  --jobs JOBS, -j JOBS  Number of AMR finder jobs to run in parallel. (default: 16)
  --identity IDENTITY, -i IDENTITY
                        Set the minimum identity of matches with amrfinder (0 - 1.0). Defaults to amrfinder preset, which is 0.9
                        unless a curated threshold is present for the gene. (default: )
  --amrfinder_db AMRFINDER_DB, -d AMRFINDER_DB
                        Path to amrfinder DB to use (default:
                        /<path_to_installation>/abritamr/abritamr/db/amrfinderplus/data/2021-09-30.1)
  --species {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes}, -sp {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes}
                        Set if you would like to use point mutations, please provide a valid species. (default: )You can also run abriTAMR inreportmode, this will output a spreadsheet which is based on reportable/not-reportable requirements in Victoria. You will need to supply a quality control file (comma separated) (-q), with the following columns:ISOLATESPECIES_EXP (the species that was expected)SPECIES_OBS (the species that was observed during the quality control analysis)TEST_QC (PASS or FAIL)--soprefers to the type of collation and reporting pipelinegeneralstandard reporting structure for aquired genes, output as reportable and non-reportableplusInferred AST based on validation undertaken at MDUabritamr report --help

optional arguments:
  -h, --help            show this help message and exit
  --qc QC, -q QC        Name of checked MDU QC file. (default: )
  --runid RUNID, -r RUNID
                        MDU RunID (default: Run ID)
  --matches MATCHES, -m MATCHES
                        Path to matches, concatentated output of abritamr (default: summary_matches.txt)
  --partials PARTIALS, -p PARTIALS
                        Path to partial matches, concatentated output of abritamr (default: summary_partials.txt)
  --sop {general,plus}  The MDU pipeline for reporting results. (default: general)OutputabritAMR runOutputs 4 summary files and retains the raw AMRFinderPlus output for each sequence input.amrfinder.outraw output from AMRFinder plus (per sequence). For more information please see AMRFinderPlus helpheresummary_matches.txtTab-delimited file, with a row per sequence, and columns representing functional drug classesOnly genes recovered from sequence which have >90% coverage of the gene reported and greater than the desired identity threshold (default 90%).I. Genes annotated with*indicate >90% coverage and > identity threshold < 100% identity.II. No further annotation indicates that the gene recovered exhibits 100% coverage and 100% identity to a gene in the gene catalog.III. Point mutations detected (if--speciessupplied) will also be present in this file in the form ofgene_AAchange.summary_partials.txtTab-delimited file, with a row per sequence, and columns representing functional drug classesGenes recovered from sequence which have >50% but <90% coverage of the gene reported and greater than the desired identity threshold (default 90%).summary_virulence.txtTab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classificationGenes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%).Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with^.Genes annotated with*indicate >90% coverage and > identity threshold < 100% identity.abritamr.txtTab-delimited file, combiningsummary_matches.txt,summary_partials.txt,summary_virulence.txtwith a row per sequence, and columns representing AMRFinderPlus virulence gene classification and/or functional drug classes.Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%).Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with^.Genes annotated with*indicate >90% coverage and > identity threshold < 100% identity.abritamr reportwill output spreadsheetsgeneral_runid.xlsx(NATA accredited) orplus_runid.xlsx(validated - not yet accredited) depending upon the sop chosen.general_rundid.xlsxhas two tabs, one for matches and one for partials (corresponding to genes reported in thesummary_matches.txtandsummary_partials.txt). Each tab has 7 columnsColumnInterpretationMDU sample IDSample IDItem codesuffix (MDU specific)Resistance genes (alleles) detectedgenes detected that are reportable (based on species and drug classification)Resistance genes (alleles) det (non-rpt)other genes detected that are not not reportable for the species detected.Species_obsSpecies observed (supplied in input file)Species_expSpecies expected (supplied in input file)db_versionVersion of the AMRFinderPlus DB usedplus_runid.xlsxoutput is a spreadsheet with the different drug resistance mechanims and the corresponding interpretation (based on validation of genotype and phenotype) for drug-classes relevant to reporting of anti-microbial resistance inSalmonella enterica(other species will be added as validation of genotype vs phenotype is performed).AmpicillinCefotaxime (ESBL)Cefotaxime (AmpC)TetracyclineGentamicinKanamycinStreptomycinSulfathiazoleTrimethoprimTrim-SulphaChloramphenicolCiprofloxacinMeropenemAzithromycinAminoglycosides (RMT)Colistin