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AMR genes

Use atb amr to query AMR (antimicrobial resistance), stress, and virulence gene hits across AllTheBacteria genomes, using AMRFinderPlus v4.2.5 results run across all ATB genomes. All AMR, stress, and virulence data is in amrfinderplus.parquet (~58.5M rows, ~1.18 GB), downloaded automatically by atb fetch and partitioned by genus for fast queries.

ENA metadata requirement

Commands that filter by country, collection date, or sequencing platform require the ena_20250506.parquet file. Fetch it with atb fetch --tables ena_20250506.parquet. Any ENA filter flag automatically implies --with-ena, which appends country, collection_date, and instrument_platform columns to the output. Without --with-ena, the ENA table is not read and default AMR queries remain in the millisecond tier.

Query AMR genes

# Get all AMR gene hits for E. coli (high-quality genomes only)
atb amr --species "Escherichia coli" --hq-only --limit 100

# Filter by drug class
atb amr --species "Escherichia coli" --hq-only --class "BETA-LACTAM"

# Wildcard gene search (all beta-lactamase genes)
atb amr --species "Escherichia coli" --gene "bla%"

# Compare resistance across multiple species
atb amr --species "Escherichia coli,Klebsiella pneumoniae" --class "BETA-LACTAM"

# Find a gene across ALL genera (no species filter needed)
atb amr --gene "blaCTX-M-15" --limit 100

# Filter by ENA metadata -- country, platform, or collection date
# (requires ena_20250506.parquet: run 'atb fetch --tables ena_20250506.parquet')
# Any ENA filter implies --with-ena, so country/collection_date/instrument_platform
# are appended to the output automatically.
atb amr --species "Escherichia coli" --class "BETA-LACTAM" \
  --country "United Kingdom" --platform ILLUMINA --limit 50
atb amr --species "Salmonella enterica" --gene "blaCTX-M-15" \
  --collection-date-from 2022-01-01

# Add ENA columns to the output without filtering
# (requires ena_20250506.parquet). Without --with-ena the ENA table is not read,
# so default AMR queries stay in the millisecond tier.
atb amr --species "Escherichia coli" --class "BETA-LACTAM" --with-ena --limit 50

# Search by drug class across all genera
atb amr --class "CARBAPENEM" --limit 50

# Filter by detection quality
atb amr --species "Escherichia coli" --min-coverage 95 --min-identity 98

# Query stress response genes
atb amr --species "Escherichia coli" --type stress

# Query virulence factors
atb amr --species "Escherichia coli" --type virulence

# Query all three categories at once
atb amr --species "Escherichia coli" --type all

# Output to file (CSV)
atb amr --species "Klebsiella pneumoniae" --hq-only --format csv -o kpn_amr.csv

# Auto-gzip when -o ends in .gz; format inferred from filename (.csv.gz -> CSV)
atb amr --species "Escherichia coli" --hq-only -o ecoli_amr.tsv.gz

# Restrict to a specific list of samples (comma-separated)
atb amr --samples SAMD00093868,SAMEA104470147 --type all

# Or read accessions from a file (one per line, '#' comments allowed)
atb amr --sample-file my_isolates.txt --class "BETA-LACTAM"

# Download matching assemblies directly
atb amr --species "Escherichia coli" --class "BETA-LACTAM" --hq-only --download -d ./genomes

# Preview what would be downloaded (no actual download)
atb amr --species "Klebsiella pneumoniae" --gene "blaCTX-M-15" --download --dry-run

# Cap number of assemblies to download
atb amr --species "Escherichia coli" --gene "bla%" --download --max-samples 20 -d ./bla_genomes

--species accepts comma-separated values for multi-species comparison. When omitted, --gene or --class is required to search across all genera.

The --download flag downloads the FASTA assembly for each unique sample in the results. Query output is always printed first. Use --dry-run to preview URLs without downloading, and --max-samples to cap the number of assemblies.

Output columns

AMR output preserves the AMRFinderPlus v4.2.5 TSV header verbatim, so all 26 columns are present in the original case and ordering: Name, Protein id, Contig id, Start, Stop, Strand, Element symbol, Element name, Scope, Type, Subtype, Class, Subclass, Method, Target length, Reference sequence length, % Coverage of reference, % Identity to reference, Alignment length, Closest reference accession, Closest reference name, HMM accession, HMM description, Hierarchy node, genus, species.

With --with-ena (or any ENA filter), three extra columns are appended: country, collection_date, instrument_platform.