ABRicate

Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: Resfinder, CARD, ARG-ANNOT, NCBI BARRGD, NCBI, EcOH, PlasmidFinder, Ecoli_VF and VFDB.

Is this the right tool for me?

1. It only supports contigs, not FASTQ reads (including Genbank and .gz compressed files)
2. It only detects acquired resistance genes, NOT point mutations
3. It needs BLAST+ >= 2.2.30 and EMBOSS to be installed
4. It's written in Perl

If you are happy with the above, then please continue! Otherwise consider using Ariba, Resfinder, RGI, SRST2, etc.

Quick Start

% abricate 6159.fasta
Using database resfinder:  2130 sequences -  Mar 17, 2017
Processing: 6159.fna
Found 3 genes in 6159.fna
#FILE     SEQUENCE     START   END     GENE     COVERAGE     COVERAGE_MAP     GAPS  %COVERAGE  %IDENTITY  DATABASE   ACCESSION  PRODUCT
6159.fna  NC_017338.1  39177   41186   mecA_15  1-2010/2010  ===============  0/0   100.00     100.000    resfinder  AB505628   n/a
6159.fna  NC_017338.1  727191  728356  norA_1   1-1166/1167  ===============  0/0   99.91      92.367     resfinder  M97169     n/a
6159.fna  NC_017339.1  10150   10995   blaZ_32  1-846/846    ===============  0/0   100.00     100.000    resfinder  AP004832   betalactamase

Installation

Brew

If you are using the OSX Brew or LinuxBrew packaging system:

brew install brewsci/bio/abricate
abricate --check
abricate --list

Bioconda

If you use Conda follow the instructions to add the Bioconda channel:

conda install abricate
abricate --check
abricate --list

Source

If you install from source, Abricate has the following package dependencies:

• EMBOSS for seqret
• BLAST+ >2.3.0 for blastn, makeblastdb, blastdbcmd
• Decompression tools gzip and unzip
• Perl modules: LWP::Simple, Text::CSV, Bio::Perl, JSON, File::Slurp

These are easy to install on an Ubuntu-based system:

sudo apt-get install emboss bioperl ncbi-blast+ gzip unzip \
  libjson-perl libtext-csv-perl libfile-slurp-perl liblwp-protocol-https-perl libwww-perl
git clone https://github.com/tseemann/abricate.git
./abricate/bin/abricate --check
./abricate/bin/abricate --setupdb
./abricate/bin/abricate ./abricate/test/assembly.fa

Input

Abricate takes any sequence file that EMBOSS seqret can convert to FASTA files (eg. Genbank, EMBL), and they can be optionally gzip compressed.

abricate assembly.fa 
abricate assembly.fa.gz
abricate assembly.gbk 
abricate assembly.gbk.gz

It can take multiple files at once too:

abricate assembly.*
abricate /mnt/ncbi/bacteria/*.gbk.gz 

It does not accept raw FASTQ reads; please use Ariba or SRTS2 for that.

Output

Abricate produces a tap-separated output file with the following columns:

Column	Example	Description
FILE	Ecoli.fna	The filename this hit came from
SEQUENCE	contig000324	The sequence in the filename
START	23423	Start coordinate in the sequence
END	24117	End coordinate
GENE	tet(M)	AMR gene name
COVERAGE	1-1920/1920	What proportion of the gene is in our sequence
COVERAGE_MAP	===============	A visual represenation
GAPS	1/4	Openings / gaps in subject and query - possible psuedogene?
%COVERAGE	100.00%	Proportion of gene covered
%IDENTITY	99.95%	Proportion of exact nucleotide matches
DATABASE	card	The database this sequence comes from
ACCESSION	NC_009632:49744-50476	The genomic source of the sequence
PRODUCT	aminoglycoside O-phosphotransferase APH(3')-IIIa	Gene product (if available)

Caveats

• Does not find mutational resistance, only acquired genes.
• Gap reporting incomplete
• Sometimes two heavily overlapping genes will be reported for the same locus
• Possible coverage calculation issues

Databases

ABRicate comes with some pre-downloaded databases:

• Resfinder
• ARG-ANNOT
• CARD
• NCBI Bacterial Antimicrobial Resistance Reference Gene Database
• EcOH
• PlasmidFinder
• VFDB
• Ecoli_VF

You can check what you have installed with the --list command. This lists the available databases in TSV (or CSV with --csv) and three columns:

% abricate --list

DATABASE       SEQUENCES  DBTYPE  DATE
abricate       4981       nucl    2018-Jul-28
argannot       1749       nucl    2018-Jul-28
card           2241       nucl    2018-Jul-28
ecoh           597        nucl    2018-Jul-28
ecoli_vf       2701       nucl    2018-Jul-28
ncbi           4324       nucl    2018-Jul-28
plasmidfinder  263        nucl    2018-Jul-28
resfinder      2434       nucl    2018-Jul-28
vfdb           2597       nucl    2018-Jul-28

The default database is currently resfinder. You can choose a different database using the --db option:

% abricate --db vfdb --quiet 6159.fa

6159.fna  NC_017338.1  2724620  2726149  aur      1-1530/1530     ===============  0/0    100.00     99.346     vfdb      NP_647375	zinc metalloproteinase aureolysin
6159.fna  NC_017338.1  2766595  2767155  icaR     1-561/561       ===============  0/0    100.00     98.930     vfdb      NP_647402	N-acetylglucosaminyltransferase
6159.fna  NC_017338.1  2767319  2768557  icaA     1-1239/1239     ===============  0/0    100.00     99.677     vfdb      NP_647403	n/a
6159.fna  NC_017338.1  2768521  2768826  icaD     1-306/306       ===============  0/0    100.00     99.020     vfdb      NP_647404	n/a
6159.fna  NC_017338.1  2768823  2769695  icaB     1-873/873       ===============  0/0    100.00     99.542     vfdb      NP_647405	n/a
6159.fna  NC_017338.1  2769682  2770734  icaC     1-1053/1053     ===============  0/0    100.00     98.955     vfdb      NP_647406	n/a
6159.fna  NC_017338.1  2771040  2773085  lip      1-2046/2046     ===============  0/0    100.00     98.778     vfdb      NP_647407	triacylglycerol lipase precursor

Combining reports across samples

ABRicate can combine results into a simple matrix of gene presence/absence.

# Run abricate on each .fa file
% abricate 1.fna > 1.tab
% abricate 2.fna > 2.tab

# Combine
% abricate --summary 1.tab 2.tab

#FILE     NUM_FOUND  aac(6')-aph(2'')_1  aadD_1  blaZ_32  blaZ_36  erm(A)_1  mecA_15  norA_1  spc_1  tet(M)_7
1.tab     8          100.00              100.00  .        100.00   100.00    100.00   99.91   100.00  100.00
2.tab     3          .                   .       100.00   .        .         100.00   99.91   .       .

Updating the databases

# force download of latest version
% abricate-get_db --db resfinder --force

# re-use existing download and just regenerate the database
% abricate-get_db --db resfinder

Making your own database

Let's say you want to make your own database called tinyamr. All you need is a FASTA file of nucleotide sequences, say tinyamr.fa. Idealy the sequence IDs would have the format >DB~~~ID~~~ACC DESC where DB is tinyamr, ID is the gene name, and ACC is an accession number of the sequence source. The DESC can be any textual description.

% cd /path/to/abricate/db     # this is the --datadir default option
% mkdir tinyamr
% cp /path/to/tinyamr.fa sequences
% abricate --setupdb
% # or just do this: makeblastdb -in sequences -title tinyamr -dbtype nucl -parse_seqids -hash_index

% abricate --list
DATABASE           SEQUENCES  DATE
tinyamr            173        2017-Aug-28

% abricate --db tinyamr screen_this.fasta

Etymology

The name "ABRicate" was chosen as the first 3 letters are a common acronym for "Anti-Biotic Resistance". It laso has the form of an English verb, which suggests the tool actual taking "action" against the problem of antibiotic resistance. It is also relatively unique in Google, and is unlikely to receive an infamous JABBA Award.

Issues

Please report problems to the Issues Page.

License

GPLv2

Author

Torsten Seemann | @torstenseemann | blog