Installation#
Dependencies#
AMRrules requires Python 3.12 or higher, and needs pip to be installed.
Download and install AMRrules#
Currently, AMRrules is only available for installation via source. We recommend you set up a new conda environment.
# create your conda environment
conda create -n amrrules -c bioconda python=3.12 pip
conda activate amrrules
# clone the repository
git clone https://github.com/AMRverse/AMRrules
cd AMRrules
# install AMRrules
make dev
After installation, you must download the required AMRFinderPlus resource files. Run:
amrrules --download-resources
This will download and cache the necessary files for AMRrules to function. You only need to run this once after installation, or when updating resources (eg a new AMRFinderPlus database has been released).
Check the installation#
Check which organisms have rule-sets available in the installation:
amrrules --list-organisms
Test on one of the included example dataset:
amrrules --input tests/data/input/test_ecoli_wildtype.tsv --output-prefix test_ecoli_wildtype --organism 's__Escherichia coli'
Compare these resulting output files to those in tests/data/example_output…
tests/data/example_output/test_ecoli_wildtype_interpreted.tsv:
Name |
status |
comments |
Protein identifier |
Contig id |
Start |
Stop |
Strand |
Gene symbol |
Sequence name |
Scope |
Element type |
Element subtype |
Class |
Subclass |
Method |
Target length |
Reference sequence length |
% Coverage of reference sequence |
% Identity to reference sequence |
Alignment length |
Accession of closest sequence |
Name of closest sequence |
HMM id |
HMM description |
Hierarchy node |
Species |
HQ |
variation type |
gene |
mutation |
ruleID |
gene context |
drug |
drug class |
phenotype |
clinical category |
evidence grade |
version |
organism |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00002 |
288840 |
291941 |
acrF |
multidrug efflux RND transporter permease subunit AcrF |
plus |
AMR |
AMR |
EFFLUX |
EFFLUX |
BLASTX |
1034 |
1034 |
100 |
99.52 |
1034 |
AAC76298.1 |
multidrug efflux RND transporter permease subunit AcrF |
NA |
NA |
acrF |
Escherichia coli |
TRUE |
Gene presence detected |
acrF |
1.0.0 |
||||||||||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
113923 |
115011 |
pmrB_Y358N |
Escherichia colistin resistant PmrB |
core |
AMR |
POINT |
COLISTIN |
COLISTIN |
POINTX |
363 |
363 |
100 |
99.45 |
363 |
WP_001300761.1 |
two-component system sensor histidine kinase PmrB |
NA |
NA |
pmrB |
Escherichia coli |
TRUE |
Protein variant detected |
pmrB |
p.Tyr358Asn |
ECO0081 |
core |
colistin |
wildtype |
S |
moderate |
1.0.0 |
s__Escherichia coli |
||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0001 |
core |
penicillin beta-lactam |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0002 |
core |
ampicillin |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0003 |
core |
amoxicillin |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0004 |
core |
piperacillin |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0005 |
core |
first-generation cephalosporin |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0006 |
core |
cefazolin |
wildtype |
I |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0007 |
core |
second-generation cephalosporin |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0008 |
core |
cefoxitin |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0009 |
core |
cefuroxime |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0011 |
core |
cefotaxime |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0012 |
core |
third-generation cephalosporin |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0013 |
core |
ceftriaxone |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0014 |
core |
ceftazidime |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0015 |
core |
cefixime |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0016 |
core |
carbapenem |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0017 |
core |
imipenem |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0018 |
core |
aztreonam |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0084 |
core |
cefepime |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00005 |
159556 |
160686 |
blaEC |
BlaEC family class C beta-lactamase |
plus |
AMR |
AMR |
BETA-LACTAM |
BETA-LACTAM |
BLASTX |
377 |
377 |
100 |
98.41 |
377 |
WP_063610930.1 |
extended-spectrum class C beta-lactamase EC-15 |
NA |
NA |
blaEC |
Escherichia coli |
TRUE |
Gene presence detected |
blaEC |
ECO0085 |
core |
cefpirome |
wildtype |
S |
high |
1.0.0 |
s__Escherichia coli |
|||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00007 |
68693 |
70048 |
glpT_E448K |
Escherichia fosfomycin resistant GlpT |
core |
AMR |
POINT |
FOSFOMYCIN |
FOSFOMYCIN |
POINTX |
452 |
452 |
100 |
99.78 |
452 |
WP_000948731.1 |
glycerol-3-phosphate transporter GlpT |
NA |
NA |
glpT |
Escherichia coli |
TRUE |
Protein variant detected |
glpT |
p.Glu448Lys |
ECO0082 |
core |
fosfomycin |
wildtype |
S |
moderate |
1.0.0 |
s__Escherichia coli |
||
SAMN26308439 |
PASS |
NA |
NA |
SAMN26308439.contig00039 |
5645 |
6871 |
mdtM |
multidrug efflux MFS transporter MdtM |
plus |
AMR |
AMR |
EFFLUX |
EFFLUX |
BLASTX |
409 |
410 |
99.76 |
98.04 |
409 |
AAC77293.1 |
multidrug efflux MFS transporter MdtM |
NA |
NA |
mdtM |
Escherichia coli |
TRUE |
Gene presence detected |
mdtM |
1.0.0 |
tests/data/example_output/test_ecoli_wildtype_genome_summary.tsv:
sample |
drug |
drug class |
clinical category |
phenotype |
evidence grade |
markers (non-S) |
markers (no rule) |
markers (S) |
ruleIDs |
combo rules |
organism |
|---|---|---|---|---|---|---|---|---|---|---|---|
SAMN26308439 |
(all) |
carbapenem |
S |
wildtype |
high |
blaEC |
ECO0016 |
s__Escherichia coli |
|||
SAMN26308439 |
imipenem |
carbapenem |
S |
wildtype |
high |
blaEC |
ECO0016;ECO0017 |
s__Escherichia coli |
|||
SAMN26308439 |
(all) |
first-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0005 |
s__Escherichia coli |
|||
SAMN26308439 |
cefazolin |
first-generation cephalosporin |
I |
wildtype |
high |
blaEC |
blaEC |
ECO0005;ECO0006 |
s__Escherichia coli |
||
SAMN26308439 |
cefepime |
fourth-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0084 |
s__Escherichia coli |
|||
SAMN26308439 |
cefpirome |
fourth-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0085 |
s__Escherichia coli |
|||
SAMN26308439 |
aztreonam |
monobactam |
S |
wildtype |
high |
blaEC |
ECO0018 |
s__Escherichia coli |
|||
SAMN26308439 |
(all) |
penicillin beta-lactam |
S |
wildtype |
high |
blaEC |
ECO0001 |
s__Escherichia coli |
|||
SAMN26308439 |
amoxicillin |
penicillin beta-lactam |
S |
wildtype |
high |
blaEC |
ECO0001;ECO0003 |
s__Escherichia coli |
|||
SAMN26308439 |
ampicillin |
penicillin beta-lactam |
S |
wildtype |
high |
blaEC |
ECO0001;ECO0002 |
s__Escherichia coli |
|||
SAMN26308439 |
piperacillin |
penicillin beta-lactam |
S |
wildtype |
high |
blaEC |
ECO0001;ECO0004 |
s__Escherichia coli |
|||
SAMN26308439 |
fosfomycin |
phosphonic acid antibiotic |
S |
wildtype |
moderate |
glpT:p.Glu448Lys |
ECO0082 |
s__Escherichia coli |
|||
SAMN26308439 |
colistin |
polymyxin antibiotic |
S |
wildtype |
moderate |
pmrB:p.Tyr358Asn |
ECO0081 |
s__Escherichia coli |
|||
SAMN26308439 |
(all) |
second-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0007 |
s__Escherichia coli |
|||
SAMN26308439 |
cefoxitin |
second-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0007;ECO0008 |
s__Escherichia coli |
|||
SAMN26308439 |
cefuroxime |
second-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0007;ECO0009 |
s__Escherichia coli |
|||
SAMN26308439 |
(all) |
third-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0012 |
s__Escherichia coli |
|||
SAMN26308439 |
cefixime |
third-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0012;ECO0015 |
s__Escherichia coli |
|||
SAMN26308439 |
cefotaxime |
third-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0011;ECO0012 |
s__Escherichia coli |
|||
SAMN26308439 |
ceftazidime |
third-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0012;ECO0014 |
s__Escherichia coli |
|||
SAMN26308439 |
ceftriaxone |
third-generation cephalosporin |
S |
wildtype |
high |
blaEC |
ECO0012;ECO0013 |
s__Escherichia coli |
|||
SAMN26308439 |
(n/a) |
antibiotic efflux |
none |
acrF;mdtM |
s__Escherichia coli |
Usage info and test data#
More info on usage options can be found on the Usage page.
Additional test data and example commands can be found on the Tests page.