<s>
The	O
AMRFinderPlus	B-Application
tool	O
from	O
the	O
National	O
Center	O
for	O
Biotechnology	O
Information	O
(	O
NCBI	O
)	O
is	O
a	O
bioinformatic	O
tool	O
that	O
allows	O
users	O
to	O
identify	O
antimicrobial	O
resistance	O
determinants	O
,	O
stress	O
response	O
,	O
and	O
virulence	O
genes	O
in	O
bacterial	O
genomes	O
.	O
</s>
<s>
AMRFinderPlus	B-Application
is	O
used	O
by	O
,	O
which	O
clusters	O
and	O
finds	O
similar	O
pathogen	O
genomic	O
sequences	O
from	O
food	O
,	O
environmental	O
sources	O
,	O
and	O
patients	O
.	O
</s>
<s>
AMRFinderPlus	B-Application
is	O
run	O
for	O
each	O
bacterial	O
isolate	O
in	O
the	O
Pathogen	O
Detection	O
Project	O
,	O
and	O
the	O
findings	O
are	O
provided	O
for	O
public	O
use	O
.	O
</s>
<s>
AMRFinderPlus	B-Application
can	O
detect	O
acquired	O
antibiotic	O
resistance	O
,	O
stress	O
response	O
,	O
and	O
virulence	O
genes	O
,	O
and	O
genetic	O
mutations	O
that	O
are	O
known	O
to	O
confer	O
antibiotic	O
resistance	O
.	O
</s>
<s>
When	O
AMRFinderPlus	B-Application
was	O
initially	O
developed	O
and	O
distributed	O
,	O
there	O
were	O
already	O
multiple	O
databases	O
containing	O
antibiotic	O
resistance	O
determinants	O
.	O
</s>
<s>
While	O
some	O
AMR	O
gene	O
identification	O
tools	O
rely	O
on	O
BLAST-based	O
methodologies	O
,	O
others	O
employ	O
hidden	O
Markov	O
model	O
(	O
HMM	O
)	O
approaches	O
.	O
</s>
<s>
BLAST-based	O
methods	O
can	O
identify	O
particular	O
alleles	O
and	O
genes	O
that	O
are	O
closely	O
related	O
,	O
but	O
they	O
often	O
apply	O
arbitrary	O
cutoffs	O
that	O
can	O
misidentify	O
AMR	O
genes	O
or	O
assign	O
resistance	O
to	O
non-AMR	O
genes	O
.	O
</s>
<s>
In	O
AMRFinderPlus	B-Application
,	O
custom	O
BLAST	B-Application
cutoffs	O
are	O
created	O
for	O
each	O
gene	O
to	O
optimize	O
sensitivity	O
and	O
specificity	O
of	O
detection	O
.	O
</s>
<s>
Unlike	O
BLAST-based	O
approaches	O
,	O
which	O
apply	O
the	O
same	O
penalty	O
for	O
sequence	O
mismatches	O
across	O
any	O
sequence	O
,	O
HMMs	O
allow	O
for	O
the	O
weighing	O
of	O
sequence	O
mismatches	O
based	O
on	O
how	O
prevalent	O
they	O
are	O
in	O
nature	O
,	O
resulting	O
in	O
higher	O
accuracy	O
in	O
detecting	O
true	O
homologs	O
than	O
BLAST-based	O
approaches	O
,	O
but	O
these	O
models	O
require	O
curation	O
and	O
validation	O
to	O
ensure	O
accuracy	O
.	O
</s>
<s>
Under	O
the	O
rules	O
of	O
the	O
United	O
States	O
Copyright	O
Act	O
,	O
NCBI	O
AMRFinderPlus	B-Application
is	O
classed	O
as	O
"	O
United	O
States	O
Government	O
Work.	O
"	O
</s>
