Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Фев. 7, 2025
The
history
of
clinical
resistance
to
tetracycline
antibiotics
is
characterized
by
cycles
whereby
the
deployment
a
new
generation
drug
molecules
quickly
followed
discovery
mechanism
resistance.
This
suggests
mechanism-specific
selection
each
generation;
however,
evolutionary
dynamics
this
remain
unclear.
Here,
we
evaluate
24
recombinant
Escherichia
coli
strains
expressing
genes
from
(efflux
pumps,
ribosomal
protection
proteins,
and
enzymatic
inactivation)
in
context
generation.
We
employ
high-throughput
barcode
sequencing
protocol
that
can
discriminate
between
mixed
culture
quantify
their
relative
abundances.
find
preferentially
selected
for
specific
antibiotic
generations,
leading
expansion.
Remarkably,
minimum
inhibitory
concentration
associated
with
individual
secondary
inter-mechanism
fitness,
but
it
does
explain
intra-mechanism
fitness.
These
patterns
match
drugs
pathogens.
Nucleic Acids Research,
Год журнала:
2019,
Номер
unknown
Опубликована: Окт. 9, 2019
The
Comprehensive
Antibiotic
Resistance
Database
(CARD;
https://card.mcmaster.ca)
is
a
curated
resource
providing
reference
DNA
and
protein
sequences,
detection
models
bioinformatics
tools
on
the
molecular
basis
of
bacterial
antimicrobial
resistance
(AMR).
CARD
focuses
high-quality
data
sequences
within
controlled
vocabulary,
Ontology
(ARO),
designed
by
biocuration
team
to
integrate
with
software
development
efforts
for
resistome
analysis
prediction,
such
as
CARD's
Gene
Identifier
(RGI)
software.
Since
2017,
has
expanded
through
extensive
curation
revision
ontological
structure,
over
500
new
AMR
models,
classification
paradigm
expansion
analytical
tools.
Most
notably,
Resistomes
&
Variants
module
provides
statistical
summary
in
silico
predicted
variants
from
82
pathogens
100
000
genomes.
By
adding
these
CARD,
we
are
able
summarize
using
information
included
identify
trends
mobility
determine
previously
undescribed
novel
variants.
Here,
describe
updates
recent
expansions
its
process,
including
resources
community
data.
Frontiers in Public Health,
Год журнала:
2019,
Номер
7
Опубликована: Сен. 4, 2019
The
recent
advancements
in
rapid
and
affordable
DNA
sequencing
technologies
have
revolutionized
diagnostic
microbiology
microbial
surveillance.
availability
of
bioinformatics
tools
online
accessible
databases
has
been
a
prerequisite
for
this.
We
conducted
scientific
literature
review
here
we
present
description
examples
available
AMR
detection
provide
future
perspectives
recommendations.
At
least
47
resources
antimicrobial
resistance
(AMR)
determinants
or
amino
acid
sequence
data
developed
to
date.
These
include,
among
others
but
not
limited
to,
ARG-ANNOT,
CARD,
SRST2,
MEGARes,
Genefinder,
ARIBA,
KmerResistance,
AMRFinder
ResFinder.
Bioinformatics
differ
several
parameters
including
type
accepted
input
data,
presence/absence
software
search
within
database
that
can
be
specific
tool
cloned
from
other
resources,
the
approach
employed,
which
based
on
mapping
alignment.
As
consequence,
each
strengths
limitations
sensitivity
specificity
application,
some
highlighted
benchmarking
exercises
articles.
identified
are
either
at
public
genome
centers,
GitHub
run
locally
online.
NCBI
ENA
possibilities
submission
both
accompanying
phenotypic
susceptibility
allowing
researchers
further
analyze
develop
test
new
tools.
advancement
whole
application
real-time
is
essential
control
prevention
strategies
combat
increasing
threat
AMR.
Accessible
expanding
establish
global
pathogen
surveillance
tracking
genomics.
There
however,
need
standardization
pipelines
as
well
predictions
data.
Antimicrobial Resistance and Infection Control,
Год журнала:
2021,
Номер
10(1)
Опубликована: Март 31, 2021
Abstract
Data
on
comprehensive
population-based
surveillance
of
antimicrobial
resistance
is
lacking.
In
low-
and
middle-income
countries,
the
challenges
are
high
due
to
weak
laboratory
capacity,
poor
health
systems
governance,
lack
information
systems,
limited
resources.
Developing
countries
struggle
with
political
social
dilemma,
bear
a
economic
burden
communicable
diseases.
Available
data
fragmented
representativeness
which
limits
their
use
advice
policy
makers
orientate
efficient
allocation
funding
financial
resources
programs
mitigate
resistance.
Low-quality
means
soaring
rates
inability
track
map
spread
resistance,
detect
early
outbreaks,
set
national
tackle
Here,
we
review
barriers
limitations
conducting
effective
surveillance,
highlight
multiple
incremental
approaches
that
may
offer
opportunities
strengthen
if
tailored
context
each
country.
Nucleic Acids Research,
Год журнала:
2020,
Номер
49(D1), С. D644 - D650
Опубликована: Сен. 17, 2020
Abstract
An
increasing
prevalence
of
hospital
acquired
infections
and
foodborne
illnesses
caused
by
pathogenic
multidrug-resistant
bacteria
has
stimulated
a
pressing
need
for
benchtop
computational
techniques
to
rapidly
accurately
classify
from
genomic
sequence
data,
based
on
that,
trace
the
source
infection.
BacWGSTdb
(http://bacdb.org/BacWGSTdb)
is
free
publicly
accessible
database
we
have
developed
bacterial
whole-genome
typing
tracking.
This
incorporates
extensive
resources
genome
sequencing
data
corresponding
metadata,
combined
with
specialized
bioinformatics
tools
that
enable
systematic
characterization
isolates
recovered
infections.
Here,
present
2.0,
which
encompasses
several
major
updates,
including
(i)
integration
core
multi-locus
(cgMLST)
approach,
highly
scalable
appropriate
belonging
different
lineages;
(ii)
addition
multiple
analysis
module
can
process
dozens
user
uploaded
sequences
in
batch
mode;
(iii)
new
tracking
comparing
plasmid
those
deposited
public
databases;
(iv)
number
species
encompassed
2.0
increased
9
20,
represents
pathogens
medical
importance;
(v)
newly
designed,
user-friendly
interface
set
visualization
providing
convenient
platform
users
are
also
included.
Overall,
updated
bears
great
utility
continuing
provide
users,
epidemiologists,
clinicians
bench
scientists,
one-stop
solution
analysis.
Abstract
Whole
genome
sequencing
(WGS)
of
foodborne
pathogens
has
become
an
effective
method
for
investigating
the
information
contained
in
sequence
bacterial
pathogens.
In
addition,
its
highly
discriminative
power
enables
comparison
genetic
relatedness
between
bacteria
even
on
a
sub-species
level.
For
this
reason,
WGS
is
being
implemented
worldwide
and
across
sectors
(human,
veterinary,
food,
environment)
investigation
disease
outbreaks,
source
attribution,
improved
risk
characterization
models.
order
to
extract
relevant
from
large
quantity
complex
data
produced
by
WGS,
host
bioinformatics
tools
been
developed,
allowing
users
analyze
interpret
data,
starting
simple
gene-searches
phylogenetic
studies.
Depending
research
question,
complexity
dataset
their
skill
set,
can
choose
great
variety
analysis
data.
review,
we
describe
approaches
phylogenomic
studies
outbreak
give
overview
selected
based
Despite
efforts
last
years,
harmonization
standardization
typing
are
still
urgently
needed
allow
easy
laboratories,
moving
towards
one
health
surveillance
system
