China CDC Weekly,
Год журнала:
2022,
Номер
4(49), С. 1110 - 1116
Опубликована: Янв. 1, 2022
Salmonella
is
a
key
intestinal
pathogen
of
foodborne
disease,
and
the
plasmids
in
are
related
to
many
biological
characteristics,
including
virulence
drug
resistance.
A
large
number
plasmid
contigs
have
been
sequenced
bacterial
draft
genomes,
however,
these
often
difficult
distinguish
from
chromosomal
contigs.In
this
study,
three
different
customized
Kraken
databases
were
used
build
classifiers.
Complete
genome
benchmark
datasets
simulated
constructed.
Five-fold
cross-validation
was
evaluate
performance
classifiers
by
two
datasets.The
predictive
classifier
based
on
all
National
Center
for
Biotechnology
Information
complete
genomes
optimal.
This
optimal
performed
with
isolated
China.
The
carrying
rate
China
91.01%,
it
found
that
could
find
more
antibiotic
resistance
genes
(ARGs)
than
results
derived
replicon-based
method
(PlasmidFinder).
Moreover,
strains
ARGs,
carried
ARGs
[three,
95%
confidence
interval
(CI):
1-14]
chromosomes
(one,
CI:
1-7).We
building
high-quality
database
as
be
ideal
prediction
sequences
genomes.
In
future,
established
study
will
play
significant
role
ARG
monitoring.
Nucleic Acids Research,
Год журнала:
2022,
Номер
51(D1), С. D744 - D752
Опубликована: Ноя. 16, 2022
Antimicrobial
resistance
(AMR)
is
considered
a
critical
threat
to
public
health,
and
genomic/metagenomic
investigations
featuring
high-throughput
analysis
of
sequence
data
are
increasingly
common
important.
We
previously
introduced
MEGARes,
comprehensive
AMR
database
with
an
acyclic
hierarchical
annotation
structure
that
facilitates
computational
analysis,
as
well
AMR++,
customized
bioinformatic
pipeline
specifically
designed
use
MEGARes
in
for
characterizing
genes
(ARGs)
metagenomic
data.
Here,
we
present
v3.0,
published
ARG
sequences
antimicrobial
drugs,
biocides,
metals,
AMR++
update
our
(available
at
MEGLab.org).
Database
annotations
have
been
expanded
include
information
regarding
specific
genomic
locations
single-nucleotide
polymorphisms
(SNPs)
insertions
and/or
deletions
(indels)
when
required
by
ARGs
expression,
the
updated
uses
this
check
presence
resistance-conferring
genetic
variants
sequenced
reads.
This
new
encompasses
337
ARGs,
whose
could
not
be
confirmed
such
manner.
In
3.0,
nodes
ontology
4
compound
types,
59
classes,
233
mechanisms
1448
gene
groups
classify
8733
accessions.
Foods,
Год журнала:
2025,
Номер
14(2), С. 253 - 253
Опубликована: Янв. 15, 2025
Infections
caused
by
human
pathogenic
bacteria
in
food
sources
pose
significant
and
widespread
concerns,
leading
to
substantial
economic
losses
adverse
impacts
on
public
health.
This
review
seeks
shed
light
the
recent
literature
addressing
prevalence
of
Salmonella
supply
chains
North
African
countries.
Additionally,
it
aims
provide
an
overview
available
information
regarding
health-related
such
as
virulence
genes,
presence
antibiotic
resistance
Salmonella.
highlights
a
gap
our
comprehensive
understanding
nations,
with
limited
molecular
characterization
efforts
identify
its
sources.
Studies
at
level
across
region
have
shown
diversity
strains
their
profiles,
thus,
these
results
show
difficulty
controlling
infections
region.
In
addition,
discussion
makes
clear
that
there
is
need
for
development
strategies
fight
potential
threat
antimicrobial
strains.
Despite
common
reports
animal-derived
foods
this
region,
underscores
persistent
challenges
may
safety
health
Microbiology Spectrum,
Год журнала:
2024,
Номер
12(4)
Опубликована: Фев. 27, 2024
The
prevalence
and
dissemination
of
the
plasmid-mediated
fluoroquinolone
(FQ)
resistance
gene
qnr
in
Salmonella
are
considered
serious
public
health
concerns
worldwide.
So
far,
no
comprehensive
large-scale
studies
have
focused
on
genetic
characteristics
isolated
from
chickens.
Herein,
this
study
aimed
to
investigate
prevalence,
antimicrobial
(AMR)
patterns,
molecular
chicken-originated
qnr-positive
strains
chicken
farms,
slaughterhouses,
markets
12
provinces
China
2020-2021.
overall
was
21.13%
(56/265),
with
highest
(36.11%,
26/72),
followed
farms
(17.95%,
21/117),
slaughterhouses
(10.53%,
9/76).
Only
qnrS
qnrB
genes
were
detected,
rate
(19.25%,
51/265)
higher
than
that
(1.89%,
5/265).
Whole
genome
sequencing
identified
37
distinct
AMR
15
plasmid
replicons,
most
frequent
mutation
quinolone
determining
regions
parC
(T57S;
91.49%,
43/47).
Meanwhile,
four
different
two
environments
discovered
among
47
strains.
In
total,
21.28%
(10/47)
capable
conjugative
transfer,
all
qnrS1-positive
strains,
majority
transferable
plasmids
being
IncHI2
types
(n
=
4).
Overall,
chickens
their
carriage
multiple
virulence
is
a
major
concern,
which
calls
for
continuous
surveillance
development
measures
control
its
transmission.IMPORTANCESalmonella
common
foodborne
pathogen
responsible
155,000
deaths
annually
Fluoroquinolones
(FQs)
used
as
first-line
drugs
treatment
infections
several
countries
regions.
However,
emergence
increasing
FQ-resistant
been
widely
reported.
Gaining
insight
into
mechanisms
could
lead
preventive
reduce
risk
drug
resistance.
study,
we
Salmonellae
patterns
genome-wide
characteristics,
providing
theoretical
basis
further
transmission.
Frontiers in Microbiology,
Год журнала:
2023,
Номер
14
Опубликована: Март 16, 2023
The
presence
of
mobile
genetic
elements
in
Salmonella
isolated
from
a
chicken
farm
constitutes
potential
risk
for
the
appearance
emerging
bacteria
present
food
industry.
These
contribute
to
increased
pathogenicity
and
antimicrobial
resistance
through
genes
that
are
related
formation
biofilms
contained
plasmids,
integrons,
transposons.
One
hundred
thirty-three
isolates
different
stages
production
line,
such
as
feed
manufacturing,
hatchery,
broiler
farm,
poultry
slaughterhouse,
were
identified,
serotyped
sequenced.
most
predominant
serotype
was
Infantis.
Phylogenetic
analyses
demonstrated
diversity
spread
strains
pipeline
serotype-independent,
belonging
same
very
closely
genetically.
On
other
hand,
Infantis
carried
pESI
IncFIB
plasmid
harboring
wide
variety
genes,
all
linked
elements,
among
carriers
these
antibiograms
showed
differences
profiles
this
structure,
similarly
observed
Heidelberg
carrying
IncI1-Iα
plasmid.
Mobile
encoding
virulence
also
contributed
gene
content.
Antibiotic
genotypes
matched
by
phenotypes,
with
high
frequency
tetracycline,
aminoglycosides,
cephalosporins
resistance.
In
conclusion,
contamination
industry
is
described
throughout
entire
leading
multi-drug
resistant
bacteria,
thus
promoting
survival
when
challenged
various
compounds.
International Journal of Food Microbiology,
Год журнала:
2024,
Номер
423, С. 110828 - 110828
Опубликована: Июль 16, 2024
Non-typhoidal
Salmonella
represents
a
significant
global
concern
for
food
safety
and
One
Health.
Despite
the
United
Arab
Emirates
(UAE)
being
leading
consumer
of
chicken
meat
globally,
there
is
lack
comprehensive
understanding
regarding
prevalence
genomic
characteristics
within
country.
This
study
aims
to
address
this
gap
by
conducting
thorough
analysis
prevalence,
antimicrobial
resistance,
profiles
isolates
obtained
from
whole
broiler
carcasses
retailed
under
chilled
conditions
in
UAE.
Our
findings
reveal
that
was
detected
41.2
%
(130/315)
sampled
carcasses,
with
notable
variability
observed
among
samples
sourced
six
different
companies.
Phenotypic
resistance
(AMR)
testing,
105
isolates,
highlighted
high
rates
tetracycline
(97.1
%),
nalidixic
acid
(93.3
ampicillin
(92.4
azithromycin
(75.2
ciprofloxacin
(63.8
ceftriaxone
(54.3
%).
Furthermore,
concerning
99
(104/105)
exhibited
multidrug
resistance.
Whole-genome
sequencing
(WGS)
60
identified
five
serovars,
S.
infantis/Sequence
Type
(ST)
32
(55
%)
Minnesota/ST-458
(28.3
most
prevalent.
WGS
unveiled
34
genes
associated
including
mcr-1.1
(only
two
isolates),
conferring
colistin.
The
major
Infantis
Minnesota,
variation
(P-values
<0.001)
distribution
AMR
(aadA1,
bla
Microorganisms,
Год журнала:
2024,
Номер
12(8), С. 1563 - 1563
Опубликована: Июль 31, 2024
Whole
genome
sequencing
is
replacing
traditional
laboratory
surveillance
methods
as
the
primary
tool
to
track
and
characterize
clusters
outbreaks
of
foodborne
zoonotic
pathogen
Frontiers in Microbiology,
Год журнала:
2025,
Номер
16
Опубликована: Фев. 13, 2025
The
emergence
of
multidrug-resistant
(MDR)
Salmonella
is
recognized
as
a
significant
public
health
problem
worldwide.
This
study
investigated
the
occurrence
MDR
serovars
in
chicken
meat
from
wet
markets
Metro
Manila,
Philippines
February
to
July
2022.
Using
whole
genome
sequencing
(WGS)
and
phenotypic
antimicrobial
resistance
(AMR)
testing,
serovar,
drug
resistance,
virulence
profiles
isolates
were
characterized.
Out
253
cut
samples,
95
S.
enterica
representing
15
distinct
recovered.
most
common
was
serovar
Infantis
(51.58%),
followed
by
Brancaster
(9.47%),
Anatum
(7.37%),
London
Uganda
(6.32%),
Derby
(4.21%).
Phenotypic
AMR
testing
revealed
that
73.68%
resistant
at
least
one
class,
45.26%
MDR.
A
wide
array
genes
(ARGs)
associated
with
12
different
classes
identified,
including
three
β-lactamase
gene
variants:
bla
CTX-M-65
,
TEM-1
TEM-176
.
Some
these
ARGs
located
on
plasmids,
such
those
IncFIB(K)_1_Kpn3,
IncFIA(HI1)_1_HI1,
IncX1_1.
total
131
detected,
some
which
conferred
pESI-like
characteristics
Infantis.
These
findings
highlight
potential
risk
posed
pathogenic
underscore
urgent
need
for
further
research
coordinated
surveillance
Philippines,
aiming
stimulate
national
efforts
combat
AMR.
