Tropical Medicine and Infectious Disease,
Год журнала:
2023,
Номер
8(8), С. 381 - 381
Опубликована: Июль 26, 2023
The
increasing
reports
of
multidrug-resistant
Klebsiella
pneumoniae
have
emerged
as
a
public
health
concern,
raising
questions
about
the
potential
routes
for
evolution
and
dissemination
pathogenic
K.
into
environmental
reservoirs.
Potential
drivers
increased
incidence
antimicrobial-resistant
include
eminent
global
climatic
variations
direct
or
indirect
effect
human
activities.
ability
microorganisms
to
adapt
grow
at
an
exponential
rate
facilitates
distribution
strains
with
acquired
resistant
mutations
water
systems,
vegetation,
soil
which
are
major
intersection
points
animals
humans.
bacterial
pathogen,
pneumoniae,
is
one
critical-priority
pathogens
listed
by
World
Health
Organization,
mostly
associated
hospital-acquired
infections.
However,
prevalence
similar
characteristics
clinical-antibiotic-resistant
isolates
concerning.
Considering
impact
in
spread
bacteria,
this
review,
we
closely
assess
factors
influencing
pathogen
resulting
interaction
environment,
beings,
animals.
We
also
look
recent
developments
rapid
detection
techniques
part
response
measures
improve
surveillance
preparedness
outbreaks.
Furthermore,
discuss
alternative
treatment
strategies
that
secondary
metabolites
such
biosurfactants
plant
extracts
high
antimicrobial
properties.
Pathogens,
Год журнала:
2024,
Номер
13(5), С. 393 - 393
Опубликована: Май 8, 2024
Medical
devices
such
as
venous
catheters
(VCs)
and
urinary
(UCs)
are
widely
used
in
the
hospital
setting.
However,
implantation
of
these
is
often
accompanied
by
complications.
About
60
to
70%
nosocomial
infections
(NIs)
linked
biofilms.
The
main
complication
ability
microorganisms
adhere
surfaces
form
biofilms
which
protect
them
help
persist
host.
Indeed,
crossing
skin
barrier,
insertion
VC
inevitably
allows
flora
or
accidental
environmental
contaminants
access
underlying
tissues
cause
fatal
complications
like
bloodstream
(BSIs).
In
fact,
80,000
central
catheters-BSIs
(CVC-BSIs)-mainly
occur
intensive
care
units
(ICUs)
with
a
death
rate
12
25%.
Similarly,
catheter-associated
tract
(CA-UTIs)
most
commonlyhospital-acquired
(HAIs)
worldwide.These
represent
up
40%
NIs.In
this
review,
we
present
summary
biofilm
formation
steps.
We
provide
an
overview
two
important
clinical
settings
medical
devices,
namely
catheter-asociated
(CA-BSIs)
(CA-UTIs),
highlight
also
multidrug
resistant
bacteria
implicated
infections.
Furthermore,
draw
attention
toseveral
useful
prevention
strategies,
advanced
antimicrobial
antifouling
approaches
developed
reduce
bacterial
colonization
on
catheter
incidence
catheter-related
Microbial Genomics,
Год журнала:
2025,
Номер
11(1)
Опубликована: Янв. 15, 2025
Phylogenetic
analyses
are
crucial
for
understanding
microbial
evolution
and
infectious
disease
transmission.
Bacterial
phylogenies
often
inferred
from
SNP
alignments,
with
SNPs
as
the
fundamental
signal
within
these
data.
alignments
can
be
reduced
to
a
‘strict
core’
by
removing
those
sites
that
do
not
have
data
present
in
every
sample.
However,
sample
size
genome
diversity
increase,
strict
core
shrink
markedly,
discarding
potentially
informative
Here,
we
propose
provide
evidence
support
use
of
‘soft
tolerates
some
missing
data,
preserving
more
information
phylogenetic
analysis.
Using
large
datasets
Neisseria
gonorrhoeae
Salmonella
enterica
serovar
Typhi,
assess
different
thresholds.
Our
results
show
cores
drastically
reduce
compared
soft
cores.
In
10
000-genome
alignment
95%
yielded
ten
times
than
100%
core.
Similar
patterns
were
observed
N.
.
We
further
evaluated
accuracy
built
strict-
soft-core
using
strong
temporal
signals.
Soft-core
generally
outperformed
producing
trees
displaying
clock-like
behaviour;
instance,
phylogeny
had
root-to-tip
regression
R
2
0.50
0.21
strict-core
phylogeny.
This
study
suggests
strategies
preferable
large,
diverse
datasets.
To
facilitate
this,
developed
Core-SNP-filter
(
https://github.com/rrwick/Core-SNP-filter
),
an
open-source
software
tool
generating
whole-genome
based
on
user-defined
Infections
caused
by
Klebsiella
pneumoniae
continue
to
be
a
global
public
health
threat;
the
treatment
of
these
infections
is
complicated
high
frequency
multidrug
resistance.
K.
produces
polysaccharide
capsule
required
for
virulence.
Hypervirulent
isolates
also
have
hypermucoviscous
(HMV)
phenotype
that
increases
virulence,
and
we
recently
demonstrated
horizontally
acquired
gene,
rmpD
,
HMV
hypervirulence
but
identity
polymeric
product(s)
in
uncertain.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Апрель 28, 2023
Adaptation
to
selective
pressures
is
crucial
for
clinically
important
pathogens
establish
epidemics,
but
the
underlying
evolutionary
drivers
remain
poorly
understood.
The
current
epidemic
of
carbapenem-resistant
Klebsiella
pneumoniae
(CRKP)
poses
a
significant
threat
public
health.
In
this
study
we
analyzed
genome
sequences
794
CRKP
bloodstream
isolates
collected
in
40
hospitals
China
between
2014
and
2019.
We
uncovered
subclonal
replacement
predominant
clone
ST11,
where
previously
prevalent
subclone
OL101:KL47
was
replaced
by
O2v1:KL64
over
time
stepwise
manner.
carried
higher
load
mobile
genetic
elements,
point
mutation
exclusively
detected
recC
significantly
promotes
recombination
proficiency.
success
further
associated
with
hypervirulent
sublineage
enhanced
resistance
phagocytosis,
sulfamethoxazole-trimethoprim,
tetracycline.
phenotypic
alterations
were
linked
overrepresentation
hypervirulence
determinants
antibiotic
genes
conferred
acquisition
an
rmpA-positive
pLVPK-like
virulence
plasmid
IncFII-type
multidrug-resistant
plasmid,
respectively.
dissemination
promoted
more
frequent
inter-hospital
transmission.
results
collectively
demonstrate
that
expansion
correlated
repertoire
genomic
convergent
subpopulation
advantages.
Oxford
Nanopore
Technologies
(ONT)
sequencing
has
rich
potential
for
genomic
epidemiology
and
public
health
investigations
of
bacterial
pathogens,
particularly
in
low-resource
settings
at
the
point
care,
due
to
its
portability
affordability.
However,
low
base-call
accuracy
limited
reliability
ONT
data
critical
tasks
such
as
antimicrobial
resistance
(AMR)
virulence
gene
detection
typing,
serotype
prediction,
cluster
identification.
Thus,
Illumina
remains
standard
surveillance
despite
higher
capital
running
costs.
We
tested
ONT-only
assemblies
common
applied
genomics
(genotyping
detection,
implemented
via
Kleborate,
Kaptive
Pathogenwatch),
using
from
54
unique
Klebsiella
pneumoniae
isolates.
reads
generated
MinION
with
R9.4.1
flowcells
were
basecalled
three
alternative
models
[Fast,
High-accuracy
(HAC)
Super-accuracy
(SUP),
available
within
ONT's
Guppy
software],
assembled
Flye
polished
Medaka.
Accuracy
typing
was
compared
that
Illumina-only
hybrid
ONT+Illumina
assemblies,
constructed
same
isolates
reference
standards.
The
most
resource-intensive
ONT-assembly
approach
(SUP
basecalling,
or
without
Medaka
polishing)
performed
best,
yielding
reliable
capsule
(K)
type
calls
all
strains
(100
%
exact
best
matching
locus),
multi-locus
sequence
(MLST)
assignment
(98.3
match
single-locus
variants),
good
acquired
AMR
genes
mutations
(88-100
correct
identification
across
various
drug
classes).
Distance-based
trees
SUP+Medaka
accurately
reflected
overall
genetic
relationships
between
definition
outbreak
clusters
problematic
inflation
SNP
counts
by
high
errors.
could
be
reliably
used
'rule
out'
distinct
lineages
suspected
transmission
clusters.
HAC
basecalling
+
polishing
similarly
SUP
polishing.
Therefore,
we
recommend
investing
compute
resources
into
model),
wherever
time
allow,
note
is
also
worthwhile
improved
performance.
Overall,
our
results
show
MLST,
K
determinants
can
identified
flowcell
data.
challenging
this
technology.
Microorganisms,
Год журнала:
2025,
Номер
13(1), С. 89 - 89
Опубликована: Янв. 5, 2025
Klebsiella
pneumoniae
represent
a
common
invasive
infection
etiological
agent,
whose
potential
carbapenem-resistance
and
hypermucoviscosity
complicate
the
patient's
management.
Infection
development
often
derives
from
gastrointestinal
colonization;
thus,
it
is
fundamental
to
monitor
asymptomatic
K.
colonization
through
surveillance
protocols,
especially
for
intensive
care
immunocompromised
patients.
We
described
six-month
routine
screening
protocol
Policlinico
of
Catania
(Italy),
while
blood
samples
were
collected
same
patients
only
in
cases
systemic
suspicion.
All
who
had
dissemination
episodes
furtherly
investigated
next-generation
sequencing,
analyzing
both
colonizing
disseminating
strains.
This
study
documents
emerging
sequence
types
such
as
ST101,
ST307,
ST395,
mainly
revealing
blaNDM
or
blaKPC
genes,
along
with
siderophores
hyperproduction
capsule
markers
virulence
factors.
Most
detected
factors
are
presumably
related
specific
plasmid
content,
which
extremely
varied
rich.
In
conclusion,
active
sequencing
essential
enhance
awareness
local
epidemiology
within
high-risk
multi-drug
resistance
areas.
A
random
analysis
on
most
warning
microorganisms
could
typing
(ST)
settings,
allowing
better
prevention
control
strategies
their
eventual
persistence
diffusion.
Antibiotics,
Год журнала:
2025,
Номер
14(3), С. 223 - 223
Опубликована: Фев. 21, 2025
Background/Objectives:
The
incidence
of
Ceftazidime/Avibactam
(CZA)-resistant
Klebsiella
pneumoniae
isolate
co-producing
carbapenemase
2
(KPC-2)
and
Vietnamese
extended-spectrum
β-lactamase
25
(VEB-25)
has
been
on
the
rise
in
Greece
over
past
five
years.
This
study
investigates
isolation
ST323
K.
isolates
co-resistant
to
CZA
cefiderocol
(FDC)
from
colonized
infected
patients
a
single
hospital
Athens.
Methods:
CZA-resistant
strains
were
isolated
5
ICU
27
December
2023
22
January
2024.
Antimicrobial
susceptibility
was
tested
against
panel
agents.
Whole-genome
sequencing
carried
out
identify
acquired
resistance
genes
mutations
that
associated
with
FDC
resistance.
Results:
belonged
harbored
blaKPC-2
blaVEB-25.
had
minimum
inhibitory
concentration
(MIC)
>256
mg/L
for
32
FDC,
due
disrupted
catecholate
siderophore
receptor
Fiu.
blaVEB-25
located
an
IncC
non-conjugative
plasmid
~14
kb
multidrug
(MDR)
region
comprising
15
further
genes.
Transformation
studies
showed
blaVEB-25-carrying
provided
most
β-lactams
tested,
including
CZA.
remained
susceptible
carbapenems,
imipenem/relebactam,
meropenem/vaborbactam.
citrate-dependent
iron
(III)
uptake
system
(fecIRABCDE),
which
increased
MIC
≤0.08
mg/L.
Conclusions:
gene
plasmids
are
important
contributors
spread
key
antibiotic
Strict
infection
control
measures
must
be
elaborated
upon
prevent
extensively
drug-resistant
organisms
such
as
those
described
here.
Abstract
Background
Resistance
to
third-generation
cephalosporins,
often
mediated
by
extended-spectrum
beta-lactamases
(ESBLs),
is
a
considerable
issue
in
hospital-associated
infections
as
few
drugs
remain
for
treatment.
ESBL
genes
are
located
on
large
plasmids
that
transfer
horizontally
between
strains
and
species
of
Enterobacteriaceae
frequently
confer
resistance
additional
drug
classes.
Whilst
plasmid
transmission
recognised
occur
the
hospital
setting,
frequency
impact
infection
burden,
compared
+
strain
transmission,
not
well
understood.
Methods
We
sequenced
genomes
clinical
carriage
isolates
Klebsiella
pneumoniae
complex
from
year-long
surveillance
study
investigate
burden
an
Australian
hospital.
Long-term
persistence
key
transmitted
was
investigated
via
sequencing
ceftriaxone-resistant
during
4
years
follow-up,
beginning
3
after
initial
study.
Results
found
25
distinct
plasmids.
identified
one
plasmid,
which
we
called
Plasmid
A,
carried
bla
CTX-M-15
IncF
backbone
similar
pKPN-307.
A
at
least
four
times
into
different
species/lineages
responsible
half
all
episodes
1-year
period.
Three
A-positive
persisted
locally
3–6
later,
detected
two
backgrounds.
Overall
accounted
21%
follow-up
Conclusions
Here,
systematically
surveyed
over
1
year
single
network.
events
were
rare
this
they
had
significant
sustained
multidrug-resistant
infections.
If
onward
A-carrying
could
have
been
prevented,
may
reduced
number
opportunities
transmit
create
novel
strains,
reducing
overall
burden.
Nature Communications,
Год журнала:
2022,
Номер
13(1)
Опубликована: Дек. 1, 2022
Abstract
Opportunistic
bacterial
pathogen
species
and
their
strains
that
colonise
the
human
gut
are
generally
understood
to
compete
against
both
each
other
commensal
colonising
this
ecosystem.
Currently
we
lacking
a
population-wide
quantification
of
strain-level
colonisation
dynamics
relationship
potential
prevalence
in
disease,
how
ecological
factors
might
be
modulating
these.
Here,
using
combination
latest
high-resolution
metagenomics
genomic
epidemiology
methods
performed
characterisation
competition
for
longitudinal
cohort
neonatal
microbiomes.
We
found
strong
inter-
intra-species
process,
but
also
number
synergistic
relationships
among
several
belonging
genus
Klebsiella
,
which
includes
prominent
pneumoniae
.
No
evidence
preferential
by
hospital-adapted
lineages
either
vaginal
or
caesarean
section
birth
groups
was
detected.
Our
analysis
further
enabled
unbiased
assessment
extra-intestinal
pathogenic
Escherichia
coli
(ExPEC)
comparison
with
propensity
cause
bloodstream
infections.
study
highlights
importance
systematic
surveillance
pathogens,
not
only
from
disease
carriage
state,
better
inform
therapies
preventive
medicine
future.
are
a
leading
cause
of
healthcare-associated
infections
worldwide.
In
particular,
strains
expressing
extended-spectrum
β-lactamases
(ESBLs)
and
carbapenemases
pose
serious
treatment
challenges,
the
World
Health
Organization
(WHO)
to
designate
ESBL
carbapenem-resistant
Enterobacteriaceae
as
'critical'
threats
human
health.
Research
efforts
combat
these
pathogens
can
be
supported
by
accessibility
diverse
clinically
relevant
isolates
for
testing
novel
therapeutics.
Here,
we
describe
panel
100