Infection Control and Hospital Epidemiology,
Год журнала:
2024,
Номер
46(2), С. 129 - 135
Опубликована: Дек. 27, 2024
Whole
genome
sequencing
(WGS)
can
help
identify
transmission
of
pathogens
causing
healthcare-associated
infections
(HAIs).
However,
the
current
gold
standard
short-read,
Illumina-based
WGS
is
labor
and
time
intensive.
Given
recent
improvements
in
long-read
Oxford
Nanopore
Technologies
(ONT)
sequencing,
we
sought
to
establish
a
low
resource
approach
providing
accurate
WGS-pathogen
comparison
within
frame
allowing
for
infection
prevention
control
(IPC)
interventions.
was
prospectively
performed
on
at
increased
risk
potential
healthcare
using
ONT
MinION
sequencer
with
R10.4.1
flow
cells
Dorado
basecaller.
Potential
assessed
via
Ridom
SeqSphere+
core
multilocus
sequence
typing
MINTyper
reference-based
single
nucleotide
polymorphisms
previously
published
cutoff
values.
The
accuracy
our
pipeline
determined
relative
Illumina.
Over
six-month
period,
242
bacterial
isolates
from
216
patients
were
sequenced
by
operator.
Compared
Illumina
standard,
achieved
mean
identity
score
Q60
assembled
genomes,
even
coverage
rate
as
40×.
initiating
DNA
extraction
complete
analysis
2
days
(IQR
2-3.25
days).
We
identified
five
clusters
comprising
21
(8.7%
strains).
Integrating
epidemiological
data,
>70%
(15/21)
putative
cluster
originated
links.
Via
stand-alone
pipeline,
detected
potentially
transmitted
HAI
rapidly
accurately,
aligning
closely
data.
Our
low-resource
method
has
assist
IPC
efforts.
This
article
advocates
for
mobilizing
pathogen
genomic
surveillance
to
contain
and
mitigate
health
threats
from
infectious
diseases
antimicrobial
resistance
(AMR),
building
upon
successes
achieved
by
large-scale
genome
sequencing
analysis
of
SARS-CoV-2
variants
in
guiding
COVID-19
monitoring
public
responses
adopting
a
One
Health
approach.
Capabilities
laboratory-based
epidemic
alert
systems
should
be
enhanced
fostering
(i)
universal
access
real-time
whole
sequence
(WGS)
data
pathogens
inform
clinical
practice,
infection
control,
policies,
vaccine
drug
research
development;
(ii)
integration
diagnostic
microbiology
data,
testing
asymptomatic
individuals,
epidemiological
into
programs;
(iii)
stronger
cross-sectorial
collaborations
between
healthcare,
health,
animal
environmental
using
approaches,
toward
understanding
the
ecology
transmission
pathways
AMR
across
ecosystems;
(iv)
international
collaboration
interconnection
networks,
harmonization
laboratory
methods,
standardization
methods
global
reporting,
including
on
variant
or
strain
nomenclature;
(v)
responsible
sharing
databases,
platforms
according
FAIR
(findability,
accessibility,
interoperability,
reusability)
principles;
(vi)
system
implementation
its
cost-effectiveness
different
settings.
Regional
policies
governance
initiatives
foster
concerted
development
efficient
utilization
protect
humans,
animals,
environment.
Medical Principles and Practice,
Год журнала:
2024,
Номер
33(3), С. 185 - 197
Опубликована: Янв. 1, 2024
The
success
in
determining
the
whole
genome
sequence
of
a
bacterial
pathogen
was
first
achieved
1995
by
complete
nucleotide
<i>Haemophilus
influenzae</i>
Rd
using
chain-termination
method
established
Sanger
et
al.
1977
and
automated
Hood
1987.
However,
this
technology
laborious,
costly,
time-consuming.
Since
2004,
high-throughput
next-generation
sequencing
technologies
have
been
developed,
which
are
highly
efficient,
require
less
time,
cost-effective
for
(WGS)
all
organisms,
including
pathogens.
In
recent
years,
data
obtained
WGS
coupled
with
bioinformatics
analyses
sequenced
genomes
projected
to
revolutionize
clinical
bacteriology.
used
identification
species,
strains,
genotypes
from
cultured
organisms
directly
specimens.
has
also
helped
resistance
antibiotics
detection
antimicrobial
genes
point
mutations.
Furthermore,
epidemiological
tracking
surveillance
pathogenic
bacteria
healthcare
settings
as
well
communities.
This
review
focuses
on
applications
Journal of Antimicrobial Chemotherapy,
Год журнала:
2024,
Номер
79(3), С. 656 - 668
Опубликована: Фев. 7, 2024
WGS
is
increasingly
being
applied
to
healthcare-associated
vancomycin-resistant
Enterococcus
faecium
(VREfm)
outbreaks.
Within-patient
diversity
could
complicate
transmission
resolution
if
single
colonies
are
sequenced
from
identified
cases.
medRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 22, 2024
ABSTRACT
Background
Current
methods
are
insufficient
alone
for
outbreak
detection
in
hospitals.
Real-time
genomic
surveillance
using
offers
the
potential
to
detect
otherwise
unidentified
outbreaks.
We
initiated
and
evaluated
Enhanced
Detection
System
Healthcare-associated
Transmission
(EDS-HAT),
a
real-time
program
mitigation.
Methods
This
study
was
conducted
at
UPMC
Presbyterian
Hospital
from
November
2021
October
2023.
Whole
genome
sequencing
(WGS)
performed
weekly
on
healthcare-associated
clinical
bacterial
isolates
identify
undetected
Interventions
were
implemented
based
identified
transmission.
A
economic
impact
analysis
estimate
infections
averted
net
cost
savings.
Results
There
3,921
patient
that
underwent
WGS,
of
which
476
(12.1%)
clustered
into
172
outbreaks
(size
range
2-16
patients).
Of
isolates,
292
(61.3%)
had
an
epidemiological
link.
Among
with
interventions,
95.6%
showed
no
further
transmission
intervened
route.
The
estimated
that,
over
two-year
period,
62
averted,
gross
savings
$1,011,146,
$695,706,
translates
3.2-fold
return
investment.
Probabilistic
sensitivity
EDS-HAT
cost-saving
more
effective
98%
simulations.
Conclusion
enabled
rapid
control
our
hospital
resulted
benefits
improvement
safety.
demonstrates
feasibility
effectiveness
integrating
routine
infection
prevention
practice,
offering
paradigm
shift
healthcare
control.
medRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 20, 2024
Abstract
Objective
Routine
use
of
whole
genome
sequencing
(WGS)
has
been
shown
to
help
identify
transmission
pathogens
causing
healthcare-associated
infections
(HAIs).
However,
the
current
gold
standard
short-read,
Illumina-based
WGS
is
labor
and
time-intensive.
In
light
recent
improvements
in
long-read
Oxford
Nanopore
Technologies
(ONT)
sequencing,
we
sought
establish
a
low
resource
utilization
approach
capable
providing
accurate
WGS-based
comparisons
HAI
within
time
frame
allowing
for
infection
prevention
control
(IPC)
interventions.
Methods
was
prospectively
performed
on
antimicrobial-resistant
at
increased
risk
potential
healthcare
using
ONT
MinION
sequencer
with
R10.4.1
flow
cells
Dorado
basecalling
algorithm.
Potential
assessed
via
Ridom
SeqSphere+
core
multilocus
sequence
typing
MINTyper
reference-based
single
nucleotide
polymorphisms
previously
published
cut-off
values.
The
accuracy
our
pipeline
determined
relative
data
generated
from
same
genomic
DNA
sample.
Results
Over
six-month
period,
242
bacterial
isolates
216
patients
were
sequenced
by
operator.
Compared
Illumina
gold-standard
data,
achieved
Q
score
60
assembled
genomes,
even
coverage
rate
as
40X.
mean
initiating
extraction
complete
genetic
analysis
2
days
(IQR
2-3.25
days).
We
identified
five
clusters
comprising
21
(8.7%
all
strains).
Combining
epidemiological
>70%
(15/21)
originated
links.
Conclusions
Via
stand-alone
pipeline,
detected
potentially
transmitted
rapidly
accurately,
aligning
closely
data.
Our
low-resource
method
assist
efficient
detection
deployment
preventative
measures
against
transmission.
Expert Review of Molecular Diagnostics,
Год журнала:
2024,
Номер
unknown, С. 1 - 10
Опубликована: Окт. 9, 2024
Introduction
Approximately
15
million
deaths
occur
globally
each
year
due
to
infectious
diseases.
Timely
diagnosis
is
crucial
in
promoting
cure
and
preventing
disease
transmission.
Currently,
molecular
diagnostics
have
replaced
many
conventional
diagnostic
tools
their
inherent
limitations.
However,
the
full
potential
of
Immuno
Polymerase
Chain
Reaction
(IPCR)
remains
largely
untapped.
