Advantage of precision metagenomics for urinary tract infection diagnostics
Frontiers in Cellular and Infection Microbiology,
Год журнала:
2023,
Номер
13
Опубликована: Июль 4, 2023
Urinary
tract
infections
(UTIs)
remain
a
diagnostic
challenge
and
often
promote
antibiotic
overuse.
Despite
urine
culture
being
the
gold
standard
for
UTI
diagnosis,
some
uropathogens
may
lead
to
false-negative
or
inconclusive
results.
Although
PCR
testing
is
fast
highly
sensitive,
its
yield
limited
targeted
microorganisms.
Metagenomic
next-generation
sequencing
(mNGS)
hypothesis-free
approach
with
potential
of
deciphering
urobiome.
However,
clinically
relevant
information
buried
in
enormous
amount
data.Precision
metagenomics
(PM)
hybridization
capture-based
method
enhanced
discovery
power
better
without
diluting
information.
We
collected
47
samples
suspected
parallel
tested
each
sample
by
microbial
culture,
PCR,
PM;
then,
we
comparatively
analyzed
Next,
phenotypically
classified
cumulative
population
using
Explify®
data
analysis
platform
pathogenicity.Results
revealed
100%
positive
predictive
agreement
(PPA)
results,
which
identified
only
13
different
microorganisms,
compared
19
62
organisms
PM,
respectively.
All
were
into
phenotypic
groups
(0-3)
increasing
pathogenic
clinical
relevance.
This
PM
can
simultaneously
quantify
classify
readily
through
bioinformatic
platforms
like
Explify®,
essentially
providing
dissected
quantitative
results
timely
accurate
empiric
treatment.PM
offers
building
effective
models
beyond
usual
care
complex
diseases.
Future
studies
should
assess
impact
PM-guided
management
on
outcomes.
Язык: Английский
Navigating the New Norm: The FDA's Final Rule on Laboratory Developed Tests (LDTs) and Its Impact on Clinical Laboratory Operations
Clinical Microbiology Newsletter,
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 1, 2024
Язык: Английский
Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential
Advances in respiratory medicine,
Год журнала:
2023,
Номер
91(1), С. 49 - 65
Опубликована: Фев. 2, 2023
Although
it
is
clinically
important
for
acute
respiratory
tract
(co)infections
to
have
a
rapid
and
accurate
diagnosis,
critical
that
medicine
understands
the
advantages
of
current
laboratory
methods.
In
this
study,
we
tested
nasopharyngeal
samples
(n
=
29)
with
commercially
available
PCR
assay
compared
results
those
hybridization-capture-based
mNGS
workflow.
Detection
criteria
positive
was
Ct
<
35
>40%
target
coverage,
median
depth
1X
RPKM
>
10.
A
high
degree
concordance
(98.33%
PPA
100%
NPA)
recorded.
However,
yielded
positively
29
additional
microorganisms
(23
bacteria,
4
viruses,
2
fungi)
beyond
PCR.
We
then
characterized
each
method
into
three
phenotypic
categories
using
IDbyDNA
Explify®
Platform
(Illumina®
Inc,
San
Diego,
CA,
USA)
consideration
infectivity
trafficking
potential
lower
region.
The
findings
are
significant
providing
comprehensive
yet
relevant
microbiology
profile
upper
infection,
especially
in
immunocompromised
or
immunocompetent
comorbidity
cases
where
traditional
syndromic
approaches
fail
identify
pathogenicity.
Accordingly,
technology
can
be
used
supplement
syndrome-based
tests,
data
quickly
effectively
phenotypically
potential,
clinical
(co)infection,
comorbid
consideration-with
promise
reduce
morbidity
mortality.
Язык: Английский
The use of NGS sequencing in Illumina technology as a method for examining the genetic variability of the SARS-CoV-2 virus
Diagnostyka Laboratoryjna,
Год журнала:
2024,
Номер
60(4), С. 296 - 307
Опубликована: Дек. 19, 2024
Next-Generation
Sequencing
(NGS)
is
an
advanced
technology
that
enables
quick
and
precise
analyzes
of
DNA
RNA
sequences.
The
use
the
Illumina
MiniSeq
NGS
platform
(Illumina,
USA)
for
sequencing
SARS-CoV-2
coronavirus
genome
allows
accurate
identification
virus,
analysis
its
genetic
variants
monitoring
evolution.
It
a
valuable
tool
supporting
epidemiological
research,
developing
effective
strategies
to
combat
virus
better
understanding
COVID-19
disease
it
causes.Molecular
surveillance
variability
using
this
has
been
carried
out
at
Interdisciplinary
Molecular
Research
Laboratory
Provincial
Sanitary
Epidemiological
Station
in
Katowice
since
September
2021.
used
identify
track
new
subvariants
Silesian,
Lesser
Poland
Opole
Voivodeships.
During
research
WSSE
laboratory
Katowice,
many
with
different
levels
infectivity
consequences
public
health
were
documented,
i.e.
Alpha
(B.1.1.7),
Gamma
(P.1),
Delta
(B.1.617.
2)
or
Omicron
(B.1.1.529).
Язык: Английский