High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater
Environmental Research,
Год журнала:
2024,
Номер
255, С. 119156 - 119156
Опубликована: Май 16, 2024
Comprehensive
data
on
bacterial
and
viral
pathogens
of
diarrhea
studies
applying
culture-independent
methods
for
examining
antibiotic
resistance
in
wastewater
are
lacking.
This
study
aimed
to
simultaneously
quantify
genes
(ARGs),
class
1
integron-integrase
(int1),
diarrhea,
16S
rRNA,
other
indicators
using
a
high-throughput
quantitative
PCR
(HT-qPCR)
system.
Thirty-six
grab
samples
from
treatment
plant
Japan
three
times
month
between
August
2022
July
2023
were
centrifuged,
followed
by
nucleic
acid
extraction,
reverse
transcription,
HT-qPCR.
Fourteen
targets
included,
HT-qPCR
was
performed
the
Biomark
X9™
System
(Standard
BioTools).
For
all
qPCR
assays,
R2
≥
0.978
efficiencies
ranged
90.5%
117.7%,
exhibiting
high
performance.
Of
36
samples,
20
(56%)
positive
Norovirus
genogroup
II
(NoV-GII),
whereas
Salmonella
spp.
Campylobacter
jejuni
detected
24
(67%)
coli
13
(36%)
with
mean
concentrations
ranging
3.2
±
0.8
4.7
0.3
log10
copies/L.
NoV-GII
detection
rates
higher
winter
spring.
None
correlated
acute
gastroenteritis
cases,
except
NoV-GII,
suggesting
need
specific
infections
validate
wastewater-based
epidemiology
(WBE).
All
tested
sul1,
int1,
blaCTX-M,
irrespective
season.
The
less
explored
blaNDM-1
showed
wide
prevalence
(>83%)
consistent
abundance
4.3
1.0
4.9
0.2
copies/L
seasons.
sul1
predominant
ARG,
absolute
abundances
blaCTX-M
varied
seasonally.
int1
significantly
autumn
spring,
it
no
correlation
blaNDM-1,
questioning
applicability
as
sole
indicator
overall
determinants.
exhibited
that
system
is
pivotal
WBE.
Язык: Английский
Optimization of a 6-plex Crystal Digital PCR® assay and its application to simultaneous surveillance of enteric and respiratory viruses in wastewater
The Science of The Total Environment,
Год журнала:
2025,
Номер
970, С. 178939 - 178939
Опубликована: Март 1, 2025
Multiplex
digital
PCR
(dPCR)
approaches
are
commonly
employed
in
wastewater-based
epidemiology
(WBE)
studies.
However,
optimizing
the
dPCR
workflow
is
a
critical
step
to
ensure
its
reliability
and
accuracy
before
application.
In
this
study,
6-plex
Crystal
Digital
PCR®
(cdPCR)
was
optimized
for
simultaneous
detection
of
six
epidemiologically
important
pathogens,
including
three
enteric
viruses,
noroviruses
genogroups
I
II
(NoV-GI
GII)
enteroviruses
(EnV),
respiratory
severe
acute
syndrome
coronavirus
2
(SARS-CoV-2),
which
causative
agent
disease
2019
(COVID-19),
influenza
A
virus
(InfA),
syncytial
B
(RSVB),
wastewater.
Four
cDNA
input
ratios
(20
%-70
%)
two
extraction
kits
were
evaluated
optimization,
with
30
%
AllPrep
PowerViral
DNA/RNA
Kit
(Qiagen)
exhibiting
optimal
performance.
The
cdPCR
assay
applied
year-long
wastewater
surveillance
study
Japan
(n
=
52),
revealing
distinct
trends
prevalence
viruses.
NoV-GII
detected
96
samples
highest
mean
concentration
(6.1
±
0.6
log10
copies/L),
while
SARS-CoV-2
InfA
60
50
samples,
respectively,
reflected
circulation
these
pathogens
within
community.
Notably,
RSVB
less
frequently
(25
%),
line
fewer
cases
reported
during
period.
concentrations
EnV
showed
significant
positive
correlations
hand
foot
mouth
herpangina
cases,
respectively.
no
observed
RSV
COVID-19,
possibly
due
testing
RSVA
more
prevalent
also
cluster
outbreaks.
These
findings
demonstrated
utility
detecting
provided
insights
into
community
trends,
representing
an
advancement
WBE.
Язык: Английский
Validation and application of high-throughput quantitative PCR for the simultaneous detection of microbial source tracking markers in environmental water
The Science of The Total Environment,
Год журнала:
2024,
Номер
940, С. 173604 - 173604
Опубликована: Май 29, 2024
No
single
microbial
source
tracking
(MST)
marker
can
be
applied
to
determine
the
sources
of
fecal
pollution
in
all
water
types.
This
study
aimed
validate
a
high-throughput
quantitative
polymerase
chain
reaction
(HT-qPCR)
method
for
simultaneous
detection
multiple
MST
markers.
A
total
26
fecal-source
samples
that
had
been
previously
collected
from
human
sewage
(n
=
6)
and
ruminant
3),
dog
6),
pig
chicken
duck
2)
feces
Kathmandu
Valley,
Nepal,
were
used
10
host-specific
markers,
i.e.,
Bacteroidales
(BacHum,
gyrB,
BacR,
Pig2Bac),
mitochondrial
DNA
(mtDNA)
(swine,
bovine,
Dog-mtDNA),
viral
(human
adenovirus,
porcine
chicken/turkey
parvovirus)
via
HT-qPCR.
Only
Dog-mtDNA
showed
100
%
accuracy.
All
tested
bacterial
markers
sensitivity
%.
Nine
further
identify
contamination
groundwater
49),
tanker
filling
stations
14),
drinking
treatment
plants
5),
river
6).
The
human-specific
BacHum
ruminant-specific
BacR
was
detected
at
high
ratio
(83
%,
respectively).
results
HT-qPCR
agreement
with
standard
qPCR.
comparable
performances
qPCR
as
well
successful
demonstrated
potential
applicability
these
detecting
Язык: Английский
Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region
Water Research X,
Год журнала:
2024,
Номер
22, С. 100221 - 100221
Опубликована: Янв. 1, 2024
Wastewater
surveillance
using
RT-qPCR
has
now
been
widely
adopted
to
track
circulating
levels
of
SARS-CoV-2
virus
in
many
sewersheds.
The
CDC
qPCR
assays
targeting
two
regions
(N1
and
N2)
within
the
N
gene
are
commonly
used,
but
a
discrepancy
between
biomarkers
noticed
by
independent
studies
these
methods
since
late
2021.
reason
is
presumed
be
due
mutations
targeted
N1
probe.
In
this
study,
we
systematically
investigated
unequivocally
confirmed
that
underlying
for
was
probe
target,
single
mutation
could
cause
significant
drop
signal.
We
first
proportion
related
wastewater
samples
(Jan
2021-Dec
2022)
nested
PCR
LC-MS.
Based
on
relative
proportions
alleles,
separated
data
into
four
time
periods
corresponding
different
variant
waves:
Period
I
(Alpha
Delta
waves
with
0
mutation),
II
(BA.1/BA.2
found
all
Omicron
strains),
III
(BA.5.2*
wave
mutations),
IV
(BQ.1*
mutations).
Significantly
lower
copies
N2
from
Periods
II-IV
compared
those
observed
wastewater.
To
further
pinpoint
extent
which
each
impacted
quantification,
response
among
synthetic
oligomers
mutations.
This
study
highlighted
impact
even
just
one
or
qPCR-based
SARS-CoV-2.
Язык: Английский
Mechanisms of intestinal injury in polychaete Perinereis aibuhitensis caused by low-concentration fluorene pollution: Microbiome and metabonomic analyses
Journal of Hazardous Materials,
Год журнала:
2024,
Номер
475, С. 134925 - 134925
Опубликована: Июнь 15, 2024
Язык: Английский
DEVELOPMENT OF A LOW-CONCENTRATION VERSION OF THE EPISENS-M METHOD SUITABLE FOR TREATED WASTEWATER AND EVALUATION OF VIRUS REMOVAL PERFORMANCE BY MBR
Japanese Journal of JSCE,
Год журнала:
2024,
Номер
80(25), С. n/a - n/a
Опубликована: Янв. 1, 2024
Язык: Английский
Investigation the Prevalence of Norovirus, Rotavirus, Human Bocavirus, and Adenovirus in Inpatient Children with Gastroenteritis in Tehran, Iran, During 2021-2022
Iranian Journal of Medical Microbiology,
Год журнала:
2024,
Номер
18(4), С. 230 - 237
Опубликована: Сен. 9, 2024
Язык: Английский