Advancing Microbial Comparative Genomics Through Tumor-Normal Inspired Framework
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 5, 2025
Abstract
Comparative
genomics
has
emerged
as
a
pivotal
methodology
for
elucidating
genetic
variations
in
microbial
studies.
However,
conventional
analytical
approaches
diploid
and
polyploid
microorganisms
have
demonstrated
limited
efficacy
discriminating
new
mutations
from
background
heterozygosity.
This
study
presents
an
innovative
comparative
framework
adapted
tumor-normal
sequencing
methodology.
Our
approach
establishes
the
original
strain
“normal
sample”
derived
“tumor
sample”,
enabling
precise
identification
of
(“somatic
variants”)
while
filtering
pre-existing
heterozygous
sites
(“germline
variations”).
The
pipeline
also
includes
assessment
loss-of-heterozygosity
(LOH)
events
genome-wide
detection
copy
number
(CNVs)
with
resolution
to
identify
both
regional
CNV
whole-chromosome
aneuploidy
through
integrated
variant
allele
frequency
analysis.
We
validated
this
using
Saccharomyces
cerevisiae
strains
before
successfully
extending
its
application
Kluyveromyces
marxianus
,
Candida
spp.,
Hortaea
werneckii
encompassing
haploid,
diploid,
polyploid,
aneuploid
states.
revealed
previously
undetected
across
experimental
evolution
studies,
demonstrating
superior
compared
approaches.
adaptable
platform
paradigm
genome
particularly
organisms
or
states
where
traditional
methods
prove
inadequate.
Язык: Английский
Tolerance and heteroresistance to echinocandins in Candida auris : conceptual issues, clinical implications, and outstanding questions
mSphere,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 16, 2025
ABSTRACT
Candida
auris
is
a
significant
public
health
threat
due
to
its
environmental
persistence
and
multidrug
resistance,
with
echinocandins
being
the
preferred
treatment.
However,
in
addition
echinocandin
tolerance
heteroresistance
may
contribute
treatment
challenges.
Echinocandin
involves
reduced
drug-mediated
killing,
while
ability
of
small
cell
subset
grow
at
high
drug
concentrations.
These
phenomena
facilitate
emergence
full
resistance
complicate
clinical
outcomes.
The
significance
these
mechanisms
remains
unclear,
limited
data
correlating
them
failures.
Research
needed
understand
their
impact,
develop
streamlined
robust
methods
detect
settings,
explore
mitigation
strategies.
pathogen’s
range
adaptations
demands
innovative
approaches
like
spatial
transcriptomics
dissect
complex
responses
improve
patient
Язык: Английский
Hotspot gene conversion between FKS1 and FKS2 in echinocandin resistant Candida glabrata serial isolates
npj Antimicrobials and Resistance,
Год журнала:
2025,
Номер
3(1)
Опубликована: Апрель 17, 2025
Candida
glabrata
(Nakaseomyces
glabratus)
is
the
most
common
cause
of
drug-resistant
candidemia
and
associated
with
a
high
mortality
rate.
Only
few
mechanisms
drug
resistance
are
known
in
C.
glabrata,
predominantly
involving
recurrent
single
nucleotide
polymorphisms.
The
importance
structural
variation
acquired
not
understood.
We
performed
comparative
phenotypic
genomic
analyses
six
serial
bloodstream
isolates
identified
novel
mutations
to
echinocandins.
Critically,
we
gene
conversion
event
between
hotspot
2
regions
FKS1
FKS2
that
was
increased
micafungin.
further
analyzed
621
publicly
available
genomes
found
three
additional
examples
FKS2.
Ultimately,
involves
variants
missed
current
diagnostic
methods
need
be
considered
when
designing
implementing
more
effective
antifungal
management
strategies.
Язык: Английский
Understanding adaptation to fluconazole: comparative insights into tolerance and resistance in Saccharomyces cerevisiae and Candida albicans
Frontiers in Cellular and Infection Microbiology,
Год журнала:
2025,
Номер
15
Опубликована: Май 5, 2025
Introduction
Antifungal
resistance
and
tolerance
are
distinct
responses
exhibited
by
fungi
when
exposed
to
drugs.
While
considerable
research
has
focused
on
azole
in
the
human
pathogen
Candida
albicans
,
studies
other
fungal
species
remain
limited.
Objective
This
study
aims
conduct
a
comparative
investigation
of
adaptation
model
organism
Saccharomyces
cerevisiae
C.
fluconazole
vitro
.
Methods
We
performed
experiments
using
laboratory
strains
S.
evaluate
their
under
varying
temperature
conditions.
High
concentrations
were
administered,
subsequent
changes
phenotypes
analyzed
through
techniques
such
as
transcriptome
analysis
monitoring
petite
formation.
Results
Our
results
revealed
that
is
present
wild-type
influenced
temperature,
albeit
manner
opposite
observed
Importantly,
subjected
high
fluconazole,
developed
without
displaying
tolerance;
all
resistant
adaptors
identified
petites.
Chemical
induction
formation
led
an
increase
accompanied
decrease
tolerance.
Conclusion
Transcriptome
indicated
petites
up-regulated
efflux
mechanisms
while
down-regulating
most
ERG
genes.
suggests
that,
unlike
petite-negative
petite-positive
swiftly
transitions
phenotype
upon
exposure
resulting
enhanced
but
diminished
evolutionary
divergence
emphasizes
need
for
additional
pathogenic
fungi.
Язык: Английский
Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Май 13, 2025
The
diploid
genome
of
the
fungal
pathogen
Candida
albicans
is
highly
heterozygous,
with
most
allele
pairs
diverging
at
either
coding
or
regulatory
level.
When
faced
selection
pressure
like
antifungal
exposure,
this
hidden
genetic
diversity
can
provide
a
reservoir
adaptive
mutations
through
loss
heterozygosity
(LOH)
events.
Validating
potential
phenotypic
impact
LOH
events
observed
in
clinical
experimentally
evolved
strains
be
difficult
due
to
challenge
precisely
targeting
one
over
other.
Here,
we
show
that
CRISPR-Cas9
system
used
overcome
challenge.
By
designing
allele-specific
guide
RNA
sequences,
induce
targeted,
directed
events,
which
validate
by
whole-genome
long-read
sequencing.
Using
approach,
efficiently
recapitulate
recently
described
event
increases
resistance
fluconazole.
Additionally,
find
recombination
tracts
these
induced
have
similar
lengths
those
naturally.
To
facilitate
future
use
method,
database
sgRNA
sequences
for
Cas9
near
genome-wide
coverage
heterozygous
sites
direct
indirect
targeting.
This
approach
will
useful
probing
role
important
human
pathogen.
Язык: Английский
Stress-driven emergence of heritable non-genetic drug resistance
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 21, 2024
Abstract
Drug
resistance
is
the
chief
cause
of
treatment
failure
for
therapies
targeting
chronic
and
infectious
diseases.
Whether
emergence
accelerated
by
environmental
exposure
to
low
levels
therapeutics
remains
controversial.
Here,
we
report
a
non-genetic
mechanism
stress
adaptation
that
promotes
heritable
widely
used
antifungal
drug
fluconazole.
In
human
fungal
pathogen
Candida
albicans,
transient
subtherapeutic
fluconazole
doses
induces
protective
response
term
para-resistance.
Like
conventional
mechanisms,
para-resistance
heritable.
However,
it
does
not
arise
from
genetic
mutations
can
revert
spontaneously.
Systematic
analyses
para-resistant
isolates
suggest
its
key
regulators
include
stress-activated
MAP
kinase
Hog1,
histone
deacetylase
subunit
Snt1,
chromatin
regulator
Rap1,
Sko1
transcriptional
factor.
Notably,
molecules
disrupt
biomolecular
condensation
prion
propagation
–
crucial
inheritance
protein
assemblies
block
induction
para-resistance,
whereas
inhibiting
deacetylases
facilitates
induction.
We
find
common
in
clinical
and,
remarkably,
passage
through
mammalian
gut
triggers
acquisition,
compromising
fluconazole’s
therapeutic
efficacy.
Our
work
defines
pervasive,
prion-like
epigenetic
highlights
potential
strategies
mitigate
rapid
resistance.
Язык: Английский