1,721,013 research outputs found
Phase variation in pneumococcal populations during carriage in the human nasopharynx
Full text linkStreptococcus pneumoniae is one of the world’s leading bacterial pathogens, responsible for pneumonia,
septicaemia and meningitis. Asymptomatic colonisation of the nasopharynx is considered to be a
prerequisite for these severe infections, however little is understood about the biological changes
that permit the pneumococcus to switch from asymptomatic coloniser to invasive pathogen. A phase
variable type I restriction-modification (R-M) system (SpnIII) has been linked to a change in capsule
expression and to the ability to successfully colonise the murine nasopharynx. Using our laboratory
data, we have developed a Markov change model that allows prediction of the expected level of phase
variation within a population, and as a result measures when populations deviate from those expected
at random. Using this model, we have analysed samples from the Experimental Human Pneumococcal
Carriage (EHPC) project. Here we show, through mathematical modelling, that the patterns of dominant
SpnIII alleles expressed in the human nasopharynx are significantly different than those predicted by
stochastic switching alone. Our inter-disciplinary work demonstrates that the expression of alternative
methylation patterns should be an important consideration in studies of pneumococcal colonisation
Lipopeptidomimetics derived from teixobactin have potent antibacterial activity against Staphylococcus aureus
No full textA series of lipopeptidomimetics derived from teixobactin have been
prepared that probe the role of residues (1–6) as a membrane anchor
and the function of enduracididine. The most active compounds,
with a farnesyl tail and End10 to Lys10 or Orn10 substitution have
potent activity (MIC 8 lg mL1) against S. aureus. These results
pave the way for the synthesis of simple, cost-effective yet potent
lipopeptidomimetic antimicrobials
Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition
Full text linkPhase-variation of Type I restriction-modification
systems can rapidly alter the sequence motifs they
target, diversifying both the epigenetic patterns
and endonuclease activity within clonally descended
populations. Here, we characterize the Streptococcus
pneumoniae SpnIV phase-variable Type I RMS,
encoded by the translocating variable restriction
(tvr) locus, to identify its target motifs, mechanism
and regulation of phase variation, and effects
on exchange of sequence through transformation.
The specificity-determining hsdS genes were
shuffled through a recombinase-mediated excisionreintegration
mechanism involving circular intermediatemolecules,
guided by two types of direct repeat.
The rate of rearrangements was limited by an attenuator
and toxin-antitoxin system homologs that inhibited
recombinase gene transcription. Target motifs
for both the SpnIV, and multiple Type II, MTases were
identified through methylation-sensitive sequencing
of a panel of recombinase-null mutants. This demonstrated
the species-wide diversity observed at the
tvr locus can likely specify nine different methylation
patterns. This will reduce sequence exchange in
this diverse species, as the native form of the SpnIV
RMS was demonstrated to inhibit the acquisition of
genomic islands by transformation. Hence the tvr locus
can drive variation in genome methylation both
within and between strains, and limits the genomic
plasticity of S. pneumoniae
Selective and non-selective bottlenecks as drivers of the evolution of hypermutable bacterial loci
Full text linkBottlenecks reduce the size of the gene pool within populations of all life forms with
implications for their subsequent survival. Here, we examine the effects of bottlenecks
on bacterial commensal-pathogens during transmission between, and dissemination
within, hosts. By reducing genetic diversity, bottlenecks may alter individual
or population-wide adaptive potential. A diverse range of hypermutable mechanisms
have evolved in infectious agents that allow for rapid generation of genetic diversity
in specific genomic loci as opposed to the variability arising from increased genomewide
mutation rates. These localised hypermutable mechanisms include multi-gene
phase variation (PV) of outer membrane components, multi-allele PV of restriction
systems and recombination-driven antigenic variation. We review selected experimental
and theoretical (mathematical) models pertaining to the hypothesis that localised
hypermutation (LH) compensates for fitness losses caused by bottlenecks and
discuss whether bottlenecks have driven the evolution of hypermutable loci
Phase-variable methylation and epigenetic regulation by type I restriction-modification systems
No full textEpigenetic modifications in bacteria, such as DNA methylation, have been shown to affect gene regulation, thereby
generating cells that are isogenic but with distinctly different phenotypes. Restriction–modification (RM) systems contain
prototypic methylases that are responsible for much of bacterial DNA methylation. This review focuses on a distinctive
group of type I RM loci that , through phase variation, can modify their methylation target specificity and can thereby
switch bacteria between alternative patterns of DNA methylation. Phase variation occurs at the level of the target
recognition domains of the hsdS (specificity) gene via reversible recombination processes acting upon multiple hsdS alleles.
We describe the global distribution of such loci throughout the prokaryotic kingdom and highlight the differences in loci
structure across the various bacterial species. Although RM systems are often considered simply as an evolutionary
response to bacteriophages, these multi-hsdS type I systems have also shown the capacity to change bacterial phenotypes.
The ability of these RM systems to allow bacteria to reversibly switch between different physiological states, combined with
the existence of such loci across many species of medical and industrial importance, highlights the potential of
phase-variable DNA methylation to act as a global regulatory mechanism in bacteria
Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations
No full textEvaluation of the apportionment of genetic diversity of human bacterial commensals within and between human populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among human populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oro-nasopharyngeal healthy-carriage Streptococcus mitis and Streptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119 S. mitis genomes showed higher within- and among-host variation than 810 S. pneumoniae genomes in European, East Asian and African populations. Summary statistics of the sitefrequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher ancestral bacterial population effective size (Ne) in S. mitis, whose genomic variation has been maintained close to mutation-drift equilibrium across (at least many) generations, whereas S. pneumoniae has been expanding from a smaller ancestral bacterial population. Strikingly, both species show limited differentiation among human populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem), we argue that large Ne have led to similar differentiation patterns, even if m is very low for S. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to large Ne
Recombination of the phase variable spnIII locus is independent of all known pneumococcal site-specific recombinases
No full textStreptococcus pneumoniae is one of the world’s leading bacterial pathogens,
causing pneumonia, septicemia, and meningitis. In recent years, it has been
shown that genetic rearrangements in a type I restriction-modification system
(SpnIII) can impact colony morphology and gene expression. By generating a
large panel of mutant strains, we have confirmed a previously reported result that
the CreX (also known as IvrR and PsrA) recombinase found within the locus is not
essential for hsdS inversions. In addition, mutants of homologous recombination
pathways also undergo hsdS inversions. In this work, we have shown that these genetic
rearrangements, which result in different patterns of genome methylation, occur
across a wide variety of serotypes and sequence types, including two strains (a
19F and a 6B strain) naturally lacking CreX. Our gene expression analysis, by transcriptome
sequencing (RNAseq), confirms that the level of creX expression is impacted
by these genomic rearrangements. In addition, we have shown that the frequency
of hsdS recombination is temperature dependent. Most importantly, we have
demonstrated that the other known pneumococcal site-specific recombinases
XerD, XerS, and SPD_0921 are not involved in spnIII recombination, suggesting that
a currently unknown mechanism is responsible for the recombination of these
phase-variable type I systems
Lineage specific evolution and gene flow in Listeria monocytogenes is independent of bacteriophages
Full text linkListeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure
and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes
Deletion of the zinc transporter lipoprotein AdcAII causes hyperencapsulation of Streptococcus pneumoniae associated with distinct alleles of the Type I restriction modification system
Full text linkThe capsule is the dominant Streptococcus pneumoniae virulence factor,
yet how variation in capsule thickness is regulated is poorly understood. Here, we
describe an unexpected relationship between mutation of adcAII, which encodes a
zinc uptake lipoprotein, and capsule thickness. Partial deletion of adcAII in three of
five capsular serotypes frequently resulted in a mucoid phenotype that biochemical
analysis and electron microscopy of the D39 adcAII mutants confirmed was caused
by markedly increased capsule thickness. Compared to D39, the hyperencapsulated
adcAII mutant strain was more resistant to complement-mediated neutrophil killing
and was hypervirulent in mouse models of invasive infection. Transcriptome analysis
of D39 and the adcAII mutant identified major differences in transcription of
the Sp_0505-0508 locus, which encodes an SpnD39III (ST5556II) type I restrictionmodification
system and allelic variation of which correlates with capsule thickness.
A PCR assay demonstrated close linkage of the SpnD39IIIC and F alleles with the hyperencapsulated
adcAII strains. However, transformation of adcAII with fixed
SpnD39III alleles associated with normal capsule thickness did not revert the hyperencapsulated
phenotype. Half of hyperencapsulated adcAII strains contained the
same single nucleotide polymorphism in the capsule locus gene cps2E, which is required
for the initiation of capsule synthesis. These results provide further evidence
for the importance of the SpnD39III (ST5556II) type I restriction-modification system
for modulating capsule thickness and identified an unexpected linkage between
capsule thickness and mutation of adcAII. Further investigation will be needed to
characterize how mutation of adcAII affects SpnD39III (ST5556II) allele dominance
and results in the hyperencapsulated phenotype
Pathogenic differences of type 1 restriction-modification allele variants in experimental Listeria monocytogenes meningitis
Full text linkBackground: L. monocytogenes meningoencephalitis has a mortality rate of up to
50% and neurofunctional sequelae are common. Type I restriction-modification systems
(RMS) are capable of adding methyl groups to the host genome. Some contain multiple
sequence recognition (hsdS) genes that recombine, resulting in distinct DNA methylation
patterns and patterns of gene expression. These phenotypic switches have been linked
to virulence and have recently been discovered in multiple clonal complexes of L.
monocytogenes. In the present study, we investigated the significant of RMS on L.
monocytogenes virulence during the acute phase of experimental meningitis.
Methods: L. monocytogenes strains containing RMS systems were identified, and
purified clones enriched for single hsdS alleles were isolated. In vivo, 11-day old Wistar
rats were infected with an inoculum containing (a) one of 4 single RMS allele variants
(A, B, C, D) treated with amoxicillin (AMX 50 mg/kg/dosis, q8h), (b) a mixture of all 4
variants with or without AMX treatment, or (c) differentmixtures of 2 RMS allele variants. At
selected time points after infection, clinical and inflammatory parameters, bacterial titers
and brain damage were determined. Changes in the relative frequency of the occurring
RMS alleles in the inoculum and in CSF or cerebellum of infected animals were analyzed
by capillary electrophoresis.
Results: We have identified a phase variable RMS locus within L. monocytogenes
CC4 and generated stocks that stably expressed each of the possible hsdS genes
within that loci. Generation of these allele variants (A, B, C, D) allowed us to determine
the methylation pattern associated with each hsdS through SMRT sequencing. In vivo
infections with these single allele variants revealed differences in disease severity in that
C induced the worst clinical outcome and more pronounced hippocampal apoptosis;
D showed the most pronounced weight loss and the highest bacterial titer in the
cerebellum. A caused the least severe disease.
Conclusion: We identified that L. monocytogenes expressing hsdS (A) causes less
damage than when other hsdS genes are expressed. While expression of hsdSC and
D worsened the outcome in L. monocytogenes meningitis. We also demonstrate a
competitive advantage of variants C and B over variant A in this model. Phenotypical
switching may therefore represent a mechanism of virulence regulation during the acute
phase of CNS infections with L. monocytogenes
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