216 research outputs found
Multiresistant Salmonella enterica serovar 4,[5],12:i:- in Europe: a new pandemic strain?
A marked increase in the prevalence of S. enterica serovar 4,[5],12:i:- with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines (R-type ASSuT) has been noted in food-borne infections and in pigs/pig meat in several European countries in the last ten years. One hundred and sixteen strains of S. enterica serovar 4,[5],12:i:- from humans, pigs and pig meat isolated in England and Wales, France, Germany, Italy, Poland, Spain and the Netherlands were further subtyped by phage typing, pulsed-field gel electrophoresis and multilocus variable number tandem repeat analysis to investigate the genetic relationship among strains. PCR was performed to identify the fljB flagellar gene and the genes encoding resistance to ampicillin, streptomycin, sulphonamides and tetracyclines. Class 1 and 2 integrase genes were also sought. Results indicate that genetically related serovar 4,[5],12:i:- strains of definitive phage types DT193 and DT120 with ampicillin, streptomycin, sulphonamide and tetracycline resistance encoded by blaTEM, strA-strB, sul2 and tet(B) have emerged in several European countries, with pigs the likely reservoir of infection. Control measures are urgently needed to reduce spread of infection to humans via the food chain and thereby prevent the possible pandemic spread of serovar 4,[5],12:i:- of R-type ASSuT as occurred with S. Typhimurium DT104 during the 1990s
Microevolution during the emergence of a monophasic Salmonella Typhimurium epidemic in the United Kingdom
Microevolutionary events associated with the emergence and clonal expansion of new 27 epidemic clones of bacterial pathogens hold the key to understanding the drivers of 28 epidemiological success. We describe a comparative whole genome sequence and 29 phylogenomic analysis of monophasic Salmonella Typhimurium isolates from the UK 30 and Italy from 2005-2012. Monophasic isolates from this time formed a single clade 31 distinct from recent monophasic epidemic clones described previously from North 32 America and Spain. The current UK monophasic epidemic clones encode a novel 33 genomic island encoding resistance to heavy metals (SGI-3), and composite transposon 34 encoding antibiotic resistance genes not present in other Typhimurium isolates, that 35 may have contributed to the epidemiological success. We also report a remarkable 36 degree of genotypic variation that accumulated during clonal expansion of a UK 37 epidemic including multiple independent acquisitions of a novel prophage carrying the 38 sopE gene and multiple deletion events affecting the phase II flagellin locus
Incidence, management and outcomes of the first cfr-mediated linezolid-resistant Staphylococcus epidermidis outbreak in a tertiary referral centre in the Republic of Ireland.
peer-reviewedAim: To report the first Irish outbreak of cfr-mediated linezolid-resistant Staphylococcus
epidermidis.
Methods: Linezolid-resistant S. epidermidis isolated at University Hospital Limerick from
four blood cultures, one wound and four screening swabs (from nine patients) between
April and June 2013 were characterized by pulsed-field gel electrophoresis (PFGE), multilocus
sequence typing (MLST) and staphylococcal cassette chromosome (SCCmec) typing.
Antibiotic susceptibilities were determined according to the guidelines of the British Society
for Antimicrobial Chemotherapy. The outbreak was controlled through prohibiting
prescription and use of linezolid, adherence to infection prevention and control practices,
enhanced environmental cleaning, isolation of affected patients, and hospital-wide education
programmes.
Findings: PFGE showed that all nine isolates represented a single clonal strain. MLST
showed that they belonged to ST2, and SCCmec typing showed that they encoded a variant
of SCCmecIII. All nine isolates were cfr positive, and eight isolates were positive for the
G2576T 23S rRNA mutation commonly associated with linezolid resistance. Isolates
exhibited multiple antibiotic resistances (i.e. linezolid, gentamicin, methicillin, clindamycin,
ciprofloxacin, fusidic acid and rifampicin). The adopted infection prevention
intervention was effective, and the outbreak was limited to the affected intensive care
unit.PUBLISHEDpeer-reviewe
Diversity of Plasmids Encoding Virulence and Resistance Functions in Salmonella enterica subsp. enterica Serovar Typhimurium Monophasic Variant 4,[5],12:i:- Strains Circulating in Europe.
Plasmids encoding resistance and virulence properties in multidrug resistant (MDR) Salmonella enterica (S.) serovar Typhimurium monophasic variant 4,[5],12:i:- isolates recovered from pigs and humans (2006-2008) in Europe were characterised. The isolates were selected based on the detection by PCR-amplification of S. Typhimurium virulence plasmid pSLT genes and were analysed by multi-locus sequence typing (MLST). The resistance genes present in the isolates and the association of these genes with integrons, transposons and insertion sequences were characterised by PCR-sequencing, and their plasmid location was determined by alkaline lysis and by S1-nuclease pulsed-field gel electrophoresis (PFGE) Southern-blot hybridisation. Plasmids were further analysed by replicon typing, plasmid MLST and conjugation experiments. The 10 S. 4,[5],12,i:- selected isolates belonged to ST19. Each isolate carried a large plasmid in which MDR with pSLT-associated virulence genes were located. After analysis, eight different plasmids of three incompatibility groups (IncA/C, IncR and IncF) were detected. Two IncA/C plasmids represented novel variants within the plasmid family of the S. 4,[5],12:i:- Spanish clone, and carried an empty class 1 integron with a conventional qacEÂż1-sul1 3' conserved segment or an In-sul3 type III with estX-psp-aadA2-cmlA1-aadA1-qacH variable region linked to tnpA440-sul3, part of Tn2, Tn21 and Tn1721 transposons, and ISCR2. Four newly described IncR plasmids contained the resistance genes within In-sul3 type I (dfrA12-orfF-aadA2-cmlA1-aadA1-qacH/tnpA440-sul3) and part of Tn10 [tet(B)]. Two pSLT-derivatives with FIIs-ST1+FIB-ST17 replicons carried cmlA1-[aadA1-aadA2]-sul3-dfrA12 and blaTEM-1 genes linked to an In-sul3 type I integron and to Tn2, respectively. In conclusion, three emerging European clones of S. 4,[5],12:i:- harboured MDR plasmids encoding additional virulence functions that could contribute significantly to their evolutionary success
Baryons: What, When and Where?
We review the current state of empirical knowledge of the total budget of
baryonic matter in the Universe as observed since the epoch of reionization.
Our summary examines on three milestone redshifts since the reionization of H
in the IGM, z = 3, 1, and 0, with emphasis on the endpoints. We review the
observational techniques used to discover and characterize the phases of
baryons. In the spirit of the meeting, the level is aimed at a diverse and
non-expert audience and additional attention is given to describe how space
missions expected to launch within the next decade will impact this scientific
field.Comment: Proceedings Review for "Astrophysics in the Next Decade: JWST and
Concurrent Facilities", ed. X. Tielens, 38 pages, 10 color figures. Revised
to address comments from the communit
Developing a predictive modelling capacity for a climate change-vulnerable blanket bog habitat: Assessing 1961-1990 baseline relationships
Aim: Understanding the spatial distribution of high priority habitats and
developing predictive models using climate and environmental variables to
replicate these distributions are desirable conservation goals. The aim of this
study was to model and elucidate the contributions of climate and topography to
the distribution of a priority blanket bog habitat in Ireland, and to examine how
this might inform the development of a climate change predictive capacity for
peat-lands in Ireland.
Methods: Ten climatic and two topographic variables were recorded for grid
cells with a spatial resolution of 1010 km, covering 87% of the mainland
land surface of Ireland. Presence-absence data were matched to these variables
and generalised linear models (GLMs) fitted to identify the main climatic and
terrain predictor variables for occurrence of the habitat. Candidate predictor
variables were screened for collinearity, and the accuracy of the final fitted GLM
was evaluated using fourfold cross-validation based on the area under the curve
(AUC) derived from a receiver operating characteristic (ROC) plot. The GLM
predicted habitat occurrence probability maps were mapped against the actual
distributions using GIS techniques.
Results: Despite the apparent parsimony of the initial GLM using only climatic
variables, further testing indicated collinearity among temperature and precipitation
variables for example. Subsequent elimination of the collinear variables and
inclusion of elevation data produced an excellent performance based on the AUC
scores of the final GLM. Mean annual temperature and total mean annual
precipitation in combination with elevation range were the most powerful
explanatory variable group among those explored for the presence of blanket
bog habitat.
Main conclusions: The results confirm that this habitat distribution in general
can be modelled well using the non-collinear climatic and terrain variables tested
at the grid resolution used. Mapping the GLM-predicted distribution to the
observed distribution produced useful results in replicating the projected
occurrence of the habitat distribution over an extensive area. The methods
developed will usefully inform future climate change predictive modelling for
Irelan
Tides in colliding galaxies
Long tails and streams of stars are the most noticeable upshots of galaxy
collisions. Their origin as gravitational, tidal, disturbances has however been
recognized only less than fifty years ago and more than ten years after their
first observations. This Review describes how the idea of galactic tides
emerged, in particular thanks to the advances in numerical simulations, from
the first ones that included tens of particles to the most sophisticated ones
with tens of millions of them and state-of-the-art hydrodynamical
prescriptions. Theoretical aspects pertaining to the formation of tidal tails
are then presented. The third part of the review turns to observations and
underlines the need for collecting deep multi-wavelength data to tackle the
variety of physical processes exhibited by collisional debris. Tidal tails are
not just stellar structures, but turn out to contain all the components usually
found in galactic disks, in particular atomic / molecular gas and dust. They
host star-forming complexes and are able to form star-clusters or even
second-generation dwarf galaxies. The final part of the review discusses what
tidal tails can tell us (or not) about the structure and content of present-day
galaxies, including their dark components, and explains how tidal tails may be
used to probe the past evolution of galaxies and their mass assembly history.
On-going deep wide-field surveys disclose many new low-surface brightness
structures in the nearby Universe, offering great opportunities for attempting
galactic archeology with tidal tails.Comment: 46 pages, 13 figures, Review to be published in "Tidal effects in
Astronomy and Astrophysics", Lecture Notes in Physics. Comments are most
welcom
All-sky search for long-duration gravitational wave transients with initial LIGO
We present the results of a search for long-duration gravitational wave transients in two sets of data collected by the LIGO Hanford and LIGO Livingston detectors between November 5, 2005 and September 30, 2007, and July 7, 2009 and October 20, 2010, with a total observational time of 283.0 days and 132.9 days, respectively. The search targets gravitational wave transients of duration 10-500 s in a frequency band of 40-1000 Hz, with minimal assumptions about the signal waveform, polarization, source direction, or time of occurrence. All candidate triggers were consistent with the expected background; as a result we set 90% confidence upper limits on the rate of long-duration gravitational wave transients for different types of gravitational wave signals. For signals from black hole accretion disk instabilities, we set upper limits on the source rate density between 3.4×10-5 and 9.4×10-4 Mpc-3 yr-1 at 90% confidence. These are the first results from an all-sky search for unmodeled long-duration transient gravitational waves. © 2016 American Physical Society
All-sky search for long-duration gravitational wave transients with initial LIGO
We present the results of a search for long-duration gravitational wave transients in two sets of data collected by the LIGO Hanford and LIGO Livingston detectors between November 5, 2005 and September 30, 2007, and July 7, 2009 and October 20, 2010, with a total observational time of 283.0 days and 132.9 days, respectively. The search targets gravitational wave transients of duration 10-500 s in a frequency band of 40-1000 Hz, with minimal assumptions about the signal waveform, polarization, source direction, or time of occurrence. All candidate triggers were consistent with the expected background; as a result we set 90% confidence upper limits on the rate of long-duration gravitational wave transients for different types of gravitational wave signals. For signals from black hole accretion disk instabilities, we set upper limits on the source rate density between 3.4×10-5 and 9.4×10-4 Mpc-3 yr-1 at 90% confidence. These are the first results from an all-sky search for unmodeled long-duration transient gravitational waves. © 2016 American Physical Society
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