Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and ...Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.
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The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, ...with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.
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The paper deals with with the on-sky performance of the pyramid wavefront sensor-based Adaptive Optics (AO) systems. These wavefront sensors are of great importance, being used in all first light AO ...systems of the ELTs (E-ELT, GMT, and TMT), currently in design phase. In particular, non-common path aberrations (NCPAs) are a critical issue encountered when using an AO system to produce corrected images in an associated astronomical instrument. The AO wavefront sensor (WFS) and the supported scientific instrument typically use a series of different optical elements, thus experiencing different aberrations. The usual way to correct for such NCPAs is to introduce a static offset in the WFS signals. In this way, when the AO loop is closed the sensor offsets are zeroed and the deformable mirror converges to the shape required to null the NCPA. The method assumes that the WFS operation is linear and completely described by some pre-calibrated interaction matrix. This is not the case for some frequently used wavefront sensors like the Pyramid sensor or a quad-cell Shack-Hartmann sensor. Here we present a method to work in closed-loop with a pyramid wavefront sensor, or more generally a non-linear WFS, introducing a wavefront offset that remains stable when AO correction quality changes due to variations in external conditions like star brightness, seeing, and wind speed. The paper details the methods with analytical and numerical considerations. Then we present results of tests executed at the LBT telescope, in daytime and on sky, using the FLAO system and LUCI2 facility instrument. The on-sky results clearly show the successful operation of the method that completely nulls NCPA, recovering diffraction-limited images with about 70% Strehl ratio in H band in variable seeing conditions. The proposed method is suitable for application to the above-mentioned ELT AO systems.
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The Hunt for Observable Signatures of Terrestrial Systems survey searches for dust near the habitable zones (HZs) around nearby, bright main-sequence stars. We use nulling interferometry in the N ...band to suppress the bright stellar light and to probe for low levels of HZ dust around the 30 stars observed so far. Our overall detection rate is 18%, including four new detections, among which are the first three around Sun-like stars and the first two around stars without any previously known circumstellar dust. The inferred occurrence rates are comparable for early-type and Sun-like stars, but decrease from % for stars with previously detected cold dust to % for stars without such excess, confirming earlier results at higher sensitivity. For completed observations on individual stars, our sensitivity is five to ten times better than previous results. Assuming a lognormal excess luminosity function, we put upper limits on the median HZ dust level of 13 zodis (95% confidence) for a sample of stars without cold dust and of 26 zodis when focusing on Sun-like stars without cold dust. However, our data suggest that a more complex luminosity function may be more appropriate. For stars without detectable Large Binocular Telescope Interferometer (LBTI) excess, our upper limits are almost reduced by a factor of two, demonstrating the strength of LBTI target vetting for future exo-Earth imaging missions. Our statistics are limited so far, and extending the survey is critical to informing the design of future exo-Earth imaging surveys.
We report the discovery of a galaxy overdensity around a Compton-thick Fanaroff–Riley type II (FRII) radio galaxy at z = 1.7 in the deep multiband survey around the z = 6.3 quasi-stellar object (QSO) ...SDSS J1030+0524. Based on a 6 h VLT/MUSE and on a 4 h LBT/LUCI observation, we identify at least eight galaxy members in this structure with spectroscopic redshift z = 1.687 − 1.699, including the FRII galaxy at z = 1.699. Most members are distributed within 400 kpc from the FRII core. Nonetheless, the whole structure is likely much more extended, as one of the members was serendipitously found at ∼800 kpc projected separation. The classic radio structure of the FRII itself extends for ∼600 kpc across the sky. Most of the identified overdensity members are blue, compact galaxies that are actively forming stars at rates of ∼8–60 M⊙ yr−1. For the brightest of them, a half-light radius of 2.2 ± 0.8 kpc at 8000 Å rest-frame was determined based on adaptive optics-assisted observations with LBT/SOUL in the Ks band. We do not observe any strong galaxy morphological segregation or concentration around the FRII core. This suggests that the structure is far from being virialized and likely constitutes the progenitor of a local massive galaxy group or cluster caught in its main assembly phase. Based on a 500 ks Chandra ACIS-I observation, we found that the FRII nucleus hosts a luminous QSO (L2 − 10 keV = 1.3 × 1044 erg s−1, intrinsic and rest-frame) that is obscured by Compton-thick absorption (NH = 1.5 ± 0.6 × 1024 cm−2). Under standard bolometric corrections, the total measured radiative power (Lrad ∼ 4 × 1045 erg s−1) is similar to the jet kinetic power that we estimated from radio observations at 150 MHz (Pkin = 6.3 × 1045 erg s−1), in agreement with what is observed in powerful jetted AGN. Our Chandra observation is the deepest so far for a distant FRII within a galaxy overdensity. It revealed significant diffuse X-ray emission within the region that is covered by the overdensity. In particular, X-ray emission extending for ∼240 kpc is found around the eastern lobe of the FRII. Four out of the six MUSE star-forming galaxies in the overdensity are distributed in an arc-like shape at the edge of this diffuse X-ray emission. These objects are concentrated within 200 kpc in the plane of the sky and within 450 kpc in radial separation. Three of them are even more concentrated and fall within 60 kpc in both transverse and radial distance. The probability of observing four out of the six z = 1.7 sources by chance at the edge of the diffuse emission is negligible. In addition, these four galaxies have the highest specific star formation rates of the MUSE galaxies in the overdensity and lie above the main sequence of field galaxies of equal stellar mass at z = 1.7. We propose that the diffuse X-rays originate from an expanding bubble of gas that is shock heated by the FRII jet, and that star formation is promoted by the compression of the cold interstellar medium of the galaxies around the bubble, which may be remarkable evidence of positive AGN feedback on cosmological scales. We emphasize that our conclusions about the feedback are robust because even assuming that the diffuse X-ray emission arises from inverse Compton scattering of photons of the cosmic microwave background by the relativistic electrons in the radio lobe, star formation may be promoted by the nonthermal pressure of the expanding lobe.
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A total of 554 samples of bean sprouts or other sprouted seeds were collected at retail sale and submitted to nine Official Control Laboratories in England and Northern Ireland during January to ...March 2011. Samples (100 g) were tested for the presence of Salmonella using the EN ISO 6579:2002 method. Products labelled as ready‐to‐eat comprised 23% of the samples and 61% were labelled as raw or to‐cook: the remaining 12% had no indication if the food was intended as ready‐to‐eat or ready‐to‐cook, and 4% were not recorded. Salmonella spp. were detected from four samples of mung‐bean sprouts (0·7% of all the 554 samples) and all four isolates were confirmed as Salmonella enterica serovar Abaetetuba (11 : k : 1,5). Two of the samples where Salmonella was detected were sold as ready‐to‐eat (labelled ‘rinse and serve’ only): The remaining two were from samples labelled as ready‐to‐cook. SIGNIFICANCE AND IMPACT OF THE STUDY: Consumption of sprouted seeds have been associated with infections from a range of foodborne pathogens, particularly Salmonella and shigatoxin producing Escherichia coli (STEC). However, there is limited data (including that from EU monitoring) on foodborne pathogens in samples of this food type which are not associated with outbreaks of infection. Out of 554 raw and ready‐to‐eat bean sprouts and sprouted seeds sampled at retail, Salmonella spp. was detected from four samples. This study illustrated the potential of this product to be contaminated with a human pathogen and the importance of considering the intended use and preparation of specific food in assessing microbiological risks.
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Since 2010, human salmonellosis outbreaks in the UK have been detected as associated with the consumption of duck eggs. Little data are available on the rate of occurrence of Salmonella in duck eggs. ...The aim of this study was to investigate the occurrence of Salmonella spp. in duck eggs on sale and from catering in England during 2011, particularly those from small‐scale production. All samples were collected independently of human salmonellosis outbreak investigations. Composite samples of 6–10 eggs (shells and contents were examined separately) were examined for the presence of Salmonella spp. using the ISO 6579:2002 method. Salmonella spp. was recovered from two of 145 samples (1·4%). In one sample, Salmonella Typhimurium DT 8 was isolated from the shells while Salm. Typhimurium DT 8 and Salm. Typhimurium DT30 were isolated from the contents. Salmonella Typhimurium DT8 was isolated from the egg shells only in the second contaminated sample. This study provides baseline data for risk assessors, regulators and the food industry and may be helpful in communicating risks associated with the consumption of this product as well as evaluating risk management options to control food safety including vaccination of ducks.
Significance and Impact of the Study
Human salmonellosis outbreaks in England and Northern Ireland due to Salmonella enterica serovar Typhimurium definitive phage type (DT) 8 have been identified as associated with the consumption of duck eggs since 2010. This study has shown that Salmonella spp. was detected in 1·4% of ducks egg samples providing baseline data for risk assessors, regulators and the food industry. This may be helpful in communicating risks associated with the consumption of this product as well as evaluating risk management options to control food safety including vaccination of ducks.
Significance and Impact of the Study: Human salmonellosis outbreaks in England and Northern Ireland due to Salmonella enterica serovar Typhimurium definitive phage type (DT) 8 have been identified as associated with the consumption of duck eggs since 2010. This study has shown that Salmonella spp. was detected in 1·4% of ducks egg samples providing baseline data for risk assessors, regulators and the food industry. This may be helpful in communicating risks associated with the consumption of this product as well as evaluating risk management options to control food safety including vaccination of ducks.
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In August to October 2012, a nationwide outbreak of Salmonella enteritidis phase type (PT) 1B with 53 cases occurred in Finland. Hypothesis generating interviews pointed toward ready-to-eat chicken ...salad from a Finnish company and at the same time Estonian authorities informed of a S. enteritidis PT 1B outbreak linked to chicken wrap prepared at an Estonian restaurant. We found that chicken salad was associated with the infection (odds ratio (OR) 16·1, 95% confidence interval (CI) 1·7–148·7 for consumption and OR 17·5. 95% CI 4·0–76·0 for purchase). The frozen pre-cooked chicken cubes used in Finnish salad and in Estonian wraps were traced back to a production plant in China. Great Britain made two Rapid Alert Systems for Food and Feed notifications on chicken cubes imported to the UK from the same Chinese production plant. Microbiological investigation confirmed that the patient isolates in Estonia and in Finland were indistinguishable from the strains isolated from chicken cubes in Estonia and in the UK. We recommend that despite certificates for tested Salmonella, food items should be analyzed when Salmonella contamination in outbreak investigations is suspected. In outbreak investigations, electronically implemented case–case study saves time, effort, and money compared with case–control study.
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