Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

International audienceSalmonella Derby (S. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK). Only two years later, in 2016, it was also recorded in the turkey and broiler sectors in Ireland and Spain. These S. Derby isolates were characterised as members of the multilocus sequence type (MLST) profile 71 (ST71). For the first time, we characterise by whole genome sequencing (WGS) analysis a panel of 90 S. Derby ST71 genomes to understand the routes of transmission of this emerging pathogen within the poultry/turkey food trade. Selected panel included strains isolated as early as 2010 in five leading European g countries for turkey meat production. Twenty-one of the 90 genomes were extracted from a public database-Enterobase. Five of these originated from the United States (n=3), China (n=1) and Taiwan (n=1) isolated between 1986 and 2016. A phylogenomic analysis at the core-genome level revealed the presence of three groups. The largest group contained 97.5% of the European strains and included both, turkey and human isolates that were genetically related by an average of 35 ± 15 single nucleotide polymorphism substitutions (SNPs). To illustrate the diversity, the presence of antimicrobial resistance genes and phages were characteised in 30, S. Derby ST71 genomes, including 11 belonging to this study This study revealed an emergent turkey-related S. Derby ST71 clone circulating in at least five European countries (the UK, Germany, Poland, Italy, and France) since 2010 that causes human gastroenteritis. A matter of concern is the identification of a gyrA mutation involved in resistance to quinolone, present in the Italian genomes. Interestingly, the diversity of phages seems to be related to the geographic origins. These results constitute a baseline for following the spread of this emerging pathogen and identifying appropriate monitoring and prevention measures

Magnetic Fields in the 3C 129 Cluster

We present multi-frequency VLA observations of the two radio galaxies 3C 129 and 3C 129.1 embedded in a luminous X-ray cluster. These radio observations reveal a substantial difference in the Faraday Rotation Measures (RMs) toward 3C 129.1 at the cluster center and 3C 129 at the cluster periphery. After deriving the density profile from available X-ray data, we find that the RM structure of both radio galaxies can be fit by a tangled cluster magnetic field with strength 6 microGauss extending at least 3 core radii (450 kpc) from the cluster center. The magnetic field makes up a small contribution to the total pressure (5%) in the central regions of the cluster. The radio morphology of 3C 129.1 appears disturbed on the southern side, perhaps by the higher pressure environment. In contrast with earlier claims for the presence of a moderately strong cooling flow in the 3C 129 cluster, our analysis of the X-ray data places a limit on the mass deposition rate from any such flow of <1.2 Msun/yr.Comment: in press at MNRA

Prevalence and molecular epidemiology of mcr-mediated colistin-resistance Escherichia coli from healthy poultry in France after national plan to reduce exposure to colistin in farm

IntroductionWithin the 2007–2014 programme for the surveillance of antimicrobial resistance (AMR) in livestock in France, mcr-1 prevalence average in commensal Escherichia coli was found to be 5.9% in turkeys and 1.8% in broilers, indicating that mobile colistin resistance had spread in farm animals. In 2017, the French national Ecoantibio2 plan was established to tackle AMR in veterinary medicine, with the objective of a 50% reduction in exposure to colistin in farm animals within 5 years (from 2014–2015 to 2020). Our objective was to update data concerning the prevalence and molecular epidemiology of colistin resistance, in consideration of colistin sales in poultry production in France.MethodsAntimicrobial susceptibility of commensal E. coli isolated from broilers and turkeys at slaughterhouse was determined by broth micro-dilution. The mcr genes were screened by polymerase chain reaction (PCR). Whole genome sequencing (WGS) was used to investigate the genetic diversity of colistin-resistant isolates. Transformation experiments enabled identification of the mcr-bearing plasmid replicon types. The correlation between prevalence of colistin resistance and colistin usage data was explored statistically.Results and discussionIn 2020, in France, the resistance prevalence to colistin in poultry production was 3% in turkeys and 1% in broilers, showing a significant highly positive correlation with a −68% decrease of poultry exposure to colistin since 2014. Only the mcr-1 gene was detected among the colistin-resistant E. coli. More than 80% of isolates are multi-drug resistant with 40% of isolates originating from turkeys and 44% originating from broilers co-resistant to the critically important antimicrobial ciprofloxacin. Most of the strains had no clonal relationship. The mcr gene was located in different plasmid types, carrying various other AMR genes. The decrease in colistin resistance among poultry in France can be considered a positive outcome of the national action plans for reduced colistin usage

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes

Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L. monocytogenes.Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses.Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering.Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories

The extended X-ray emission around HDF130 at z=1.99: an inverse Compton ghost of a giant radio source in the Chandra Deep Field North

One of the six extended X-ray sources found in the Chandra DeepField North is centred on HDF130, which has recently been shown to be a massive galaxy at z=1.99 with a compact radio nucleus. The X-ray source has a roughly double-lobed structure with each lobe about 41 arcsec long, or 345 kpc at the redshift of HDF130. We have analyzed the 2 Ms X-ray image and spectrum of the source and find that it is well fit by a power-law continuum of photon index 2.65 and has a 2--10 keV luminosity of 5.4x10^{43}ergps (if at z=1.99). Any further extended emission within a radius of 60 arcsec has a luminosity less than half this value, which is contrary to what is expected from a cluster of galaxies. The source is best explained as an inverse Compton ghost of a giant radio source, which is no longer being powered, and for which Compton losses have downgraded the energetic electrons, \gamma> 10^4, required for high-frequency radio emission. The lower energy electrons, \gamma~1000, produce X-rays by inverse Compton scattering on the Cosmic Microwave Background. Depending on the magnetic field strength, some low frequency radio emission may remain. Further inverse Compton ghosts may exist in the Chandra deep fields.Comment: 4 pages, 2 figures, accepted for publication in MNRA

Chandra X-ray observations of the 3C295 cluster core

We examine the properties of the X-ray gas in the central regions of the distant (z=0.46), X-ray luminous cluster of galaxies surrounding the powerful radio source 3C 295, using observations made with the Chandra Observatory. Between radii of 50-500 kpc, the cluster gas is approximately isothermal with an emission-weighted temperature, kT ~5 keV. Within the central 50 kpc radius this value drops to kT ~3.7 keV. The spectral and imaging Chandra data indicate the presence of a cooling flow within the central 50 kpc radius of the cluster, with a mass deposition rate of approximately 280 solar masses per year. We estimate an age for the cooling flow of 1-2 Gyr, which is approximately one thousand times older than the central radio source. We find no evidence in the X-ray spectra or images for significant heating of the X-ray gas by the radio source. We report the detection of an edge-like absorption feature in the spectrum for the central 50 kpc region, which may be due to oxygen-enriched dust grains. The implied mass in metals seen in absorption could have been accumulated by the cooling flow over its lifetime. Combining the results on the X-ray gas density profile with radio measurements of the Faraday rotation measure in 3C295, we estimate the magnetic field strength in the region of the cluster core to be B ~12 \muG.Comment: 27 pages, 16 figs, 5 tables. Accepted for publication in MNRA

The Origin of Radio Haloes and Non-thermal Emission in Clusters of Galaxies

We study the origin of the non-thermal emission from the intracluster medium, including the excess hard X-ray emission and cluster-wide radio haloes, through fitting two representative models to the Coma cluster. If the synchrotron emitting relativistic electrons are accelerated in situ from the vast pool of thermal electrons, then a quasi-stationary solution of the kinetic equation with particle acceleration through turbulence at high energies (>200 keV) naturally produces a population of supra-thermal electrons responsible for the excess hard X-ray emission through bremsstrahlung. Inverse Compton scattering is negligible at hard X-ray energies in this case. The radio halo flux density constrains the magnetic field strength to a value close to that of equipartition ~1 uG. Alternatively, if the relativistic electrons are injected from numerous localised `external' sources then the hard X-rays are best explained by inverse Compton scattering from GeV electrons, and little of the hard X-radiation has a bremsstrahlung origin. In this case, the magnetic field strength is constrained to ~0.1-0.2 uG. Both models assume that the non-thermal emissions are generated by a single electron spectrum, so that only two free parameters, well constrained by the observed hard X-ray and radio halo spectra, are needed in either case. Measurements of the cluster magnetic field will distinguish between the models.Comment: 14 pages, 7 figures, accepted by MNRA

Cosmology with clusters of galaxies

In this Chapter I review the role that galaxy clusters play as tools to constrain cosmological parameters. I will concentrate mostly on the application of the mass function of galaxy clusters, while other methods, such as that based on the baryon fraction, are covered by other Chapters of the book. Since most of the cosmological applications of galaxy clusters rely on precise measurements of their masses, a substantial part of my Lectures concentrates on the different methods that have been applied so far to weight galaxy clusters. I provide in Section 2 a short introduction to the basics of cosmic structure formation. In Section 3 I describe the Press--Schechter (PS) formalism to derive the cosmological mass function, then discussing extensions of the PS approach and the most recent calibrations from N--body simulations. In Section 4 I review the methods to build samples of galaxy clusters at different wavelengths. Section 5 is devoted to the discussion of different methods to derive cluster masses. In Section 6 I describe the cosmological constraints, which have been obtained so far by tracing the cluster mass function with a variety of methods. Finally, I describe in Section 7 the future perspectives for cosmology with galaxy clusters and the challenges for clusters to keep playing an important role in the era of precision cosmology.Comment: 49 pages, 19 figures, Lectures for 2005 Guillermo Haro Summer School on Clusters, to appear in "Lecture notes in Physics" (Springer

Identification of Genetic Markers for the Detection of <i>Bacillus thuringiensis</i> Strains of Interest for Food Safety

Bacillus thuringiensis (Bt), belonging to the Bacillus cereus (Bc) group, is commonly used as a biopesticide worldwide due to its ability to produce insecticidal crystals during sporulation. The use of Bt, especially subspecies aizawai and kurstaki, to control pests such as Lepidoptera, generally involves spraying mixtures containing spores and crystals on crops intended for human consumption. Recent studies have suggested that the consumption of commercial Bt strains may be responsible for foodborne outbreaks (FBOs). However, its genetic proximity to Bc strains has hindered the development of routine tests to discriminate Bt from other Bc, especially Bacillus cereus sensu stricto (Bc ss), well known for its involvement in FBOs. Here, to develop tools for the detection and the discrimination of Bt in food, we carried out a genome-wide association study (GWAS) on 286 complete genomes of Bc group strains to identify and validate in silico new molecular markers specific to different Bt subtypes. The analyses led to the determination and the in silico validation of 128 molecular markers specific to Bt, its subspecies aizawai, kurstaki and four previously described proximity clusters associated with these subspecies. We developed a command line tool based on a 14-marker workflow, to carry out a computational search for Bt-related markers from a putative Bc genome, thereby facilitating the detection of Bt of interest for food safety, especially in the context of FBOs

The 2023 pipeline of disease-modifying antirheumatic drugs (DMARDs) in clinical development for spondyloarthritis (including psoriatic arthritis): a systematic review of trials

Objectives The objective of this systematic review was to provide an overview of current developments and potentially available therapeutic options for spondyloarthritis (SpA) in the coming years.Methods We conducted a systematic review of 17 national and international clinical trial databases for all disease-modifying antirheumatic drugs (DMARDs) for SpA that are already marketed, in clinical development or withdrawn. The search was performed on February 2023 with the keywords “spondyloarthritis”, “ankylosing spondylitis” and “psoriatic arthritis”. For each molecule, we only considered the study at the most advanced stage of clinical development.Results Concerning axial SpA (axSpA), a total of 44 DMARDs were identified: 6 conventional synthetic DMARDs (csDMARDs), 27 biological DMARDs (bDMARDs) and 11 targeted synthetic DMARDs (tsDMARDs). Among the 18 targeted treatments (b+tsDMARDs) in current development, corresponding trials reached phase I (n=1), II (n=10) and III (n=7). Ten molecules are IL-17 inhibitors, two Janus kinase (JAK) inhibitors and two granulocyte-macrophage colony-stimulating factor inhibitors; four have another mode of action. Concerning psoriatic arthritis (PsA), 44 DMARDs were identified: 5 csDMARDs, 27 bDMARDs and 12 tsDMARDs. Among the 15 molecules in current development, corresponding trials reached phase II (n=8) and III (n=7). Six molecules are JAK inhibitors, six IL-17 inhibitors and one an IL-23 inhibitor; two have another mode of action.Conclusion This systematic review identified 18 and 15 molecules in clinical development for axSpA and PsA, respectively, which suggests a strengthening of the therapeutic arsenal in the coming years. However, with so many DMARDs but low target diversity, we will need to develop strategies or biomarkers to help clinicians make informed treatment decisions