Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. IMPORTANCE This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view of L. monocytogenes strain populations associated with specific food matrices. We clearly showed that some STs were associated with food matrices, such as meat, meat products, and dairy products. We opened the way to source attribution modeling in order to quantify the relative importance of the main food matrices

Collapse of the N=28 shell closure in 42^{42}Si

The energies of the excited states in very neutron-rich $^{42}$Si and $^{41,43}$P have been measured using in-beam $\gamma$-ray spectroscopy from the fragmentation of secondary beams of $^{42,44}$S at 39 A.MeV. The low 2$^+$ energy of $^{42}$Si, 770(19) keV, together with the level schemes of $^{41,43}$P provide evidence for the disappearance of the Z=14 and N=28 spherical shell closures, which is ascribed mainly to the action of proton-neutron tensor forces. New shell model calculations indicate that $^{42}$Si is best described as a well deformed oblate rotor.Comment: 4 pages, 3 figures, accepted for publication in Phys. Rev. let

Learning the fundamental mid-infrared spectral components of galaxies with non-negative matrix factorization

The mid-infrared (MIR) spectra observed with the Spitzer Infrared Spectrograph (IRS) provide a valuable data set for untangling the physical processes and conditions within galaxies. This paper presents the first attempt to blindly learn fundamental spectral components of MIR galaxy spectra, using non-negative matrix factorization (NMF). NMF is a recently developed multivariate technique shown to be successful in blind source separation problems. Unlike the more popular multivariate analysis technique, principal component analysis, NMF imposes the condition that weights and spectral components are non-negative. This more closely resembles the physical process of emission in the MIR, resulting in physically intuitive components. By applying NMF to galaxy spectra in the Cornell Atlas of Spitzer/IRS sources, we find similar components amongst different NMF sets. These similar components include two for active galactic nucleus (AGN) emission and one for star formation. The first AGN component is dominated by fine structure emission lines and hot dust, the second by broad silicate emission at 10 and 18 μm. The star formation component contains all the polycyclic aromatic hydrocarbon features and molecular hydrogen lines. Other components include rising continuums at longer wavelengths, indicative of colder grey-body dust emission. We show an NMF set with seven components can reconstruct the general spectral shape of a wide variety of objects, though struggle to fit the varying strength of emission lines. We also show that the seven components can be used to separate out different types of objects. We model this separation with Gaussian mixtures modelling and use the result to provide a classification tool. We also show that the NMF components can be used to separate out the emission from AGN and star formation regions and define a new star formation/AGN diagnostic which is consistent with all MIR diagnostics already in use but has the advantage that it can be applied to MIR spectra with low signal-to-noise ratio or with limited spectral range. The seven NMF components and code for classification are available at https://github.com/pdh21/NMF_software/

Structure of the N=27 isotones derived from the 44^{44}Ar(d,p)45^{45}Ar

Expérience GANIL/SPIRAL, détecteur CATS, détecteur MUST, 7 figures,International audienceThe $^{44}$Ar(d,p)$^{45}$Ar neutron transfer reaction was performed at 10~A.MeV. Measured excitation energies, deduced angular momenta and spectroscopic factors of the states populated in $^{45}$Ar are reported. A satisfactory description of these properties is achieved in the shell model framework using a new $sdpf$ interaction. The model analysis is extended to more exotic even-Z nuclei down to $^{41}_{14}$Si$_{27}$ to study how collectivity impacts the low lying structure of N~=~27 neutron-rich nuclei

Spectroscopy of 26^{26}F

The structure of the weakly-bound $^{26}_{\;\;9}$F$_{17}$ odd-odd nucleus, produced from $^{27,28}$Na nuclei, has been investigated at GANIL by means of the in-beam $\gamma$-ray spectroscopy technique. A single $\gamma$-line is observed at 657(7) keV in $^{26}_{9}$F which has been ascribed to the decay of the excited J=$2^+$ state to the J=1$^+$ ground state. The possible presence of intruder negative parity states in $^{26}$F is also discussed.Comment: 3 pages, 1 figure, accepted for publication in Physical Review

One-neutron removal reactions on light neutron-rich nuclei

A study of high energy (43--68 MeV/nucleon) one-neutron removal reactions on a range of neutron-rich psd-shell nuclei (Z = 5--9, A = 12--25) has been undertaken. The inclusive longitudinal and transverse momentum distributions for the core fragments, together with the cross sections have been measured for breakup on a carbon target. Momentum distributions for reactions on tantalum were also measured for a subset of nuclei. An extended version of the Glauber model incorporating second order noneikonal corrections to the JLM parametrisation of the optical potential has been used to describe the nuclear breakup, whilst the Coulomb dissociation is treated within first order perturbation theory. The projectile structure has been taken into account via shell model calculations employing the psd-interaction of Warburton and Brown. Both the longitudinal and transverse momentum distributions, together with the integrated cross sections were well reproduced by these calculations and spin-parity assignments are thus proposed for $^{15}$B, $^{17}$C, $^{19-21}$N, $^{21,23}$O, $^{23-25}$F. In addition to the large spectroscopic amplitudes for the $\nu2$s$_{1/2}$ intruder configuration in the N=9 isotones,$^{14}$B and $^{15}$C, significant $\nu2$s$_{1/2}^2$ admixtures appear to occur in the ground state of the neighbouring N=10 nuclei $^{15}$B and $^{16}$C. Similarly, crossing the N=14 subshell, the occupation of the $\nu2$s$_{1/2}$ orbital is observed for $^{23}$O, $^{24,25}$F. Analysis of the longitudinal and transverse momentum distributions reveals that both carry spectroscopic information, often of a complementary nature. The general utility of high energy nucleon removal reactions as a spectroscopic tool is also examined.Comment: 50 pages, 19 figures, submitted to Phys. Rev.

One-neutron removal reactions on neutron-rich psd-shell nuclei

A systematic study of high energy, one-neutron removal reactions on 23 neutron-rich, psd--shell nuclei (Z=5-9, A=12-25) has been carried out. The longitudinal momentum distributions of the core fragments and corresponding single-neutron removal cross sections are reported for reactions on a carbon target. Extended Glauber model calculations, weighted by the spectroscopic factors obtained from shell model calculations, are compared to the experimental results. Conclusions are drawn regarding the use of such reactions as a spectroscopic tool and spin-parity assignments are proposed for 15B, 17C, 19-21N, 21,23O, 23-25F. The nature of the weakly bound systems 14B and 15,17C is discussed.Comment: 11 pages + 2 figure

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

Nuclear structure and reaction studies at SPIRAL

The SPIRAL facility at GANIL, operational since 2001, is described briefly. The diverse physics program using the re-accelerated (1.2 to 25 MeV/u) beams ranging from He to Kr and the instrumentation specially developed for their exploitation are presented. Results of these studies, using both direct and compound processes, addressing various questions related to the existence of exotic states of nuclear matter, evolution of new "magic numbers", tunnelling of exotic nuclei, neutron correlations, exotic pathways in astrophysical sites and characterization of the continuum are discussed. The future prospects for the facility and the path towards SPIRAL2, a next generation ISOL facility, are also briefly presented.Comment: 48 pages, 27 figures. Accepted for publication in Journal of Physics

ISM properties in low-metallicity environments I. mid-infrared spectra of dwarf galaxies

We present new ISOCAM mid-infrared spectra of three starbursting nearby dwarf galaxies, NGC1569, IIZw40, NGC1140 and the 30Dor region of the LMC and explore the properties of the ISM in low-metallicity environments, also using additional sources from the literature. We analyse the various components of the ISM probed by the mid-infrared observations and compare them with other Galactic and extragalactic objects. The MIR spectra of the low-metallicity starburst sources are dominated by the [NeIII] and [SIV] lines, as well as a steeply rising dust continuum. PAH bands are generaly faint, both locally and averaged over the full galaxy, in stark contrast to dustier starburst galaxies, where the PAH features are very prominant and even dominate on global scales. The hardness of the modeled interstellar radiation fields for the dwarf galaxies increases as the presence of PAH band emission becomes less pronounced. The [NeIII]/[NeII] ratios averaged over the full galaxy are strikingly high, often >10. Thus, the hard radiation fields are pronounced and pervasive. We find a prominent correlation between the PAHs/VSGs and the [NeIII]/[NeII] ratios for a wide range of objects, including the low metallicity galaxies as well as Galactic HII regions and other metal-rich galaxies. This effect is consistent with the hardness of the interstellar radiation field playing a major role in the destruction of PAHs in the low metallicity ISM. We see a PAHs/VSGs and metallicity correlation, also found by Engelbracht et al. (2005) for a larger survey. Combined effects of metallicity and radiation field seem to be playing important roles in the observed behavior of PAHs in the low metallicity systems.Comment: accepted by A&