First Molecular Characterization of Siphoviridae-Like Bacteriophages Infecting Staphylococcus hyicus in a Case of Exudative Epidermitis

Exudative epidermitis (EE), also known as greasy pig disease, is one of the most frequent skin diseases affecting piglets. Zoonotic infections in human occur. EE is primarily caused by virulent strains of Staphylococcus (S.) hyicus. Generally, antibiotic treatment of this pathogen is prone to decreasing success, due to the incremental development of multiple resistances of bacteria against antibiotics. Once approved, bacteriophages might offer interesting alternatives for environmental sanitation or individualized treatment, subject to the absence of virulence and antimicrobial resistance genes. However, genetic characterization of bacteriophages for S. hyicus has, so far, been missing. Therefore, we investigated a piglet raising farm with a stock problem due to EE. We isolated eleven phages from the environment and wash water of piglets diagnosed with the causative agent of EE, i.e., S. hyicus. The phages were morphologically characterized by electron microscopy, where they appeared Siphoviridae-like. The genomes of two phages were sequenced on a MiSeq instrument (Illumina), resulting in the identification of a new virulent phage, PITT-1 (PMBT8), and a temperate phage, PITT-5 (PMBT9). Sequencing of three host bacteria (S. hyicus) from one single farm revealed the presence of two different strains with genes coding for two different exfoliative toxin genes, i.e., exhA (2 strains) and exhC (1 strain). The exhC-positive S. hyicus strain was only weakly lysed by most lytic phages. The occurrence of different virulent S. hyicus strains in the same outbreak limits the prospects for successful phage treatment and argues for the simultaneous use of multiple and different phages attacking the same host

The Stellar and Gas Kinematics of the LITTLE THINGS Dwarf Irregular Galaxy NGC 1569

In order to understand the formation and evolution of dIm galaxies, one needs to understand their three-dimensional structure. We present measurements of the stellar velocity dispersion in NGC 1569, a nearby post-starburst dIm galaxy. The stellar vertical velocity dispersion, $\sigma_{\rm z}$, coupled with the maximum rotational velocity derived from \ion{H}{1} observations, $V_{\rm max}$, gives a measure of how kinematically hot the galaxy is, and, therefore, indicates its structure. We conclude that the stars in NGC 1569 are in a thick disk with a $V_{\rm max} / \sigma_{\rm z}$ = 2.4 $\pm$ 0.7. In addition to the structure, we analyze the ionized gas kinematics from \ion{O}{3} observations along the morphological major axis. These data show evidence for outflow from the inner starburst region and a potential expanding shell near supermassive star cluster (SSC) A. When compared to the stellar kinematics, the velocity dispersion of the stars increase in the region of SSC A supporting the hypothesis of an expanding shell. The stellar kinematics closely follow the motion of the gas. Analysis of high resolution \ion{H}{1} data clearly reveals the presence of an \ion{H}{1} cloud that appears to be impacting the eastern edge of NGC 1569. Also, an ultra-dense \ion{H}{1} cloud can be seen extending to the west of the impacting \ion{H}{1} cloud. This dense cloud is likely the remains of a dense \ion{H}{1} bridge that extended through what is now the central starburst area. The impacting \ion{H}{1} cloud was the catalyst for the starburst, thus turning the dense gas into stars over a short timescale, $\sim$ 1 Gyr. We performed a careful study of the spectral energy distribution using infrared, optical, and ultraviolet photometry producing a state-of-the-art mass model for the stellar disk. This mass modeling shows that stars dominate the gravitational potential in the inner 1 kpc.Comment: 49 pages, 25 figures, accepted in A

The CO-to-H2 Conversion Factor From Infrared Dust Emission Across the Local Group

We estimate the conversion factor relating CO emission to H2 mass, alpha_CO, in five Local Group galaxies that span approximately an order of magnitude in metallicity - M31, M 33, the Large Magellanic Cloud (LMC), NGC 6822, and the Small Magellanic Cloud (SMC). We model the dust mass along the line of sight from infrared (IR) emission and then solve for the alpha_CO that best allows a single gas-to-dust ratio (delta_GDR) to describe each system. This approach remains sensitive to CO-dark envelopes of H2 surrounding molecular clouds. In M 31, M 33, and the LMC we find alpha_CO \approx 3-9 M_sun pc^-2 (K km s^-1)^-1, consistent with the Milky Way value within the uncertainties. The two lowest metallicity galaxies in our sample, NGC 6822 and the SMC (12 + log(O/H) \approx 8.2 and 8.0), exhibit a much higher alpha_CO. Our best estimates are \alpha_NGC6822 \approx 30 M_sun/pc^-2 (K km s^-1)^-1 and \alpha_SMC \approx 70 M_sun/pc^-2 (K km s-1)-1. These results are consistent with the conversion factor becoming CO a strong function of metallicity around 12 + log(O/H) \sim 8.4 - 8.2. We favor an interpretation where decreased dust-shielding leads to the dominance of CO-free envelopes around molecular clouds below this metallicity.Comment: Accepted for publication in the Astrophysical Journal, 15 pages, 7 figure

Low CO Luminosities in Dwarf Galaxies

[Abridged] We present maps of CO 2-1 emission covering the entire star-forming disks of 16 nearby dwarf galaxies observed by the IRAM HERACLES survey. The data have 13 arcsec angular resolution, ~250 pc at our average distance of 4 Mpc, and sample the galaxies by 10-1000 resolution elements. We apply stacking techniques to perform the first sensitive search for CO emission in dwarfs outside the Local Group ranging from single lines-of-sight, stacked over IR-bright regions of embedded star formation, and stacked over the entire galaxy. We detect 5 dwarfs in CO with total luminosities of L_CO = 3-28 1e6 Kkmspc2. The other 11 dwarfs remain undetected in CO even in the stacked data and have L_CO < 0.4-8 1e6 Kkmspc2. We combine our sample of dwarfs with a large literature sample of spirals to study scaling relations of L_CO with M_B and metallicity. We find that dwarfs with metallicities of Z ~ 1/2-1/10 Z_sun have L_CO about 1e2-1e4x smaller than spirals and that their L_CO per unit L_B is 10-100x smaller. A comparison with tracers of star formation (FUV and 24 micron) shows that L_CO per unit SFR is 10-100x smaller in dwarfs. One possible interpretation is that dwarfs form stars much more efficiently, however we argue that the low L_CO/SFR ratio is due to significant changes of the CO-to-H2 conversion factor, alpha_CO, in low metallicity environments. Assuming a constant H2 depletion time of 1.8 Gyr (as found for nearby spirals) implies alpha_CO values for dwarfs with Z ~ 1/2-1/10 Z_sun that are more than 10x higher than those found in solar metallicity spirals. This significant increase of alpha_CO at low metallicity is consistent with previous studies, in particular those which model dust emission to constrain H2 masses. Even though it is difficult to parameterize the metallicity dependence of alpha_CO, our results suggest that CO is increasingly difficult to detect at lower metallicities.Comment: Accepted for publication in the Astronomical Journal, 19 pages, 7 figure

The MALATANG Survey : The L GAS-L IR Correlation on Sub-kiloparsec Scale in Six Nearby Star-forming Galaxies as Traced by HCN J = 4 → 3 and HCO + J = 4 → 3

This is an author-created, un-copyedited version of an article published in The Astrophysical Journal. The Version of Record is available online at https://doi.org/10.3847/1538-4357/aac512.We present HCN J = 4→3 and HCO+ J = 4→3 maps of six nearby star-forming galaxies, NGC 253, NGC 1068, IC 342, M82, M83, and NGC 6946, obtained with the James Clerk Maxwell Telescope as part of the MALATANG survey. All galaxies were mapped in the central 2×2 region at 14 (FWHM) resolution (corresponding to linear scales of ∼0.2-1.0 kpc). The LIR-Ldense relation, where the dense gas is traced by the HCN J = 4→3 and the HCO+ J = 4→3 emission, measured in our sample of spatially resolved galaxies is found to follow the linear correlation established globally in galaxies within the scatter. We find that the luminosity ratio, LIR/Ldense, shows systematic variations with LIR within individual spatially resolved galaxies, whereas the galaxy-integrated ratios vary little. A rising trend is also found between LIR/Ldense ratio and the warm-dust temperature gauged by the 70 μm/100 μm flux ratio. We find that the luminosity ratios of IR/HCN (4-3) and IR/HCO+ (4-3), which can be taken as a proxy for the star formation efficiency (SFE) in the dense molecular gas (SFE dense), appear to be nearly independent of the dense gas fraction ( f dense) for our sample of galaxies. The SFE of the total molecular gas (SFEmol) is found to increase substantially with f dense when combining our data with those on local (ultra)luminous infrared galaxies and high-z quasars. The mean LHCN(4-3) LHCO+(4-3) line ratio measured for the six targeted galaxies is 0.9±0.6. No significant correlation is found for the L'HCN(4-3) L'HCO+(4-3) ratio with the star formation rate as traced by L IR, nor with the warm-dust temperature, for the different populations of galaxies.Peer reviewe

Molecular Gas and Star Formation in Nearby Disk Galaxies

We compare molecular gas traced by ^(12)CO (2-1) maps from the HERACLES survey, with tracers of the recent star formation rate (SFR) across 30 nearby disk galaxies. We demonstrate a first-order linear correspondence between Σ_(mol) and Σ_(SFR) but also find important second-order systematic variations in the apparent molecular gas depletion time, τ_(dep)^(mol) = ∑_(mol)/∑_(SFR). At the 1 kpc common resolution of HERACLES, CO emission correlates closely with many tracers of the recent SFR. Weighting each line of sight equally, using a fixed α_(CO) equivalent to the Milky Way value, our data yield a molecular gas depletion time, τ_(dep)^(mol)= ∑_(mol)∑_(SFR) ≈ 2.2 Gyr with 0.3 dex 1σ scatter, in very good agreement with recent literature data. We apply a forward-modeling approach to constrain the power-law index, N, that relates the SFR surface density and the molecular gas surface density, ∑_(SFR) ∝ ∑_(mol)^N. We find N = 1 ± 0.15 for our full data set with some scatter from galaxy to galaxy. This also agrees with recent work, but we caution that a power-law treatment oversimplifies the topic given that we observe correlations between τ_(dep)^(mol) and other local and global quantities. The strongest of these are a decreased τ_(dep)^(mol) in low-mass, low-metallicity galaxies and a correlation of the kpc-scale τ_(dep)^(mol) with dust-to-gas ratio, D/G. These correlations can be explained by a CO-to-H_2 conversion factor (α_(CO)) that depends on dust shielding, and thus D/G, in the theoretically expected way. This is not a unique interpretation, but external evidence of conversion factor variations makes this the most conservative explanation of the strongest observed τ_(dep)^(mol) trends. After applying a D/G-dependent α_(CO), some weak correlations between τ_(dep)^(mol) and local conditions persist. In particular, we observe lower τ_(dep)^(mol) and enhanced CO excitation associated with nuclear gas concentrations in a subset of our targets. These appear to reflect real enhancements in the rate of star formation per unit gas, and although the distribution of τ_(dep) does not appear bimodal in galaxy centers, τ_(dep) does appear multivalued at fixed Σ_(H2), supporting the idea of "disk" and "starburst" modes driven by other environmental parameters

Variations in the Star Formation Efficiency of the Dense Molecular Gas across the Disks of Star-Forming Galaxies

Date of Acceptance: 15/05/2015We present a new survey of HCN(1-0) emission, a tracer of dense molecular gas, focused on the little-explored regime of normal star-forming galaxy disks. Combining HCN, CO, and infrared (IR) emission, we investigate the role of dense gas in Star Formation (SF), finding systematic variations in both the apparent dense gas fraction and the apparent SF efficiency (SFE) of dense gas. The latter may be unexpected, given the popularity of gas density threshold models to explain SF scaling relations. We used the IRAM 30-m telescope to observe HCN(1-0) across 29 nearby disk galaxies whose CO(2-1) emission has previously been mapped by the HERACLES survey. Because our observations span a range of galactocentric radii, we are able to investigate the properties of the dense gas as a function of local conditions. We focus on how the IR/CO, HCN/CO, and IR/HCN ratios (observational cognates of the SFE, dense gas fraction, and dense gas SFE) depend on the stellar surface density and the molecular/atomic ratio. The HCN/CO ratio correlates tightly with these two parameters across a range of 2.1 dex and increases in the high surface density parts of galaxies. Simultaneously, the IR/HCN ratio decreases systematically with these same parameters and is ~6-8 times lower near galaxy centers than in the outer regions. For fixed line-mass conversion factors, these results are incompatible with a simple model in which SF depends only on the gas mass above some density threshold. Only a specific set of environment-dependent conversion factors can render our observations compatible with such a model. Whole cloud models, such as the theory of turbulence regulated SF, do a better job of matching our data. We explore one such model in which variations in the Mach number and in the mean density would respectively drive the trends within galaxy disks and the differences between disk and merging galaxies (abridged).Peer reviewe

Impact of wet-lab protocols on quality of whole-genome short-read sequences from foodborne microbial pathogens

For successful elucidation of a food-borne infection chain, the availability of high-quality sequencing data from suspected microbial contaminants is a prerequisite. Commonly, those investigations are a joint effort undertaken by different laboratories and institutes. To analyze the extent of variability introduced by differing wet-lab procedures on the quality of the sequence data we conducted an interlaboratory study, involving four bacterial pathogens, which account for the majority of food-related bacterial infections: Campylobacter spp., Shiga toxin-producing Escherichia coli, Listeria monocytogenes, and Salmonella enterica. The participants, ranging from German federal research institutes, federal state laboratories to universities and companies, were asked to follow their routine in-house protocols for short-read sequencing of 10 cultures and one isolated bacterial DNA per species. Sequence and assembly quality were then analyzed centrally. Variations within isolate samples were detected with SNP and cgMLST calling. Overall, we found that the quality of Illumina raw sequence data was high with little overall variability, with one exception, attributed to a specific library preparation kit. The variability of Ion Torrent data was higher, independent of the investigated species. For cgMLST and SNP analysis results, we found that technological sequencing artefacts could be reduced by the use of filters, and that SNP analysis was more suited than cgMLST to compare data of different contributors. Regarding the four species, a minority of Campylobacter isolate data showed the in comparison highest divergence with regard to sequence type and cgMLST analysis. We additionally compared the assembler SPAdes and SKESA for their performance on the Illumina data sets of the different species and library preparation methods and found overall similar assembly quality metrics and cgMLST statistics