High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

<p>Abstract</p> <p>Background</p> <p>Next-Generation Sequencing (NGS) is increasingly being used as a molecular epidemiologic tool for discerning ancestry and traceback of the most complicated, difficult to resolve bacterial pathogens. Making a linkage between possible food sources and clinical isolates requires distinguishing the suspected pathogen from an environmental background and placing the variation observed into the wider context of variation occurring within a serovar and among other closely related foodborne pathogens. Equally important is the need to validate these high resolution molecular tools for use in molecular epidemiologic traceback. Such efforts include the examination of strain cluster stability as well as the cumulative genetic effects of sub-culturing on these clusters. Numerous isolates of <it>S</it>. Montevideo were shot-gun sequenced including diverse lineage representatives as well as numerous replicate clones to determine how much variability is due to bias, sequencing error, and or the culturing of isolates. All new draft genomes were compared to 34 <it>S</it>. Montevideo isolates previously published during an NGS-based molecular epidemiological case study.</p> <p>Results</p> <p>Intraserovar lineages of <it>S</it>. Montevideo differ by thousands of SNPs, that are only slightly less than the number of SNPs observed between <it>S</it>. Montevideo and other distinct serovars. Much less variability was discovered within an individual <it>S</it>. Montevideo clade implicated in a recent foodborne outbreak as well as among individual NGS replicates. These findings were similar to previous reports documenting homopolymeric and deletion error rates with the Roche 454 GS Titanium technology. In no case, however, did variability associated with sequencing methods or sample preparations create inconsistencies with our current phylogenetic results or the subsequent molecular epidemiological evidence gleaned from these data.</p> <p>Conclusions</p> <p>Implementation of a validated pipeline for NGS data acquisition and analysis provides highly reproducible results that are stable and predictable for molecular epidemiological applications. When draft genomes are collected at 15×-20× coverage and passed through a quality filter as part of a data analysis pipeline, including sub-passaged replicates defined by a few SNPs, they can be accurately placed in a phylogenetic context. This reproducibility applies to all levels within and between serovars of <it>Salmonella </it>suggesting that investigators using these methods can have confidence in their conclusions.</p

Enhanced biofilm and extracellular matrix production by chronic carriage versus acute isolates of Salmonella Typhi.

Salmonella Typhi is the primary causative agent of typhoid fever; an acute systemic infection that leads to chronic carriage in 3-5% of individuals. Chronic carriers are asymptomatic, difficult to treat and serve as reservoirs for typhoid outbreaks. Understanding the factors that contribute to chronic carriage is key to development of novel therapies to effectively resolve typhoid fever. Herein, although we observed no distinct clustering of chronic carriage isolates via phylogenetic analysis, we demonstrated that chronic isolates were phenotypically distinct from acute infection isolates. Chronic carriage isolates formed significantly thicker biofilms with greater biomass that correlated with significantly higher relative levels of extracellular DNA (eDNA) and DNABII proteins than biofilms formed by acute infection isolates. Importantly, extracellular DNABII proteins include integration host factor (IHF) and histone-like protein (HU) that are critical to the structural integrity of bacterial biofilms. In this study, we demonstrated that the biofilm formed by a chronic carriage isolate in vitro, was susceptible to disruption by a specific antibody against DNABII proteins, a successful first step in the development of a therapeutic to resolve chronic carriage

Transport regimes of cold gases in a two-dimensional anisotropic disorder

We numerically study the dynamics of cold atoms in a two-dimensional disordered potential. We consider an anisotropic speckle potential and focus on the classical regime, which is relevant to some recent experiments. First, we study the behavior of particles with a fixed energy and identify different transport regimes. For low energy, the particles are classically localized due to the absence of a percolating cluster. For high energy, the particles undergo normal diffusion and we show that the diffusion constants scale algebraically with the particle energy, with an anisotropy factor which significantly differs from that of the disordered potential. For intermediate energy, we find a transient sub-diffusive regime, which is relevant to the time scale of typical experiments. Second, we study the behavior of a cold-atomic gas with an arbitrary energy distribution, using the above results as a groundwork. We show that the density profile of the atomic cloud in the diffusion regime is strongly peaked and, in particular, that it is not Gaussian. Its behavior at large distances allows us to extract the energy-dependent diffusion constants from experimental density distributions. For a thermal cloud released into the disordered potential, we show that our numerical predictions are in agreement with experimental findings. Not only does this work give insights to recent experimental results, but it may also serve interpretation of future experiments searching for deviation from classical diffusion and traces of Anderson localization.Comment: 19 pages, 16 figure

The evolution of ultraviolet emission lines from the circumstellar material surrounding SN 1987A

The presence of narrow high-temperature emission lines from nitrogen-rich gas close to SN 1987A has been the principal observational constraint on the evolu- tionary status of the supernova's progenitor. A new analysis of the complete five-year set of low and high resolution IUE ultraviolet spectra of SN 1987A (1987.2--1992.3) provide fluxes for the N V 1240, N IV] 1486, He II 1640, OIII] 1665, NIII] 1751, and CIII] 1908 lines with significantly reduced random and systematic errors and reveals significant short-term fluctuations in the light curves. The N V, N IV] and N III] lines turn on sequentially over 15 to 20 days and show a progression from high to low ionization potential, implying an ioni- zation gradient in the emitting region. The line emission turns on suddenly at 83+/-4 days after the explosion, as defined by N IV]. The N III] line reaches peak luminosity at 399+/-15 days. A ring radius of (6.24+/-0.20)E{17} cm and inclination of 41.0+/-3.9 is derived from these times, assuming a circular ring. The probable role of resonant scattering in the N V light curve introduces systematic errors that leads us to exclude this line from the timing analysis. A new nebular analysis yields improved CNO abundance ratios N/C=6.1+/-1.1 and N/O=1.7+/-0.5, confirming the nitrogen enrichment found in our previous paper. From the late-time behavior of the light curves we find that the emission origi- nates from progressively lower density gas. We estimate the emitting mass near maximum (roughly 400 days) to be roughly 4.7E{-2} solar masses, assuming a filling factor of unity and an electron density of 2.6E4 cm^{-3}. These results are discussed in the context of current models for the emission and hydrodynamics of the ring.Comment: 38 pages, AASTeX v.4.0, 13 Postscript figures; ApJ, in pres

Morphological Variation Among Herring Gulls (Larus Argentatus) And Great Black-Backed Gulls (Larus Marinus) In Eastern North America

Herring Gull (Larus argentatus) and Great Black-backed Gull (L. marinus) morphometric data from various eastern North American locations was collected to examine the sources of variation in body size within and among geographic regions. For Herring Gulls, significant differences in all commonly taken measurements at local and regional scales were found. However, most of the variation in measurements was due to sex differences and the natural variance seen within local populations. Herring Gulls breeding in the Arctic did not show any evidence of being morphologically different from other groups. A discriminant function derived from a Newfoundland, Canada, breeding population of Herring Gulls successfully assigned the sex of birds in Atlantic Canada and Nunavut, Canada, further emphasizing that most of the variation seen is between sexes and not among local or even regional populations. It also indicates that the evitable variation introduced by inter-individual differences in measurements was insufficient to compromise the utility of the discriminant function. The correct classification rate was lower for Great Lakes breeding Herring Gulls, indicating that these birds have different morphologies than those of populations in easterly regions. In contrast, few differences and no clear geographic patterns were found in measurements for Great Black-backed Gulls. These results were consistent with recent genetic information, suggesting an older west to east radiation of Herring Gulls across North America and a lack of isolation among Great Black-Backed Gull populations

Blood and Imaging Biomarkers in the Long-term Follow-up of Bicuspid Aortic Valve Patients

Background: Bicuspid aortic valve (BAV) is a common congenital heart defect. Patients with BAV are at risk for long-term complications such as valve stenosis and regurgitation. This study aimed to investigate sex differences in blood and imaging biomarkers and to describe the long-term prognostic value of blood and echocardiographic biomarkers. Methods:Patients were included from 2 prospective observational cohort studies; they underwent venous blood sampling and transthoracic echocardiography including speckle tracking. Analyzed blood biomarkers were red-cell distribution width (RDW), creatinine, C-reactive protein (CRP), troponin T, N-terminal pro B-type natriuretic peptide (NT-proBNP), and transforming growth factor-beta (TGF-β). Sex differences were analyzed at baseline. Associations between biomarkers and arrhythmia-free and intervention-free survival were determined by Cox regression, adjusted for age and sex. Results:A total of 182 patients with BAV were included: median age 34; interquartile range [IQR]: 23-46 years; 55.5% male. CRP, NT-proBNP, and RDW were higher in women, whereas creatinine, troponin T and TGF-β were higher among men. After a median follow-up time of 6.9 (IQR: 6.5-9.9) years, arrhythmia-free and intervention-free survival was, 81.0% and 73.1%, respectively. NT-proBNP was associated with both arrhythmia-free and intervention-free survival (hazard ratio [HR], 1.94, P = 0.005 and HR, 2.06, P = 0.002, respectively). On echocardiography higher left atrial (LA) size, left ventricular end-diastolic diameter (LVEDD), left ventricular (LV) mass index and E/e’ ratio were associated with lower arrhythmia-free survival, whereas higher LA size, LV mass index, aortic valve peak velocity, and aortic regurgitation were associated with lower intervention-free survival. Conclusions: Differences were observed in blood biomarkers between men and women with BAV. Besides LV systolic parameters, diastolic LV function and NT-proBNP should have a more prominent role as prognostic markers in clinical care.</p

CXC chemokines exhibit bactericidal activity against multidrug-resistant gram-negative pathogens

The continued rise and spread of antimicrobial resistance among bacterial pathogens pose a serious challenge to global health. Countering antimicrobial-resistant pathogens requires a multifaceted effort that includes the discovery of novel therapeutic approaches. Here, we establish the capacity of the human CXC chemokines CXCL9 and CXCL10 to kill multidrug-resistant Gram-negative bacteria, including New Delhi metallo-beta-lactamase-1-producing Klebsiella pneumoniae and colistin-resistant members of the family Enterobacteriaceae that harbor the mobile colistin resistance protein MCR-1 and thus possess phosphoethanolamine-modified lipid A. Colistin-resistant K. pneumoniae isolates affected by genetic mutation of the PmrA/PmrB two-component system, a chromosomally encoded regulator of lipopolysaccharide modification, and containing 4-amino-4-deoxy-l-arabinose-modified lipid A were also found to be susceptible to chemokine-mediated antimicrobial activity. However, loss of PhoP/PhoQ autoregulatory control, caused by disruption of the gene encoding the negative regulator MgrB, limited the bactericidal effects of CXCL9 and CXCL10 in a variable, strain-specific manner. Cumulatively, these findings provide mechanistic insight into chemokine-mediated antimicrobial activity, highlight disparities amongst determinants of colistin resistance, and suggest that chemokine-mediated bactericidal effects merit additional investigation as a therapeutic avenue for treating infections caused by multidrug-resistant pathogens

Detection of brown dwarf-like objects in the core of NGC3603

We use near-infrared data obtained with the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope to identify objects having the colors of brown dwarfs (BDs) in the field of the massive galactic cluster NGC 3603. These are identified through use of a combination of narrow and medium band filters spanning the J and H bands, and which are particularly sensitive to the presence of the 1.3-1.5{\mu}m H2O molecular band - unique to BDs. We provide a calibration of the relationship between effective temperature and color for both field stars and for BDs. This photometric method provides effective temperatures for BDs to an accuracy of {\pm}350K relative to spectroscopic techniques. This accuracy is shown to be not significantly affected by either stellar surface gravity or uncertainties in the interstellar extinction. We identify nine objects having effective temperature between 1700 and 2200 K, typical of BDs, observed J-band magnitudes in the range 19.5-21.5, and that are strongly clustered towards the luminous core of NGC 3603. However, if these are located at the distance of the cluster, they are far too luminous to be normal BDs. We argue that it is unlikely that these objects are either artifacts of our dataset, normal field BDs/M-type giants or extra-galactic contaminants and, therefore, might represent a new class of stars having the effective temperatures of BDs but with luminosities of more massive stars. We explore the interesting scenario in which these objects would be normal stars that have recently tidally ingested a Hot Jupiter, the remnants of which are providing a short-lived extended photosphere to the central star. In this case, we would expect them to show the signature of fast rotation.Comment: 26 Pages, 8 Figures, Accepted for publication on Ap