Whole-genome sequencing revealed independent emergence of vancomycin-resistant Enterococcus faecium causing sequential outbreaks over 3 years in a tertiary care hospital.

Vancomycin-resistant Enterococcus faecium (VREfm) emerged as an important cause of nosocomial infections worldwide. Previous studies based on molecular typing revealed that VREfm outbreaks are mainly associated with a particular genetic lineage, namely clonal complex 17 (CC17), which harbours either vanA or vanB gene cluster. The University Hospital of Lausanne faced several VREfm episodes of transmissions between 2014 and 2017. In this study, we used whole-genome sequencing (WGS) to investigate the relatedness of 183 VREfm isolates collected from 156 patients. Sequence types (ST) 17, ST80 and ST117 were the most predominant clones. Based on epidemiological data, 10 outbreaks were identified, which were caused by at least 13 distinct genotypes. The majority of isolates involved in outbreaks (91%) differed by only 0 to 3 SNPs. Four outbreaks involved more than one genotype and half of the cases considered as sporadic were possibly linked to an outbreak. By sequencing all isolates, we were able to better understand our local epidemiology of VREfm. The polyclonal structure observed between the different outbreaks strains, the high level of recombination detected in isolates, the time elapsed between admission and the first VREfm detection and the negative screening at admission support the hypothesis of the emergence of new VREfm clones within the hospitalised population

Directed evolution of colE1 plasmid replication compatibility: a fast tractable tunable model for investigating biological orthogonality

Plasmids of the ColE1 family are among the most frequently used in molecular biology. They were adopted early for many biotechnology applications, and as models to study plasmid biology. Their mechanism of replication is well understood, involving specific interactions between a plasmid encoded sense-antisense gene pair (RNAI and RNAII). Due to such mechanism, two plasmids with the same origin cannot be stably maintained in cells-a process known as incompatibility. While mutations in RNAI and RNAII can make colE1 more compatible, there has been no systematic effort to engineer new compatible colE1 origins, which could bypass technical design constraints for multi-plasmid applications. Here, we show that by diversifying loop regions in RNAI (and RNAII), it is possible to select new viable colE1 origins compatible with the wild-type one. We demonstrate that sequence divergence is not sufficient to enable compatibility and pairwise interactions are not an accurate guide for higher order interactions. We identify potential principles to engineer plasmid copy number independently from other regulatory strategies and we propose plasmid compatibility as a tractable model to study biological orthogonality

Coeficientes de difusión durante la deshidratación osmótica de anco (<i>Cucurbita moschata</i>) : Efecto del tamaño

La deshidratación osmótica del anco surge como un tratamiento mínimo que permite prolongar su vida útil. Esta hortaliza se consume en el Noroeste argentino por su sabor suave, bajo costo y disponibilidad; es rica en fibra, vitaminas y potasio. El objetivo del presente trabajo fue evaluar el ajuste al modelo de Azuara de la cinética de la deshidratación osmótica de cubos de anco de 0,5; 1 y 1,5 cm de espesor y analizar el efecto de la dimensión característica en las difusividades que determinan las transferencias de masa. Se determinaron gravimétricamente la pérdida de peso y la ganancia de sólidos; la pérdida de agua se obtuvo a partir de las variables anteriores. Las mayores pérdidas de agua y ganancias de sólidos se obtuvieron para cubos de menor espesor. Se calcularon los parámetros cinéticos mediante el modelo matemático, lográndose muy buenos ajustes y se determinaron las difusividades para la pérdida de agua y la ganancia de sólidos, obteniéndose coeficientes menores para la ganancia de sólidos. Los valores de difusividad másica calculados aumentaron linealmente con el cuadrado de la dimensión característica de los cubos.Centro de Investigación y Desarrollo en Criotecnología de Alimento

Ocean deoxygenation caused non-linear responses in the structure and functioning of benthic ecosystems

Les teneurs en O2 de l'océan mondial ont diminué progressivement au cours des dernières décennies, principalement en raison des activités humaines et du réchauffement climatique. Néanmoins, les effets à long terme de la désoxygénation sur les communautés macrobenthiques, la biogéochimie des sédiments et leurs interactions mutuelles demeurent mal compris. Dans cette étude, nous évaluons la réponse des assemblages de macrofaune benthiques et de la dynamique biogéochimique sédimentaire aux concentrations décroissantes d'O2 le long du gradient persistant d'O2 dissous dans l'eau de fond de l'estuaire et du golfe du Saint-Laurent (QC, Canada). Nous avons observé plusieurs réponses non linéaires de la biodiversité et de la dynamique biogéochimique sédimentaire face à la diminution de la concentration en O2 avec un seuil situé à environ 63 μM. En dessous de ce seuil, les assemblages de communautés macrobenthiques changent, et les taux de bioturbation diminuent drastiquement pour atteindre des niveaux presque nuls. En conséquence, la séquence des accepteurs d'électrons utilisés pour minéraliser la matière organique sédimentaire se contracte vers la surface du sédiment, tandis que les composés réduits s'accumulent plus près (jusqu'à 0.5 à 2.5 cm selon le composé) de l'interface sédiment-eau. Nos résultats illustrent la capacité des espèces bioturbatrices à compenser les conséquences biogéochimiques de la désoxygénation et peuvent contribuer à prédire les futurs changements dans les écosystèmes benthiques. The O2 content of the global ocean has been declining progressively over the past decades, mainly because of human activities and global warming. Nevertheless, how long-term deoxygenation affects macrobenthic communities, sediment biogeochemistry and their mutual feedback remains poorly understood. Here, we evaluate the response of the benthic assemblages and biogeochemical functioning to decreasing O2 concentrations along the persistent bottom-water dissolved O2 gradient of the Estuary and Gulf of St. Lawrence (QC, Canada). We report several of non-linear biodiversity and functional responses to decreasing O2 concentrations, and identify an O2 threshold that occurs at approximately at 63 μM. Below this threshold, macrobenthic community assemblages change, and bioturbation rates drastically decrease to near zero. Consequently, the sequence of electron acceptors used to metabolize the sedimentary organic matter is squeezed towards the sediment surface while reduced compounds accumulate closer (as much as 0.5–2.5 cm depending on the compound) to the sediment–water interface. Our results illustrate the capacity of bioturbating species to compensate for the biogeochemical consequences of hypoxia and can help to predict future changes in benthic ecosystems. -- Keywords : benthic biodiversity ; benthic fluxes ; biogeochemistry ; bioturbation ; hypoxia ; nutrients ; oxygen ; sediment

Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production

Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol. We determined the complete genome sequences of the reuterin-producing L. reuteri JCM 1112T and its closely related species Lactobacillus fermentum IFO 3956. Both are in the same phylogenetic group within the genus Lactobacillus. Comparative genome analysis revealed that L. reuteri JCM 1112T has a unique cluster of 58 genes for the biosynthesis of reuterin and cobalamin (vitamin B12). The 58-gene cluster has a lower GC content and is apparently inserted into the conserved region, suggesting that the cluster represents a genomic island acquired from an anomalous source. Two-dimensional nuclear magnetic resonance (2D-NMR) with 13C3-glycerol demonstrated that L. reuteri JCM 1112T could convert glycerol to reuterin in vivo, substantiating the potential of L. reuteri JCM 1112T to produce reuterin in the intestine. Given that glycerol is shown to be naturally present in feces, the acquired ability to produce reuterin and cobalamin is an adaptive evolutionary response that likely contributes to the probiotic properties of L. reuteri

Commentary on Viewpoint: Human skeletal muscle wasting in hypoxia: a matter of hypoxic dose?: Skeletal muscle wasting in hypoxia; a matter of altitude.

SKELETAL MUSCLE WASTING IN HYPOXIA; A MATTER OF ALTITUDE TO THE EDITOR: D’Hulst and Deldicque (1) argue that the severity of muscle atrophy incurred at high altitude is dependent on the combined effect of duration and degree of hypoxia exposure, or “hypoxic dose” (1). We do see a limitation of this concept, as it implies that someone residing in Leuven (altitude: 28 m) for 10 years would be subjected to a hypoxic dose of 2,454 km·h and incur 5% atrophy. Although the authors wrote that “it is unknown which parameter, altitude, or time spent at altitude is most decisive in the overall metric of hypoxic dose,” our illustration suggests that altitude is the prime determinant. This is further supported by the cut-off point at 4,000 m in a plot of the degree of atrophy vs. altitude (using the data in Table 1), whereas there was no clear relationship with duration of altitude residence. This cut-off point is likely related to the shape of the hemoglobin dissociation curve, where the oxygen tension at 4,000 m is such that physiologically significant arterial hemoglobin desaturation occurs (2). We acknowledge that one cannot entirely dismiss the importance of duration of hypoxic exposure, simply because skeletal muscle atrophy can only be noticed some time after net protein breakdown is initiated. However, muscle atrophy will not continue indefinitely, but will reach a new steady state (how otherwise can Tibetans still have muscle?). Finally, other adaptations than atrophy, such as an increase in hematocrit and capillarization, serve to attenuate muscle tissue hypoxia and atrophy (3) during residence at altitude. REFERENCES 1. D=Hulst G, Deldicque L. Viewpoint: Human skeletal muscle wasting in hypoxia: a matter of hypoxic dose? J Appl Physiol. doi:10.1152/ japplphysiol.00264.2016. 2. Wagner PD, Wagner HE, Groves BM, Cymerman A, Houston CS. Hemoglobin P(50) during a simulated ascent of Mt. Everest, Operation Everest II. High Alt Med Biol 8: 32–42, 2007. doi:10.1089/ham.2006. 1049. 3. Wüst RCI, Jaspers RT, van Heijst AF, Hopman MT, Hoofd LJ, van der Laarse WJ, Degens H. Region-specific adaptations in determinants of rat skeletal muscle oxygenation to chronic hypoxia. Am J Physiol Heart Circ Physiol 297: H364–H374, 2009. doi:10.1152/ajpheart.00272.2009

Conversion of rice straw to bio-based chemicals: an integrated process using Lactobacillus brevis

Commercialization of lignocellulosic biomass as a feedstock for bio-based chemical production is problematic due to the high processing costs of pretreatment and saccharifying enzymes combined with low product yields. Such low product yield can be attributed, in large part, to the incomplete utilization of the various carbohydrate sugars found in the lignocellulosic biomass. In this study, we demonstrate that Lactobacillus brevis is able to simultaneously metabolize all fermentable carbohydrates in acid pre-processed rice straw hydrolysate, thereby allowing complete utilization of all released sugars. Inhibitors present in rice straw hydrolysate did not affect lactic acid production. Moreover, the activity of exogenously added cellulases was not reduced in the presence of growing cultures of L. brevis. These factors enabled the use of L. brevis in a process termed simultaneous saccharification and mixed sugar fermentation (SSMSF). In SSMSF with L. brevis, sugars present in rice straw hydrolysate were completely utilized while the cellulase maintained its maximum activity due to the lack of feedback inhibition from glucose and/or cellobiose. By comparison to a sequential hydrolysis and fermentation process, SSMSF reduced operation time and the amount of cellulase enzyme necessary to produce the same amount of lactic acid

A model for uranium, rhenium, and molybdenum diagenesis in marine sediments based on results from coastal locations

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 73 (2009): 2938-2960, doi:10.1016/j.gca.2009.02.029.The purpose of this research is to characterize the mobilization and immobilization processes that control the authigenic accumulation of uranium (U), rhenium (Re) and molybdenum (Mo) in marine sediments. We analyzed these redox– sensitive metals (RSM) in benthic chamber, pore water and solid phase samples at a site in Buzzards Bay, Massachusetts, U.S.A., which has high bottom water oxygen concentrations (230–300 mol/L) and high organic matter oxidation rates (390 mol C/cm2/y). The oxygen penetration depth varies from 2–9 mm below the sediment–water interface, but pore water sulfide is below detection (< 2M). The RSM pore water profiles are modeled with a steady–state diagenetic model that includes irrigation, which extends 10–20 cm below the sediment–water interface. To present a consistent description of trace metal diagenesis in marine sediments, RSM results from sediments in Buzzards Bay are compared with previous research from sulfidic sediments (Morford et al., GCA 71). Release of RSM to pore waters during the remineralization of solid phases occurs near the sediment–water interface at depths above the zone of authigenic RSM formation. This release occurs consistently for Mo at both sites, but only in the winter for Re in Buzzards Bay and intermittently for U. At the Buzzards Bay site, Re removal to the solid phase extends to the bottom of the profile, while the zone of removal is restricted to ~2–9 cm for U and Mo. Authigenic Re formation is independent of the anoxic remineralization rate, which is consistent with an abiotic removal mechanism. The rate of authigenic U formation and its modeled removal rate constant increase with increasing anoxic remineralization rates, and is consistent with U reduction being microbially mediated. Authigenic Mo formation is related to the formation of sulfidic microenvironments. The depth and extent of Mo removal from pore water is closely associated with the balance between iron and sulfate reduction and the consumption of pore water sulfide via iron sulfide formation. Pore water RSM reach constant asymptotic concentrations in sulfidic sediments, but only pore water Re is constant at depth in Buzzards Bay. The increases in pore water U at the Buzzards Bay site are consistent with addition via irrigation and subsequent upward diffusion to the removal zone. Deep pore water Mo concentrations exceed its bottom water concentration due to irrigation–induced oxidation and remobilization from the solid phase. In sulfidic sediments, there is no evidence for higher pore water U or Mo concentrations at depth due to the absence of irrigation and/or the presence of more stable authigenic RSM phases. There are good correlations between benthic fluxes and authigenic accumulation rates for U and Mo in sulfidic sediments. However, results from Buzzards Bay suggest irrigation ultimately results in the partial loss of U and Mo from the solid phase, with accumulation rates that are 20–30% of the modeled flux. Irrigation can augment (Re, possibly U) or compromise (U, Mo) authigenic accumulation in sediments, and is important when determining burial rates in continental margin sediments.The authors also acknowledge financial support from the National Science Foundation (JLM, WRM: OCE–0220892), Research Corporation (JLM, CMC), Franklin & Marshall College, and the Hackman Summer Research Program at F&M