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

Recent turbidite deposition in the eastern Atlantic: Early diagenesis and biotic recovery

An interface core taken in Capbreton canyon shows a succession of sedimentary facies interpreted as classical Bouma turbiditic sequences. Activities of 234Th and 210Pb suggest that the deposition of the most recent turbidite was triggered by the violent storm that affected the Atlantic coast of southern France on the 27th of December 1999, about four months before the sampling of the core. This turbidite allows us to study the ongoing diagenesis of the new sediment layer and of the previous sediment-water interface, which has been buried and only slightly eroded. A study of benthic foraminiferal populations informs us about the rate of benthic ecosystem recovery after such a major ecosystem disturbance event. The composition of the benthic foraminiferal fauna suggests that the benthic ecosystem in Capbreton canyon remains in an early stage of colonization. The rare agglutinant taxon Technitella melo appears to be the first colonizing species. It is suggested that Technitella melo is advantaged by the food-impoverished conditions in the days following turbidite deposition. Almost all of the turbidite layer and the previous oxic sediment-water interface contain reduced dissolved metal species and were anoxic. The buried interface contains Fe- and Mn-oxides inherited from its recent oxic past. The reduction of manganese oxides was in progress at the time of core collection. The reduced Mn remained trapped in the sediment as Mn-containing carbonates. Iron-oxides did not undergo significant reductive dissolution. The top of the newly deposited turbidite formed an oxic layer, which was rapidly enriched in metal-oxides. The enrichment of manganese oxides was mostly due to the oxidation of dissolved Mn2+, which diffused from below. The enrichment of iron oxides is explained both by the oxidation of the upward flux of dissolved Fe2+, and by the input of detrital iron oxide after, or as a result of the turbidite deposition

Degradation state of organic matter in surface sediments from the Southern Beaufort Sea: a lipid approach

For the next decades significant climatic changes should occur in the Arctic zone. The expected destabilisation of permafrost and its consequences for hydrology and plant cover should increase the input of terrigenous carbon to coastal seas. Consequently, the relative importance of the fluxes of terrestrial and marine organic carbon to the seafloor will likely change, strongly impacting the preservation of organic carbon in Arctic marine sediments. Here, we investigated the lipid content of surface sediments collected on the Mackenzie basin in the Beaufort Sea. Particular attention was given to biotic and abiotic degradation products of sterols and monounsaturated fatty acids. By using sitosterol and campesterol degradation products as tracers of the degradation of terrestrial higher plant inputs and brassicasterol degradation products as tracers of degradation of phytoplanktonic organisms, it could be observed that autoxidation, photooxidation and biodegradation processes act much more intensively on higher plant debris than on phytoplanktonic organisms. Examination of oxidation products of monounsaturated fatty acids showed that photo- and autoxidation processes act more intensively on bacteria than on phytodetritus. Enhanced damages induced by singlet oxygen (transferred from senescent phytoplanktonic cells) in bacteria were attributed to the lack of an adapted antioxidant system in these microorganisms. The strong oxidative stress observed in the sampled sediments resulted in the production of significant amounts of epoxy acids and unusually high proportions of monounsaturated fatty acids with a <i>trans</i> double bond. The formation of epoxy acids was attributed to peroxygenases (enzymes playing a protective role against the deleterious effects of fatty acid hydroperoxides in vivo), while <i>cis/trans</i> isomerisation was probably induced by thiyl radicals produced during the reaction of thiols with hydroperoxides. Our results confirm the important role played by abiotic oxidative processes in the degradation of marine bacteria and do not support the generally expected refractory character of terrigenous material deposited in deltaic systems

Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705

The nucleotide sequences of plasmids pRC12 (12,342 bp; GC 43.99%) and pRC18 (18,664 bp; GC 34.33%), harbored by the bacteriocin-producer Lactobacillus curvatus CRL 705, were determined and analyzed. Plasmids pRC12 and pRC18 share a region with high DNA identity (> 83% identity between RepA, a Type II toxin-antitoxin system and a tyrosine integrase genes) and are stably maintained in their natural host L. curvatus CRL 705. Both plasmids are low copy number and belong to the theta-type replicating group. While pRC12 is a pUCL287-like plasmid that possesses iterons and the repA and repB genes for replication, pRC18 harbors a 168 amino acid replication protein affiliated to RepB, which was named RepB’. Plasmid pRC18 also possesses a pUCL287-like repA gene but it was disrupted by an 11 kb insertion element that contains RepB’, several transposases/IS elements, and the lactocin Lac705 operon. An Escherichia coli / Lactobacillus shuttle vector, named plasmid p3B1, carrying the pRC18 replicon (i.e. repB’ and replication origin), a chloramphenicol resistance gene and a pBluescript backbone, was constructed and used to define the host range of RepB’. Chloramphenicol-resistant transformants were obtained after electroporation of Lactobacillus plantarum CRL 691, Lactobacillus sakei 23K and a plasmid-cured derivative of L. curvatus CRL 705, but not of L. curvatus DSM 20019 or Lactococcus lactis NZ9000. Depending on the host, transformation efficiency ranged from 102 to 107 per μg of DNA; in the new hosts, the plasmid was relatively stable as 29–53% of recombinants kept it after cell growth for 100 generations in the absence of selective pressure. Plasmid p3B1 could therefore be used for cloning and functional studies in several Lactobacillus species.Fil: Teran, Lucrecia Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Cuozzo, Sergio Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Aristimuño Ficoseco, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Fadda, Silvina G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Chaillou, Stéphane. Institut National de la Recherche Agronomique; FranciaFil: Champomier Vergès, Marie Christine. Institut National de la Recherche Agronomique; FranciaFil: Zagorec, Monique. Institut National de la Recherche Agronomique; FranciaFil: Hebert, Elvira Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentin

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

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

Nunataryuk field campaigns: understanding the origin and fate of terrestrial organic matter in the coastal waters of the Mackenzie Delta region

Climate warming and related drivers of soil thermal change in the Arctic are expected to modify the distribution and dynamics of carbon contained in perennially frozen grounds. Thawing of permafrost in the Mackenzie River watershed of northwestern Canada, coupled with increases in river discharge and coastal erosion, triggers the release of terrestrial organic matter (OMt) from the largest Arctic drainage basin in North America into the Arctic Ocean. While this process is ongoing and its rate is accelerating, the fate of the newly mobilized organic matter as it transits from the watershed through the delta and into the marine system remains poorly understood. In the framework of the European Horizon 2020 Nunataryuk programme, and as part of the Work Package 4 (WP4) Coastal Waters theme, four field expeditions were conducted in the Mackenzie Delta region and southern Beaufort Sea from April to September 2019. The temporal sampling design allowed the survey of ambient conditions in the coastal waters under full ice cover prior to the spring freshet, during ice breakup in summer, and anterior to the freeze-up period in fall. To capture the fluvial–marine transition zone, and with distinct challenges related to shallow waters and changing seasonal and meteorological conditions, the field sampling was conducted in close partnership with members of the communities of Aklavik, Inuvik and Tuktoyaktuk, using several platforms, namely helicopters, snowmobiles, and small boats. Water column profiles of physical and optical variables were measured in situ, while surface water, groundwater, and sediment samples were collected and preserved for the determination of the composition and sources of OMt, including particulate and dissolved organic carbon (POC and DOC), and colored dissolved organic matter (CDOM), as well as a suite of physical, chemical, and biological variables. Here we present an overview of the standardized datasets, including hydrographic profiles, remote sensing reflectance, temperature and salinity, particle absorption, nutrients, dissolved organic carbon, particulate organic carbon, particulate organic nitrogen, CDOM absorption, fluorescent dissolved organic matter intensity, suspended particulate matter, total particulate carbon, total particulate nitrogen, stable water isotopes, radon in water, bacterial abundance, and a string of phytoplankton pigments including total chlorophyll. Datasets and related metadata can be found in Juhls et al. (2021) (https://doi.org/10.1594/PANGAEA.937587).</p