Genomics of three new bacteriophages useful in the biocontrol of Salmonella

Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large terminase subunits confirms their packaging strategies and grouping to the different phage genus type. All these studies are necessary for the development and the use of an efficient cocktail with commercial applications in bacteriophage therapy against Salmonella

Analysis of the evolution of hake (Merluccius hubbsi and Merluccius australis) catch and effort by Spanish vessels operating in the Patagonian shelf area since the beginning of this industrial fishery

The hake fishery (Merluccius hubbsi and Merluccius australis) is one of the most important ones for Spanish vessels operating in the Southwest Atlantic. Both species are widely distributed along the Patagonian shelf, although M. australis occupies mainly more southern waters. This paper presents a historical review of fishery data on the Spanish fishing fleet operating in the SW Atlantic collected and collated during the EC Study Project 99/016 “Data collection for stock assessment of two hakes (Merluccius hubbsi and M. australis) in International and Falkland waters of the SW Atlantic”, in order to analyse the evolution of catch and effort in the hake fishery since 1983 to 2000. Data on landings and effort by Spanish vessels from 1983 onwards were utilised to study trends and shifts within the fishery. These data were provided by Asociación Nacional de Armadores de Buques Congeladores de Pesca de Merluza (ANAMER), the most important Spanish ship-owners fishing association operating in distant fishing grounds. Catch and effort data collected by observer’s programmes carried out by Instituto Español de Oceanografía (IEO) and the Falkland Islands Government Fisheries Department (FIGFD), as well as by observers provided by the project were used to estimate CPUE by area and season.The data included landings in kgs by commercial size category of hake (both species together) and effort made by vessels appertaining to ANAMER in number of fishing days and number of vessels by vessel size category. Conversion factors obtained by scientific observers onboard of these vessels were used to obtain the whole catch from landings. Total effort of the Spanish fleet was estimated from ANAMER logbooks, assuming a similar pattern for the whole fleet and taking into account the different ratio of ANAMER fleet compared to the total Spanish fleet. An increase of the catches and effort was observed from 1983 to a maximum in 1990 coinciding with the closure of Namibian fisheries. After that, catches and effort decreased corresponding to the development of the Greenland halibut fishery in the NW Atlantic, until its stabilisation from 1993. CPUE showed different patterns of fishing activity by area and season

Low-cost, easy-to-build noninvasive pressure support ventilator for under-resourced regions: open source hardware description, performance and feasibility testing

Aim: Current pricing of commercial mechanical ventilators in low-/middle-income countries (LMICs) markedly restricts their availability, and consequently a considerable number of patients with acute/chronic respiratory failure cannot be adequately treated. Our aim was to design and test an affordable and easy-to- build noninvasive bilevel pressure ventilator to allow a reduction in the serious shortage of ventilators in LMICs. Methods: The ventilator was built using off-the-shelf materials available via e-commerce and was based on a high-pressure blower, two pressure transducers and an Arduino Nano controller with a digital display (total retail cost <75 USD), with construction details provided open source for free replication. The ventilator was evaluated, and compared with a commercially available device (Lumis 150 ventilator; Resmed, San Diego, CA, USA): 1) in the bench setting using an actively breathing patient simulator mimicking a range of obstructive/restrictive diseases; and b) in 12 healthy volunteers wearing high airway resistance and thoracic/abdominal bands to mimic obstructive/restrictive patients. Results: The designed ventilator provided inspiratory/expiratory pressures up to 20/10cmH2O, respectively, with no faulty triggering or cycling; both in the bench test and in volunteers. The breathing difficulty score rated (1-10 scale) by the loaded breathing subjects was significantly (p<0.005) decreased from 5.45±1.68 without support to 2.83±1.66 when using the prototype ventilator, which showed no difference with the commercial device (2.80±1.48; p=1.000). Conclusion: The low-cost, easy-to-build noninvasive ventilator performs similarly to a high-quality commercial device, with its open-source hardware description, which will allow for free replication and use in LMICs, facilitating application of this life-saving therapy to patients who otherwise could not be treated

Preliminary study of the variations on the spatio-temporal distribution of a potentially exploitable species (Patagonotothen spp.) in the southwest Atlantic, using GIS techniques

The genus Patagonotothen is the most common Nototheniid on the Patagonian Shelf and slope and is part of the by-catch species in the bottom trawl fisheries. This paper presents preliminary results from the EC CRAFT project “Promoting higher added value to a finfish species rejected to sea”, aiming to develop the research and the technology necessary to promote higher added value to fishing activity by taking profit from a finfish species (Rockcod, Patagonotothen spp.) not known to consumers and currently discarded by the EU fishing fleet operating in the South West Atlantic in order to supply the EU seafood industry with a good quality raw material for human food manufacturing. Historical fishery data series (26 168 commercial hauls of which 12 745 were positive), including effort, catches and discards, as well as biological and environmental information, from 1988 onwards was used to describe and quantify patterns and spatio-temporal changes in the rockcod fishery. These data was collected by scientific observers on board commercial vessels.GIS analysis was carried out in order to study the seasonal geographical changes in the distribution of abundance, SST and densities calculated from CPUE. Fishery and environmental data as well as SST data derived from the NOAA Advanced Very High Resolution Radiometer (AVHRR), were analysed in order to find monthly variations in spatial and depth distribution of Patagonotothen spp. Preliminary results demonstrated that, within areas of occurrence, there are significant correlations between fish abundance (CPUE), the oceanographic conditions of the area (SST gradients) and depth in certain months

Data collection for stock assessment of two Hakes (Merluccius Hubbsi and M. Australis) in international and Falkland Waters of the SW Atlantic

Study Project 99/016 “Data collection for stock assessment of two hakes (Merluccius hubbsi and M. australis) in international and Falkland waters of the SW Atlantic” ran from January 2000 to December 2001. The main objective of the project was the collection and collation of already existing and newly acquired fishery and biological data needed for preliminary assessment of two hake species occurring in the study area. In addition to this basic remit, additional objectives included the creation of a common database, study of spawning seasons and areas, discard pattern and length-frequency composition of target and non-target species, estimation of annual by-catch rates, analysis of trophic relationships, marine mammals by-catch and sightings, morphometric analysis for stock differentiation, and developing GIS applications for analysis of the data collected. Historical fishery and biological data series available from IEO and FIGFD (since 1988 and 1987 respectively) were provided to the project. New fishery and biological data were collected by scientific observers provided by IEO, ANAMER and FIGFD, and placed on board Spanish fishing vessels operating in the study area during the project period. Data on fishing activity included effort, catches and discards of target and non-target species on a haul-by-haul basis. Biological information (size, sex, maturity stage, etc) of target and non-target species was recorded on a daily basis. Data on landings and effort were provided by ANAMER to its subcontractor (MG OTERO) for processing and estimation of total catch and effort of the whole Spanish fishing fleet in the area; MG OTERO was also responsible for organisation of observers in collaboration with ANAMER staff in Vigo and Port Stanley. Ancillary data on location, time of fishing, depth, SST, SBT, sea roughness, wind, etc, was recorded on a haul-by-haul basis. This type of information was essential for development of GIS at AU to relate the species distribution to physical and environmental factors. Other information collected was about by-catches and sightings of small cetaceans and seabirds, and biological samples such as otoliths, stomachs and whole specimens of hakes for subsequent studies on growth (IEO, FIGFD), diet and morphometrics (AU). All the historical and new data collected during the project were collated and integrated into a common database designed by all participants and built at IEO. The information was used for preliminary assessment of two hake populations co-ordinated by RRAG during a workshop held in London in July 2001. All these data will be analysed and written up for future publications. Discard rates of target species were generally low in all areas and seasons with the highest discard rate for Notothen sp. (around 100% of the catch). Illex squid was found to be the major by-catch for hake fishery in the 46 S area. IEO observers reported data on incidental catches of marine mammals and sea birds since 1993 and the analysis of this information was made by AU. The observed mortality in the fishing gears comprised small numbers of black-browed albatross, gentoo penguin and the hourglass dolphin. The species most frequently sighted was the Peale’s dolphin, although this species did not appear in by-catches, followed by the hourglass dolphin. The project provided an opportunity to collect and integrate for the first time at European level the necessary fishery and biological data for the development of partial stock assessment for the future rational management of the fisheries in the area. Such management is needed for the sustainability of the commercial fisheries, the conservation of the onshore and offshore jobs and the supply of fish to the most important markets worldwide.EUROPEAN COMMISSION DIRECTORATE GENERAL FISHERIES – DG XI

Biodistribution of liposome-encapsulated bacteriophages and their transcytosis during oral phage therapy

This study sheds light on the biodistribution of orally administered, liposome-encapsulated bacteriophages, and their transcytosis through intestinal cell layers. Fluorochrome-labeled bacteriophages were used together with a non-invasive imaging methodology in the in vivo visualization of bacteriophages in the stomach and intestinal tract of mice. In those studies, phage encapsulation resulted in a significant increase of the labeled phages in the mouse stomach, even 6 h after their oral administration, and without a decrease in their concentration. By contrast, the visualization of encapsulated and non-encapsulated phages in the intestine were similar. Our in vivo observations were corroborated by culture methods and ex vivo experiments, which also showed that the percentage of encapsulated phages in the stomach remained constant (50%) compared to the amount of initially administered product. However, the use of conventional microbiological methods, which employ bile salts to break down liposomes, prevented the detection of encapsulated phages in the intestine. The ex vivo data showed a higher concentration of non-encapsulated than encapsulated phages in liver, kidney, and even muscle up to 6 h post-administration. Encapsulated bacteriophages were able to reach the liver, spleen, and muscle, with values of 38% ± 6.3%, 68% ± 8.6%, and 47% ± 7.4%, respectively, which persisted over the course of the experiment. Confocal laser scanning microscopy of an in vitro co-culture of human Caco-2/HT29/Raji-B cells revealed that Vybrant-Dil-stained liposomes containing labeled bacteriophages were preferably embedded in cell membranes. No transcytosis of encapsulated phages was detected in this in vitro model, whereas SYBR-gold-labeled non-encapsulated bacteriophages were able to cross the membrane. Our work demonstrates the prolonged persistence of liposome-encapsulated phages in the stomach and their adherence to the intestinal membrane. These observations could explain the greater long-term efficacy of phage therapy using liposome-encapsulated phages

Molecular epidemiology of an enterovirus A71 outbreak associated with severe neurological disease, Spain, 2016

Altres ajuts: We wish to thank I Bustillo, H del Pozo and P Higueras for their technical assistance. We also sincerely wish to thank all technical staff from microbiology departments and medical staff from paediatrics departments from all participating hospitals. Some of the samples are included in an ongoing project (PI15CIII-00020) which was supported by a grant by the Health Research System (AES).Introduction: Enterovirus A71 (EV-A71) is an emerging pathogen that causes a wide range of disorders including severe neurological manifestations. In the past 20 years, this virus has been associated with large outbreaks of hand, foot and mouth disease with neurological complications in the Asia-Pacific region, while in Europe mainly sporadic cases have been reported. In spring 2016, however, an EV-A71 outbreak associated with severe neurological cases was reported in Catalonia and spread further to other Spanish regions. Aim: Our objective was to investigate the epidemiology and clinical characteristics of the outbreak. Methods: We carried out a retrospective study which included 233 EV-A71-positive samples collected during 2016 from hospitalised patients. We analysed the clinical manifestations associated with EV-A71 infections and performed phylogenetic analyses of the 3'-VP1 and 3Dpol regions from all Spanish strains and a set of EV-A71 from other countries. Results: Most EV-A71 infections were reported in children (mean age: 2.6 years) and the highest incidence was between May and July 2016 (83%). Most isolates (218/233) were classified as subgenogroup C1 and 217 of them were grouped in one cluster phylogenetically related to a new recombinant variant strain associated with severe neurological diseases in Germany and France in 2015 and 2016. Moreover, we found a clear association of EV-A71-C1 infection with severe neurological disorders, brainstem encephalitis being the most commonly reported. Conclusion: An emerging recombinant variant of EV-A71-C1 was responsible for the large outbreak in 2016 in Spain that was associated with many severe neurological cases

Molecular epidemiology of an enterovirus A71 outbreak associated with severe neurological disease, Spain, 2016

IntroductionEnterovirus A71 (EV-A71) is an emerging pathogen that causes a wide range of disorders including severe neurological manifestations. In the past 20 years, this virus has been associated with large outbreaks of hand, foot and mouth disease with neurological complications in the Asia-Pacific region, while in Europe mainly sporadic cases have been reported. In spring 2016, however, an EV-A71 outbreak associated with severe neurological cases was reported in Catalonia and spread further to other Spanish regions.AimOur objective was to investigate the epidemiology and clinical characteristics of the outbreak.MethodsWe carried out a retrospective study which included 233 EV-A71-positive samples collected during 2016 from hospitalised patients. We analysed the clinical manifestations associated with EV-A71 infections and performed phylogenetic analyses of the 3'-VP1 and 3Dpol regions from all Spanish strains and a set of EV-A71 from other countries.ResultsMost EV-A71 infections were reported in children (mean age: 2.6 years) and the highest incidence was between May and July 2016 (83%). Most isolates (218/233) were classified as subgenogroup C1 and 217 of them were grouped in one cluster phylogenetically related to a new recombinant variant strain associated with severe neurological diseases in Germany and France in 2015 and 2016. Moreover, we found a clear association of EV-A71-C1 infection with severe neurological disorders, brainstem encephalitis being the most commonly reported.ConclusionAn emerging recombinant variant of EV-A71-C1 was responsible for the large outbreak in 2016 in Spain that was associated with many severe neurological cases.S

Overview of the Spanish fisheries in the Patagonian Shelf

The fishing grounds of the Patagonian Shelf support some of the most important fisheries in the world. The great abundance of marine resources among parallels 35º and 54º South, is associated with the Subtropical Convergence formed by the Brazil and Falkland/Malvinas currents. The mixing of the flow of La Plata River and the western branch of the Falkland/Malvinas Current generates areas of high plankton production on the shelf. Hakes (Merluccius hubbsi and Merluccius australis) and cephalopods (Illex argentinus and Loligo gahi) have been found the main commercial species, with important amounts of accompanying species in the catches such as Patagonian toothfish (Dissostichus eleginoides), Kingclip (Genypterus blacodes), Hoki (Macruronus magellanicus), Red cod (Salilota australis), Southern blue whiting (Micromesistius australis), etc. These fisheries are currently among the most important to the Spanish bottom trawler freezing fleet that has around 40 vessels fishing in this area, besides another 20 that operate in joint ventures sailing Falkland flag. It is estimated that this fleet generates approximately 2,000 direct offshore jobs, and more than 10,000 indirect onshore jobs. This paper presents results from the EC Study Project 99/016 “Data collection for stock assessment of two hakes (Merluccius hubbsi and M. australis) in international and Falkland waters of the SW Atlantic”. Historical fishery and biological data series available from the Instituto Español de Oceanografía (IEO) and the Falkland Islands Fishery Department (FIFD) were used during the project to describe fishing patterns and spatio-temporal changes in the abundance and distribution of target and accompanying species, as well as to give an overview of these important fisheries

Bona fide atypical scrapie faithfully reproduced for the first time in a rodent model

Atypical Scrapie, which is not linked to epidemics, is assumed to be an idiopathic spontaneous prion disease in small ruminants. Therefore, its occurrence is unlikely to be controlled through selective breeding or other strategies as it is done for classical scrapie outbreaks. Its spontaneous nature and its sporadic incidence worldwide is reminiscent of the incidence of idiopathic spontaneous prion diseases in humans, which account for more than 85% of the cases in humans. Hence, developing animal models that consistently reproduce this phenomenon of spontaneous PrP misfolding, is of importance to study the pathobiology of idiopathic spontaneous prion disorders. Transgenic mice overexpressing sheep PrPC with I112 polymorphism (TgShI112, 1–2 × PrP levels compared to sheep brain) manifest clinical signs of a spongiform encephalopathy spontaneously as early as 380 days of age. The brains of these animals show the neuropathological hallmarks of prion disease and biochemical analyses of the misfolded prion protein show a ladder-like PrPres pattern with a predominant 7–10 kDa band. Brain homogenates from spontaneously diseased transgenic mice were inoculated in several models to assess their transmissibility and characterize the prion strain generated: TgShI112 (ovine I112 ARQ PrPC), Tg338 (ovine VRQ PrPC), Tg501 (ovine ARQ PrPC), Tg340 (human M129 PrPC), Tg361 (human V129 PrPC), TgVole (bank vole I109 PrPC), bank vole (I109I PrPC), and sheep (AHQ/ARR and AHQ/AHQ churra-tensina breeds). Our analysis of the results of these bioassays concludes that the strain generated in this model is indistinguishable to that causing atypical scrapie (Nor98). Thus, we present the first faithful model for a bona fide, transmissible, ovine, atypical scrapie prion disease.info:eu-repo/semantics/publishedVersio