Salmonella enterica 4,5,12:b:- serotipo berriaren karakterizazioa eta etxeko dortokekin erlazionatutako arriskua

Salmonellosis, is one of the most common toxinfection caused by bacteria of the genus Salmonella in developed countries. In general, human salmonellosis is associated with contaminated food. However, contact with animals can be an important transmission route for Salmonella. Turtles have been shown to be reservoirs of different Salmonella serotypes. Considering that these reptiles are very common domestic pets, they can be a risk for public health, especially among children. In this work, a new monophasic serotype with the antigenic formula 4,5,12:b:- has been characterized. Most of the isolates analyzed have been isolated from children under 5 years of age in different regions of Spain. By means of different molecular techniques, it has been confirmed that 4,5,12:b:- isolates are genetically related to the biphasic isolates of Paratyphi B Java and that this serotype is their possible ancestor. The great homogeneity between the studied strains suggests that the origin of the turtles infected by these strains is closely related and that in Spain turtle shops have a common distribution point that contributes to the spread of this pathogen.; Salmonelosia, herrialde garatuetako toxiinfekzio ohikoenetariko bat da, Salmonella generoko bakterioek eragindakoa. Oro har, giza salmonelosia elikagai kutsatuekin lotzen da. Hala ere, animaliekin izandako kontaktua Salmonella generoaren transmisio bide garrantzitsua izan daiteke. Dortokak Salmonella serotipo desberdinen gordailuak direla frogatu da. Narrasti hauek etxeko maskota oso ohikoak direla kontuan izanda, osasun publikorako arriskutsuak izan daitezke, batez ere haurren artean. Horregatik, lan honetan 4,5,12:b:- formula antigenikoa duen serotipo monofasiko berri bat karakterizatu da. Aztertutako isolatu gehienak 5 urtetik beherako haurretan isolatu dira, Espainiako eskualde desberdinetan. Teknika molekular ezberdinen bidez, baieztatu da 4,5,12:b:- isolatuak Paratyphi B Javako iso- latu bifasikoekin genetikoki erlazionatuta daudela eta serotipo hori dela haren arbaso posiblea. Aztertutako anduien arteko homogeneotasun handiak iradokitzen du, andui horietaz infektatutako dortoken jatorria estuki lotuta dagoela, Espainian dortoken saltokiek banaketa-puntu komuna dutela, eta horrek patogeno honen sakabanaketan laguntzen duela

Anianabacter salinae gen. nov., sp. nov. ASV31T, a Facultative Alkaliphilic and Extremely Halotolerant Bacterium Isolated from Brine of a Millennial Continental Saltern

During a prokaryotic diversity study in Añana Salt Valley, a new Rhodobacteraceae member, designated ASV31T, was isolated from Santa Engracia spring water. It was extremely halotolerant, tolerating up to 23% NaCl, and facultatively alkaliphilic, growing at pH 6.5–9.5 (optimum at 7.0–9.5). The isolate was a Gram-negative, rod-shaped, aerobic and non-motile bacterium that formed beige-to-pink colonies on marine agar. According to a 16S rRNA gene-based phylogenetic analysis, strain ASV31T forms a distinct branch of the family Rhodobacteraceae, with Thioclava pacifica DSM 10166T being its closest type strain (95.3%). This was confirmed with a phylogenomic tree and the values of ANI (73.9%), dDDH (19.3%), AAI (63.5%) and POCP (56.0%), which were below the genus/species level boundary. Additionally, an ability to degrade aromatic compounds and biosynthesise secondary metabolites was suggested by the genome of strain ASV31T. Distinguishing fatty acid profiles and polar lipid content were also observed. The genome size was 3.6 Mbp, with a DNA G+C content of 65.7%. Based on the data obtained, it was considered that strain ASV31T (=CECT 30309T = LMG 32242T) represents a new species of a new genus in the family Rhodobacteraceae, for which the name Anianabacter salinae gen. nov., sp. nov. is proposed.This research was funded by the University of the Basque Country UPV/EHU (grant number US19/01) and the Añana Salt Valley Foundation (specific agreement between the Añana Salt Valley Foundation and the University of the Basque Country UPV/EHU)

Liquid-Core Microstructured Polymer Optical Fiber as Fiber-Enhanced Raman Spectroscopy Probe for Glucose Sensing

This work reports the development and application of two liquid-core microstructured polymer optical fibers (LC-mPOF) with different microstructure sizes. They are used in a fiber-enhanced Raman spectroscopy sensing platform, with the aim of detecting glucose in aqueous solutions in the clinically relevant range for sodium-glucose cotransporter 2 inhibitor therapy. The sensing platform is tested for low-concentration glucose solutions using each LC-mPOF. Results confirm that a significant enhancement of the Raman signal is achieved in comparison to conventional Raman spectroscopy. Additional measurements are carried out to obtain the valid measurement range, the resolution, and the limit of detection, showing that the LC-mPOF with 66-µm-diameter central hollow core has the highest potential for future clinical applications. Finally, preliminary tests successfully demonstrate glucose identification in urine. © 1983-2012 IEEE

Fungal Diversity and Composition of the Continental Solar Saltern in Añana Salt Valley (Spain)

The Añana Salt Valley in Spain is an active continental solar saltern formed 220 million years ago. To date, no fungal genomic studies of continental salterns have been published, although DNA metabarcoding has recently expanded researchers’ ability to study microbial community structures. Accordingly, the aim of this present study was to evaluate fungal diversity using the internal transcribed spacer (ITS) metabarcoding at different locations along the saltern (springs, ponds, and groundwater) to describe the fungal community of this saline environment. A total of 380 fungal genera were detected. The ubiquity of Saccharomyces was observed in the saltern, although other halotolerant and halophilic fungi like Wallemia, Cladosporium, and Trimmatostroma were also detected. Most of the fungi observed in the saltern were saprotrophs. The fungal distribution appeared to be influenced by surrounding conditions, such as the plant and soil contact, cereal fields, and vineyards of this agricultural region.This research was funded by the University of the Basque Country UPV/EHU grant number US19/01 and the Añana Salt Valley Foundation (Specific Agreement between the Añana Salt Valley Foundation and the University of the Basque Country UPV/EHU)

U-Shaped and Surface Functionalized Polymer Optical Fiber Probe for Glucose Detection

In this work we show an optical fiber evanescent wave absorption probe for glucose detection in different physiological media. High selectivity is achieved by functionalizing the surface of an only-core poly(methyl methacrylate) (PMMA) polymer optical fiber with phenilboronic groups, and enhanced sensitivity by using a U-shaped geometry. Employing a supercontinuum light source and a high-resolution spectrometer, absorption measurements are performed in the broadband visible light spectrum. Experimental results suggest the feasibility of such a fiber probe as a low-cost and selective glucose detector.This work has been funded in part by the European Regional Development Fund; in part by the Ministerio de Economia y Competitividad under project TEC2015-638263-C03-1-R; and in part by the Gobierno Vasco/Eusko Jaurlaritza under projects IT933-16, IT718-13, and ELKARTEK (KK-2016/0030, KK-2017/00033, KK-2017/00089, KK-2016/0059). Authors are also grateful to the technical and human support provided by SGIKER (UPV/EHU, MICINN, GV/EJ, ERDF, and ESF). The work of Mikel Azkune was supported in part by a research fellowship from the Universidad del Pais Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vicerrectorado de Euskera y Formacion Continua

INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens

Abstract In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole-genome sequencing in surveillance and outbreak investigation of food-borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross-sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user-centered design strategy involving the end-users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand-alone, portable, open-source, end-to-end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species-specific protocols that can be run using a user-friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species-specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene-by-gene methodology; quality control measures from raw reads to allele calling; reporting system; a built-in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof-of-concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web-sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open-source software in genomic epidemiology.Peer reviewe

Salmonella enterica espeziearen andui monofasikoen karakterizazio molekularra eta epidemiologikoa

Salmonellosis, is one of the most common food-poisoning disease caused by bacteria of the genus Salmonella in developed countries. More than 2,500 serotypes of Salmonella enterica species are described today, but a few serotypes have been re-ceived a harbor epidemiological monitoring. On the first decade of the 21th century, thanks to advances in molecular biology techniques, the Spanish National Center of Microbiology detected an emergence and increase of monophasic variants of Salmo-nella enterica. Typification methods allow us the analysis and characterization of 4 monophasic variants. As a result, it has been possible to determine their evolutionary origin and provide epidemiological markers designed for their detection, monitoring and control to facilitate the work in epidemiology of the health authorities.; Salmonelosia, herrialde garatuetako toxiinfekzio ohikoenetariko bat da, Salmonella generoko bakterioek eragindako elikagaien bidezkoa. Salmonella ente-ricaespeziearen barruan 2.500 serotipo baino gehiago deskribatuta daude gaur egun, baina serotipo gutxi batzuk izan dira jarraipen epidemiologiko sakonagoa jaso dutenak. XXI. mendearen lehenengo hamarkadan, biologia molekularreko tekniken aurrerakun-tzei esker, Salmonella enterica espeziearen aldaera monofasikoen gehikuntza detek-tatu zen Espainiako Mikrobiologiako Zentru Nazionalean. Lan honetan, aldaera mo-nofasiko horietako 4 aztertu eta karakterizatu dira tipikazio metodoen bidez. Ondorioz, posible izan da lau aldaeren eboluzio-jatorri zehaztea eta euren detekziorako, jarraipe-nerako eta kontrolerako diseinatu diren markatzaile epidemiologikoak eskaintzen dira, osasun agintariei epidemiologia esparruan lana erraztearren

Online exercise for the design and simulation of PCR and PCR-RFLP experiments

[EN] Background: Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings: An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes,compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions: The exercise is freely available at http://insilico.ehu.es/edu

Genotyping Study of Salmonella 4,[5],12:i:- Monophasic Variant of Serovar Typhimurium and Characterization of the Second-Phase Flagellar Deletion by Whole Genome Sequencing

After Salmonella Enteritidis and S. Typhimurium, S. 4,[5],12:i:- is the most reported serovar in human clinical cases. During the past 20 years, many tools have been used for its typing and second-phase flagellar deletion characterization. Currently, whole genome sequencing (WGS) and different bioinformatic programs have shown the potential to be more accurate than earlier tools. To assess this potential, we analyzed by WGS and in silico typing a selection of 42 isolates of S. 4,[5],12:i:- and S. Typhimurium with different in vitro characteristics. Comparative analysis showed that SeqSero2 does not differentiate fljB-positive S. 4,[5],12:i:- strains from those of serovar Typhimurium. Our results proved that the strains selected for this work were non-clonal S. 4,[5],12:i:- strains circulating in Spain. Using WGS data, we identified 13 different deletion types of the second-phase flagellar genomic region. Most of the deletions were generated by IS26 insertions, showing orientation-dependent conserved deletion ends. In addition, we detected S. 4,[5],12:i:- strains of the American clonal line that would give rise to the Southern European clone in Spain. Our results suggest that new S. 4,[5],12:i:- strains are continuously emerging from different S. Typhimurium strains via different genetic events, at least in swine products