Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

Complete circularized genome data of two Spanish strains of xylella fastidiosa (IVIA5235 and IVIA5901) using hybrid assembly approaches

Xylella fastidiosa is an economically important plant pathogenic bacterium of global importance associated, since 2013, with a devastating epidemic in olive trees in Italy. Since then, several outbreaks of this pathogen have been reported in other European member countries including Spain, France, and Portugal. In Spain, the three major subspecies (subsp. fastidiosa, multiplex, and pauca) of the bacterium have been detected in the Balearic Islands, but only subspecies multiplex in the mainland (Alicante). We present the first complete genome sequences of two Spanish strains: X. fastidiosa subsp. fastidiosa IVIA5235 from Mallorca and X. fastidiosa subsp. multiplex IVIA5901 from Alicante, using Oxford Nanopore and Illumina sequence reads, and two hybrid approaches for genome assembly. These completed genomes will provide a resource to better understand the biology of these X. fastidiosa strains

Complete Genome Resources for Xylella fastidiosa Strains AlmaEM3 and BB08-1 Reveal Prophage-Associated Structural Variation Among Blueberry-Infecting Strains

This work was funded by the United States Department of Agriculture–Agricultural Research Service appropriated project 2034-22000-012-00D and the Xylella fastidiosa Active Containment Through a Multidisciplinary-Oriented Research Strategy (XF-ACTORS) project. Illumina sequencing for BB08-1 was carried out at the University of California, Davis, Genome Center DNA Technologies and Expression Analysis Cores, supported by National Institute of Health Shared Instrumentation Grant 1S10OD010786-01.Peer reviewe

Genome comparison of two Spanish strains of Xylella fastidiosa subsp. multiplex ST6 and their potential relationship with phenotypic traits associated to pathogenicity

Study supported by Projects XF-ACTORS 727987 (EU-H2020), AGL2016-75606-R (MICINN Spain and FEDER-EU) and COST Action CA16107 EuroXanth.The ability of Xylella fastidiosa (Xf) to acquire new genetic information, via horizontal gene transfer and homologous recombination, has been related with its capacity to colonize new hosts and environments. In this study we have performed a comparative genome analysis of the complete circularized sequences of two Xf subsp. multiplex ST6 strains (ESVL and IVIA5901) isolated from almond trees showing almond leaf scorch (ALS) symptoms, located at the Guadalest Valley in Alicante province, in mainland Spain. Genome differences detected between both strains and with the reference strain Temecula1 of Xf subsp. fastidiosa ST1 were then related with phenotypic traits differences associated to infection and disease development observed among those strains. Genome analysis of both strains indicated an average nucleotide identity at the chromosomal level of 99.99%, but main differences were due to the presence of plasmids pXF64-Hb_ESVL and pUCLA-ESVL only present in the ESVL strain. Our results showed that the ESVL strain had a higher cell motility and a greater surface attachment capability being able to form larger aggregates, while IVIA5901 strain showed a higher planktonic growth. Despite the high genetic similarity between the two strains, we have found important differences in their genomes. The presence of the two plasmids in the ESVL strain provided 48 unique genes to ESVL strain. Also, when comparing the two chromosomes, some unique genes and SNPs differences were found associated to genes potentially related with adhesion, motility, cell wall degradation, toxin-antitoxin system and the development of outer membrane protein, which might have an influence on some of the studied traits associated to pathogenicity

Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids

Xylella fastidiosa (Xf) is a vascular plant pathogenic bacterium native to the Americas that is causing significant epidemics and economic losses in olive and almonds in Europe, where it is a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys across Europe revealed the presence of the bacterium also in France, Spain, and Portugal. Combining ONT and Illumina sequencing data, we assembled high-quality complete genomes of seven Xf subsp. fastidiosa strains isolated from different plants in Spain, the USA, and Mexico. Comparative genomic analyses discovered differences in plasmid content among strains, including plasmids that had been overlooked previously when using Illumina sequencing platform alone. Interestingly, in strain CFBP8073, intercepted in France from plants imported from Mexico, three plasmids were identified, including two (plasmid pXF-P1.CFBP8073 and pXF-P2.CFBP8073) not previously described in X. fastidiosa, and one (pXF5823.CFBP8073) almost identical to a plasmid described in a Xf strain from citrus. Plasmids found in the Spanish strains here were similar to those described previously in other strains from the same subspecies and ST1 isolated in the Balearic Islands and the USA. The genome resources from this work will assist in further studies on the role of plasmids in the epidemiology, ecology, and evolution of this plant pathogen.This research was funded by Project BeXyl (Beyond Xylella, Integrated Management Strategies for Mitigating Xylella fastidiosa impact in Europe; Grant ID No 101060593) from European Union’s Horizon Action ‘Food, Bioeconomy Natural Resources, Agriculture and Environment’ Programme; Project E-RTA2017-00004-C06-02 (Desarrollo de estrategias de erradicación, contención y control de X. fastidiosa enEspaña) from ‘Programa Estatal de I+D+I Orientada a los Retos de la Sociedad of the Spanish Government AEI-INIA Spain’ and The Spanish Olive Oil Interprofesional; and the Thematic Interdisciplinary Platform on X. fastidiosa from CSIC (PTI Sol-Xyl). Financial support from the Spanish Ministry of Agriculture and Fisheries to the Institute for Sustainable Agriculture is also acknowledged. L.D.F. was a recipient of a research fellowship awarded by the Organization for Economic Co-operation and Development (OECD), Co-operative Research Programme (CRP), during the writing of this manuscript. M. P. Velasco Amo is recipient of a contract financed by the Intramural Project 178 201840E111 from CSIC.Peer reviewe

Detection of recombination events in Xylella fastidiosa genomes of different Spanish strains

Trabajo presentado en la 3rd European Conference on Xylella fastidiosa (Building knowledge, protecting plant health), celebrada online el 29 y 30 de abril de 2021.Xylella fastidiosa (Xf) has the capacity of uptaking extracellular DNA from the environment and incorporate it into its genome by homologous recombination, process known as Natural Competence. The process of genetic acquisition and recombination of extracellular DNA could be related to the acquisition of new traits such as antibiotic resistance and virulence factors, giving rise to the origin of new pathotypes. We took a step forward in comparative genomics analysis of Spanish populations of Xf by determining the complete genome of several isolates from Alicante, Mallorca and Ibiza and established potential recombination events that may have occurred with isolates from other places in the world. For this purpose, we used combined Illumina and Oxford Nanopore sequencing platforms and combined assembly approaches to obtain complete circularized genomes. Our results showed that olive and almond isolates belonging to subspecies pauca ST80 from Ibiza (Balearic Islands), the only place where this ST has been detected, showed an unusual level of recombination, being so far the isolates showing the highest number of recombination events among all the Xf isolates sequenced to date. On the order hand, we have confirmed the high degree of homology among genomes from Xf strains from Mallorca and California belonging to subspecies fastidiosa ST1 and subspecies multiplex ST81 isolated from almond and grapes, and we have also identified specific long-size genomic rearrangements in isolates of Xf subspecies multiplex ST6 from Alicante, compared to their homologous strains from the Americas. Research is now underway to determine the source and the functionality of these recombinant genes and their role in pathogenicity.Peer reviewe

Pacientes con sello de toráx hospitalizados en el área de quirúrgicas del HUSJ de Pereira en el año 2002

Para identificar las características de los pacientes con sello de tórax en el HUSJ de la ciudad de Pereira durante el año 2002, se diseñó un instrumento tomando como fuente la historia clínica de estos pacientes