A new serotype 14 variant of the pneumococcal Spain9V-3 international clone detected in the central region of Argentina

The penicillin-resistant Spain9V-3 clone of Streptococcus pneumoniae is widespread and presents different serotype variants originating from recombination of the capsular genes. In this work, the genetic relatedness of 29 invasive pneumococci isolated from the central region of Argentina (Cordoba, Buenos Aires, Santa Fe and La Pampa provinces) was assessed by multilocus sequence typing (MLST). All of the penicillin-non-susceptible isolates studied (21/29) belonged to a serotype 14 variant of the Spain 9V-3 clone. This clone was predominant, suggesting that it was responsible for the penicillin resistance spread in this region. Interestingly, this serotype 14 variant (named Cordoba S14V) could be differentiated from the European one by its pbp1a gene, suggesting a different recombinational replacement of the capsular genes. The putative recombination sites were analysed, resulting in the proximal crossover point being clearly localized in the spr0309 gene, with the distal site restricted to the recU gene, confirming a different recombination event. Analysis of the dexB, cpsB, aliA and pbp1a genes from these strains showed a high similarity with the corresponding genes of the Spain14-5 clone, suggesting that the capsular genes were provided by this international clone. Analysis of the genetic polymorphisms of the pbp1a (nt 1473-1922) and spr0309 (nt 1-790) genes is proposed as an epidemiological tool to help recognize the Cordoba S14V of the Spain9V-3 clone. On the other hand, BOX-repeat-based PCR and MLST analyses of serotype 14 strains revealed a divergent epidemiology of the Cordoba S14V, suggesting a non-recent dissemination in the paediatric population. It is suggested that this molecular epidemiology work will be a reference for monitoring the evolution of S14Vs of Spain9V-3, the emergence of new clones and the impact of pneumococcal vaccination programmes in Argentina.Fil: Albarracín Orio, Andrea Georgina. Universidad Católica de Córdoba. Instituto de Investigaciones en Recursos Naturales y Sustentabilidad José Sanchez Labrador S. J. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Recursos Naturales y Sustentabilidad José Sanchez Labrador S. J.; ArgentinaFil: Cortes, Paulo. Hospital Pediátrico del Niño Jesús; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Tregnaghi, Miguel. Centro de Desarrollo de Proyectos Avanzados en Pediatria; ArgentinaFil: Piñas, German Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Echenique, Jose Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Yudowski, Silvia. Centro de Desarrollo de Proyectos Avanzados en Pediatria; ArgentinaFil: Carvajal, Lydia. Centro de Desarrollo de Proyectos Avanzados en Pediatria; ArgentinaFil: Culasso, Catalina. Centro de Desarrollo de Proyectos Avanzados en Pediatria; ArgentinaFil: Nobile, Carmen Beatriz. Centro de Desarrollo de Proyectos Avanzados en Pediatria; ArgentinaFil: Figueroa, Myriam Haydee. Centro de Desarrollo de Proyectos Avanzados en Pediatria; ArgentinaFil: Lopardo, Horacio. Fundacion Hospital de Pediatria Professor Dr. Juan P. Garrahan; ArgentinaFil: Hernández, Claudia. Fundacion Hospital de Pediatria Professor Dr. Juan P. Garrahan; ArgentinaFil: Regueira, Mabel. Instituto Nacional de Enfermedades Infecciosas; Argentin

El cultivo de garbanzo (Cicer arietinum L.) en Argentina

El Programa Transferencia de Resultados de Investigación y Comunicación Pública de la Ciencia (PROTRI), de la Secretaría de Ciencia y Tecnología del Gobierno de la Provincia de Córdoba, financió la realización del libro El cultivo de garbanzo en Argentina con el objeto de promover la transferencia de resultados, experiencias o saberes entre las áreas del sector social y productivo para una mejor calidad de vida. Para la ejecución de esta obra han sido convocados técnicos e investigadores de las Ciencias Agropecuarias, Biológicas y Económicas, quienes en una forma clara y sencilla, aunque no menos consistente, ponen a disposición del lector sus experiencias adquiridas a lo largo de varios años de trabajo. El desarrollo de los diferentes temas se realiza a través de dieciséis Capítulos que abarcan desde la domesticación de Cicer y su llegada a la Argentina (Capítulo 1), pasando por el estudio morfológico de las diferentes partes de la planta en relación a los cultivares locales (Capítulo 2), además del manejo del suelo y sus nutrientes, en cuanto a requerimientos edáficos en los sistemas productivos (Capítulo 3). También se contempla el análisis de la influencia de los diversos factores ambientales para la determinación de zonas productivas (Capítulo 4). En el Capítulo 5 se hace referencia a la ecofisiología del cultivo, sus requerimientos en las diferentes etapas fenológicas, y cuándo y cómo se expresan en los cultivares. Un tema de indudable importancia para las leguminosas en general, y para el garbanzo en particular, es la simbiosis con las bacterias fijadoras de nitrógeno y su influencia en la productividad, el cual se desarrolla en el Capítulo 6. La mejora genética en el país es abordada en el Capítulo 7, donde se exponen sus inicios, desarrollo, disponibilidad de recursos, bondades y potencial del germoplasma disponible. A lo largo del ciclo biológico de la planta, el cultivo es visitado por insectos e infectado por hongos. Identificarlos y conocer sus ciclos biológicos y comportamientos es un aspecto importante para seleccionar las medidas de manejo y control más adecuadas (Capítulos 8 y 9). Quizás pocos sepan que el volumen de semilla genética de un cultivar, alcanza sólo unos pocos gramos (alrededor de 20). Para llevar este pequeño volumen a toneladas, se requiere del trabajo y tesón de investigadores, fitomejoradores y productores. Resultado de ese esfuerzo es la difusión de los seis cultivares obtenidos en el país, y se sigue trabajando para lograr nuevos materiales que se adapten a las diversas áreas y sistemas de producción (Capítulo 10). El desarrollo de los diferentes cultivares, que dan lugar a diversas arquitecturas de plantas, sumado a la adopción de diversos sistemas de producción, hace que el tema de la mecanización ocupe un lugar importante. Maquinas pequeñas y grandes intervienen en las etapas de siembra y de cosecha tratando de lograr la mayor eficiencia posible y un producto de calidad (Capítulo 11). Un cuello de botella para la expansión del cultivo es su comercialización, tanto para consumo interno como externo. En el Capítulo 12 se analizan los diferentes mercados y la necesidad de lograr un producto rentable de alta calidad, para mercados muy diversos. En el Capítulo 13 se hace un recorrido por las diferentes Provincias que actualmente producen garbanzo. Sus autores comentan como se incorporó el cultivo a los sistemas productivos de la región, sobre posibilidades y limitaciones, manejos y potencial de rendimiento, entre otros aportes. Los Capítulos 14 y 15 presentan dos temas de relevancia actual: la composición química del grano y las posibilidades de brindar valor agregado a éste, aspectos reforzados en la última década por el auge de las tendencias que promueven un nuevo estilo de vida y una alimentación sana, con alimentos naturales, bajos en grasa y con un buen balance nutricional. En el último Capítulo (16) se presentan experiencias de investigación en las que se utilizó al garbanzo como materia prima o como sustrato para diversas experimentaciones. La interacción docente-investigador-alumno permitió que vieran la luz diversos trabajos que, además de la formación de recursos humanos, brindan una información útil y novedosa al incursionar en temas tales como manejo de fechas de siembra, riego, alimento para pollos, cerdos y abejas. Estimado lector, tiene en sus manos un libro que es una invitación a un viaje con dieciséis estaciones. En cada una de ellas encontrará información sobre el cultivo del garbanzo en la Argentina. Estos datos fueron obtenidos por docentes, investigadores, productores, estudiantes que trabajaron y siguen trabajando para aportar al conocimiento del cultivo en nuestro país, bajo la realidad local y el contexto regional, ya que la mayoría de los trabajos y publicaciones son de origen extranjero y la aplicación de muchas de las tecnologías de manejo requieren una correcta adaptación y validación. Esperamos que este libro, además de serle útil, pueda ser disfrutado, sintiendo la pasión y el entusiasmo de cada uno de los autores por brindar y compartir sus conocimientos y logros

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

Background Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press