A Whole-Genome sequencing-based study of the emergent multidrug-resistant Salmonella enterica subspecies enterica serovar Infantis clones in German broiler farms

Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) places the fourth position in the ranking of most reported Salmonella serovars in Europe. During the last decade, a multi-drug resistant (MDR) S. Infantis population has rapidly increased and widespread in European and non-European broiler production. The study proposed here aimed to i) implement and evaluate the performance of a bioinformatics pipeline named WGSBAC for Salmonella in silico serotyping, and ii) identify the genetic determinants for the increased emergence of broiler-derived S. Infantis observed in Germany. First, we conducted an evaluation of WGSBAC and three bioinformatic tools (SISTR, SeqSero, and SeqSero2) for the characterization and genoserotyping of 43 Salmonella strains of 26 different serovars. Second, we performed sequencing of 30 broiler-derived S. Infantis isolates collected from two distant decades (the 1990s and the 2010s). We applied the WGSBAC pipeline and external bioinformatics software to i) assess and control the quality of the sequenced reads ii) assembly and quality control of assemblies, and iii) annotation, typing by classical MLST, cgMLST, genoserotyping, SNPs-based phylogenetic reconstruction and in silico phenotype prediction including antimicrobial resistance genes (AMR), virulence genes and plasmid replicons detection. To detect possible clonal relatedness with other S. Infantis clones from Europe, we performed a further comparative genome analysis using 17 public genomes of other S. Infantis clones circulating in Europe. WGSBAC was feasible for the serovar prediction of most of the 43 Salmonella strains. The tool SISTR reported the highest correlation (79.1%) followed by SeqSero2 (72.1%) and SeqSero (60.5%). The study of the S. Infantis strains revealed that in contrast to the isolates from the 1990s, the majority of the strains from the 2010s revealed the presence of a megaplasmid that carried a multidrug-resistant genes (MDR) pattern, a virulence genes pattern, and several fitness-associated determinants. We termed the MDR gene pattern “ESIr” and it coded for at least three antimicrobial families: ant(3”)-Ia (aminoglycosides), sul1 (sulfonamides), and tet(A) (tetracyclines). Besides, we termed the virulence pattern as “ESIv” which includes genes for fimbriae cluster, yersiniabactin siderophore, mercury resistance, and antitoxin/antitoxin systems. Furthermore, the genotyping analysis revealed the presence of a novel sequence type (ST2283) among the majority of the strains from the 2010s and ST32 and ST1032 within the strains from the 1990s. This genetic traits may promote the rapid incidence and dissemination of a novel MDR S. Infantis population. Following a WGS-based approach, this study evidences that MDR S. Infantis ST2283 strains carrying a pESI-like plasmid have emerged during the last decade and are currently circulating in the German poultry production chain. This event results in an urgent public health hazard, thus, control measures and the support of epidemiological studies are needed to prevent the entrance, transmission, and further dissemination of this clonal population in the food chain.Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) nimmt die vierte Position in der Rangliste der am häufigsten gemeldeten Salmonella-Serovare in Europa ein. Während des letzten Jahrzehnts hat das Auftreten einer multiresistenten Salmonella enterica subspecies enterica serovar Infantis (S. Infantis)-Population rapide zugenommen und ist in der europäischen und außereuropäischen Broilerproduktion weit verbreitet. Die Studie zielte darauf ab, i) eine bioinformatische Pipeline für die in silico-Serotypisierung von Salmonellen zu implementieren und deren Leistungsfähigkeit zu bewerten, und ii) die genetischen Determinanten für das in der deutschen Broilerproduktion während des letzten Jahrzehnts beobachtete vermehrte Auftreten von S. Infantis zu identifizieren. Zunächst wurde eine Bioinformatik-Pipeline (WGSBAC) und drei bioinformatische Tools (SISTR, SeqSero und SeqSero2) zur Genoserotypisierung von 43 Salmonella spp.-Stämmen von 26 verschiedenen Serovaren durchgeführt. Zweitens führten wir die Genomsequenzierung von 30 S. Infantis Broiler-Isolaten durch, die in zwei unterschiedlichen Jahrzehnten (den 1990er und den 2010er Jahren) gesammelt wurden. Wir setzen die WGSBAC-Pipeline und externe Bioinformatik-Software ein, um i) die Qualität der sequenzierten Reads zu bewerten und zu kontrollieren, ii) Assemblierungen und Qualitätskontrollen von und iii) Annotation, Typisierung durch klassischen MLST, cgMLST, Genoserotypisierung, phylogenetische Rekonstruktion mittels Einzelnukleotidänderungen (SNPs) und in-silico-Phänotyp-Vorhersage, einschließlich antimikrobieller Resistenzgene (AMR), Virulenzgene und Plasmid-Replikons zu erkennen. Die Bioinformatik-Pipeline WGSBAC ist geeignet, das antigene Profil der meisten der in der Studie verwendeten Salmonella-Stämme zu bestimmen. Das Tool SISTR zeigte dabei die höchste Übereinstimmung (79,1 %), gefolgt von SeqSero2 (72,1 %) und SeqSero (60,5 %). Die Untersuchung der S. Infantis-Stämme ergab, dass im Gegensatz zu den Isolaten aus den 1990er Jahren, die Mehrheit der Stämme aus den 2010er Jahren das Vorhandensein eines Megaplasmids zeigte, das homolog zu dem pESI-Plasmid aus Israel und anderen pESIähnlichen Plasmiden aus europäischen Isolaten ist. Das deutsche pESI-ähnliche Plasmid kodierte für ein Muster von multiresistenten Genen (MDR), ein Muster von Virulenzgenen und mehrere Fitness-assoziierte Determinanten, welches wir 'ESIr' nannten. Dieses korrelierte mit mindestens drei antimikrobiellen Familien: ant(3')-Ia (Aminoglykoside), sul1 (Sulfonamide) und tet(A) (Tetracycline). Der Genotyp korreliert hier vollständig mit dem antimikrobiellen Phänotyp. Außerdem bezeichneten wir das Virulenzmuster als 'ESIv', welches Gene für Fimbrien-Cluster, Yersiniabactin-Siderophore, Quecksilberresistenz und Antitoxin/Antitoxin- Systeme mit einschließt. Die Genotypisierungsanalyse ergab das Vorhandensein eines neuen Sequenztyps (ST2283) bei der Mehrzahl der Stämme aus den 2010er Jahren und ST32 und ST1032 bei den Stämmen aus den 1990er Jahren. Anhand eines auf Gesamtgenomsequenzierung-basierten Ansatzes zeigte diese Studie, dass MDR S. Infantis ST2283 Stämme, die ein pESI-ähnliches Plasmid tragen, während des letzten Jahrzehnts entstanden sind und derzeit in der deutschen Geflügelproduktionskette zirkulieren. Der Erwerb eines Megaplasmids, das für Resistenzen, Virulenz-assoziierte Determinanten und Fitnessmechanismen kodiert, könnte dieses schnelle und besorgniserregende epidemiologische Ereignis erklären. Dieses Ereignis stellt eine Gefahr für die öffentliche Gesundheit dar. Daher sind Kontrollmaßnahmen und die Unterstützung epidemiologischer Studien erforderlich, um den Eintritt, die Übertragung und die weitere Verbreitung dieser klonalen Population in der Lebensmittelkette zu verhindern

Meta-DiSc 2.0:a web application for meta-analysis of diagnostic test accuracy data

BACKGROUND: Diagnostic evidence of the accuracy of a test for identifying a target condition of interest can be estimated using systematic approaches following standardized methodologies. Statistical methods for the meta-analysis of diagnostic test accuracy (DTA) studies are relatively complex, presenting a challenge for reviewers without extensive statistical expertise. In 2006, we developed Meta-DiSc, a free user-friendly software to perform test accuracy meta-analysis. This statistical program is now widely used for performing DTA meta-analyses. We aimed to build a new version of the Meta-DiSc software to include statistical methods based on hierarchical models and an enhanced web-based interface to improve user experience. RESULTS: In this article, we present the updated version, Meta-DiSc 2.0, a web-based application developed using the R Shiny package. This new version implements recommended state-of-the-art statistical models to overcome the limitations of the statistical approaches included in the previous version. Meta-DiSc 2.0 performs statistical analyses of DTA reviews using a bivariate random effects model. The application offers a thorough analysis of heterogeneity, calculating logit variance estimates of sensitivity and specificity, the bivariate I-squared, the area of the 95% prediction ellipse, and the median odds ratios for sensitivity and specificity, and facilitating subgroup and meta-regression analyses. Furthermore, univariate random effects models can be applied to meta-analyses with few studies or with non-convergent bivariate models. The application interface has an intuitive design set out in four main menus: file upload; graphical description (forest and ROC plane plots); meta-analysis (pooling of sensitivity and specificity, estimation of likelihood ratios and diagnostic odds ratio, sROC curve); and summary of findings (impact of test through downstream consequences in a hypothetical population with a given prevalence). All computational algorithms have been validated in several real datasets by comparing results obtained with STATA/SAS and MetaDTA packages. CONCLUSION: We have developed and validated an updated version of the Meta-DiSc software that is more accessible and statistically sound. The web application is freely available at www.metadisc.es

Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis

Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq® technology was used to sequence 66 C. jejuni isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0–26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in C. jejuni isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). The wlaN gene associated with the Guillain–Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin (blaOXA), tetracycline [tet(O)], neomycin [aph(3')-IIIa], streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. jejuni using WGS. A gene cluster comprising the genes sat4, aph(3′)-IIIa and aadE was present in six isolates. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes (blaOXA variants) was detected in 58 C. jejuni isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. jejuni. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection

Returning to work in cancer survivors: a multi-center cross-sectional study in Spain

Objetivo: Analizar la situación laboral, así como variables sociodemográficas (edad, sexo, estado civil y titulación) relacionadas con el cáncer (tipo de cáncer, estrategia de tratamiento primario y fase de supervivencia) en supervivientes españoles de cáncer. Método y procedimiento: Estudio transversal sobre una muestra heterogénea de 772 supervivientes de cáncer de inicio en la edad adulta en edad laboral. Se realizaron análisis correlacionales y de regresión logística para estudiar la capacidad predictiva de las variables sociodemográficas y relacionadas con el cáncer sobre la situación laboral y la posible modulación de los resultados por la CVRS evaluada mediante el QLACS. Resultados: Sólo el 55% de los supervivientes de cáncer estaban empleados. La edad, la cualificación y el tipo de cáncer fueron predictores independientes de la situación laboral, así como de la fase de supervivencia en los supervivientes con una CVRS baja. Conclusiones: Un alto porcentaje de supervivientes en edad laboral no vuelve a trabajar tras la experiencia oncológica. Algunas variables sociodemográficas y relacionadas con la enfermedad pueden ayudar a la identificación precoz de la población de riesgo en la que centrar la atención. Objective: To analyze the employment status as well as sociodemographic (age, gender, marital status, and qualification) and cancer-related variables (cancer type, primary treatment strategy, and survival phase) in Spanish cancer survivors. Method and procedure: Cross-sectional study on a heterogeneous sample of 772 working-age survivors of adult-onset cancer. Correlational and logistic regression analyses were performed to study the predictive ability of sociodemographic and cancer-related variables on employment status and the possible modulation of results by HRQOL assessed by the QLACS. Results: Only 55% of cancer survivors were employed. Age, qualification, and type of cancer were independent predictors of employment status as well as the survival phase in survivors with a low HRQOL. Conclusions: A high percentage of working-age survivors do not return to work after the cancer experience. Some sociodemographic and disease-related variables can help in the early identification of the risk population on which to focus attention

Redes de conocimiento en torno a la complejidad organizacional: aprendizaje de la autorregulación, disipación adaptabilidad y dinamismo ante los cambios

SE PRESENTA EL ARTÍCULO REDES DE CONOCIMIENTO ANTE EL DINAMISMO Y LOS CAMBIOSEN RELACIÓN CON LOS MARCOS TEÓRICOS Y CONCEPTUALES SE PROPONE EL ESTUDIO DE LA COMPLEJIDAD A PARTIR DE LAS DIFERENCIAS Y SIMILITUDES DE SUS PROCESOS IMPLICITOS EN LAS REDES DE CONOCIMIENTO.NINGUN

Fluctuación poblacional de Xyleborus volvulus (F.) (Coleoptera: Curculionidae), en localidades de Tabasco, México

The aim of this study is to show the population dynamics of Xyleborus volvulus in six localities of Tabasco, Mexico. The trapping methods used were alcohol traps, light traps and directly capture from their host plants. The total number of specimens collected was 4 600, using the three methods of collection. Most organisms were collected using alcohol traps 2 927, followed by light traps with 1 595 and finally from their host plants with 78. The fluctuation of X. volvulus showed two population peaks in all the localities studied, one at the beginning (January-April) and another one towards the end (September, November and December) of study period, which, in most cases, coincides with those periods of rain in the  area. Also, it was determined that this species is present throughout the year but with low populations.El objetivo de este estudio es dar a conocer la fluctuación poblacional de Xyleborus volvulus en seis localidades de Tabasco, México. Los métodos de captura utilizados fueron las trampas dealcohol, trampa de luz y captura directa sobre sus plantas huésped. Se obtuvo como resultado un total de 4 600 especímenes con los tres métodos de colecta, siendo las trampas de alcohol las que registraron el mayor número de organismos con 2 927, seguidos de las trampas de luz con 1 595 y por último sobre sus plantas huésped con 78. La fluctuación de X. volvulus presentó dos picos poblacionales en todas las localidades estudiadas, uno al inicio (enero-abril) y otro hacia el final (septiembre, noviembre y diciembre) del periodo de estudio, coincidiendo en la mayoría de los casos con el periodo de lluvia de la zona.Además se determinó que esta especie se encuentra presente todo el año pero con poblaciones bajas.

Cartilla 2.1: ¿Quién soy?

Con la lectura de esta cartilla encontrará temas que ayudarán al lector a comprender mejor y a conocerse a sí mismo, lo cual debe ser la base de todo conocimiento.With the reading of this booklet, you will find topics that will help the reader to better understand and know himself, which should be the basis of all knowledge.Quien soy -- Mi familia -- Nuestro ambiente social -- Que podemos hacer.naDirigido especialmente a alumnos SENA.Campaña de Instrucción Nacional (CAMINA)Documento sin fecha, se aproxima fecha a la década20 página

Grado de conocimiento sobre su enfermedad en pacientes diabéticos que se controlan en el servicio de Endocrinología del Hospital “José F. de San Martin”. Año 2016

LLa Diabetes Mellitus es una enfermedad crónica las complicaciones asociadas a la misma se vinculan con el grado de conocimiento que tenga elpaciente sobre su enfermedad. Se realizó un estudio cuantitativo, transversal y descriptivo con el objetivo de estimar el grado de conocimiento sobre Diabetes relacionándola con edad, sexo, nivel de instrucción, situación laboral, estado civil, situaciónde convivencia, presencia o no de antecedentes de Diabetes de tipo II en familiares directos y tipo de tratamiento que recibían. La población en estudio fue una muestra de 90 pacientes controlados en el servicio de Endocrinología del Hospital “José F. de San Martin”, durante el año 2016. Se analizó el grado de conocimiento mediante un instrumento basado en un cuestionario realizado por la Universidad de Michigan (EUA) y un cuestionario de Diabetes ECODI (Escala de conocimientos de Diabetes). Las operaciones estadísticas utilizadas fueron porcentajes y promedios en el programa “Excel”.RESULTADOSEl 69% de los pacientes encuestados obtuvo un grado de conocimiento aceptable; de estos la mayoría no tenían antecedentes de Diabetes, eran adultos maduros (36 a 59años de edad), pertenecían al sexo femenino, tenían riesgo educativo (personas con escolaridad básica incompleta), trabajaban de forma independiente, eran solteros, vivían solos y tenían la alimentación como principal tratamiento.DISCUSIÓNExisten estudios antecedentes que demuestran que el grado de conocimientos de pacientes diabéticos sobre su enfermedad influye directamente en el autocuidado de los mismos. Este estudio evidenció que el grado de conocimiento sobre su enfermedad es aceptable en los sujetos estudiados resultados similares a lo obtenido por Rodríguez en Buenos Aires Argentina 2015.CONCLUSIONESSe encontró un nivel de conocimientos aceptable, se sugiere implementar talleres supervisados para evaluar autocuidado, estrategias demostrativas sobre complicaciones para concientizar y lograr mantener un buen nivel de conocimientos o mejorarlo

Yield evaluation of rocoto pepper (Capsicum pubescens R and P) with application of calcium carbonate in greenhouses

The manzano chili is native to South America. It is characterized by having a fleshy pulp and is very popular in Latin American cuisine. In the state of Chihuahua, Mexico, Chili peppers of the jalapeño, serrano, chilaca and cayenne varieties are grown, while the manzano chili can be an option for greenhouse cultivation. The objective of the present work was to evaluate if the applications of calcium carbonate to the soil and to the plant (foliar route) influence the weight and number of fruits in manzano peppers under greenhouse conditions. The study was carried out in the greenhouse of the Faculty of Agrotechnological Sciences, of the Autonomous University of Chihuahua. For the generation of the treatments, the Taguchi method was used, creating 13 treatments, for 2 factors and 5 levels each factor, with 5 repetitions per treatment, using 65 plants in the study. Data analysis was performed using the quadratic response surface technique, adjusting the surface to determine the factor levels for optimal response. In order to obtain the highest weight in the three harvests 234.8 g, it is necessary to reduce the CaCO3 to the soil by 9%, while increasing the CaCO3 to the foliar by 100%. To increase the number of peppers from 59 to 70 in the three harvest periods, it is necessary to increase CaCO3 in the soil and foliar by 8.5% and 100%.Objective: To evaluate if the application of calcium carbonate on the soil and to the leaf influences the weight and number of fruits in rocoto pepper grown under greenhouse conditions. Design/Methodology/Approach: The study was carried out in the greenhouse of the Facultad de Ciencias Agrotecnológicas, of the Universidad Autónoma de Chihuahua. The Taguchi method was used to develop the 13 treatments, with two factors, five levels per factor, and five repetitions per treatment, using 65 plants under study. Data was analyzed using the quadratic response surface technique, fitting the surface to determine factor levels for optimal response. Results: Reducing soil CaCO3 by 9% and increasing leaf CaCO3 by 100% was necessary to obtain the highest weight in the three harvests (234.8 g). Findings/Conclusions: A rise in the number of rocoto peppers (from 59 to 70, in the three harvest periods) required an increase in the soil and foliar CaCO3 by 8.5% and 100%, respectively