Dual RNA-Seq Uncovers Metabolic Amino Acids Dependency of the Intracellular Bacterium Piscirickettsia salmonis Infecting Atlantic Salmon

High-throughput sequencing technologies have offered the possibility to understand the complexity of the transcriptomic responses of an organism during a wide variety of biological scenarios, such as the case of pathogenic infections. Recently, the simultaneous sequencing of both pathogen and host transcriptomes (dual RNA-seq) during the infection has become a promising approach to uncover the complexity of the host–pathogen interactions. In this study, through a double rRNA depletion and RNA sequencing protocols, we simultaneously analyzed the transcriptome of the intracellular bacterium Piscirickettsia salmonis and its host the Atlantic salmon (Salmo salar) during the course of the infection. Beyond canonical host immune-related response and pathogen virulent factors, both bacteria and host displayed a large number of genes associated with metabolism and particularly related with the amino acid metabolism. Notably, genome-wide comparison among P. salmonis genomes and different fish pathogens genomes revealed a lack of the biosynthetic pathway for several amino acids such as valine, leucine, and isoleucine. To support this finding, in vitro experiments evidenced that when these amino acids are restricted the bacterial growth dynamics is significantly affected. However, this condition is phenotypically reversed when the amino acids are supplemented in the bacterial growth medium. Based on our results, a metabolic dependency of P. salmonis on S. salar amino acids is suggested, which could imply novel mechanisms of pathogenesis based on the capacity to uptake nutrients from the host. Overall, dual transcriptome sequencing leads to the understanding of host–pathogen interactions from a different perspective, beyond biological processes related to immunity

Long noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-Infected Atlantic salmon (Salmo salar)

Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of theSalmo salarresponse to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection

Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi

The sea louse Caligus rogercresseyi has become one of the main constraints for the sustainable development of salmon aquaculture in Chile. Although this parasite's negative impacts are well recognized by the industry, some novel potential threats remain unnoticed. The recent sequencing of the C. rogercresseyi genome revealed a large bacterial community associated with the sea louse, however, it is unknown if these microorganisms should become a new focus of sanitary concern. Herein, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the C. rogercresseyi microbiota. Through deconvolution analysis, we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen Tenacibacullum ovolyticum (97.87% completeness), followed by Dokdonia sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the T. ovolyticum genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between C. rogercresseyi and its associated microbiota. Taken together, our data highlight the relevance of Hi-C techniques to discover pathogenic bacteria, VF, and ARGs and also suggest novel host-microbiota mutualism in sea lice biology.info:eu-repo/semantics/publishedVersio

Whole-genome resequencing in the sea louse Caligus rogercresseyi uncovers gene duplications and copy number variants associated with pesticide resistance

The sea louse Caligus rogercresseyi is a marine ectoparasite that constitutes one of the major threats to the salmon farming industry, where the primary control strategy is the use of delousing drugs through immersion treatments. The emergence of pharmacological resistance in this copepodid species has previously been described using transcriptome data. However, the molecular mechanisms underlying chromosome rearrangements have not yet been explored. This study aimed to identify structural genomic variations and gene expression in C. rogercresseyi associated with pesticide sensitivity. In this study, genome resequencing was conducted using Oxford Nanopore Technology on lice strains with contrasting sensitivity to azamethiphos to detect genome duplications. Transcriptome profiling of putative gene duplications was performed by Illumina sequencing. Copy Number Variants (CNVs) were identified through comparative coverage, and collinear/tandem gene duplications over all the chromosomal regions by sequence homology. Duplications or CNVs in functional genes were primarily identified in transposable elements and genes related to the drug response, with differential expression values calculated by RNA-seq analyses of the same strains. Notably, differentially duplicated genes were found in coding regions related to cuticle proteins, suggesting that a putative resistance mechanism may be associated with cuticular structure formation and the proteins involved. Collectively, the results revealed that the intensive use of pesticides on sea lice populations increases the frequency of gene duplication, expanding the molecular elements involved in drug response. This study is the first to report an association between genome rearrangements and pharmacological resistance in sea lice populations

Long noncoding RNAs: unexplored players in the drug response of the sea louse Caligus rogercresseyi

Long non-coding RNAs (lncRNAs), endogenous RNAs with restricted or null coding potential, are emerging as key regulators of multiple biological processes in several species. Despite the importance of these transcripts, few studies have characterized marine crustacean lncRNAs or the modulation of these in response to chemical exposure. Therefore, the present study mainly focused on identifying lncRNAs in the sea louse Caligus rogercresseyi, an ectoparasite of primary concern to the Chilean salmon industry. A bioinformatics pipeline for lncRNAs discovery was designed, revealing 1835 putative lncRNA sequences in the C. rogercresseyi transcriptome. Furthermore, C. rogercresseyi lncRNAs evidenced features classical of lncRNAs, such as lower values of GC content, length, transcription activity, and minimum free energy as compared with coding transcripts. Furthermore, since developed resistance against delousing drugs is a major threat to the management and control of sea lice, the transcriptional modulation of C. rogercresseyi lncRNAs during exposure to delousing drugs was also evaluated. Unlike coding transcripts, lncRNAs were mainly downregulated after exposure to either deltamethrin or azamethiphos, showing transcription patterns similar to other, better studied non-coding RNAs in arthropods. Finally, a subset of lncRNAs exhibited a strong transcriptional correlation to genes commonly associated with the drug response, such as ABC transporters, cytochrome p450, and glutathione S-transferase, among others. Our findings provide one of the first comprehensive lncRNA characterizations in a crustacean, contributing towards understandings on the regulatory role of lncRNAs during the drug response in Caligus rogercresseyi

Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment

The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical–chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex

Sistema de apoyo para la toma de decisiones en programación de oferta médica para listas de espera no GES y consultas médicas del hospital de Santa Cruz

195 p.En la actualidad el sistema hospitalario se ve enfrentado a un auge a nivel nacional, con ello la necesidad de poseer sistemas de información que tengan la capacidad de adaptarse a una demanda y entorno que evoluciona día a día y que busca facilitar las labores esenciales dentro del área de salud, sin embargo, la implementación real de Sistemas de información hospitalarios es muy baja, ello queda evidenciado en el Hospital de Santa Cruz, demostrado el uso de sistema basados en Excel, que, si bien aportan en la recolección de datos de forma efectiva, solo pueden ser incrementados hasta cierto punto, con registros estáticos y una interfaz poco amigable, además de contar con un uso activo en muchas áreas, tiende a generar errores en el ingreso de datos, los cuales pueden generar duplicidad e inconsistencia para calcular los rendimientos finales, provocando la perdida de eficiencia a la hora de generar cálculos estadísticos y medición de las distintas variables de consultas médicas y listas de espera, áreas que son las más afectadas y que poseen una mayor demanda por la población chilena provocando un bottleneck en el sistema que gestiona las horas de los pacientes, además es necesario agilizar sus registros y estadísticas. La eficiencia es necesaria para poder llevar a cabo tareas tales como la programación médica, la cual involucra la capacidad resolutiva de equipo médico especialista hacia las prestaciones de consulta y Lista de espera no ges, la toma de decisiones por el equipo de Control y Gestión del Hospital de Santa Cruz, deben ser bajo criterios de rendimientos e indicadores fáciles de interpretar y entender, no contar con dicha información en el momento oportuno genera pérdida de tiempo y confusión al crear dicha agenda. Como resultado de este trabajo implementar un HIS en el área de Control y Gestión del Hospital de Santa Cruz ayudara a la toma de decisiones sobre consultas médicas y listas de espera, reduciendo de manera enorme el tiempo que lleva analizar los datos y generar sus cálculos específicos, Con ello permitir a los profesionales del área de Control y Gestión tomar decisiones basados en proyecciones e indicadores de rendimiento críticos de ambas áreas. Además, con la implementación de este sistema se busca poder enfrentar de mejor manera la evolución tecnológica del sistema hospitalario. // ABSTRACT: The demand of the hospital system and the improvement in its technologies, have a high demand, however, even this implementation process has not been completely generated, this is evidenced in the Hospital of Santa Cruz, demonstrating the use of an Excel-based system , which, although they contribute to the data collection in an effective way, can only be increased to a certain point, the registry system and the unfriendly interface, in addition to having an active use in many areas, it tends to generate errors in the data entry, which can generate duplication and inconsistency to calculate the final returns. Efficiency is necessary to be able to carry out tasks such as medical programming and decision-making by the Control and Management team of the Hospital of Santa Cruz, it must be under performance criteria and indicators that are easy to interpret and understand, and not having A HIS also generates losses in the analysis time, creating the medical programming of each specialist, according to the current demand both in the area of medical consultations and surgery programs, which are of great importance for the local population. As a result of the implementation of a hospital information system to help decision-making in medical consultations and waiting lists, at the Hospital of Santa Cruz, there was a reduction in time in generating the medical agenda of specialists, focused on the capture of information of medical consultations and scheduled surgeries, showing the performance and the necessary goals for; be able to schedule quickly and be able to achieve decisionmaking based on quick and intuitive indicators, in this way professionals can speed up the analysis necessary to solve a growing demand that accumulates month by month, evidenced in the results obtained with the HIS implemented. In addition, they would modularize it, allowing the system to fully cover the REM data capture system and its performance and indicators in the future, providing greater capacity for details and traceability. The result of the implementation seeks to point towards the modernization of current hospital systems, generating a single system that can standardize the collection of medical records, results and projections, can help in part to solve bottleneck problems established in the hospital system

The wastewater microbiome: a novel insight for COVID-19 surveillance

Wastewater-Based Epidemiology is a tool to face and mitigate COVID-19 outbreaks by evaluating conditions in a specic community. This study aimed to analyze the microbiome proles using nanopore technology for full-length 16S rRNA sequencing in wastewater samples collected from a penitentiary (P), a residential care home (RCH), and a quarantine or health care facilities (HCF). The HCF microbiome was strongly associated with enteric bacteria previously reported in patients with chronic disease and psychological disorders. During the study, the wastewater samples from the RCH and the P were negative for SARS-CoV-2 based on qPCRs, except during the fourth week when was detected. Unexpectedly, the wastewater microbiome from RCH and P prior to week four was correlated with the samples collected from the HCF, suggesting a core bacterial community is expelled from the digest tract of individuals infected with SARS-CoV-2. We provide novel evidence that the wastewater microbiome associated with gastrointestinal manifestations appears to precede the SARS-CoV-2 detection in sewage. This nding suggests that the wastewaters microbiome can be applied as an indicator of community-wide SARS-CoV2 surveillance.This study was funded by “Fondo de Emergencia Sanitaria COVID-19, Intendencia Región de Ñuble, Chile” and FONDAP #15110027 granted by National Research and Development Agency (ANID), Chile. We also thank MINSAL and MinCiencia to support this research and provide the epidemiological data.N

Impact of Biological Agents on Postsurgical Complications in Inflammatory Bowel Disease : A Multicentre Study of Geteccu

Background: The impact of biologics on the risk of postoperative complications (PC) in inflammatory bowel disease (IBD) is still an ongoing debate. This lack of evidence is more relevant for ustekinumab and vedolizumab. Aims: To evaluate the impact of biologics on the risk of PC. Methods: A retrospective study was performed in 37 centres. Patients treated with biologics within 12 weeks before surgery were considered "exposed". The impact of the exposure on the risk of 30-day PC and the risk of infections was assessed by logistic regression and propensity score-matched analysis. Results: A total of 1535 surgeries were performed on 1370 patients. Of them, 711 surgeries were conducted in the exposed cohort (584 anti-TNF, 58 vedolizumab and 69 ustekinumab). In the multivariate analysis, male gender (OR: 1.5; 95% CI: 1.2-2.0), urgent surgery (OR: 1.6; 95% CI: 1.2-2.2), laparotomy approach (OR: 1.5; 95% CI: 1.1-1.9) and severe anaemia (OR: 1.8; 95% CI: 1.3-2.6) had higher risk of PC, while academic hospitals had significantly lower risk. Exposure to biologics (either anti-TNF, vedolizumab or ustekinumab) did not increase the risk of PC (OR: 1.2; 95% CI: 0.97-1.58), although it could be a risk factor for postoperative infections (OR 1.5; 95% CI: 1.03-2.27). Conclusions: Preoperative administration of biologics does not seem to be a risk factor for overall PC, although it may be so for postoperative infections

Enfermedades crónicas

Adherencia al tratamiento farmacológico y relación con el control metabólico en pacientes con DM2Aluminio en pacientes con terapia de reemplazo renal crónico con hemodiálisis en Bogotá, ColombiaAmputación de extremidades inferiores: ¿están aumentando las tasas?Consumo de edulcorantes artificiales en jóvenes universitariosCómo crecen niños normales de 2 años que son sobrepeso a los 7 añosDiagnóstico con enfoque territorial de salud cardiovascular en la Región MetropolitanaEfecto a corto plazo de una intervención con ejercicio físico, en niños con sobrepesoEfectos de la cirugía bariátrica en pacientes con síndrome metabólico e IMC < 35 KG/M2Encuesta mundial de tabaquismo en estudiantes de profesiones de saludEnfermedades crónicas no transmisibles: Consecuencias sociales-sanitarias de comunidades rurales en ChileEpidemiología de las muertes hospitalarias por patologías relacionadas a muerte encefálica, Chile 2003-2007Estado nutricional y conductas alimentarias en adolescentes de 4º medio de la Región de CoquimboEstudio de calidad de vida en una muestra del plan piloto para hepatitis CEvaluación del proceso asistencial y de resultados de salud del GES de diabetes mellitus 2Factores de riesgo cardiovascular en población universitaria de la Facsal, universidad de TarapacáImplicancias psicosociales en la génesis, evolución y tratamiento de pacientes con hipertensión arterial esencialInfarto agudo al miocardio (IAM): Realidad en el Hospital de Puerto Natales, 2009-2010Introducción de nuevas TIC y mejoría de la asistencia a un programa de saludNiños obesos atendidos en el Cesfam de Puerto Natales y su entorno familiarPerfil de la mortalidad por cáncer de cuello uterino en Río de JaneiroPerfil del paciente primo-consultante del Programa de Salud Cardiovascular, Consultorio Cordillera Andina, Los AndesPrevalencia de automedicación en mujeres beneficiarias del Hospital Comunitario de Til-TiPrevalencia de caries en población preescolar y su relación con malnutrición por excesoPrevalencia de retinopatía diabética en comunas dependientes del Servicio de Salud Metropolitano Occidente (SSMOC)Problemas de adherencia farmacológica antihipertensiva en población mapuche: Un estudio cualitativoRol biológico de los antioxidantes innatos en pacientes portadores de VIH/SidaSobrepeso en empleados de un restaurante de una universidad pública del estado de São Paul