Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.

Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.

We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US $5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial.

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes.

Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic 'signatures' that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen.

BACKGROUND: Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows. RESULTS: Here we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of >8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning. CONCLUSIONS: This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset can be explored to assess a wide range of ecological questions with regards to antimicrobial resistance, host-associated microbial and phage communities, and their dynamics during the aging of the host.

Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring.

Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.

Importância do cuidado domiciliar de enfermagem para o controle pressórico de pessoas com hipertensão arterial / Importancia del cuidado domiciliario de enfermería para el control de la presión arterial en personas con hipertensión / Importance of nursing home care for blood pressure control in people with hypertension

Objetivo: descrever o efeito do acompanhamento domiciliar de enfermagem no conhecimento, internação hospitalar e níveis pressóricos de pacientes portadores de hipertensão arterial com tratamento comprometido. Método: pesquisa quantitativa com delineamento retrospectivo, realizada a partir do banco de dados do projeto de extensão desenvolvido em uma Unidade Básica de Saúde de um município da região metropolitana de Curitiba-PR. As atividades desenvolvidas pelo projeto incluíram ações educativas em grupo e acompanhamentos no domicílio durante 12 meses. A amostra foi composta por 16 usuários com hipertensão arterial. Resultados: Houve maior frequência de mulheres, com média de idade de 63 anos. Observou-se melhora no conhecimento acerca da hipertensão arterial, redução na taxa de internação hospital decorrente de crise hipertensiva e aumento na proporção de indivíduos com pressão arterial controlada. Conclusão: O acompanhamento domiciliar mostrou-se eficaz no controle pressórico.

Objective: To describe the effect of home care nursing in knowledge, hospitalization and blood pressure levels in patients with hypertension treated impaired. Method: quantitative research with a retrospective design, made from the database extension project developed in a basic health unit of a municipality in the metropolitan region of Curitiba-PR. The activities included in the project were educational group and follow-up at home for 12 months. The sample consisted of 16 users with hypertension. Results: There was a higher frequency of women with a mean age of 63 year old. There was improvement in knowledge about hypertension, reduction in the rate of hospital admission due to hypertensive crisis and increase in the proportion of individuals with controlled blood pressure. Conclusion: The home care was effective in controlling blood pressure.

Objetivo: Describir el efecto de la atención domiciliaria de enfermería en lo conocimiento, hospitalización y niveles de presión arterial en pacientes con hipertensión tratada con discapacidad. Método: investigación cuantitativa con un diseño retrospectivo, a partir de una base de datos del proyecto de extensión desarrollado en una unidad básica de salud de un municipio en la región metropolitana de Curitiba-PR. Las actividades desarrolladas en el proyecto fueron las acciones educativas en grupo y el seguimiento en el hogar durante 12 meses. La muestra constó de 16 usuarios con hipertensión. Resultados: Hubo una mayor frecuencia de mujeres con una edad media de 63 años. Hubo una mejora en el conocimiento sobre la hipertensión, la reducción en la tasa de ingreso hospitalario por una crisis hipertensiva y el aumento de la proporción de individuos con presión arterial controlada. Conclusión: La atención en el hogar fue eficaz en el control de la presión arterial.

As representações dos usuários sobre a doença crônica e a prática educativa / User's representations of chronic diseases and educational practice / Necesidades de los ancianos en la enfermedad crónica

Trata-se de pesquisa qualitativa realizada no período de outubro de 2008 a março de 2009 com 45 usuários maiores de 60 anos de uma unidade de saúde, com o objetivo de identificar as representações dos usuários sobre a doença crônica. A obtenção das representações da doença foi feita por meio de entrevistas e, após foram realizadas três reuniões em grupo, com a média de oito usuários cada. Desta etapa participaram 24 usuários, e os temas oriundos dos discursos foram os seguintes: "A chegada da doença: fatores explicativos", "O mistério das transformações corporais: obrigatoriedade de mudar" e "A importância de aprender e partilhar experiências". Os participantes reconhecem os fatores ligados ao aparecimento da doença e de suas incumbências, as transformações necessárias para continuar vivendo e para postergar complicações valorizam a troca de experiências mediante o diálogo nas atividades educativas.

IThis is a qualitative research study held between October, 2008, and March, 2009, with 45 users over 60 years of age from a Health Unit, which aimed to identify their representations of chronic disease. Inerviews were carried out to collect chronic disease's representation. Three team meetings were also carried out, with an average of 8 users. Twenty-four (24) users participated in this step. The themes brought out of their discourses were: "The arrival of the disease: explanatory factors"; "The mystery of the bodyly changes: an obligation to change", and "The importance of learning and sharing the experience". Participants recognized the factors related to the disease onset and their commitments, the changes necessary to keep living and put off complications, and they also valued the exchange of experiences through dialogue in educational activities.

Se trata de una investigación cualitativa realizada durante el periodo de octubre de 2008 a marzo de 2009, con 45 usuarios mayores de 60 años de una unidad de salud, con el objetivo de comprender las necesidades educativas de las enfermedades crónicas y las percepciones de los usuarios en el mismo. El diagnóstico educativo fue obtenido por medio de entrevistas. Fueron realizadas tres reuniones en grupo, con un promedio de ocho usuarios cada. De esta etapa participaron 24 usuarios, y los temas oriundos de los discursos fueron los siguientes: "La llegada de la enfermedad: factores explicativos", "El misterio de las transformaciones corporales: obligatoriedad de mudar" y "La importancia de aprender y compartir experiencias". Los participantes reconocen los factores ligados al aparecimiento de la enfermedad y de sus incumbencias, las transformaciones necesarias para continuar viviendo y para postergar complicaciones valorizan el intercambio de experiencias mediante el diálogo en las actividades educativas.

Dificuldades no tratamento da doença crônica: relato de experiência de atividade de extensão / Difficulties in the treatment of a cronic disease: a case study of extension activity / Dificultades en el tratamiento de la enfermedad crónica: relato dela experiencia de actividad de extensión

Este trabalho tem como objetivo relatar os resultados de uma roda de conversa utilizada como estratégiaeducativa com portadores de hipertensão arterial e diabetes Mellitus, acerca das dificuldades na adesão aotratamento. Participaram desta atividade treze usuários acompanhados pelo programa de hipertensos ediabéticos de uma unidade básica de saúde de um município da região metropolitana de Curitiba – PR.Primeiramente, conduzimos uma entrevista para identificar as principais dificuldades em relação às enfermidadese ao tratamento. Dos resultados emergiram os temas abordados na roda de conversa, os quais foram divididosem três eixos: alimentação, exercício físico e tratamento farmacológico. Esta experiência nos permitiu umareflexão sobre as atividades desenvolvidas e a importância da participação ativa do portador de hipertensão ediabetes no seu tratamento. Acreditamos que essa iniciativa pode contribuir no desenvolvimento de estratégiasde educação em saúde para aumentar a adesão à terapêutica, evitar e/ou diminuir as complicações decorrentesda patologia e melhorar a qualidade de vida dessa população.

The present work aims to report the results of using conversation circle as an educational strategy in patients withHypertension and Mellitus Diabetes. The topics of conversation were the difficulties in compliance to therapy.Thirteen patients took part in this activity through the Hypertension and Diabetes Program of a Health Basic Unitof a township in a metropolitan area of Curitiba – PR. An interview was conducted in first place, in order to identifythe main difficulties in regard to the disease and to the treatment. The topics approached in the conversationcircle resulted from the interview. They were divided in three main topics: nutrition, physical activity and drugtherapy. This experience led us to reflect on the carried out activities and the importance of the active participationof hypertensive and diabetic patients in their treatments. We believe that this initiative will contribute to thedevelopment of health education strategies in order to increase the compliance to therapy, to avoid and/or todiminish complications arising from the pathology and to improve the quality of life of these individuals.

Este trabajo tiene como objetivo relatar los resultados del uso de una rueda de conversación como estrategiaeducativa con portadores de hipertensión arterial y diabetes melitus, acerca de las dificultades en la adhesión altratamiento. Participaron de esta actividad 13 usuarios acompañados por el programa de hipertensión ydiabéticos de una Unidad Básica de Salud en un municipio de la región metropolitana de Curitiba – PR.Primeramente, realizamos una entrevista para identificar las principales dificultades en relación a la enfermedady al tratamiento. De los resultados emergieron los temas que fueron abarcados en la rueda de conversación,siendo divididos en tres ejes temáticos: alimentación, ejercicio físico y tratamiento farmacológico. Estaexperiencia nos permitió reflexionar sobre las actividades desarrolladas y la importancia de la participación activadel portador de hipertensión y diabetes en la realización de su tratamiento. Creemos que esta iniciativa puedecontribuir al desarrollo de estrategias de educación en salud para aumentar la adhesión a la terapéutica, evitary/o disminuir las complicaciones consecuentes de la patología y mejorar la calidad de vida de esa clientela.

[User's representations of chronic diseases and educational practice]. / As representações dos usuários sobre a doença crônica e a prática educativa.

This is a qualitative research study held between October, 2008, and March, 2009, with 45 users over 60 years of age from a Health Unit, which aimed to identify their representations of chronic disease. Inerviews were carried out to collect chronic disease's representation. Three team meetings were also carried out, with an average of 8 users. Twenty-four (24) users participated in this step. The themes brought out of their discourses were: "The arrival of the disease: explanatory factors"; "The mystery of the bodyly changes: an obligation to change", and "The importance of learning and sharing the experience". Participants recognized the factors related to the disease onset and their commitments, the changes necessary to keep living and put off complications, and they also valued the exchange of experiences through dialogue in educational activities.

Panorama da produção do conhecimento em enfermagem na saúde do trabalhador: impacto e perspectivas: [revisão] / Overview of nursing knowledge production on the professional's health: impact and outlooks: [review] / Panorama de la producción de conocimineto en enfermería de la salud del trabajador: impactos y perspectivas: [revisión]

Trata-se de pesquisa bibliográfica realizada no banco de dados de teses e dissertações da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) no período de 1997 a 2006, utilizando as palavras: saúde do trabalhador e enfermagem. Foram identificados 172 resumos. As palavras-chave mais utilizadas foram trabalho de enfermagem e trabalho (14,3 por cento), riscos ocupacionais (10 por cento) e acidentes de trabalho (10 por cento). Das 172 produções, 52,9 por cento de abordagem quantitativa de várias modalidades, principalmente estudos descritivos ou exploratórios, ou os dois em conjunto. Os locais e os sujeitos do estudo foram os trabalhadores de enfermagem, de saúde. As perspectivas para o futuro desta área de produção talvez seja a busca de evidências científicas e metodologias modernas de investigação.

It is a literature review held by means of abstract consultation in the theses and dissertations data base of the Coordination of Specialization for the Superior Level Staff (CAPES - in Portuguese), from 1997 to 2006, using the words: professional's health and nursing. 172 abstracts were identified. Most used key words were: nursing job and work (14.3 percent), occupational hazards (10 percent) and work accidents (10 percent). Only 119 out of 172 productions referred to the nature of the study, 52.9 percent have a quantitative approach in many research studies, ultimately descriptive or exploratory studies or both. Future outlook in this production field may be the issue of changing the study typology, putting aside descriptive and exploratory qualitative or quantitative studies in order to search scientific evidences and modern investigative methodologies besides the implementation of intervention proposals as well as the appreciation of nurses' educational function.

Se trata de uma pesquisa bibliográfica realizada por medio de consulta de resúmenes en el banco de datos de tesis y disertaciones de la Coordinación de Capacitación de Personas de Nivel Superior (CAPES) durante los años de 1997 a 2006, utilizándose las palabras: salud del trabajador y enfermería. Fueron identificados 172 resúmenes. Las palabras claves más utilizadas fueron el trabajo de enfermería y el trabajo (14,3 por ciento), los riesgos ocupacionales (10 por ciento) y los accidentes de trabajo (10 por ciento). De las 172 producciones, solamente 119 presentaban referencias sobre el tema, 52,9 por ciento sobre abordajes cuantitativas sobre varias modalidades, principalmente estudios descriptivos o exploratorios, o los dos conjuntamente. Las perspectivas para el futuro de esta área de producción talvez sea la forma de modificación de las tipologias de estudio dejando de lado la forma descriptiva y exploratoria, tanto cuantitativo como cualitativo para buscar evidencias cientifícas y metodologías modernas de investigación mas allá de la implementación de las intervenciones propuestas y a la valorización de la función educativa del enfermero.

[Overview of nursing knowledge production on the professional's health: impact and outlooks]. / Panorama da produção do conhecimento em enfermagem na saúde do trabalhador: impacto e perspectivas.

It is a literature review held by means of abstract consultation in the theses and dissertations data base of the Coordination of Specialization for the Superior Level Staff (CAPES - in Portuguese), from 1997 to 2006, using the words: professional's health and nursing. 172 abstracts were identified. Most used key words were: nursing job and work (14.3%), occupational hazards (10%) and work accidents (10%). Only 119 out of 172 productions referred to the nature of the study, 52.9% have a quantitative approach in many research studies, ultimately descriptive or exploratory studies or both. Future outlook in this production field may be the issue of changing the study typology, putting aside descriptive and exploratory qualitative or quantitative studies in order to search scientific evidences and modern investigative methodologies besides the implementation of intervention proposals as well as the appreciation of nurses' educational function.