School Nursing Practice in Education Settings in Spain.

School nurses and pediatric nurses play vital roles in providing healthcare for children and adolescents in educational and healthcare settings. School nurses operate within educational institutions, serving as caregivers and facilitating communication between the school, families, and the healthcare system. These professionals closely collaborate with pediatric nurses. The primary objective of this study was to examine the state of school nursing in Spain. The research comprised 27 nurses, including 18 school nurses and 9 pediatric nurses, chosen through theoretical sampling. These nurses participated in in-depth interviews as part of the data collection process. Grounded theory, following Charmaz's process, was employed for data analysis. The findings underscore the nurses' call for their mandated presence and regulation in all Spanish educational institutions to address contemporary health challenges and ensure inclusive education.

Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software.

RNA and DNA modifications occur in eukaryotes and prokaryotes, as well as in their viruses, and serve a wide range of functions, from gene regulation to nucleic acid protection. Although the first nucleotide modification was discovered almost 100 years ago, new and unusual modifications are still being described. Nucleotide modifications have also received more attention lately because of their increased significance, but also because new sequencing approaches have eased their detection. Chiefly, third generation sequencing platforms PacBio and Nanopore offer direct detection of modified bases by measuring deviations of the signals. These unusual modifications are especially prevalent in bacteriophage genomes, the viruses of bacteria, where they mostly appear to protect DNA against degradation from host nucleases. In this Opinion article, we highlight and discuss current approaches to detect nucleotide modifications, including hardwares and softwares, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages. The ability to distinguish between several types of nucleotide modifications may even shed new light on metagenomic studies.

ChEMBL: towards direct deposition of bioassay data.

ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.

Role of Atypical Bacteria in Hospitalized Patients With Nursing Home-Acquired Pneumonia.

Background: Nursing home-acquired pneumonia (NHAP) has been identified as one of the leading causes of mortality and hospitalization for long-term care residents. However, current and previous pneumonia guidelines differ on the appropriate management of NHAP in hospitalized patients, specifically in regard to the role of atypical bacteria such as Chlamydiae pneumonia, Mycoplasma pneumoniae, and Legionella. Objectives: The purpose of this review is to evaluate clinical trials conducted in hospitalized patients with NHAP to determine the prevalence of atypical bacteria and thus the role for empiric antibiotic coverage of these pathogens in NHAP. Methods: Comprehensive MEDLINE (1966-April 2016) and Embase (1980-April 2016) searches were performed using the terms "atypical bacteria", "atypical pneumonia", "nursing-home acquired pneumonia", "pneumonia", "elderly", "nursing homes", and "long term care". Additional articles were retrieved from the review of references cited in the collected studies. Thirteen published clinical trials were identified. Results: In the majority of studies, atypical bacteria were infrequently identified in patients hospitalized with NHAP. However, when an active community-acquired pneumonia (CAP) cohort was available, the rate of atypical bacteria between NHAP and CAP study arms was similar. Only 3 studies in this review adhered to recommended strategies for investigating atypical bacteria; in 2 of these studies, C. pneumoniae was the most common pathogen identified in NHAP cohorts. Conclusion: Although atypical bacteria were uncommon in most NHAP studies in this review, suboptimal microbial investigations were commonly performed. To accurately describe the role of atypical bacteria in NHAP, more studies using validated diagnostic tests are needed.

Creation of a Didactic Clinical Pharmacology Lecture Series for Internal Medicine Residents.

INTRODUCTION: One of the noted areas of weakness for internal medicine residents is pharmacology. However, there is little data documenting the creation and effect of a comprehensive pharmacology didactic program. Our goal was to create a two-year clinical pharmacology didactic program focused on areas of stated weakness and to evaluate this program for an increase in knowledge and prescribing confidence of the participants. METHODS: From August 2020 to June 2022, a two-year pharmacology program was developed, which included 20 didactic lectures on a variety of topics. Pre- and post-tests were given for 15 of the lectures, and four surveys were given, two during each year of the program. Four questions on each survey were the same and asked about confidence in choosing an appropriate medication based on current guidelines, patient-specific factors, primary literature, and pharmacokinetics. RESULTS:  Over the two years, participation in the pharmacology sessions ranged from 17 to 29 residents (65-74% of the residency class). The average pre- and post-test scores increased by an average of 25.1%, which was a statistically significant increase (p<0.001, 95% CI [17.5, 32.8]). A Kruskal-Wallis H test showed a statistically significant difference in resident-reported confidence adjusting medications based on primary literature between the different survey groups, χ2 = 9.871, p = 0.02. CONCLUSION: A two-year, didactic pharmacology program improved the knowledge of resident participants and confidence in their ability to choose an appropriate medication based on primary literature.

Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria.

Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 108 virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.

Teachers and Parents' Perceptions of Care for Students with Type 1 Diabetes Mellitus and Their Needs in the School Setting.

The high incidence of Type 1 Diabetes Mellitus (DM1) increases the likelihood of teachers having students with this illness in their classrooms. The objective of this study is to investigate the needs of students with DM1 during the school day from the perspective of both teachers and parents. A mixed methods study was designed and a questionnaire was administered to practicing teachers in Pre-primary Education, Primary Education, Compulsory Secondary Education, and Further Education, as well as Vocational Education within both the province and the city of Burgos (Castile and Leon, Spain) who may have students with DM1. Semi-structured interviews were also conducted with mothers and fathers, members of the Burgos Diabetics Association (ASDIBUR). In the questionnaires administered to the teaching staff, 54.8% affirmed that they knew of students with DM1 at their centers. Of those questioned, 51.2% affirmed that they knew of the existence of action protocols on DM, and 45.2% declared that they had received specialized information on the illness; 92.8% believed that there was no discrimination at their center towards students with DM, and 82.8% thought that the educational center raised no objections to students with DM departing on trips during the school year. In their interviews, both family and teachers assessed the material and human resources as insufficient and called for the presence of school nurses at the educational centers. It is important to raise the awareness of the educational community about the needs of students with DM1 and to provide guidelines on emergency situations to teachers and staff at the centers.

Application Site Reactions from the Buprenorphine Transdermal Patch: A Case Series.

Buprenorphine is a partial mu-opioid agonist available as a transdermal patch for use in patients with chronic pain. Transdermal products can be associated with application site reactions (ASRs). The incidence of ASRs to the buprenorphine transdermal patch (BTP) have been described as low and seldom requiring patch discontinuation. In this case series, we describe four patients who developed an erythematous, rash-like ASR to the BTP leading to treatment discontinuation or rotation to buprenorphine buccal films (BBF). All subjects had demonstrated tolerability to lower patch strengths before developing an ASR with titration to a BTP of a higher strength. The strength at which an ASR emerged varied among subjects; however, all ASRs developed with BTP strengths 10 mcg/hr or higher. The dose-response relationship and prolonged onset to ASR emergence may be suggestive of an allergic delayed hypersensitivity reaction. However, in this case series three subjects demonstrated tolerability to BBF either before or after developing a skin reaction to BTP.

Can we do it all? Reflections on the development of a collaborative, three day a week internal medicine rounding experience.

PURPOSE: Interdisciplinary training is a critical part of pharmacy education, and often much of the interdisciplinary participation occurs during the advanced practice experiences of the final professional year of pharmacy education. Creation and maintenance of these experiences can be difficult for faculty members, especially faculty at community hospitals or those with multiple roles and responsibilities at their practice site. The purpose of this article is to reflect on the development process and student acceptance of a collaborative, three-day a week internal medicine rounding student experience. DESCRIPTION: Instead of a traditional five-day a week rounding schedule with a single, primary faculty preceptor, students participated in a three-day a week internal medicine rounding experience where their primary faculty preceptor had a faculty partner who functioned as a substitute. The student activities on the other days were adapted by each faculty preceptor based on their internal medicine subspecialty duties and needs of the practice site. ANALYSIS/INTERPRETATION: Results from a seven-question, anonymous survey to students who participated in the three-day a week internal medicine rounds found high impact on their reported confidence and knowledge. Those responding "positive impact" or "extreme positive impact" ranged from 67% to 100%. In addition, 78% indicated comfort with the substitute faculty preceptor. CONCLUSIONS: This collaborative, three-day a week rounding experience was well received by pharmacy students. IMPLICATIONS: Non-traditional rounding may be an option that could help decrease pharmacy student and faculty burnout, while still providing a positive learning experience for students.

Bacteriophages Roam the Wheat Phyllosphere.

The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried out until now. In this study, we extracted, sequenced, and characterized the dsDNA and ssDNA viral community from a phyllosphere for the first time. We sampled leaves from winter wheat (Triticum aestivum), where we identified a total of 876 virus operational taxonomic units (vOTUs), mostly predicted to be bacteriophages with a lytic lifestyle. Remarkably, 848 of these vOTUs corresponded to new viral species, and we estimated a minimum of 2.0 × 106 viral particles per leaf. These results suggest that the wheat phyllosphere harbors a large and active community of novel bacterial viruses. Phylloviruses have potential applications as biocontrol agents against phytopathogenic bacteria or as microbiome modulators to increase plant growth-promoting bacteria.

Computational Tools for the Analysis of Uncultivated Phage Genomes.

Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.

Time to Deprescribe: A Time-Centric Model for Deprescribing at End of Life.

In end-of-life care, deprescribing practices may vary considerably from one practitioner to the next, although most published frameworks for evaluating medication appropriateness in advanced illness consider three key principles (1) patient and caregiver goals, (2) remaining life expectancy (LE), and (3) medication time to benefit (TTB). The objective of this article is to provide clinicians with a structured, consistent approach for deprescribing that does not replace clinical judgment or the preferences of patients and their families but enhances it through clinical data. The emphasis will be on the time component of published models, including how to estimate remaining LE and medication TTB. Through case examples of two new hospice admissions, LE and TTB will be estimated and applied to deprescribing decisions. This time-centric approach may satisfy the palliative and hospice clinicians' desire for clear clinical justification for medication discontinuation while at the same time providing a strategy for communicating deprescribing rationale to patients and families.

Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay.

Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.

Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment.

Phages drive bacterial diversity, profoundly influencing microbial communities, from microbiomes to the drivers of global biogeochemical cycling. Aiming to broaden our understanding of Escherichiacoli (MG1655, K-12) phages, we screened 188 Danish wastewater samples and isolated 136 phages. Ninety-two of these have genomic sequences with less than 95% similarity to known phages, while most map to existing genera several represent novel lineages. The isolated phages are highly diverse, estimated to represent roughly one-third of the true diversity of culturable virulent dsDNA Escherichia phages in Danish wastewater, yet almost half (40%) are not represented in metagenomic databases, emphasising the importance of isolating phages to uncover diversity. Seven viral families, Myoviridae, Siphoviridae, Podoviridae,Drexlerviridae,Chaseviridae,Autographviridae, and Microviridae, are represented in the dataset. Their genomes vary drastically in length from 5.3 kb to 170.8 kb, with a guanine and cytosine (GC) content ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, substantial diversity remains to be uncovered. These results expand and underline the range of coliphage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.

DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.

Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.

NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.

A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.