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Background: Team-based palliative care interventions have shown positive results for patients at the end of life in both hospital and community settings. However, evidence on the effectiveness of transmural, that is, spanning hospital and home, team-based palliative care collaborations is limited. Aim: To systematically review whether transmural team-based palliative care interventions can prevent hospital admissions and increase death at home. Design: Systematic review and meta-analysis. Data sources: MEDLINE (Ovid), Embase (Ovid), CINAHL (Ebsco), PsychINFO (Ovid), and Cochrane Library (Wiley) were systematically searched until January 2021. Studies incorporating teams in which hospital and community professionals co-managed patients, hospital-based teams with community follow-up, and case-management interventions led by palliative care teams were included. Data was extracted by two researchers independently. Results: About 19 studies were included involving 6614 patients, of whom 2202 received an intervention. The overall pooled odds ratio of at least one hospital (re)admissions was 0.46 (95% confidence interval (CI) 0.34–0.68) in favor of the intervention group. The highest reduction in admission was in the hospital-based teams with community follow-up: OR 0.21 (95% CI 0.07–0.66). The pooled effect on home deaths was 2.19 (95% CI 1.26–3.79), favoring the intervention, with also the highest in the hospital-based teams: OR 4.77 (95% CI 1.23–18.47). However, studies had high heterogeneity regarding intervention, study population, and follow-up time. Conclusion: Transmural team-based palliative care interventions, especially hospital-based teams that follow-up patients at home, show an overall effect on lowering hospital admissions and increasing the number of patients dying at home. However, broad clinical and statistical heterogeneity of included studies results in uncertainty about the effect size.

Purpose: Intensive care is a stressful environment in which team-family conflicts commonly occur. If managed poorly, conflicts can have negative effects on all parties involved. Previous studies mainly investigated these conflicts and their management in a retrospective way. This study aimed to prospectively explore team-family conflicts, including its main topics, complicating factors, doctors’ conflict management strategies and the effect of these strategies. Methods: Conversations between doctors in the neonatal, pediatric, and adult intensive care unit of a large university-based hospital and families of critically ill patients were audio-recorded from the moment doubts arose whether treatment was still in patients’ best interest. Transcripts were coded and analyzed using a qualitative deductive approach. Results: Team-family conflicts occurred in 29 out of 101 conversations (29%) concerning 20 out of 36 patients (56%). Conflicts mostly concerned more than one topic. We identified four complicating context- and/or family-related factors: diagnostic and prognostic uncertainty, families’ strong negative emotions, limited health literacy, and burden of responsibility. Doctors used four overarching strategies to manage conflicts, namely content-oriented, process-oriented, moral and empathic strategies. Doctors mostly used content-oriented strategies, independent of the intensive care setting. They were able to effectively address conflicts in most conversations. Yet, if they did not acknowledge families’ cues indicating the existence of one or more complicating factors, conflicts were likely to linger on during the conversation. Conclusion: This study underlines the importance of doctors tailoring their communication strategies to the concrete conflict topic(s) and to the context- and family-related factors which complicate a specific conflict.

Background Accessible and high-quality primary health care (PHC) is fundamental to countries moving towards universal health coverage. In order to improve the quality of patient-centered care provided in PHC, a comprehensive understanding of patients’ values is crucial to address any gaps in the health care system. This systematic review aimed to identify patients’ values relevant to PHC. Methods We searched primary qualitative and quantitative studies about patients’ values related to primary care in PubMed and EMBASE (Ovid) from 2009 to 2020. The studies’ quality was assessed using Joanna Briggs Institute (JBI) Critical Appraisal Checklist for both quantitative and qualitative studies and Consolidated Criteria for Reporting Qualitative Studies (COREQ) for qualitative studies. A thematic approach was used in the data synthesis. Outcome The database search resulted in 1,817 articles. A total of 68 articles were full-text screened. Data were extracted from nine quantitative and nine qualitative studies that met the inclusion criteria. The participants of the studies were mainly the general population in high-income countries. Four themes emerged from the analysis: patients’ values related to privacy and autonomy; values associated with the general practitioners including virtuous characteristics, knowledge and competence; values involving patient-doctor interactions such as shared decision-making and empowerment; and core values related to the primary care system such as continuity, referral, and accessibility. Conclusions This review reveals that the doctor’s personal characteristics and their interactions with the patients are critical considerations concerning the primary care services from the patients’ point of view. The inclusion of these values is essential to improve the quality of primary care.

BackgroundThe importance and attention to patient privacy in recent decades have been directed mostly toward medical data protection in electronic means. Hence, other aspects of patients’ privacy were overlooked, particularly in the primary health care (PHC) level. In the attempt of many countries, including Indonesia, to strive toward universal healthcare provision, a strong and accessible PHC is essential. This situation may create a tension in privacy provision where patients who need to disclose secrets may opt for other facilities, such as hospitals. This study aimed to describe and discuss patients’ and doctors’ perspectives and experiences about privacy in PHC in Indonesia, particularly since the universal coverage started.Design and methodsWe used in-depth interviews and observations to gather information. Inductive and thematic data analyses were conducted. We interviewed PHC users (n = 17), doctors (n = 16), other PHC staff (n = 7), and non-PHC users (n = 5) and observed the PHC activities.ResultsWe found that privacy is imperative for both patients and doctors. Design and conditions in PHC, including consultation room doors open, separate rooms for treatment, and patients’ symptoms asked by other staff were aspects that undermine privacy in PHC. Inadequate physical and informational privacy protection during a patient’s visit has affected the quality of care negatively in ways that impede proper anamneses and physical examination.ConclusionEnsuring patients’ and doctors’ physical and informational privacy is essential to creating PHC as the primary source of care that responds to the privacy values of its users, but it has been overlooked. The PHC building designs and care provision guidelines should incorporate the privacy needs of patients and doctors.

In this article, we use the theory of Information Ethics to argue that deceased people have a prima facie moral right to privacy in the context of health data research, and that this should be reflected in regulation and guidelines. After death, people are no longer biological subjects but continue to exist as informational entities which can still be harmed/damaged. We find that while the instrumental value of recognising post-mortem privacy lies in the preservation of the social contract for health research, its intrinsic value is grounded in respect for the dignity of the post-mortem informational entity. However, existing guidance on post-mortem data protection is available only in the context of genetic studies. In comparing the characteristics of genetic data and other health-related data, we identify two features of DNA often given as arguments for this genetic exceptionalism: relationality and embodiment. We use these concepts to show that at the appropriate Level of Abstraction, there is no morally relevant distinction between posthumous genetic and other health data. Thus, genetic data should not automatically receive special moral status after death. Instead we make a plea for ‘contextual exceptionalism’. Our analysis concludes by reflecting on a real-world case and providing suggestions for contextual factors that researchers and oversight bodies should take into account when designing and evaluating research projects with health data from deceased subjects.

Background: The life expectancy of people with profound intellectual and multiple disabilities (PIMD) is increasing and parents express concerns about being possibly outlived by their child with PIMD. However, little is known about the nature of these concerns. Method: We interviewed 27 parents of persons with PIMD and analysed the data thematically, to explore parents’ concerns about being outlived by their child. Results: Most parents hoped to outlive their child with PIMD and related this to the expectation of a decreased quality of life (QoL) of their child, when they would have passed away. The uncertainty about who would fulfil their parental roles in the future contributed to parents’ concerns and sometimes resulted in feelings of despair. Conclusions: Our study provides insight into the nature and gravity of parents’ concerns. The division of parents’ concerns into roles helps to address future care and support gaps for people with PIMD.

Persons with profound intellectual and multiple disabilities (PIMD) cannot speak about their Quality of Life (QoL), which makes it necessary to involve others. In current approaches, these ‘others’ are seen as assessors trying to describe QoL as objectively as possible, which involves a reduction of their experiences, through which they develop knowledge on the QoL of the person with PIMD. The objective of this paper is to give caregivers’ knowledge on the QoL of a person with PIMD a theoretical basis that values these experiences. We will argue that caregivers should be seen as witnesses, not assessors, and their statements on QoL as testimonies, not assessments. Audiences judge the trustworthiness of these witnesses intersubjectively, which implies a relationship characterized by trust and suspicion. Trust supports the witness to tell in her own words about the QoL of the person with PIMD; it demands receptivity, indicating that both the witness and the audience are willing to reconsider their perspective on QoL. Suspicion is necessary too, which helps the witness to critically approach her own interpretations and supports her to create more trustworthy testimonies. We conclude that the concept of witnessing helps to acknowledge caregivers’ experiential knowledge of QoL of a person with PIMD, which may also apply to other persons who cannot speak about their own QoL. We hope that our study will empower caregivers to give testimonies on QoL of a person with PIMD, which is crucial when complex decisions about the life of this person have to be made.

IntroductionThe human gut microbiota is an important reservoir of ESBL-producing Escherichia coli (ESBL-Ec). Community surveillance studies of ESBL-Ec to monitor circulating clones and ESBL genes are logistically challenging and costly.ObjectivesTo evaluate if isolates obtained in routine clinical practice can be used as an alternative to monitor the distribution of clones and ESBL genes circulating in the community.MethodsWGS was performed on 451 Dutch ESBL-Ec isolates (2014–17), including 162 community faeces and 289 urine and blood isolates. We compared proportions of 10 most frequently identified STs, PopPUNK-based sequence clusters (SCs) and ESBL gene subtypes and the degree of similarity using Czekanowski’s proportional similarity index (PSI).ResultsNine out of 10 most prevalent STs and SCs and 8/10 most prevalent ESBL genes in clinical ESBL-Ec were also the most common types in community faeces. The proportions of ST131 (39% versus 23%) and SC131 (40% versus 25%) were higher in clinical isolates than in community faeces (P ConclusionsDistributions of the 10 most prevalent clones and ESBL genes from ESBL-Ec community gut colonization and extra-intestinal infection overlapped in majority, indicating that isolates from routine clinical practice could be used to monitor ESBL-Ec clones and ESBL genes in the community.

Clinical biobanks processing data of participants in the European Union (EU) fall under the scope of the General Data Protection Regulation (GDPR), which among others includes requirements for consent. These requirements are further specified by the Article 29 Working Party (WP29)—an EU advisory body currently known as the European Data Protection Board (EDPB). Unfortunately, their guidance is cause for some confusion. While the GDPR allows participants to give broad consent for research when specific research purposes are still unknown, the WP29 guidelines suggest that additional consent for specific uses should be obtained in addition to broad consent when this becomes applicable. This discrepancy elicits the question whether clinical biobanks can fail the requirement of consent if they obtain broad consent, but not a specific consent for each biomedical study. We analysed this discrepancy within the framework of contextual integrity, in order to describe the context-relative informational norms that govern information flows in clinical biobanks. However, our analysis demonstrates that there is no uniform set of norms that can be applied to all clinical biobanks. As such, neither the GDPR nor the WP29 guidance can act as a “one size fits all” approach to all clinical biobanks. Rather, differences between clinical biobanks—especially regarding the scientific aims and patient populations—make the case for context-relative norms that determine the appropriate type of consent.

Background Colistin is an antibiotic that targets the LPS molecules present in the membranes of Gram-negative bacteria. It is used as a last-resort drug to treat infections with MDR strains. Colistin is also used in selective decontamination of the digestive tract (SDD), a prophylactic therapy used in patients hospitalized in ICUs to selectively eradicate opportunistic pathogens in the oropharyngeal and gut microbiota. Objectives To unravel the mechanisms of acquired colistin resistance in Gram-negative opportunistic pathogens obtained from SDD-treated patients. Results Routine surveillance of 428 SDD-treated patients resulted in 13 strains with acquired colistin resistance (Escherichia coli, n = 9; Klebsiella aerogenes, n = 3; Enterobacter asburiae, n = 1) from 5 patients. Genome sequence analysis showed that these isolates represented multiple distinct colistin-resistant clones but that colistin-resistant strains within the same patient were clonally related. We identified previously described mechanisms that lead to colistin resistance, i.e. a G53 substitution in the response regulator PmrA/BasR and the acquisition of the mobile colistin resistance gene mcr-1.1, but we also observed novel variants of basR with an 18 bp deletion and a G19E substitution in the sensor histidine kinase BasS. We experimentally confirmed that these variants contribute to reduced colistin susceptibility. In a single patient, we observed that colistin resistance in a single E. coli clone evolved through two unique variants in basRS. Conclusions We show that prophylactic use of colistin during SDD can select for colistin resistance in species that are not intrinsically colistin resistant. This highlights the importance of continued surveillance for strains with acquired colistin resistance in patients treated with SDD.

International audience; Various species of the intestinal microbiota have been associated with the development of colorectal cancer(1,2), but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin(3). This compound is believed to alkylate DNA on adenine residues(4,5) and induces double-strand breaks in cultured cells(3). Here we expose human intestinal organoids to genotoxic pks(+)E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in colorectal cancer. Our study describes a distinct mutational signature in colorectal cancer and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.Organoids derived from human intestinal cells that are co-cultured with bacteria carrying the genotoxic pks(+) island develop a distinct mutational signature associated with colorectal cancer.

Intensive care is a stressful environment in which team-family conflicts commonly occur. If managed poorly, conflicts can have negative effects on all parties involved. Previous studies mainly investigated these conflicts and their management in a retrospective way. This study aimed to prospectively explore team-family conflicts, including its main topics, complicating factors, doctors' conflict management strategies and the effect of these strategies.Conversations between doctors in the neonatal, pediatric, and adult intensive care unit of a large university-based hospital and families of critically ill patients were audio-recorded from the moment doubts arose whether treatment was still in patients' best interest. Transcripts were coded and analyzed using a qualitative deductive approach.Team-family conflicts occurred in 29 out of 101 conversations (29%) concerning 20 out of 36 patients (56%). Conflicts mostly concerned more than one topic. We identified four complicating context- and/or family-related factors: diagnostic and prognostic uncertainty, families' strong negative emotions, limited health literacy, and burden of responsibility. Doctors used four overarching strategies to manage conflicts, namely content-oriented, process-oriented, moral and empathic strategies. Doctors mostly used content-oriented strategies, independent of the intensive care setting. They were able to effectively address conflicts in most conversations. Yet, if they did not acknowledge families' cues indicating the existence of one or more complicating factors, conflicts were likely to linger on during the conversation.This study underlines the importance of doctors tailoring their communication strategies to the concrete conflict topic(s) and to the context- and family-related factors which complicate a specific conflict.

The genomic relationships amongWe collected short-read sequence data from invited groups that had previously publishedWe assembled a collection of 1095 hospitalA2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect ofWellcome Trust.

Background The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups-A and B-corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium. Methods We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality. Findings We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events. Interpretation A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd.

Contains fulltext : 248234.pdf (Publisher’s version ) (Open Access) AIM: To investigate the main factors which facilitate or hinder end-of-life decision-making (EoLDM) in neonates and children. METHODS: A qualitative inductive, thematic analysis was performed of interviews with a total of 73 parents and 71 physicians. The end-of-life decisions mainly concern decisions to withhold or withdraw life-sustaining treatment. RESULTS: The importance of taking sufficient time and exchanging clear, neutral and relevant information was main facilitators expressed by both parents and physicians. Lack of time, uncertain information and changing doctors were seen as important barriers by both parties. Most facilitators and barriers could be seen as two sides of the same coin, but not always. For example, some parents and physicians considered the fact that parents hold strong opinions as a barrier while others considered this a facilitator. Furthermore, parents and physicians showed differences. Parents especially underlined the importance of physician-related facilitators, such as a personalised approach, empathy and trust. On the contrary, physicians underlined the importance of the child's visible deterioration and parents' awareness of the seriousness of their child's condition and prognosis as facilitators of EoLDM. CONCLUSIONS: This study gained insight into what parents and physicians experience as the main barriers and facilitators in EoLDM for neonates and children.

The purpose of this study was to characterize the patient and provider engagement in the sudden telehealth implementation that occurred with the onset of the COVID-19 pandemic. Patients and providers from 3 nurse-led models of care (federally qualified health centers, nurse midwifery practices, and the Nurse-Family partnership program) in Colorado were surveyed. Data from the Patient Attitude toward Telehealth survey and Provider Perceptions about Telehealth were collected. Patient respondents (n = 308) who resided primarily in rural or frontier communities were female, white, and Hispanic. Patients in urban areas used telehealth more frequently than in rural or frontier areas ( P

Enterococcus faecium is a nosocomial, multidrug-resistant pathogen. Whole genome sequence studies revealed that hospital-associated E. faecium isolates are clustered in a separate clade A1. Here, we investigated the distribution, integration site and function of a putative iol gene cluster that encodes for myo-inositol (MI) catabolism. This iol gene cluster was found as part of an ~20 kbp genetic element (iol element), integrated in ICEEfm1 close to its integrase gene in E. faecium isolate E1679. Among 1644 E. faecium isolates, ICEEfm1 was found in 789/1227 (64.3 %) clade A1 and 3/417 (0.7 %) non-clade A1 isolates. The iol element was present at a similar integration site in 180/792 (22.7 %) ICEEfm1-containing isolates. Examination of the phylogenetic tree revealed genetically closely related isolates that differed in presence/absence of ICEEfm1 and/or iol element, suggesting either independent acquisition or loss of both elements. E. faecium iol gene cluster containing isolates E1679 and E1504 were able to grow in minimal medium with only myo-inositol as carbon source, while the iolD-deficient mutant in E1504 (E1504∆iolD) lost this ability and an iol gene cluster negative recipient strain gained this ability after acquisition of ICEEfm1 by conjugation from donor strain E1679. Gene expression profiling revealed that the iol gene cluster is only expressed in the absence of other carbon sources. In an intestinal colonization mouse model the colonization ability of E1504∆iolD mutant was not affected relative to the wild-type E1504 strain. In conclusion, we describe and functionally characterise a gene cluster involved in MI catabolism that is associated with the ICEEfm1 island in hospital-associated E. faecium isolates. We were unable to show that this gene cluster provides a competitive advantage during gut colonisation in a mouse model. Therefore, to what extent this gene cluster contributes to the spread and ecological specialisation of ICEEfm1-carrying hospital-associated isolates remains to be investigated.

Summary Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data. Availability and implementation Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https://gitlab.com/sirarredondo/gplas.git. Supplementary information Supplementary data are available at Bioinformatics online.

Total phenolic chromatographic indices (TPCI) of three commercially grown saskatoon berry varieties and a pomace from commercial juice production were determined. Northline was shown to have the highest TPCI of 504.2 mg/100 g FW. These results agreed with total phenolic content results for these varieties. The TPCI of the commercial pomace was 404.2 mg/100 g pomace indicating that a significant concentration of phenolics were present in this co-product, showing the commercial relevance of this material. A phenolic rich extract (PRE; 500 ppm) of the Northline variety was compared to BHT (0.02% w:w) and Rosamox (0.2% w:w) for delaying the oxidation of borage oil via rancimat analysis. Induction times were 1.46 h (borage oil), 1.44 h (Rosamox), 2.18 h (BHT), and 2.42 h (PRE), which was a ∼65% delay in the oxidation of borage oil. These results clearly support the value of this material as an antioxidant ingredient in foods, pharmaceuticals, nutriceuticals and cosmetics.

IntroductionSudden cardiac death (SCD) is the leading cause of death in patients with myocardial infarction (MI) and can be prevented by the implantable cardioverter defibrillator (ICD). Currently, risk stratification for SCD and decision on ICD implantation are based solely on impaired left ventricular ejection fraction (LVEF). However, this strategy leads to over- and under-treatment of patients because LVEF alone is insufficient for accurate assessment of prognosis. Thus, there is a need for better risk stratification. This is the study protocol for developing and validating a prediction model for risk of SCD in patients with prior MI.Methods and AnalysisThe EU funded PROFID project will analyse 23 datasets from Europe, Israel and the US (∼225,000 observations). The datasets include patients with prior MI or ischemic cardiomyopathy with reduced LVEFEthics and disseminationLocal ethical approval was obtained. The final model will be disseminated through scientific publications and a web-calculator. Statistical code will be published through open-source repositories.

The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed.Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. They use either assembly graph information (plasmidSPAdes, gplas), reference databases (MOB-Suite, FishingForPlasmids) or both (HyAsP and SCAPP) to produce plasmid predictions. The benchmark data set consisted of 240 E. coli strains, harboring 631 plasmids, which were representative for the diversity of E. coli in public databases. Notably, these strains were not used for training any of the tools.We found that two thirds (n=425, 66.3.%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n=85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n=317, 50.23%), and performed best at reconstructing large plasmids (n=166, 46.37%) and ARG-plasmids (n=41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n=168, 61.54%). Large ARG-plasmids, however, were recovered with small precision values (median=0.47, IQR=0.61), indicating that plasmidSPAdes frequently merged sequences derived from distinct replicons. Additionally, only 63% of all plasmid-borne ARGs were correctly predicted by plasmidSPAdes.The remaining four tools (FishingForPlasmids, HyAsP, SCAPP and gplas) were able to correctly reconstruct a combined total of 18 plasmids that were missed by MOB-suite and plasmidSPAdes.Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

Physician-assisted death (PAD) for patients suffering from a mental illness is allowed in the Netherlands under certain conditions but is a very controversial topic, mainly discussed by ethicists and physicians. The voice of the patient is rarely included in the debate, so we know little about what their views on the topic are. We aim to understand the views of patients with mental illness and wish to die with regard to the possibility of PAD in the Netherlands. The data for this qualitative study were collected through 21 in-depth interviews with Dutch patients who have a wish for PAD as a result of suffering from a mental illness. We identified four themes in relation to the meaning of PAD for the patients suffering from mental illness and wish to die. These themes are (1) Autonomy and self-determination, (2) ending the suffering, (3) recognition, and (4) a dignified end-of-life. The option of PAD for patients suffering from mental illnesses was considered of great importance to the patients who have a wish to die. We highlight the importance of ‘recognition’ for the situation of the patient, as this could lead to new perspective. We argue that psychiatrists need to reflect on providing this recognition in earlier phases of treatment, taking seriously and discussing a wish for PAD in treatment is beneficial to patients. It provides space for the patient to discuss their wishes and could cause them not wanting to die anymore.

Broad-spectrum antibiotics for suspected early-onset neonatal sepsis (sEONS) may have pronounced effects on gut microbiome development and selection of antimicrobial resistance when administered in the first week of life, during the assembly phase of the neonatal microbiome. Here, 147 infants born at ≥36 weeks of gestational age, requiring broad-spectrum antibiotics for treatment of sEONS in their first week of life were randomized 1:1:1 to receive three commonly prescribed intravenous antibiotic combinations, namely penicillin + gentamicin, co-amoxiclav + gentamicin or amoxicillin + cefotaxime (ZEBRA study, Trial Register NL4882). Average antibiotic treatment duration was 48 hours. A subset of 80 non-antibiotic treated infants from a healthy birth cohort served as controls (MUIS study, Trial Register NL3821). Rectal swabs and/or faeces were collected before and immediately after treatment, and at 1, 4 and 12 months of life. Microbiota were characterized by 16S rRNA-based sequencing and a panel of 31 antimicrobial resistance genes was tested using targeted qPCR. Confirmatory shotgun metagenomic sequencing was executed on a subset of samples. The overall gut microbial community composition and antimicrobial resistance gene profile majorly shift directly following treatment (R

BackgroundA key aim of palliative care is to improve the quality of life of patients and their families. To help ensure quality of life for the families of patients with migrant backgrounds, this study sought insights into the dignity of informal caregivers in migrant communities. This could improve understanding of family-centered care for migrant patients.MethodsTwenty semi-structured interviews with informal caregivers of Turkish, Moroccan, or Surinamese background living in the Netherlands were analyzed thematically.ResultsThe dignity of the patient and that of their informal caregivers were found to be strongly interrelated. Most important for the dignity of caregivers was ensuring good care for their patients and preserving the patients’ dignity. Ensuring good care involved advocating for good and dignified care and for satisfaction of a patient’s wishes. For many informal caregivers, it also included delivering care to the patient by themselves or together with other family members, despite having to give up part of their own lives. Providing care themselves was part of maintaining a good relationship with the patient; the care was to cater to the patient’s preferences and help preserve the patient’s dignity, and it could be accompanied by valuable aspects such as times for good conversations. Positive interaction between an informal caregiver and a patient positively influenced the informal caregiver’s dignity. Informal caregiver and patient dignity were often compromised simultaneously; when informal caregivers felt healthcare professionals were undermining a patient’s dignity, their own dignity suffered. According to informal caregivers, healthcare professionals can help them preserve dignity by taking seriously their advice about the patient, keeping them informed about the prognosis of the disease and of the patient, and dealing respectfully with differences in values at the end of life.ConclusionThe dignity of migrant patients’ informal caregivers in the last phase of a patient’s life is closely entwined with ensuring good care and dignity for the patient. Healthcare professionals can strengthen the dignity of informal caregivers by supporting their caregiving role.

Background To identify genetic associations of quantitative metabolic syndrome (MetS) traits and characterize heterogeneity across ethnic groups. Methods Data was collected from GENetics of Noninsulin dependent Diabetes Mellitus (GENNID), a multiethnic resource of Type 2 diabetic families and included 1520 subjects in 259 African-American, European-American, Japanese-Americans, and Mexican-American families. We focused on eight MetS traits: weight, waist circumference, systolic and diastolic blood pressure, high-density lipoprotein, triglycerides, fasting glucose, and insulin. Using genotyped and imputed data from Illumina’s Multiethnic array, we conducted genome-wide association analyses with linear mixed models for all ethnicities, except for the smaller Japanese-American group, where we used additive genetic models with gene-dropping. Results Findings included ethnic-specific genetic associations and heterogeneity across ethnicities. Most significant associations were outside our candidate linkage regions and were coincident within a gene or intergenic region, with two exceptions in European-American families: (a) within previously identified linkage region on chromosome 2, two significant GLI2-TFCP2L1 associations with weight, and (b) one chromosome 11 variant near CADM1-LINC00900 with pleiotropic blood pressure effects. Conclusions This multiethnic family study found genetic heterogeneity and coincident associations (with one case of pleiotropy), highlighting the importance of including diverse populations in genetic research and illustrating the complex genetic architecture underlying MetS.

Additional file 1. Interview guide. Semi-structured interview guide used for interviews. The interview guide includes questions on researchers’ perception of diversity, responsiveness and their role in contributing to responsiveness of palliative care in their projects. It also includes suggestions for strategies to improve responsiveness roughly following the domains of the equity standards – equity in policy; equitable access and utilisation; equitable quality of care; equity in participation; and, promoting equity – used to discuss the feasibility of implementing such strategies and identify factors influencing researchers’ effort to contribute to responsiveness of palliative care in their projects.

Additional file 1.

Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium . Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving single-nucleotide polymorphisms (SNPs). We identified three genomic regions harbouring large numbers of SNPs in tight linkage that are not proximal to each other based on the completely assembled chromosome of the clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS30-like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS30-like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.

Introduction The human gut microbiota is an important reservoir of ESBL-producing Escherichia coli (ESBL-Ec). Community surveillance studies of ESBL-Ec to monitor circulating clones and ESBL genes are logistically challenging and costly. Objectives To evaluate if isolates obtained in routine clinical practice can be used as an alternative to monitor the distribution of clones and ESBL genes circulating in the community. Methods WGS was performed on 451 Dutch ESBL-Ec isolates (2014–17), including 162 community faeces and 289 urine and blood isolates. We compared proportions of 10 most frequently identified STs, PopPUNK-based sequence clusters (SCs) and ESBL gene subtypes and the degree of similarity using Czekanowski’s proportional similarity index (PSI). Results Nine out of 10 most prevalent STs and SCs and 8/10 most prevalent ESBL genes in clinical ESBL-Ec were also the most common types in community faeces. The proportions of ST131 (39% versus 23%) and SC131 (40% versus 25%) were higher in clinical isolates than in community faeces (P

BackgroundEnterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and especially to vancomycin, a first-line antibiotic to treat infections with multidrug-resistant Gram-positive pathogens, has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or Tn1546 transposition between different genomic locations. Here, we reconstructed all nested genetic elements (clone, plasmid, transposon) to study how the dissemination of vanA-type vancomycin resistance occurred in Dutch hospitals (2012-2015).MethodsWe performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterisation was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. This allowed determining all nested genomic elements (clone, plasmid and transposon) involved in the dissemination of the vanA gene cluster. Next, we conducted an “all vs. all” pairwise comparison between isolates sharinga potential epidemiological link to elucidate whether clonal, plasmid or Tn1546 spread accounted for the dissemination of vanA resistance.ResultsThe 309 VRE isolates belonged to 18 different SCs of which SC13 (n = 102, 33%), SC17 (n = 52, 16.8%) and SC18 (n = 42, 13.6%) were predominant. We identified seven different plasmid types bearing the vanA gene cluster, four of which were highly similar (identity ∼99%, coverage∼84%) to previously described complete plasmid sequences. We estimated that clonal dissemination contributed most (∼45%) to the spread of vancomycin-resistance in Dutch hospitals, followed by Tn1546 mobilisation (∼12%) and plasmid dissemination (∼6%).ConclusionsThe dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of Tn1546 transposition and/or plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides one of the first quantitative assessments to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type vancomycin resistance cluster.

Background The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among patients in hospitals. There is currently a lack of data on the mechanisms that are responsible for the ability of E. faecium to survive in the absence of nutrients. Results We performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20 °C. A total of 24 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS was usp (locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant in usp, we were able to confirm that usp significantly contributes to survival in PBS and this defect was restored by in trans complementation. The usp gene is present in 99% of a set of 1644 E. faecium genomes that collectively span the diversity of the species. Conclusions We postulate that usp is a key determinant for the remarkable environmental robustness of E. faecium. Further mechanistic studies into usp and other genes identified in this study may shed further light on the mechanisms by which E. faecium can survive in the absence of nutrients for prolonged periods of time.

The purpose of the study was to investigate the molecular characteristics and genetic relatedness of the first reported cases of vancomycin-resistant enterococci (VRE) from the Tripoli Medical Center, Libya. In total, 43 VRE isolates were obtained from various clinical sites throughout the years 2013-2014, including 40