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Abstract Background The emergence of artificial intelligence (AI) in medicine has prompted the development of numerous ethical guidelines, while the involvement of patients in the creation of these documents lags behind. As part of the European PROFID project we explore patient perspectives on the ethical implications of AI in care for patients at increased risk of sudden cardiac death (SCD). Aim Explore perspectives of patients on the ethical use of AI, particularly in clinical decision-making regarding the implantation of an implantable cardioverter-defibrillator (ICD). Methods Semi-structured, future scenario-based interviews were conducted among patients who had either an ICD and/or a heart condition with increased risk of SCD in Germany (n = 9) and the Netherlands (n = 15). We used the principles of the European Commission’s Ethics Guidelines for Trustworthy AI to structure the interviews. Results Six themes arose from the interviews: the ability of AI to rectify human doctors’ limitations; the objectivity of data; whether AI can serve as second opinion; AI explainability and patient trust; the importance of the ‘human touch’; and the personalization of care. Overall, our results reveal a strong desire among patients for more personalized and patient-centered care in the context of ICD implantation. Participants in our study express significant concerns about the further loss of the ‘human touch’ in healthcare when AI is introduced in clinical settings. They believe that this aspect of care is currently inadequately recognized in clinical practice. Participants attribute to doctors the responsibility of evaluating AI recommendations for clinical relevance and aligning them with patients’ individual contexts and values, in consultation with the patient. Conclusion The ‘human touch’ patients exclusively ascribe to human medical practitioners extends beyond sympathy and kindness, and has clinical relevance in medical decision-making. Because this cannot be replaced by AI, we suggest that normative research into the ‘right to a human doctor’ is needed. Furthermore, policies on patient-centered AI integration in clinical practice should encompass the ethics of everyday practice rather than only principle-based ethics. We suggest that an empirical ethics approach grounded in ethnographic research is exceptionally well-suited to pave the way forward.

Abstract Background In the last decade, there has been a growing concern to make palliative care more culturally sensitive and contextually appropriate. This concern is also relevant in Indonesia, where the progress of palliative care, particularly in home-based care, has been slow. Like elsewhere in the world, there has been a growing awareness of the importance of shifting from a curative orientation towards a palliative one, especially in cases where further medical treatment is futile. In this paper we argue that the development of palliative care practices would benefit greatly from learning about the values that are important for patients, families, and health professionals. It is important to understand these values to support forms of care that aim to enhance quality of life. To demonstrate this, we analyse the care values people in rural Java evoke in their home palliative care practices. Methods We conducted an eight-month ethnographic study involving forty-nine patients, families, and health professionals. Results We identified three specific Javanese Islamic values: making an effort (ikhtiar), being sincere (ikhlas), and being in a state of surrender (pasrah). These values influenced the participants’ activities in a palliative care setting. Based on our findings, we suggest three strategies to incorporate these values into palliative care practices and to better facilitate palliative care’s integration into Javanese Muslim communities. The first strategy is to include efforts to reduce suffering and improve the quality of life using the concept of ikhtiar. The second strategy is to foster sincerity (ikhlas) to help patients and families accept the realities of their condition and provide care for patients at home. The last strategy is to clarify that palliative care is not synonymous with ‘giving up’ but can be seen as an act of pious surrender. Conclusions Our study identified three Islamic-Javanese values that can be incorporated to strategies aiming at enhancing palliative care practices, resulting in care focused on improving quality of life rather than futile attempts at a cure.

Abstract Background To improve transmural palliative care for older adults acutely admitted to hospital, the PalliSupport intervention, comprising an educational programme and transmural palliative care pathway, was developed. This care pathway involves timely identification of palliative care needs, advance care planning, multidisciplinary team meetings, warm handover, and follow-up home visits. With this study, we evaluate changes in patient-related outcomes and transmural collaboration after implementation of the care pathway. Methods We conducted a before-after study, in which we compared 1) unplanned hospital admission and death at place of preference and 2) transmural collaboration before implementation, up to six months, and six to 18 months after implementation. Data from palliative care team consultations were collected between February 2017 and February 2020 in a teaching hospital in the Netherlands. Results The palliative care team held 711 first-time consultations. The number of consultation, as well as the number of consultations for patients with non-malignant diseases, and consultations for advance care planning increased after implementation. The implementation of the pathway had no statistically significant effect on unplanned hospitalization but associated positively with death at place of preference more than six months after implementation (during/shortly after adjusted OR: 2.12; 95% CI: 0.84–5.35; p-value: 0.11, long term after adjusted OR: 3.14; 95% CI: 1.49–6.62; p-value: 0.003). Effects on transmural collaboration showed that there were more warm handovers during/shortly after implementation, but not on long term. Primary care professionals attended multidisciplinary team meetings more often during and shortly after implementation, but did not more than six months after implementation. Conclusions The pathway did not affect unplanned hospital admissions, but more patients died at their place of preference after implementation. Implementation of the pathway increased attention to- and awareness for in-hospital palliative care, but did not improve transmural collaboration on long-term. For some patients, the hospital admissions might helped in facilitating death at place of preference.

Aim: Out-of-hospital cardiac arrest is a major health problem, and the overall survival rate is low (4.6%–16.4%). The initiation of the current chain of survival depends on the presence of a witness of the cardiac arrest, which is not present in 29.7%–63.4% of the cases. Furthermore, a delay in starting this chain is common in witnessed out-of-hospital cardiac arrest. This project aims to reduce morbidity and mortality due to out-of-hospital cardiac arrest by developing a smartwatch-based solution to expedite the chain of survival in the case of (un)witnessed out-of-hospital cardiac arrest. Methods: Within the ‘Beating Cardiac Arrest’ project, we aim to develop a demonstrator product that detects out-of-hospital cardiac arrest using photoplethysmography and accelerometer analysis, and autonomously alerts emergency medical services. A target group study will be performed to determine who benefits the most from this product. Furthermore, several clinical studies will be conducted to capture or simulate data on out-of-hospital cardiac arrest cases, as to develop detection algorithms and validate their diagnostic performance. For this, the product will be worn by patients at high risk for out-of-hospital cardiac arrest, by volunteers who will temporarily interrupt blood flow in their arm by inflating a blood pressure cuff, and by patients who undergo cardiac electrophysiologic and implantable cardioverter defibrillator testing procedures. Moreover, studies on psychosocial and ethical acceptability will be conducted, consisting of surveys, focus groups, and interviews. These studies will focus on end-user preferences and needs, to ensure that important individual and societal values are respected in the design process.

BackgroundSpecialist palliative care teams are consulted during hospital admission for advice on complex palliative care. These consultations need to be timely to prevent symptom burden and maintain quality of life. Insight into specialist palliative care teams may help improve the outcomes of palliative care.MethodsIn this retrospective observational study, we analyzed qualitative and quantitative data of palliative care consultations in a six-month period (2017 or 2018) in four general hospitals in the northwestern part of the Netherlands. Data were obtained from electronic medical records.ResultsWe extracted data from 336 consultations. The most common diagnoses were cancer (54.8%) and organ failure (26.8%). The estimated life expectancy was less than three months for 52.3% of all patients. Within two weeks after consultation, 53.2% of the patients died, and the median time until death was 11 days (range 191) after consultation. Most patients died in hospital (49.4%) but only 7.5% preferred to die in hospital. Consultations were mostly requested for advance care planning (31.6%). End-of-life preferences focused on last wishes and maintaining quality of life.ConclusionThis study provides detailed insight into consultations of palliative care teams and shows that even though most palliative care consultations were requested for advance care planning, consultations focus on end-of-life care and are more crisis-oriented than prevention-oriented. Death often occurs too quickly after consultation for end-of-life preferences to be met and these preferences tend to focus on dying. Educating healthcare professionals on when to initiate advance care planning would promote a more prevention-oriented approach. Defining factors that indicate the need for timely palliative care team consultation and advance care planning could help timely identification and consultation.

ABSTRACT Enterococcus faecalis is a commensal bacterium of the human gastrointestinal tract that causes opportunistic infections. The E. faecalis genetic changes associated with pathogenicity, particularly gut-to-bloodstream translocation, remain poorly understood. Here, we performed a genome-wide association study (GWAS) of 736 whole-genome sequences of fecal and bloodstream E. faecalis isolates from hospitalized and nonhospitalized individuals, respectively, to identify E. faecalis genetic signatures associated with the patient’s hospitalization status and body isolation source. We found that infection by hospitalization status and extraintestinal infection are heritable traits, with ~40% and ~30% of their variation explained by E. faecalis genetics, respectively. Furthermore, a GWAS using linear mixed models did not pinpoint any clear overrepresentation of individual genetic changes by hospitalization status or body isolation source after controlling for the population structure. However, we observed elevated signals in a genomic region containing a prophage element. However, the lineages themselves and their associated virulence factors and antibiotic resistance genes showed variable frequency among blood and fecal isolates and in hospitalized and nonhospitalized individuals. Altogether, our findings indicate that E. faecalis infection by hospitalization status and body sites is partially influenced by the overall genetic background of the isolates and antibiotic resistance patterns rather than genetic variation at individual loci, which suggests a greater role of other host and environmental factors and ultimately the opportunistic pathogenic lifestyle of this versatile host generalist bacterium. IMPORTANCE Enterococcus faecalis causes life-threatening invasive hospital- and community-associated infections that are usually associated with multidrug resistance globally. Although E. faecalis infections cause opportunistic infections typically associated with antibiotic use, immunocompromised immune status, and other factors, they also possess an arsenal of virulence factors crucial for their pathogenicity. Despite this, the relative contribution of these virulence factors and other genetic changes to the pathogenicity of E. faecalis strains remain poorly understood. Here, we investigated whether specific genomic changes in the genome of E. faecalis isolates influence its pathogenicity—infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection and intestinal colonization. Our findings indicate that E. faecalis genetics partially influence the infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection, possibly due to gut-to-bloodstream translocation, highlighting the potential substantial role of host and environmental factors, including gut microbiota, on the opportunistic pathogenic lifestyle of this bacterium.

ABSTRACT This study investigated the gut microbiome dynamics of index patients colonized with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) (n = 5) or extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) (n = 3) and their household contacts (n = 9) up to 4 months after hospital discharge of the index patient using 16S rRNA amplicon gene sequencing. Samples were collected at the day of hospital discharge of the index patient, 1 week and 2 and 4 months after discharge. Compared to household contacts, we observed a significant lower alpha diversity (P < 0.001) among index patients and significant (P < 0.05) separation between the two groups for beta diversity. Principal component analysis of the samples from each household (i.e., index patient and respective household contact) showed a clear shift in microbiome composition, in 4/8 index patients, from dissimilar to more similar to the household contact group. This suggests recovery of the microbiome to a healthier status, which was also reflected by de novo colonization of (health-associated) taxa. In contrast, the four time-point samples of the household contacts clustered together indicating a stable microbiome composition over time irrespective of low-level ESBL-Ec (n = 3) or ESBL-Kp (n = 2) colonization. In conclusion, here we show that, at the day of hospital discharge, the microbiome composition of index patients is dissimilar from that of household contacts. Over time, signals of microbiome recovery were observed in half of the index patients. The stable microbiome composition in household contacts irrespective of low-level ESBL-Ec or ESBL-Kp colonization suggests that the gut microbiome in these healthy people provided colonization resistance against ESBL-PE outgrowth. IMPORTANCE Colonization with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) often precedes infections and is therefore considered as a great threat for public health. Here, we studied the gut microbiome dynamics in eight index patients colonized with ESBL-PE after hospital discharge and the impact of exposure to this index patient on the gut microbiome dynamics of their household contacts. We showed that the microbiome composition from index patients is different from their household contacts upon hospital discharge and that, in some of the index patients, their microbiome composition over time shifted toward the composition of their household contacts. In contrast, household contacts showed a stable microbiome composition over time irrespective of low-level extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) or extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) gut colonization, suggesting that, in healthy microbiomes, colonization resistance is able to prevent ESBL-PE expansion.

Abstract 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.

A major challenge for interdisciplinary teamwork on complex sustainability issues is the often-conflicting disciplinary perspectives and underlying values and assumptions among collaborators. Interdisciplinary collaboration among researchers and practitioners therefore requires interdisciplinary consciousness (IC): epistemological and metaphysical understanding and appreciation of one’s own and others’ disciplinary views and their differences. Since it cannot be assumed that professionals have IC, there is a need for explicit training, for instance in higher education. We developed Frame Reflection Lab (FRL)—a playful intervention to stimulate the development of IC through frame reflection—and investigated its application among cross-disciplinary student teams collaborating on sustainability issues. We aimed to understand how frame reflection can contribute to enhancing IC, by analyzing the written and oral reflections of 23 Master’s degree students. We found that the FRL intervention contributed to the development of IC as it sparked cognitive, affective, and critical reflection; created a safe space for reflection; helped participants to articulate values and assumptions; and balanced structure and freedom. Our findings demonstrate that to prepare sustainability professionals for interdisciplinary collaboration, deeply rooted and possibly unconscious preconceptions have to be challenged to build awareness and appreciation of disciplinary differences. This calls for explicitly facilitating affective processes, for instance using playfulness, whereas training in reflection and interdisciplinarity usually focuses on cognitive processes. These findings are promising in terms of informing and inspiring future efforts to use playful frame reflection in education, research, and practice to support interdisciplinary collaboration to address complex sustainability issues.

ABSTRACT Quaternary ammonium compounds (QACs) have been extensively used in the community, healthcare facilities, and food chain, in concentrations between 20 and 30,000 mg/L. Enterococcus faecalis and Enterococcus faecium are ubiquitous in these settings and are recognized as nosocomial pathogens worldwide, but QACs’ activity against strains from diverse epidemiological and genomic backgrounds remained largely unexplored. We evaluated the role of Enterococcus isolates from different sources, years, and clonal lineages as hosts of QACs tolerance genes and their susceptibility to QACs in optimal, single-stress and cross-stress growth conditions. Only 1% of the Enterococcus isolates included in this study and 0.5% of publicly available Enterococcus genomes carried qacA/B, qacC, qacG, qacJ, qacZ, qrg, bcrABC or oqxAB genes, shared with >60 species of Bacillota, Pseudomonadota, Actinomycetota, or Spirochaetota. These genes were generally found within close proximity of antibiotics and/or metals resistance genes. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) of benzalkonium chloride (BC) and didecyldimethylammonium chloride ranged between 0.5 and 4 mg/L (microdilution: 37°C/20 h/pH = 7/aerobiosis) for 210 E. faecalis and E. faecium isolates (two isolates carrying qacZ). Modified growth conditions (e.g., 22°C/pH = 5) increased MICBC/MBCBC (maximum of eightfold and MBCBC = 16 mg/L) and changed bacterial growth kinetics under BC toward later stationary phases in both species, including in isolates without QACs tolerance genes. In conclusion, Enterococcus are susceptible to in-use QACs concentrations and rarely carry QACs tolerance genes. However, their potential gene exchange with different microbiota, the decreased susceptibility to QACs under specific environmental conditions, and the presence of subinhibitory QACs concentrations in various settings may contribute to the selection of particular strains and, thus, require a One Health strategy to maintain QACs effectiveness. IMPORTANCE Despite the increasing use of quaternary ammonium compounds (QACs), the susceptibility of pathogens to these antimicrobials remains largely unknown. Enterococcus faecium and Enterococcus faecalis are susceptible to in-use QACs concentrations and are not main hosts of QACs tolerance genes but participate in gene transfer pathways with diverse bacterial taxa exposed to these biocides. Moreover, QACs tolerance genes often share the same genetic contexts with antibiotics and/or metals resistance genes, raising concerns about potential co-selection events. E. faecium and E. faecalis showed increased tolerance to benzalkonium chloride under specific environmental conditions (22°C, pH = 5), suggesting that strains might be selected in settings where they occur along with subinhibitory QACs concentrations. Transcriptomic studies investigating the cellular mechanisms of Enterococcus adaptation to QACs tolerance, along with longitudinal metadata analysis of tolerant populations dynamics under the influence of diverse environmental factors, are essential and should be prioritized within a One Health strategy.

Background: Observational studies using large-scale databases and biobanks help improve prevention and treatment of sudden cardiac arrest (SCA) but the lack of guidance on data protection issues in this setting may harm patients’ rights and the research enterprise itself. This qualitative study explored the ethical aspects of observational SCA research, as well as solutions. Methods: European experts in SCA research, medical ethics and health law reflected on this topic through semi-structured interviews (N = 29) and a virtual roundtable conference (N = 18). The ESCAPE-NET project served as a discussion case. Findings were coded and thematically analysed. Results: The first theme concerned the potential benefits and harms (at individual and group level) of observational data-based SCA studies and included the following sub-themes: societal value, scientific validity, data privacy, disclosure of genetic findings, stigma and discrimination, and medicalisation of sudden death. The second theme involved governance through ‘privacy by design’, ‘privacy by policy’ and associated regulation and oversight. Sub-themes were: de-identification of data, informed consent (broad and deferred), ethics review, and harmonisation. Conclusions: Researchers and scientific societies should be aware that ethico-legal issues may arise during data-driven studies in SCA and other emergencies. These can be mitigated by combining technical data protection safeguards with appropriate informed consent policies and proportional ethics oversight. To ensure responsible conduct of data research in emergency medicine, we recommend the establishment of ‘codes of conduct’ which should be developed in interdisciplinary groups and together with patient representatives.

ABSTRACT The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.

Here, in a randomized trial of 147 infants receiving distinct antibiotic regimens for early-onset neonatal sepsis, Reyman et al. characterize the gut microbiome and resistance profiles, finding differential effects of antibiotic combinations on microbial community composition and antimicrobial resistance genes.

Abstract The human gut microbiome plays a central role in health and disease. Environmental factors, such as lifestyle and diet, are known to shape the gut microbiome as well as the reservoir of resistance genes that these microbes harbour; the resistome. In this study we assessed whether long-term dietary habits within a single geographical region (the Netherlands) impact the human gut resistome. Faecal samples from Dutch omnivores, pescatarians, vegetarians and vegans were analysed by metagenomic shotgun sequencing (MSS) (n = 149) and resistome capture sequencing approach (ResCap) (n = 64). Among all diet groups, 119 and 145 unique antibiotic resistance genes (ARGs) were detected by MSS or ResCap, respectively. Five or fifteen ARGs were shared between all diet groups, based on MSS and ResCap, respectively. The total number of detected ARGs by MSS or ResCap was not significantly different between the groups. MSS also revealed that vegans have a distinct microbiome composition, compared to other diet groups. Vegans had a lower abundance of Streptococcus thermophilus and Lactococcus lactis compared to pescatarians and a lower abundance of S. thermophilus when compared to omnivores. In summary, our study showed that long-term dietary habits are not associated with a specific resistome signature.

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

ABSTRACT Diet is an important determinant of the human gut microbiome. Here, we analyzed fecal metagenomes of Dutch adults following omnivorous, pescatarian, vegan, and vegetarian diets. We compared the taxonomic composition of individuals from our study with publicly available gut metagenomes from westernized and non-westernized societies. We observed that, despite long-term transition to diets rich in plant fibers (vegan or vegetarian), the microbiomes of these were typical of westernized populations, and similar in composition to omnivores. Although there were no major differences in metabolic modules, we identified differences in the species that contributed to particular functions, such as carbohydrate degradation and short-chain fatty acid metabolism. Overall, this study shows functional redundancy of the microbiomes among westernized populations, which is independent of long-term individual dietary habits. IMPORTANCE Diet is an important modulator of the human gut microbiome, which is susceptible to increased consumption of plant fibers in vegan or vegetarian lifestyles. To investigate this, we compared the gut microbiome of Dutch adults following omnivorous, pescatarian, vegan and vegetarian diets. We did not observe major differences in the gut microbiome composition and function between individuals with different dietary habits. However, we observed differences in the species that contribute to the core functions of the gut microbiome. Our study thus emphasizes the need to better understand the species-specific functional changes associated with dietary habits in the human gut microbiome.

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.

Abstract 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.

The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids’ transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem.

Background In the Netherlands, physician-assisted death (PAD) is allowed under certain conditions. Patients who suffer from mental illnesses are not excluded from this practice. In 2018, general practitioners (GPs) performed 20 out of a total of 67 cases of EAS for psychiatric suffering Objective More insight into GPs’ experiences and views with regard to PAD in psychiatry. Design The data for this study were obtained through a survey amongst 500 randomly selected Dutch GPs and by in-depth interviews with 20 Dutch GPs. Setting A survey study and in-depth interviews. Subjects Dutch GPs. Results 86 out of 101 GPs found it conceivable to perform EAS in case of somatic disease, and 51 out of 104 GPs found it conceivable in the case a patient suffered from a mental illness only. The main reason given for refusing an PAD request was that the criteria of due care were not met. Reasons for supporting psychiatric PAD related to responsibility, self-determination, compassion, fairness, and preventing suicide. Reasons for not supporting psychiatric PAD were related to the scope of medicine, a perceived lack of experience, uncertainties regarding the criteria of due care and life-expectancy. Conclusion GPs are less likely to perform PAD for suffering from a mental illness, compared to somatic suffering. Some GPs apply an extra criterion of ‘life-expectancy’ in case of PAD for suffering from a mental illness. Refusing PAD based on a long life expectancy keeps open the possibility of recovery, but may also just prolong the suffering and add to the unbearableness of it.KEY POINTS Currently, there is no qualitative research on what the views are of general practitioners regarding the subject of physician-assisted death (PAD) for patients suffering from severe mental disorders. General practitioners are less likely to consider a request for physician-assisted death by a patient suffering from a psychiatric disorder, compared to somatic suffering. Reasons for supporting psychiatric PAD related to responsibility, self-determination, compassion, fairness, and preventing suicide. Reasons for not supporting psychiatric PAD were related to the scope of medicine, a perceived lack of experience, uncertainties regarding the criteria of due care and life-expectancy. Significance for the reader: Although allowed in the Netherlands, PAD in case of severe mental suffering remains a controversial topic. We need in-depth information about the actual practice of it to have an informed debate with regard to this subject.

Abstract Background The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood. Methods A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of Enterococcus faecium was assembled (n = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes. Results Two main modes of genomic evolution continue to shape E. faecium: the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes. Conclusions The ability of A1 E. faecium to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.

Enterococcus faecalis is a commensal microorganism of animals, insects and humans, but also a nosocomial pathogen. Here, the authors analyse genomic sequences from E. faecalis isolates from animals and humans, and find that the last common ancestors of multiple hospital-associated lineages date to the pre-antibiotic era.

Abstract Background A 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. Methods Twenty semi-structured interviews with informal caregivers of Turkish, Moroccan, or Surinamese background living in the Netherlands were analyzed thematically. Results The 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. Conclusion The 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.

Abstract Background The aging of migrant populations across Europe challenges researchers in palliative care to produce knowledge that can be used to respond to the needs of the growing group of patients with a migration background and address ethnic disparities in palliative care. The aim of this study was to identify what factors influence researchers’ efforts to address responsiveness of palliative care to patients with a migration background and other underserved populations in their projects. Methods We conducted semi-structured interviews with 11 researchers involved in seven projects under the Dutch national program for palliative care innovation. Results Researchers’ efforts to address responsiveness of palliative care in their projects were influenced by individual factors, i.e. awareness of the need for responsiveness to patients with a migration background; experience with responsiveness; and, differences in perceptions on responsiveness in palliative care. Researchers’ efforts were furthermore influenced by institutional factors, i.e. the interaction with healthcare institutions and healthcare professionals as they rely on their ability to identify the palliative patient with a migration background, address the topic of palliative care, and enrol these patients in research; scientific standards that limit the flexibility needed for responsive research; and, the responsiveness requirements set by funding agencies. Conclusion Researchers play a key role in ensuring research addresses responsiveness to patients with a migration background. Such responsiveness may also benefit other underserved populations. However, at times researchers lack the knowledge and experience needed for responsive research. To address this we recommend training in responsiveness for researchers in the field of palliative care. We also recommend training for healthcare professionals involved in research projects to increase enrolment of patients with a migration background and other underrepresented populations. Lastly, we encourage researchers as well as research institutions and funding agencies to allow flexibility in research practices and set a standard for responsive research practice.

Abstract Background Consent for data research in acute and critical care is complex as patients become at least temporarily incapacitated or die. Existing guidelines and regulations in the European Union are of limited help and there is a lack of literature about the use of data from this vulnerable group. To aid the creation of a patient-centred framework for responsible data research in the acute setting, we explored views of patients and next-of-kin about the collection, storage, sharing and use of genetic and health-related data for observational research. Methods We conducted qualitative interviews (n = 19) with Dutch sudden cardiac arrest survivors who donated clinical and socio-economic data and genetic samples to research. We also interviewed their next-of-kin. Topics were informed by ethics literature and we used scenario-sketches to aid discussion of complex issues. Results Sudden cardiac arrest survivors displayed limited awareness of their involvement in health data research and of the content of their given consent. We found that preferences regarding disclosure of clinically actionable genetic findings could change over time. When data collection and use were limited to the medical realm, patients trusted researchers to handle data responsibly without concern for privacy or other risks. There was no consensus as to whether deferred consent should be explicitly asked from survivors. If consent is asked, this would ideally be done a few months after the event when cognitive capacities have been regained. Views were divided about the need to obtain proxy consent for research with deceased patients’ data. However, there was general support for the disclosure of potentially relevant post-mortem genetic findings to relatives. Conclusions Sudden cardiac arrest patients’ donation of data for research was grounded in trust in medicine overall, blurring the boundary between research and care. Our findings also highlight questions about the acceptability of a one-time consent and about responsibilities of patients, researchers and ethics committees. Finally, further normative investigation is needed regarding the (continued) use of participants’ data after death, which is of particular importance in this setting. Our findings are thought to be of relevance for other acute and life-threatening illnesses as well.

Abstract Background Enterococcus 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 to vancomycin 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 by Tn1546 transposition between different genomic locations. Methods We 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 characterization 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. Next, we conducted a pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid, or Tn1546 spread accounted for vanA-type resistance dissemination. Results On average, we estimated that 59% of VRE cases with a potential epidemiological link were unrelated which was defined as VRE pairs with a distinct Tn1546 variant. Clonal dissemination accounted for 32% cases in which the same SC and Tn1546 variants were identified. Horizontal plasmid dissemination accounted for 7% of VRE cases, in which we observed VRE pairs belonging to a distinct SC but carrying an identical plasmid and Tn1546 variant. In 2% of cases, we observed the same Tn1546 variant in distinct SC and plasmid types which could be explained by mixed and consecutive events of clonal and plasmid dissemination. Conclusions In related VRE cases, the 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 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 a novel assessment to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type resistance.

Abstract Background A transitional care pathway (TCP) could improve care for older patients in the last months of life. However, barriers exist such as unidentified palliative care needs and suboptimal collaboration between care settings. The aim of this study was to determine the feasibility of a TCP, named PalliSupport, for older patients at the end of life, prior to a stepped-wedge randomized controlled trial. Methods A mixed-method feasibility study was conducted at one hospital with affiliated primary care. Patients were ≥ 60 years and acutely hospitalized. The intervention consisted of (1) training on early identification of the palliative phase and end of life conversations, (2) involvement of a transitional palliative care team during admission and post-discharge and (3) intensified collaboration between care settings. Outcomes were feasibility of recruitment, data collection, patient burden and protocol adherence. Experiences of 14 professionals were assessed through qualitative interviews. Results Only 16% of anticipated participants were included which resulted in difficulty assessing other feasibility criteria. The qualitative analysis identified misunderstandings about palliative care, uncertainty about professionals’ roles and difficulties in initiating end of life conversations as barriers. The training program was well received and professionals found the intensified collaboration beneficial for patient care. The patients that participated experienced low burden and data collection on primary outcomes and protocol adherence seems feasible. Discussion This study highlights the importance of performing a feasibility study prior to embarking on effectiveness studies. Moving forward, the PalliSupport care pathway will be adjusted to incorporate a more active recruitment approach, additional training on identification and palliative care, and further improvement on data collection.

Abstract Early in its evolution, Enterococcus faecium acquired traits that allowed it to become a successful nosocomial pathogen. E. faecium inherent tenacity to build resistance to antibiotics and environmental stressors that allows the species to thrive in hospital environments. The continual wide use of antibiotics in medicine has been an important driver in the evolution of E. faecium becoming a highly proficient hospital pathogen. For successful prevention and reduction of nosocomial infections with vancomycin resistant E. faecium (VREfm), it is essential to focus on reducing VREfm carriage and spread. The aim of this review is to incorporate microbiological insights of E. faecium into practical infection control recommendations, to reduce the spread of hospital-acquired VREfm (carriage and infections). The spread of VREfm can be controlled by intensified cleaning procedures, antibiotic stewardship, rapid screening of VREfm carriage focused on high-risk populations, and identification of transmission routes through accurate detection and typing methods in outbreak situations. Further, for successful management of E. faecium, continual innovation in the fields of diagnostics, treatment, and eradication is necessary.

Abstract 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.

Summary: 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. Funding: Wellcome Trust.

Abstract Background Physicians who receive a request for euthanasia or assisted suicide may experience a conflict of duties: the duty to preserve life on the one hand and the duty to relieve suffering on the other hand. Little is known about experiences of physicians with receiving and granting a request for euthanasia or assisted suicide. This study, therefore, aimed to explore the concerns, feelings and pressure experienced by physicians who receive requests for euthanasia or assisted suicide. Methods In 2016, a cross-sectional study was conducted. Questionnaires were sent to a random sample of 3000 Dutch physicians. Physicians who had been working in adult patient care in the Netherlands for the last year were included in the sample (n = 2657). Half of the physicians were asked about the most recent case in which they refused a request for euthanasia or assisted suicide, and half about the most recent case in which they granted a request for euthanasia or assisted suicide. Results Of the 2657 eligible physicians, 1374 (52%) responded. The most reported reason not to participate was lack of time. Of the respondents, 248 answered questions about a refused euthanasia or assisted suicide request and 245 about a granted EAS request. Concerns about specific aspects of the euthanasia and assisted suicide process, such as the emotional burden of preparing and performing euthanasia or assisted suicide were commonly reported by physicians who refused and who granted a request. Pressure to grant a request was mostly experienced by physicians who refused a request, especially if the patient was ≥80 years, had a life-expectancy of ≥6 months and did not have cancer. The large majority of physicians reported contradictory emotions after having performed euthanasia or assisted suicide. Conclusions Society should be aware of the impact of euthanasia and assisted suicide requests on physicians. The tension physicians experience may decrease their willingness to perform euthanasia and assisted suicide. On the other hand, physicians should not be forced to cross their own moral boundaries or be tempted to perform euthanasia and assisted suicide in cases that may not meet the due care criteria.

Abstract Background European migrant populations are aging and will increasingly be in need of palliative and end of life care. However, migrant patients are often underrepresented in palliative care research populations. This poses a number of drawbacks, such as the inability to generalize findings or check the appropriateness of care innovations amongst migrant patients. The aim of this study was to develop a self-assessment instrument to help palliative care researchers assess and find ways to improve their projects’ diversity responsiveness in light of the aging migrant population, and determine whether in addition to older migrants other groups should be included in the instrument’s focus. Methods After developing a concept instrument based on the standards for equity in healthcare for migrants and other vulnerable groups, literature review and interviews with palliative care researchers, we conducted a Delphi study to establish the content of the self-assessment instrument and used think aloud methods in a study involving seven projects for usability testing of the self-assessment instrument. Results A Delphi panel of 22 experts responded to a questionnaire consisting of 3 items concerning the target group and 30 items on diversity responsiveness measures. Using an a priori set consensus rate of 75% to include items in the self-assessment instrument, experts reached consensus on 25 out of 30 items on diversity responsiveness measures. Findings furthermore indicate that underserved groups in palliative care other than migrant patients should be included in the instrument’s focus. This was stressed by both the experts involved in the Delphi study and the researchers engaged in usability testing. Usability testing additionally provided insights into learnability, error-rate, satisfaction and applicability of the instrument, which were used to revise the self-assessment instrument. Conclusions The final self-assessment instrument includes a list of 23 diversity responsiveness measures to be taken at varying stages of a project, and targets all groups at risk of being underrepresented. This instrument can be used in palliative care research to assess diversity responsiveness of projects and instigate action for improvement.

Abstract Background Patient-reported outcomes (PROs) are frequently used for medical decision making, at the levels of both individual patient care and healthcare policy. Evidence increasingly shows that PROs may be influenced by patients’ response shifts (changes in interpretation) and dispositions (stable characteristics). Main text We identify how response shifts and dispositions may influence medical decisions on both the levels of individual patient care and health policy. We provide examples of these influences and analyse the consequences from the perspectives of ethical principles and theories of just distribution. Conclusion If influences of response shift and disposition on PROs and consequently medical decision making are not considered, patients may not receive optimal treatment and health insurance packages may include treatments that are not the most effective or cost-effective. We call on healthcare practitioners, researchers, policy makers, health insurers, and other stakeholders to critically reflect on why and how such patient reports are used.

Abstract Background Early start of palliative care improves the quality of life of eligible patients and their relatives. However, in hospital, patients who could benefit from palliative care are often not identified timely. The aim of this study is to assess how hospital-based nurses and physicians define the palliative phase, how they identify the palliative phase and what difficulties they face. Methods Semi-structured interviews were held with ten nurses and 18 physicians working at seven hospitals in the Netherlands. Data was analysed using thematic analysis. Results Nurses and physicians feel insecure about how to define the palliative phase and differentiate between an acute and extended phase. Great variation existed in what life expectancy is attributed to each phase. A variety of ways to identify the palliative phase were described: 1) Prognostication. 2) Treatment trade-off. 3) Assessment of patients’ preferences and needs. 4) Interprofessional collaboration. Professionals base prognostication on their experience but also search for clinical indicators. When benefits of treatment no longer outweigh the negatives, this was considered an, albeit late, identification point. To start a conversation on a patients’ palliative care needs was found to be difficult. Therefore, some respondents wait for patients to vocalize preferences themselves. Many professionals rely on interprofessional collaboration for identification, however uncertainty exist about responsibilities. Difficulties in identification occurred because of variance in definitions, unpredictability of non-oncological diseases, focus on treatment and difficulties in communication and collaboration. Conclusion These results provide insight into the challenges and difficulties hospital-based professionals experience in timely identification of patients with palliative care needs.

Abstract Background There is increasing awareness of the need for an integrated palliative care approach in chronic progressive neurological diseases. Advance care planning (ACP) is an integral part of this approach. As a systematically organized and ongoing communication process about patients’ values, goals and preferences regarding medical care during serious and chronic illness, ACP aims to involve patients in decision-making before they become cognitively and communicatively incapable. However, it remains underutilized in daily neurological practice except for speciality clinics such as ALS centers. Our aim was to study ACP in the tertiary ALS center Amsterdam and to investigate patients’ reflections on it. Subsequently we used this knowledge to formulate recommendations for integration of ACP in the care of patients with other chronic progressive neurological diseases. Methods Non-participating observations of all appointments of patients with amyotrophic lateral sclerosis (ALS) or progressive muscular atrophy (PMA) with the treating physician, in various stages of disease, during 6 consecutive months, followed by single in-depth interviews, and an inductive analysis. Results Twenty-eight Dutch patients participated, varying in age, gender, disease onset and severity of physical decline. ACP started directly when the diagnosis was given, by means of a general outlook on the future with progressive disability and immediate introduction to a customized multidisciplinary team. During follow-up ACP was realized by regular appointments in which monitoring of the patient’s status and clear communication strategies formed the basis of tailor-made discussions on treatment options. Patients accepted this policy as careful professional guidance. Conclusions ACP is a professional communication process throughout the whole course of progressive disease. It is feasible to integrate ACP into follow-up of patients with ALS and PMA from diagnosis onwards. Supported by recent literature, we argue that such a well-structured approach would also enhance the quality of care and life of patients with other chronic progressive neurological diseases.

Common Variable Immunodeficiency (CVID) and X-linked agammaglobulinemia (XLA) are primary antibody deficiencies characterized by hypogammaglobulinemia and recurrent infections, which can lead to structural airway disease (AD) and interstitial lung disease (ILD). We investigated associations between serum IgA, oropharyngeal microbiota composition and severity of lung disease in these patients. In this cross-sectional multicentre study we analyzed oropharyngeal microbiota composition of 86 CVID patients, 12 XLA patients and 49 healthy controls (HC) using next-generation sequencing of the 16S rRNA gene. qPCR was used to estimate bacterial load. IgA was measured in serum. High resolution CT scans were scored for severity of AD and ILD. Oropharyngeal bacterial load was increased in CVID patients with low IgA (p = 0.013) and XLA (p = 0.029) compared to HC. IgA status was associated with distinct beta (between-sample) diversity (p = 0.039), enrichment of (Allo)prevotella, and more severe radiographic lung disease (p = 0.003), independently of recent antibiotic use. AD scores were positively associated with Prevotella, Alloprevotella, and Selenomonas, and ILD scores with Streptococcus and negatively with Rothia. In clinically stable patients with CVID and XLA, radiographic lung disease was associated with IgA deficiency and expansion of distinct oropharyngeal bacterial taxa. Our findings highlight IgA as a potential driver of upper respiratory tract microbiota homeostasis.

ABSTRACT Infections by multidrug-resistant Gram-negative bacteria are increasingly common, prompting the renewed interest in the use of colistin. Colistin specifically targets Gram-negative bacteria by interacting with the anionic lipid A moieties of lipopolysaccharides, leading to membrane destabilization and cell death. Here, we aimed to uncover the mechanisms of colistin resistance in nine colistin-resistant Escherichia coli strains and one Escherichia albertii strain. These were the only colistin-resistant strains of 1,140 bloodstream Escherichia isolates collected in a tertiary hospital over a 10-year period (2006 to 2015). Core-genome phylogenetic analysis showed that each patient was colonized by a unique strain, suggesting that colistin resistance was acquired independently in each strain. All colistin-resistant strains had lipid A that was modified with phosphoethanolamine. In addition, two E. coli strains had hepta-acylated lipid A species, containing an additional palmitate compared to the canonical hexa-acylated E. coli lipid A. One E. coli strain carried the mobile colistin resistance (mcr) gene mcr-1.1 on an IncX4-type plasmid. Through construction of chromosomal transgene integration mutants, we experimentally determined that mutations in basRS, encoding a two-component signal transduction system, contributed to colistin resistance in four strains. We confirmed these observations by reversing the mutations in basRS to the sequences found in reference strains, resulting in loss of colistin resistance. While the mcr genes have become a widely studied mechanism of colistin resistance in E. coli, sequence variation in basRS is another, potentially more prevalent but relatively underexplored, cause of colistin resistance in this important nosocomial pathogen. IMPORTANCE Multidrug resistance among Gram-negative bacteria has led to the use of colistin as a last-resort drug. The cationic colistin kills Gram-negative bacteria through electrostatic interaction with the anionic lipid A moiety of lipopolysaccharides. Due to increased use in clinical and agricultural settings, colistin resistance has recently started to emerge. In this study, we used a combination of whole-genome sequence analysis and experimental validation to characterize the mechanisms through which Escherichia coli strains from bloodstream infections can develop colistin resistance. We found no evidence of direct transfer of colistin-resistant isolates between patients. The lipid A of all isolates was modified by the addition of phosphoethanolamine. In four isolates, colistin resistance was experimentally verified to be caused by mutations in the basRS genes, encoding a two-component regulatory system. Our data show that chromosomal mutations are an important cause of colistin resistance among clinical E. coli isolates.

ABSTRACT Enterococcus faecium is a gut commensal of humans and animals but is also listed on the WHO global priority list of multidrug-resistant pathogens. Many of its antibiotic resistance traits reside on plasmids and have the potential to be disseminated by horizontal gene transfer. Here, we present the first comprehensive population-wide analysis of the pan-plasmidome of a clinically important bacterium, by whole-genome sequence analysis of 1,644 isolates from hospital, commensal, and animal sources of E. faecium. Long-read sequencing on a selection of isolates resulted in the completion of 305 plasmids that exhibited high levels of sequence modularity. We further investigated the entirety of all plasmids of each isolate (plasmidome) using a combination of short-read sequencing and machine-learning classifiers. Clustering of the plasmid sequences unraveled different E. faecium populations with a clear association with hospitalized patient isolates, suggesting different optimal configurations of plasmids in the hospital environment. The characterization of these populations allowed us to identify common mechanisms of plasmid stabilization such as toxin-antitoxin systems and genes exclusively present in particular plasmidome populations exemplified by copper resistance, phosphotransferase systems, or bacteriocin genes potentially involved in niche adaptation. Based on the distribution of k-mer distances between isolates, we concluded that plasmidomes rather than chromosomes are most informative for source specificity of E. faecium. IMPORTANCE Enterococcus faecium is one of the most frequent nosocomial pathogens of hospital-acquired infections. E. faecium has gained resistance against most commonly available antibiotics, most notably, against ampicillin, gentamicin, and vancomycin, which renders infections difficult to treat. Many antibiotic resistance traits, in particular, vancomycin resistance, can be encoded in autonomous and extrachromosomal elements called plasmids. These sequences can be disseminated to other isolates by horizontal gene transfer and confer novel mechanisms to source specificity. In our study, we elucidated the total plasmid content, referred to as the plasmidome, of 1,644 E. faecium isolates by using short- and long-read whole-genome technologies with the combination of a machine-learning classifier. This was fundamental to investigate the full collection of plasmid sequences present in our collection (pan-plasmidome) and to observe the potential transfer of plasmid sequences between E. faecium hosts. We observed that E. faecium isolates from hospitalized patients carried a larger number of plasmid sequences compared to that from other sources, and they elucidated different configurations of plasmidome populations in the hospital environment. We assessed the contribution of different genomic components and observed that plasmid sequences have the highest contribution to source specificity. Our study suggests that E. faecium plasmids are regulated by complex ecological constraints rather than physical interaction between hosts.

Abstract Sudden cardiac arrest (SCA) accounts for half of all cardiac deaths in Europe. In recent years, large-scale SCA registries have been set up to enable observational studies into risk factors and the effect of treatment approaches. The increasing scale and variety of data sources, coupled with the implementation of a new European data protection legal framework, causes researchers to struggle with how to handle these ‘big data’. Data protection in the SCA setting is especially complex since patients become at least temporarily incapacitated, and are thus unable to provide prospective informed consent, and because the majority of patients do not survive. A narrative review employing a systematic literature search was conducted to thematically analyse ethical aspects of non-interventional emergency medicine and critical care research. Although the identified issues may apply to a wider patient population, we describe them within the context of SCA research. Potential harms were found to include: privacy breaches, genetic discrimination and issues associated with the disclosure of individual findings, study design and application of research results. Measures proposed to mitigate harms were: alternative informed consent models including deferred or waived consent and data governance approaches promoting data security, responsible sharing and public engagement. The themes identified in this study may serve as a basis for a much-needed ethical framework regarding research with data from patients with acute and critical illness such as SCA.

Abstract Background The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can survive and grow in blood during an infection have not yet been characterized. Here, we identify genes that contribute to growth of E. faecium in human serum through transcriptome profiling (RNA-seq) and a high-throughput transposon mutant library sequencing approach (Tn-seq). Results We first sequenced the genome of E. faecium E745, a vancomycin-resistant clinical isolate, using a combination of short- and long read sequencing, revealing a 2,765,010 nt chromosome and 6 plasmids, with sizes ranging between 9.3 kbp and 223.7 kbp. We then compared the transcriptome of E. faecium E745 during exponential growth in rich medium and in human serum by RNA-seq. This analysis revealed that 27.8% of genes on the E. faecium E745 genome were differentially expressed in these two conditions. A gene cluster with a role in purine biosynthesis was among the most upregulated genes in E. faecium E745 upon growth in serum. The E. faecium E745 transposon mutant library was then used to identify genes that were specifically required for growth of E. faecium in serum. Genes involved in de novo nucleotide biosynthesis (including pyrK_2, pyrF, purD, purH) and a gene encoding a phosphotransferase system subunit (manY_2) were thus identified to be contributing to E. faecium growth in human serum. Transposon mutants in pyrK_2, pyrF, purD, purH and manY_2 were isolated from the library and their impaired growth in human serum was confirmed. In addition, the pyrK_2 and manY_2 mutants were tested for their virulence in an intravenous zebrafish infection model and exhibited significantly attenuated virulence compared to E. faecium E745. Conclusions Genes involved in carbohydrate metabolism and nucleotide biosynthesis of E. faecium are essential for growth in human serum and contribute to the pathogenesis of this organism. These genes may serve as targets for the development of novel anti-infectives for the treatment of E. faecium bloodstream infections.

Abstract Background The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed “selective decontamination of the digestive tract” (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes (“the resistome”) of ICU patients during SDD and of healthy subjects. Results From ten patients that were acutely admitted to the ICU, 30 fecal samples were collected during ICU stay. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. Feces from ten healthy subjects were collected twice, with a 1-year interval. Gut microbiota and resistome composition were determined using 16S rRNA gene phylogenetic profiling and nanolitre-scale quantitative PCRs. The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by lower microbial diversity, decreased levels of Escherichia coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6′)-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants, and tetracyclines, respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects. Conclusions The gut microbiota of SDD-treated ICU patients deviated strongly from the gut microbiota of healthy subjects. The negative effects on the resistome were limited to selection for four resistance genes. While it was not possible to disentangle the effects of SDD from confounding variables in the patient cohort, our data suggest that the risks associated with ICU hospitalization and SDD on selection for antibiotic resistance are limited. However, we found evidence indicating that recolonization of the gut by antibiotic-resistant bacteria may occur upon ICU discharge and cessation of SDD.

BACKGROUND:Knowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is mostly based on extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec). We determined differences in clonality and resistance and virulence gene (VG) content between non-ESBL-producing E. coli (non-ESBL-Ec) and ESBL-Ec isolates from ECB episodes with different epidemiological characteristics. METHODS:A random selection of non-ESBL-Ec isolates as well as all available ESBL-Ec blood isolates was obtained from two Dutch hospitals between 2014 and 2016. Whole genome sequencing was performed to infer sequence types (STs), serotypes, acquired antibiotic resistance genes and VG scores, based on presence of 49 predefined putative pathogenic VG. RESULTS:ST73 was most prevalent among the 212 non-ESBL-Ec (N = 26, 12.3%) and ST131 among the 69 ESBL-Ec (N = 30, 43.5%). Prevalence of ST131 among non-ESBL-Ec was 10.4% (N = 22, P value < .001 compared to ESBL-Ec). O25:H4 was the most common serotype in both non-ESBL-Ec and ESBL-Ec. Median acquired resistance gene counts were 1 (IQR 1-6) and 7 (IQR 4-9) for non-ESBL-Ec and ESBL-Ec, respectively (P value < .001). Among non-ESBL-Ec, acquired resistance gene count was highest among blood isolates from a primary gastro-intestinal focus (median 4, IQR 1-8). Median VG scores were 13 (IQR 9-20) and 12 (IQR 8-14) for non-ESBL-Ec and ESBL-Ec, respectively (P value = .002). VG scores among non-ESBL-Ec from a primary urinary focus (median 15, IQR 11-21) were higher compared to non-ESBL-Ec from a primary gastro-intestinal (median 10, IQR 5-13) or hepatic-biliary focus (median 11, IQR 5-18) (P values = .007 and .04, respectively). VG content varied between different E. coli STs. CONCLUSIONS:Non-ESBL-Ec and ESBL-Ec blood isolates from two Dutch hospitals differed in clonal distribution, resistance gene and VG content. Also, resistance gene and VG content differed between non-ESBL-Ec from different primary foci of ECB.

Abstract The aim of this study was to determine whether dietary intervention influenced luminal Ca2+ levels and Enterococcus faecium gut colonization in mice. For this purpose, mice fed semi‐synthetic food AIN93 were compared to mice fed AIN93‐low calcium (LC). Administration of AIN93‐LC resulted in lower luminal Ca2+ levels independent of the presence of E. faecium. Furthermore, E. faecium gut colonization was reduced in mice fed AIN93‐LC based on culture, and which was in concordance with a reduction of Enterococcaceae in microbiota analysis. In conclusion, diet intervention might be a strategy for controlling gut colonization of E. faecium, an important opportunistic nosocomial pathogen.

Hundreds of geothermal wells have been drilled in Hungary to exploit Pannonian Basin sandstones for district heating, agriculture, and industrial heating projects. Most of these sites suffer from reinjection issues, limiting efficient use of this vast geothermal resource and imposing significant extra costs for the required frequent workovers and maintenance. To better understand the cause of this issue requires details of reservoir rock porosity, permeability, and mineralogy. However, publicly available data for the properties of reservoir rocks at geothermal project sites in Hungary is typically very limited, because these projects often omit or limit data acquisition. Many hydrocarbon wells in the same rocks are more extensively documented, but their core, log, or production data are typically decades old and unavailable in the public domain. Furthermore, because many Pannonian sandstone formations are poorly consolidated, coring was always limited and the collected core often unsuitable for conventional analysis, only small remnant fragments typically being available from legacy hydrocarbon wells. This study aims to reduce this data gap and to showcase methods to derive reservoir properties without using core for flow experiments. The methods are thin-section analysis, XRD analysis and mercury intrusion porosimetry, and X-CT scanning followed by numerical flow simulation. We validate our results using permeability data from conventional production testing, demonstrating the effectiveness of our method for detailed reservoir characterization and to better constrain the lateral variation in reservoir properties across the Pannonian Basin. By eliminating the need for expensive bespoke coring to obtain reservoir properties, such analysis will contribute to reducing the capital cost of developing geothermal energy projects, thus facilitating decarbonization of global energy supply.