Navigating social and ethical challenges of biobanking for human microbiome research

Estimating implicit and explicit racial and ethnic bias among community pharmacists in Canada

Background

Bias, whether implicit (unconscious) or explicit (conscious), can lead to preferential treatment of specific social groups and antipathy towards others. When healthcare professionals (HCPs), including pharmacists, act on these biases, patient care and health outcomes can be adversely affected. This study aims to estimate implicit and explicit racial/ethnic bias towards Black and Arab people among community pharmacists in Ontario, Canada.

Methods

Community pharmacists participated in a secure, web-based survey using a cross-sectional design that included Harvard's Race and Arab Implicit Association Tests (IATs) to examine bias towards Black and Arab people. Explicit (stated) preferences were measured by self-report. Data were analyzed using descriptive and inferential statistics.

Results

The study surveyed 407 community pharmacists, 56.1 % of whom were women with an average age of 46.9. Implicit Association Test (IAT) results showed a statistically significant moderate preference for white people over both Black (mean IAT = 0.41) and Arab people (mean IAT = 0.35). However, most pharmacists explicitly stated that they had no racial/ethnic preference, with 75.7 % expressing a neutral preference between Black and white and 66.6 % neutral between Arab and white. However, a slight preference for white individuals was observed. Demographic factors such as age, place of birth, race/ethnicity, and experience significantly impacted IAT scores. For example, older, Canadian-born, white pharmacists with more experience displayed higher implicit bias scores. A mild correlation was found between implicit and explicit bias, indicating as implicit bias increases, explicit bias tends to become more negative.

Conclusions

This study is the first to explore the issue of pharmacist bias in Canada and concentrate on anti-Arab bias. Our findings reveal that Ontario community pharmacists tend to have an unconscious inclination towards white people, which calls for further understanding of this matter. Additionally, we discovered a moderate degree of anti-Arab bias, indicating that studies on other HCPs should consider bias against this social group. Educational interventions are needed to address the implicit biases among community pharmacists in Ontario, Canada. These findings should aim to raise self-awareness of biases, educate about the potential implications of these biases on patient care, and provide strategies to reduce bias.

(Predictable) performance bias in unsupervised anomaly detection

BACKGROUND

With the ever-increasing amount of medical imaging data, the demand for algorithms to assist clinicians has amplified. Unsupervised anomaly detection (UAD) models promise to aid in the crucial first step of disease detection. While previous studies have thoroughly explored fairness in supervised models in healthcare, for UAD, this has so far been unexplored.

METHODS

In this study, we evaluated how dataset composition regarding subgroups manifests in disparate performance of UAD models along multiple protected variables on three large-scale publicly available chest X-ray datasets. Our experiments were validated using two state-of-the-art UAD models for medical images. Finally, we introduced subgroup-AUROC (sAUROC), which aids in quantifying fairness in machine learning.

FINDINGS

Our experiments revealed empirical "fairness laws" (similar to "scaling laws" for Transformers) for training-dataset composition: Linear relationships between anomaly detection performance within a subpopulation and its representation in the training data. Our study further revealed performance disparities, even in the case of balanced training data, and compound effects that exacerbate the drop in performance for subjects associated with multiple adversely affected groups.

INTERPRETATION

Our study quantified the disparate performance of UAD models against certain demographic subgroups. Importantly, we showed that this unfairness cannot be mitigated by balanced representation alone. Instead, the representation of some subgroups seems harder to learn by UAD models than that of others. The empirical "fairness laws" discovered in our study make disparate performance in UAD models easier to estimate and aid in determining the most desirable dataset composition.

FUNDING

European Research Council Deep4MI.

A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions

Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw data, hindering the ability to perform robust data stratifications and consider confounding factors. In this comprehensive review, we categorize publicly available microbiome data into five types: shotgun sequencing, amplicon sequencing, metatranscriptomic, metabolomic, and metaproteomic data. We explore the importance of metadata for data reuse and address the challenges in collecting standardized metadata. We also, assess the limitations in metadata collection of existing public repositories collecting metagenomic data. This review emphasizes the vital role of metadata in interpreting and comparing datasets and highlights the need for standardized metadata protocols to fully leverage metagenomic data's potential. Furthermore, we explore future directions of implementation of Machine Learning (ML) in metadata retrieval, offering promising avenues for a deeper understanding of microbial communities and their ecological roles. Leveraging these tools will enhance our insights into microbial functional capabilities and ecological dynamics in diverse ecosystems. Finally, we emphasize the crucial metadata role in ML models development.

Myocardial Infarction Within 30 Days of Discharge From an Emergency Department: A Descriptive Study of Albertan Women

Background

Cardiovascular diseases (CVDs) are the leading cause of premature death for Canadian women, which may be due partly to a lack of awareness of the presentation of acute coronary events in emergency departments (EDs). To address an identified gap in women's cardiovascular care, we sought to describe the clinical and comorbid factors of women who, following discharge from an ED, suffered a myocardial infarction (MI).

Methods

Descriptive analyses were completed on a cohort of women who presented to an ED in Alberta, Canada, between January 1, 2010 and December 31, 2020, were discharged, and within 30 days of their index ED visit, were admitted to the hospital with an MI. The cohort was explored for clinical and comorbid data, ED visits pre-MI, type of MI, and presenting complaint/ primary diagnosis for the index ED visit.

Results

1380 women were included in this analysis with a mean age of 67 (standard deviation ±13) years. The frequencies of hypertension, diabetes, and dyslipidemia among the youngest women, aged 18-45 years, were 47.5%, 31.3%, and 48.8%, respectively. Women across all ages demonstrated a high prevalence of traditional CVD risk factors, and 22% of women presented to an ED 2 or more times within the 30 days pre-MI.

Conclusions

Regardless of their age, the women in this cohort had notable CVD risk factors. Future research is required to better understand the phenomenon of women presenting multiple times to an ED pre-MI. Research is needed on life-stage-specific factors of women presenting to EDs pre-MI, to help reduce MI incidence.

Ethical challenges in conducting and the clinical application of human microbiome research

The Article Abstract is not available.    

A blockchain-enabled sharing platform for personal health records

Background

Longitudinal personal health record (PHR) provides a foundation for managing patients' health care, but we do not have such a system in the U.S. except for the patients in the Department of Veterans Affairs. Such a gap exists mainly in the rest of the U.S. by the fact that patients' electronic health records are scattered across multiple health care facilities and often not shared due to privacy, security, and business interests concerns from both patients and health care organizations. In addition, patients have ethical concerns related to consent. To patients, data security, privacy, and consent are based on trustfulness, rather than patients' engagement in ensuring only authorized people can view their PHRs with patient-managed granularity. Resolving these challenges is an important step in making longitudinal PHR useful for patient care.

Objective

This research aims to design and implement a blockchain-enabled sharing platform prototype for PHR with desired patient-controlled data security, privacy, and consent granularity.

Methods

Built upon our prior work of a blockchain-enabled access control (BAC) model, we design a blockchain-enabled sharing platform for PHR with patient-controlled security, privacy, and consent granularity. We further implement the construct by building a prototypical platform among a patient and two typical health care organizations. Health organizations that hold the patient's electronic health records can join the platform with trust based on the validation from the patient. The mutual trust can be established through a rigorous validation process by both the patient and the built-in Hyperledger Fabric blockchain consensus mechanism.

Results

We proposed a system trusted by patients and health care providers and constructed a Web-based PHR sharing platform with patient-controlled security, privacy, and consent granularity. We analyzed the system scalability in three aspects and showed millisecond range of performance when simultaneously changing access permissions on hundreds of PHRs. Consent, security and privacy of the model are ensured by the merits of the BAC model. We discovered the current blockchain model limits the system scalability due to using a non-graphical database. A new graphical database is suggested for future improvements.

Conclusions

In this research, we report a solution to electronically sharing and managing patients' electronic health records originating from multiple organizations, focusing on privacy, security, and granularity control of consent in the U.S. Specifically, the system protects data security and privacy, and provides auditability, scalability, distributedness, patient consent autonomy, and zero-trust capabilities. The prototypical instantiation of the designed model suggested the feasibility of combining emerging blockchain technology with next generation access control model to tackle a longstanding longitudinal PHR problem.

Realising respiratory microbiomic meta-analyses: time for a standardised framework

In microbiome fields of study, meta-analyses have proven to be a valuable tool for identifying the technical drivers of variation among studies and results of investigations in several diseases, such as those of the gut and sinuses. Meta-analyses also represent a powerful and efficient approach to leverage existing scientific data to both reaffirm existing findings and generate new hypotheses within the field. However, there are currently limited data in other fields, such as the paediatric respiratory tract, where extension of original data becomes even more critical due to samples often being difficult to obtain and process for a range of both technical and ethical reasons. Performing such analyses in an evolving field comes with challenges related to data accessibility and heterogeneity. This is particularly the case in paediatric respiratory microbiomics - a field in which best microbiome-related practices are not yet firmly established, clinical heterogeneity abounds and ethical challenges can complicate sharing of patient data. Having recently conducted a large-scale, individual participant data meta-analysis of the paediatric respiratory microbiota (n = 2624 children from 20 studies), we discuss here some of the unique barriers facing these studies and open and invite a dialogue towards future opportunities. Video Abstract.

Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic

We assessed public perspectives of microbiome research privacy risks before and after a nationwide emergency was declared in the United States regarding the Covid-19 pandemic. From January to July of 2020, we conducted an online survey of perceived privacy risks of microbiome research among U.S. adults. Among 3,106 participants (the preemergency group), most expressed that the microbiome posed privacy risks similar to those associated with DNA (60.3%) or medical records (50.6%) and that they would prefer detailed explanations (70.2%) of risk in consent materials. Only 8.9% reported moderate to high familiarity with microbiome privacy risks. In adjusted analyses, individuals who participated in the study after the Covid-19 emergency was declared (the Covid-19 emergency group) were less likely to express that microbiome privacy risks were similar to those of DNA or medical records and more likely to report familiarity with the privacy risks of microbiomes. There was a trend toward increased concern after the Covid-19 emergency was declared (p = 0.053). Overall, the study revealed that many U.S. adults believe that microbiome privacy risks are similar to those associated with DNA or medical records, and they prefer detailed explanations in consent documents. Individuals who participated after the Covid-19 emergency was declared reported greater knowledge of microbiome privacy risks but had more concern.

Travelling to die: views, attitudes and end-of-life preferences of Israeli considering receiving aid-in-dying in Switzerland

Background

Following the increased presence of the Right-to-Die Movement, improved end-of-life options, and the political and legal status of aid-in-dying around the globe, suicide tourism has become a promising alternative for individuals who wish to end their lives. Yet, little is known about this from the perspective of those who engage in the phenomenon.

Methods

This study applied the qualitative research approach, following the grounded theory tradition. It includes 11 in-depth semi-structured interviews with Israeli members of the Swiss non-profit Dignitas who contemplated traveling to Switzerland for aid-in-dying.

Results

Seven themes emerged from the data analysis, including health and functioning; feelings regarding survivorship and existence; interacting with the health sector; attitudes regarding death and dying; suicide; choosing death; and choosing suicide tourism. A significant portion of the participants had experienced suicidal thoughts and had even previously attempted suicide, some more than once. Most of them referred to chronic illnesses, functional disability, and social isolation. They understand suffering within the subjective dimension, namely only by the person who is actually subjected to the disease, ailments, and disability. Participants regarded aid-in-dying in Switzerland as positive thanks to its guaranteed outcome: "beautiful death", compared to "disadvantaged dying" which places a burden on the participants' loved ones throughout the prolonged dying. Most of them do not necessarily want to have their loved ones beside them when they die, and they see no significant meaning in dying in a foreign country to which they have no emotional or civil attachment.

Conclusion

The desirable approval or tragic refusal by Dignitas to participants' requests for suicide tourism enhances the paradox between the perception of aid-in-dying as a mechanism for fulfilling controlled death and its bureaucratic and materialistic characteristics specifically reflected in a paid, formalized approach to aid-in-dying that cultivate dependency and collaboration.

A comprehensive approach to stool donor screening for faecal microbiota transplantation in China

Background

Faecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium difficile infections and chronic gastrointestional infections. However, the risks of FMT and the selection process of suitable donors remain insufficiently characterized. The eligibility rate for screening, underlying microbial basis, and core ethical issues of stool donors for FMT are yet to be elucidated in China.

Results

The potential stool donors were screened from December 2017 to December 2019 with the help of an online survey, clinical assessments, and stool and blood testing. Bioinformatics analyses were performed, and the composition and stability of gut microbiota in stool obtained from eligible donors were dynamically observed using metagenomics. Meanwhile, we build a donor microbial evaluation index (DoMEI) for stool donor screening. In the screening process, we also focused on ethical principles and requirements. Of the 2071 participants, 66 donors were selected via the screening process (3.19% success rate). Although there were significant differences in gut microbiota among donors, we found that the changes in the gut microbiota of the same donor were typically more stable than those between donors over time.

Conclusions

DoMEI provides a potential reference index for regular stool donor re-evaluation. In this retrospective study, we summarised the donor recruitment and screening procedure ensuring the safety and tolerability for FMT in China. Based on the latest advances in this field, we carried out rigorous recommendation and method which can assist stool bank and clinicians to screen eligible stool donor for FMT.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01705-0.

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice

Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.

Biobank networking and globalisation: perspectives and practices of Australian biobanks

Objective This study examined the practices and attitudes of Australian biobanks regarding access to samples and data, as well as local and global networking with other biobanks. Methods This was a mixed-methods study, including an online survey of Australian biobank administrators and qualitative interviews with survey participants. The survey examined the criteria applied when considering requests to share or network. The interviews explored attitudes and practices regarding sharing and networking. Results Most (90.9%; 30/33) biobanks offered access to their samples and data to others, principally for research (90.6%; 29/32). The most common criteria used to evaluate access requests included ethical oversight (84.8%; 28/33), scientific merit (84.8%; 28/33) and intended use (81.8%; 27/33). Just over two-thirds (69.7%; 23/33) of biobanks participated in Australian networks, and 39.1% (9/23) participated in global networks. Networking took the form of both sharing standardised operating procedures and policies (60.9%) and sharing samples and data (43.5%). Thirteen of the 16 interviewees participated in networks. Motivations for sharing included scientific necessity, sharing expertise and standardising operations and governance. Significant barriers to networking remain, including insufficient resources, inconsistent regulations and procedures, and cultural and political issues to do with the conduct of research. Conclusions Many Australian biobanks are already active participants in various types of global biobanking. If biobanks are to expand and make the most of their involvement in global networks, then important barriers need to be overcome. What is known about the topic? Biobanks that store human tissue and associated data are increasingly forming local, national and global networks. These networks create opportunities for enhancing the utility and sustainability of biobanks, but also raise considerable technical, legal and ethical challenges. What does this paper add? This paper reports findings from a mixed-methods study of Australian biobanks and reveals contemporary practices and perspectives concerning sample and data sharing, as well as local and global networking. It found most Australian biobanks currently take part in these activities. What are the implications for practitioners? Many Australian biobanks are networking in various ways across regional and national borders. A better understanding of current practices and views on significant and emerging issues is relevant to the diverse range of biobank stakeholders involved in any agenda to expand biobank networking, including patients, consumers, clinicians, scientists, policy makers and regulators.

Citizens' views on sharing their health data: the role of competence, reliability and pursuing the common good

Background

In this article, we address questions regarding how people consider what they do or do not consent to and the reasons why. This article presents the findings of a citizen forum study conducted by the University of Geneva in partnership with the Geneva University Hospitals to explore the opinions and concerns of members of the public regarding predictive oncology, genetic sequencing, and cancer.

Methods

This paper presents the results of a citizen forum that included 73 participants. A research tool titled "the mechanics of consent" was designed for this study. This tool is a table encouraging participants to reflect on social and research actors, types of data, and desired levels of control while sharing different types of data with different actors. Participants’ discussion that led to the completion of each table were audio-recorded, transcribed, and analyzed using thematic analysis.

Results

The results are a compilation of responses from the mechanics of consent tool divided into two sections; the first presents quantitative results of collective responses regarding attitudes to consent to donate their data. The second section present qualitative findings emerged from the discussion amongst participants.

Discussion

Choice and control of personal data is crucial for the public to be able to decide who and how to trust. Key information to be disclosed to potential research participants shall include information about potential risks and benefits; who will be accessing and using their data; as well as assurances that their choice will be respected. Furthermore, researchers ought to make sure they are trustworthy, by acting in a competent, reliable, and honest manner. Governance systems ought to be better equipped to address ethical issues raise by the growing presence of non-traditional research actors, consent of exchanges of data via digital devices and online activity such as social media and fairness of data trading. Finally, informed consent is one of the various elements that contribute to conducting ethical research. More needs to be done to strengthen governance and ensure adequate protection of research participants, particularly to address issues related to predictive health analytics.

A framework for microbiome science in public health

Human microbiome science has advanced rapidly and reached a scale at which basic biology, clinical translation and population health are increasingly integrated. It is thus now possible for public health researchers, practitioners and policymakers to take specific action leveraging current and future microbiome-based opportunities and best practices. Here we provide an outline of considerations for research, education, interpretation and scientific communication concerning the human microbiome and public health. This includes guidelines for population-scale microbiome study design; necessary physical platforms and analysis methods; integration into public health areas such as epidemiology, nutrition, chronic disease, and global and environmental health; entrepreneurship and technology transfer; and educational curricula. Particularly in the near future, there are both opportunities for the incorporation of microbiome-based technologies into public health practice, and a growing need for policymaking and regulation around related areas such as prebiotic and probiotic supplements, novel live-cell therapies and fecal microbiota transplants.

Knowledge, attitudes, ethical and social perspectives towards fecal microbiota transplantation (FMT) among Jordanian healthcare providers

BACKGROUND

Fecal microbiota transplant (FMT) is a treatment modality that involves the introduction of stool from a healthy pre-screened donor into the gastrointestinal tract of a patient. It exerts its therapeutic effects by remodeling the gut microbiota and treating microbial dysbiosis-imbalance. FMT is not regulated in Jordan, and regulatory effort for FMT therapy in Jordan, an Islamic conservative country, might be faced with unique cultural, social, religious, and ethical challenges. We aimed to assess knowledge, attitudes, and perceptions of ethical and social issues of FMT use among Jordanian healthcare professionals.

METHODS

An observational, cross-sectional study design was used to assess knowledge, attitudes, and perceptions of ethical and social issues of FMT among 300 Jordanian healthcare professionals.

RESULTS

A large proportion (39 %) thought that the safety and efficacy of this technique are limited and 29.3 % thought there is no evidence to support its use. Almost all (95 %) responded that they would only perform it in certain cases, if ethically justified, and 48.3 % would use it due to treatment failure of other approaches. When reporting about reasons for not using it, 40 % reported that they would not perform it due to concerns about medical litigation, fear of infections (38 %), and lack of knowledge of long safety and efficacy (31.3 %). Interestingly, all practitioners said they would perform this procedure through the lower rather than upper gastrointestinal tract modality and the majority will protect the patient's confidentiality via double-blinding (43.3 %). For a subset of participants (n = 100), the cultural constraints that might affect the choice of performing FMT were mainly due to donor's religion, followed by dietary intake, and alcohol consumption.

CONCLUSIONS

Our healthcare practitioners are generally reluctant to use the FMT modality due to religious and ethical reasons but would consider it if there was a failure of other treatment and after taking into consideration many legislative, social, ethical and practice-based challenges including safety, efficacy and absence of guidelines.

Recent advances in culture-based gut microbiome research

Gut microbes affect the physiology of their hosts. Studying their diversity and functions is thus of utmost importance as it will open new avenues towards the discovery of new biomolecules and the treatment of diseases. Gut microbiome research is currently boosted by the unification of metagenomics, which has dominated the field in the last two decades, and cultivation, which is experiencing a renaissance. Each of these approaches has advantages and drawbacks that can be overcome if used synergistically. In this brief article, we summarize recent literature and own studies on the cultivation of gut microbes, provide a succinct status quo of cultured fractions and collections of isolates, and give short opinions on challenges and next steps to take.

Framing the discussion of microorganisms as a facet of social equity in human health

What do “microbes” have to do with social equity? These microorganisms are integral to our health, that of our natural environment, and even the “health” of the environments we build. The loss, gain, and retention of microorganisms—their flow between humans and the environment—can greatly impact our health. It is well-known that inequalities in access to perinatal care, healthy foods, quality housing, and the natural environment can create and arise from social inequality. Here, we focus on the argument that access to beneficial microorganisms is a facet of public health, and health inequality may be compounded by inequitable microbial exposure.

What do microbes have to do with social equity? This Essay explores the argument that access to beneficial microorganisms is a facet of public health, and that health inequality may be compounded by inequitable microbial exposure.

A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition

The microbiome plays many roles in human health, often through the exclusive lens of clinical interest. The inevitable end point for all living hosts, death, has its own altered microbiome configurations. However, little is understood about the ecology and changes of microbial communities after death, or their potential utility for understanding the health condition of the recently living. Here we reveal distinct postmortem microbiomes of human hosts from a large-scale survey of death cases representing a predominantly urban population, and demonstrated these microbiomes reflected antemortem health conditions within 24–48 hours of death. Our results characterized microbial community structure and predicted function from 188 cases representing a cross-section of an industrial-urban population. We found strong niche differentiation of anatomic habitat and microbial community turnover based on topographical distribution. Microbial community stability was documented up to two days after death. Additionally, we observed a positive relationship between cell motility and time since host death. Interestingly, we discovered evidence that microbial biodiversity is a predictor of antemortem host health condition (e.g., heart disease). These findings improve the understanding of postmortem host microbiota dynamics, and provide a robust dataset to test the postmortem microbiome as a tool for assessing health conditions in living populations.

How medical technologies shape the experience of illness

In this article we explore how diagnostic and therapeutic technologies shape the lived experiences of illness for patients. By analysing a wide range of examples, we identify six ways that technology can (trans)form the experience of illness (and health). First, technology may create awareness of disease by revealing asymptomatic signs or markers (imaging techniques, blood tests). Second, the technology can reveal risk factors for developing diseases (e.g., high blood pressure or genetic tests that reveal risks of falling ill in the future). Third, the technology can affect and change an already present illness experience (e.g., the way blood sugar measurement affects the perceived symptoms of diabetes). Fourth, therapeutic technologies may redefine our experiences of a certain condition as diseased rather than unfortunate (e.g. assisted reproductive technologies or symptom based diagnoses in psychiatry). Fifth, technology influences illness experiences through altering social-cultural norms and values regarding various diagnoses. Sixth, technology influences and changes our experiences of being healthy in contrast and relation to being diseased and ill. This typology of how technology forms illness and related conditions calls for reflection regarding the phenomenology of technology and health. How are medical technologies and their outcomes perceived and understood by patients? The phenomenological way of approaching illness as a lived, bodily being-in-the-world is an important approach for better understanding and evaluating the effects that medical technologies may have on our health, not only in defining, diagnosing, or treating diseases, but also in making us feel more vulnerable and less healthy in different regards.

Ethical Considerations in Microbial Therapeutic Clinical Trials

As understanding of the human microbiome improves, novel therapeutic targets to improve human health with microbial therapeutics will continue to expand. We outline key considerations of balancing risks and benefits, optimising access, returning key results to research participants, and potential conflicts of interest.