Impact of metagenomic next-generation sequencing on clinical decision-making at an academic medical center, a retrospective study, Iowa, 2020-2022.

We assessed the impact of metagenomic next-generation sequencing (mNGS) on patient care using previously established criteria. Among 37 patients receiving mNGS testing, 16% showed results that had a positive clinical impact. While mNGS results may offer valuable supplementary information, results should be interpreted within the broader clinical context and evaluation.

Exchanging words: Engaging the challenges of sharing qualitative research data.

In January 2023, a new NIH policy on data sharing went into effect. The policy applies to both quantitative and qualitative research (QR) data such as data from interviews or focus groups. QR data are often sensitive and difficult to deidentify, and thus have rarely been shared in the United States. Over the past 5 y, our research team has engaged stakeholders on QR data sharing, developed software to support data deidentification, produced guidance, and collaborated with the ICPSR data repository to pilot the deposit of 30 QR datasets. In this perspective article, we share important lessons learned by addressing eight clusters of questions on issues such as where, when, and what to share; how to deidentify data and support high-quality secondary use; budgeting for data sharing; and the permissions needed to share data. We also offer a brief assessment of the state of preparedness of data repositories, QR journals, and QR textbooks to support data sharing. While QR data sharing could yield important benefits to the research community, we quickly need to develop enforceable standards, expertise, and resources to support responsible QR data sharing. Absent these resources, we risk violating participant confidentiality and wasting a significant amount of time and funding on data that are not useful for either secondary use or data transparency and verification.

Use of subgroup-specific hematopoietic stem cell collection efficiencies to improve truncation calculations for large-volume leukapheresis procedures.

PURPOSE: A critical component of optimizing peripheral blood (PB) hematopoietic stem cell (HSC) collections is accurately determining the processed blood volume required to collect the targeted number of HSCs. Fundamental to most truncation equations employed to determine this volume is the procedure's estimated collection efficiency (CE), which is typically applied uniformly across all HSC collections. Few studies have explored the utility of using different CEs in subpopulations of donors that have substantially different CEs than the institutional average. METHODS: Initial procedures from 343 autologous and 179 allogeneic HSC collections performed from 2018 to 2021 were retrospectively analyzed. Predictive equations were developed to determine theoretical truncation rates in various donor subgroups. RESULTS: Quantitative variables (pre-procedure cell counts) and qualitative variables (relatedness to recipient, gender, method of venous access, and mobilization strategy) were found to significantly impact CE. However, much of the variability in CE between donors could not be explained by the variables assessed. Analyses of procedures with high pre-collection PB cell counts identified lower CE values for these donors' truncation equations which still allow truncation but minimize risk of collecting less CD34+ cells than requested. CONCLUSIONS: Individualized CE does not substantially improve truncation volume calculations over use of a fixed CE and adds complexity to these calculations. The optimal fixed CE varies between autologous and allogeneic donors, and donors with high pre-collection PB cell counts in either of these groups. This model will be clinically validated and continuously refined through analysis of future HSC collections.

What Is New in Fungal Infections?

Invasive fungal infections are an increasingly important cause of morbidity and mortality. We provide a summary of important changes in the epidemiology of invasive fungal infections, citing examples of new emerging pathogens, expanding populations who are at-risk, and increasing antifungal resistance. We review how human activity and climate change may play a role in some of these changes. Finally, we discuss how these changes create the need for advances in fungal diagnostics. The limitations of existing fungal diagnostic testing emphasize the critically important role of histopathology in the early recognition of fungal disease.

Barriers to Using Legally Authorized Representatives in Clinical Research with Older Adults.

Background: Older adults are at increased risk of cognitive impairments including Alzheimer's disease dementia. Legally authorized representatives (LARs) can provide informed consent when a participant is no longer able to, but little is known about barriers to incorporating them in research. Objective: Explore reasons for not asking and documenting participant decisions to appoint LARs among researchers conducting clinical intervention trials studying older adults or individuals with cognitive impairments. Methods: Mixed method design consisting of a survey (N = 1,284) and qualitative interviews (N = 40) regarding barriers to incorporating LARs. Participants were principal investigators and clinical research coordinators. Results: 37% (N = 469) had not asked and documented participant decisions about appointing LARs in the prior year. They had significantly lower confidence in resources available to incorporate LARs and lower positive attitudes compared to their counterparts who had done so. The majority (83%) had no trials studying individuals with cognitive impairments and reported LARs were not applicable. A minority (17%) had at least one trial studying individuals with cognitive impairments and reported being unaware of LARs. Qualitative findings indicate discomfort broaching a sensitive topic especially with individuals who are not yet impaired. Conclusion: Resources and education to increase awareness and knowledge of LARs are needed. Researchers studying older adults should, at minimum, have the knowledge and resources to incorporate LARs when necessary. Stigma and discomfort discussing LARs will need to be overcome, as early proactive discussions before a participant loses decisional capacity could enhance participant autonomy and facilitate recruitment and retention of older adults to research.

A randomized implementation trial to increase adoption of evidence-informed consent practices.

Introduction: Several evidence-informed consent practices (ECPs) have been shown to improve informed consent in clinical trials but are not routinely used. These include optimizing consent formatting, using plain language, using validated instruments to assess understanding, and involving legally authorized representatives when appropriate. We hypothesized that participants receiving an implementation science toolkit and a social media push would have increased adoption of ECPs and other outcomes. Methods: We conducted a 1-year trial with clinical research professionals in the USA (n = 1284) who have trials open to older adults or focus on Alzheimer's disease. We randomized participants to receive information on ECPs via receiving a toolkit with a social media push (intervention) or receiving an online learning module (active control). Participants completed a baseline survey and a follow-up survey after 1 year. A subset of participants was interviewed (n = 43). Results: Participants who engaged more with the toolkit were more likely to have tried to implement an ECP during the trial than participants less engaged with the toolkit or the active control group. However, there were no significant differences in the adoption of ECPs, intention to adopt, or positive attitudes. Participants reported the toolkit and social media push were satisfactory, and participating increased their awareness of ECPs. However, they reported lacking the time needed to engage with the toolkit more fully. Conclusions: Using an implementation science approach to increase the use of ECPs was only modestly successful. Data suggest that having institutional review boards recommend or require ECPs may be an effective way to increase their use.

Blood culture practices in patients with a central line at an academic medical center-Iowa, 2020.

We analyzed blood-culture practices to characterize the utilization of the Infectious Diseases Society of America (IDSA) recommendations related to catheter-related bloodstream infection (CRBSI) blood cultures. Most patients with a central line had only peripheral blood cultures. Increasing the utilization of CRBSI guidelines may improve clinical care, but may also affect other quality metrics.

Pelvic and central nervous system tuberculosis complicated by a paradoxical response manifesting as a spinal tuberculoma: a case report.

BACKGROUND: The post-partum period is a risk factor for tuberculosis (TB), possibly including the period after miscarriage as illustrated here. This case demonstrates how non-specific symptoms can hide widely disseminated TB. CASE PRESENTATION: A healthy 26-year-old female with a history of recent miscarriage presented to the emergency department with non-specific symptoms of headache, abdominal pain, and sub-acute fevers. She had immigrated to the United States from the Marshall Islands 9 years prior. Two months prior to presentation she had a miscarriage at 18 weeks of pregnancy. On admission, transvaginal ultrasound revealed retained products of conception and abdominal computed tomography revealed findings consistent with tubo-ovarian abscesses and peritonitis. The obstetrics and gynecology service performed dilation and curettage (D&C) to remove retained products of conception. Acid-fast bacilli cultures from cerebrospinal fluid as well as specimens from D&C and intra-abdominal abscesses subsequently all grew TB. She was diagnosed with TB meningitis, peritonitis, endometritis, and tubo-ovarian abscesses. Her treatment course was complicated by a paradoxical response resulting in a spinal tuberculoma causing lower extremity weakness. The tuberculoma was treated with surgical decompression as well as continuation of treatment with anti-tubercular chemotherapy and steroids. CONCLUSION: Disseminated and extrapulmonary TB can present with non-specific symptoms. Recognition of risk factors for TB is critical for prompt diagnostic evaluation and treatment of this deadly disease. A paradoxical reaction needs to be taken into consideration when any new neurological symptoms occur during TB treatment.

Responding to Sexual Abuse in Health Care: Development of a Guide for Patients.

This report details the development of a stakeholder- and evidence-informed online resource guide for patients that provides information to raise awareness about sexual abuse in health care, the value of chaperones, and options for responding to sexual abuse. The guide was developed to reflect lessons learned from 10 years of researching physician wrongdoing (ie, sexual violations, improper prescribing, and unnecessary invasive procedures), a 5-year National Institutes of Health-funded mixed-methods study of 280 cases of egregious wrongdoing in medicine, and an expert working group. Focus groups were conducted with 22 patients from diverse backgrounds to obtain feedback on the acceptability of the guide. Thematic analysis of the focus groups yielded 6 key themes: 1) empowering patients, 2) recognizing and responding to sexual abuse, 3) educating patients about reporting options, 4) educating patients on availability of chaperones, 5) balancing trust and mistrust, and 6) using simple language. Qualitative data from the focus groups (ie, audio files and detailed notes taken by the research team) suggested that the guide effectively informed and empowered patients to recognize and effectively respond to sexual misconduct in health care. The guide is publicly available and has been disseminated nationally to patient health advocates and public health agencies.

Non-tuberculous mycobacterial thoracic osteomyelitis in an immunocompetent host: a rare presentation of Mycobacterium kansasii.

An immunocompetent man in his 40s presented with 3 months of mid-thoracic back pain which progressed to include progressive paraesthesias and lower extremity weakness. Investigations revealed thoracic spine osteomyelitis with signs of cord compression. He underwent neurosurgical intervention, including laminectomy, spinal cord decompression and partial resection of an epidural mass. Initial intraoperative biopsy and surgical pathology results were concerning for an acid-fast bacillus as the causative pathogen, and the patient was given empiric therapy for presumed Mycobacterium tuberculosis However, microbiology speciation revealed the presence of the non-tuberculous mycobacterium (NTM) Mycobacterium kansasii, which resulted in an alteration of his antimicrobial therapy. This case highlights the importance of considering NTM as a possible aetiology of spinal osteomyelitis, even among immunocompetent individuals or in low-prevalence regions.

Ethical, regulatory, and practical barriers to COVID-19 research: A stakeholder-informed inventory of concerns.

INTRODUCTION: SARS-CoV-2 (COVID-19) has caused death and economic injury around the globe. The urgent need for COVID-19 research created new ethical, regulatory, and practical challenges. The next public health emergency could be worse than COVID-19. We must learn about these challenges from the experiences of researchers and Research Ethics Committee professionals responsible for these COVID-19 studies to prepare for the next emergency. MATERIALS AND METHODS: We conducted an online survey to identify the ethical, oversight, and regulatory challenges of conducting COVID-19 research during the early pandemic, and proposed solutions for overcoming these barriers. Using criterion-based, convenience sampling, we invited researchers who proposed or conducted COVID-19 research to complete an anonymous, online survey about their experiences. We administered a separate but related survey to Institutional Review Board (IRB) professionals who reviewed COVID-19 research studies. The surveys included open-ended and demographic items. We performed inductive content analysis on responses to open-ended survey questions. RESULTS: IRB professionals (n = 143) and researchers (n = 211) described 19 types of barriers to COVID-19 research, related to 5 overarching categories: policy and regulatory, biases and misperceptions, institutional and inter-institutional conflicts, risks of harm, and pressure of the pandemic. Researchers and IRB professionals described 8 categories of adaptations and solutions to these challenges: enacting technological solutions; developing protocol-based solutions; disposition and team management; establishing and communicating appropriate standards; national guidance and leadership; maintaining high standards; prioritizing studies before IRB review; and identifying and incorporating experts. DISCUSSION AND CONCLUSIONS: This inventory of challenges represents ongoing barriers to studying the current pandemic, and they represent a risk to research during future public health emergencies. Delays in studies of a pandemic during a pandemic threatens the health and safety of the public. We urge the development of a national working group to address these issues before the next public health emergency arises.

Understanding the Use of Optimal Formatting and Plain Language When Presenting Key Information in Clinical Trials.

Recent revisions to the Common Rule require that consent documents begin with a focused presentation of the study's key information that is organized to facilitate understanding. We surveyed 1,284 researchers working with older adults or individuals with Alzheimer's disease, supplemented with 60 qualitative interviews, to understand current use and barriers to using evidence-based formatting and plain language in key information. Researchers reported using formatting in 42% of their key information sections, and plain language in 63% of their key information sections. Perceived barriers included lack of knowledge, Institutional Review Board, other members of their team, and the burden associated with implementation. Education and training are required to increase adoption of the practices.

Barriers and facilitators to qualitative data sharing in the United States: A survey of qualitative researchers.

Qualitative health data are rarely shared in the United States (U.S.). This is unfortunate because gathering qualitative data is labor and time-intensive, and data sharing enables secondary research, training, and transparency. A new U.S. federal policy mandates data sharing by 2023, and is agnostic to data type. We surveyed U.S. qualitative researchers (N = 425) on the barriers and facilitators of sharing qualitative health or sensitive research data. Most researchers (96%) have never shared qualitative data in a repository. Primary concerns were lack of participant permission to share data, data sensitivity, and breaching trust. Researcher willingness to share would increase if participants agreed and if sharing increased the societal impact of their research. Key resources to increase willingness to share were funding, guidance, and de-identification assistance. Public health and biomedical researchers were most willing to share. Qualitative researchers need to prepare for this new reality as sharing qualitative data requires unique considerations.

Development of a Resource Guide to Help Patients Receive Appropriate Care.

After 10 years researching physician wrongdoing (i.e., sexual violations, improper prescribing, and unnecessary procedures), we developed a resource guide to help patients receive appropriate care and respond to inappropriate care. We gathered evaluative patient feedback, engaged physicians, and disseminated the guide. It is available at beforeyourvisit.org.

Perceived barriers to assessing understanding and appreciation of informed consent in clinical trials: A mixed-method study.

INTRODUCTION: Participants and research professionals often overestimate how well participants understand and appreciate consent information for clinical trials, and experts often vary in their determinations of participant's capacity to consent to research. Past research has developed and validated instruments designed to assess participant understanding and appreciation, but the frequency with which they are utilized is unknown. METHODS: We administered a survey to clinical researchers working with older adults or those at risk of cognitive impairment (N = 1284), supplemented by qualitative interviews (N = 60). RESULTS: We found that using a validated assessment of consent is relatively uncommon, being used by only 44% of researchers who had an opportunity. Factors that predicted adoption of validated assessments included not seeing the study sponsor as a barrier, positive attitudes toward assessments, and being confident that they had the resources needed to implement an assessment. The perceived barriers to adopting validated assessments of consent included lack of awareness, lack of knowledge, being unsure of how to administer such an assessment, and the burden associated with implementing this practice. CONCLUSIONS: Increasing the use of validated assessments of consent will require educating researchers on the practice and emphasizing very practical assessments, and may require Institutional Review Boards (IRBs) or study sponsors to champion the use of assessments.

Attitudes toward genomics and precision medicine.

PURPOSE: This paper reports on a novel measure, attitudes toward genomics and precision medicine (AGPM), which evaluates attitudes toward activities such as genetic testing, collecting information on lifestyle, and genome editing - activities necessary to achieve the goals of precision medicine. DISCUSSION: The AGPM will be useful for researchers who want to explore attitudes toward genomics and precision medicine. The association of concerns about precision medicine activities with demographic variables such as religion and politics, as well as higher levels of education, suggests that further education on genomic and precision activities alone is unlikely to shift AGPM scores significantly. METHODS: We wrote items to represent psychological and health benefits of precision medicine activities, and concerns about privacy, social justice, harm to embryos, and interfering with nature. We validated the measure through factor analysis of its structure, and testing associations with trust in the health information system and demographic variables such as age, sex, education, and religion. RESULTS: The AGPM had excellent alpha reliability (.92) and demonstrated good convergent validity with existing measures. Variables most strongly associated with higher levels of concern with precision medicine activities included: regular religious practice, republican political leanings, and higher levels of education.