Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples.

Introduction: Advancements in DNA extraction and sequencing technologies have been fundamental in deciphering the significance of the microbiome related to human health and pathology. Whole metagenome shotgun sequencing (WMS) is gaining popularity in use compared to its predecessor (i.e., amplicon-based approaches). However, like amplicon-based approaches, WMS is subject to bias from DNA extraction methods that can compromise the integrity of sequencing and subsequent findings. The purpose of this study was to evaluate systematic differences among four commercially available DNA extraction kits frequently used for WMS analysis of the microbiome. Methods: Oral, vaginal, and rectal swabs were collected in replicates of four by a healthcare provider from five participants and randomized to one of four DNA extraction kits. Two extraction blanks and three replicate mock community samples were also extracted using each extraction kit. WMS was completed with NovaSeq 6000 for all samples. Sequencing and microbial communities were analyzed using nonmetric multidimensional scaling and compositional bias analysis. Results: Extraction kits differentially biased the percentage of reads attributed to microbial taxa across samples and body sites. The PowerSoil Pro kit performed best in approximating expected proportions of mock communities. While HostZERO was biased against gram-negative bacteria, the kit outperformed other kits in extracting fungal DNA. In clinical samples, HostZERO yielded a smaller fraction of reads assigned to Homo sapiens across sites and had a higher fraction of reads assigned to bacterial taxa compared to other kits. However, HostZERO appears to bias representation of microbial communities and demonstrated the most dispersion by site, particularly for vaginal and rectal samples. Conclusions: Systematic differences exist among four frequently referenced DNA extraction kits when used for WMS analysis of the human microbiome. Consideration of such differences in study design and data interpretation is imperative to safeguard the integrity of microbiome research and reproducibility of results.

Lessons Learned from Rapid Community Needs Assessment in the African American Community During the COVID-19 Pandemic.

BACKGROUND: With the accelerated spread of COVID-19 and current shelter-in-place orders from many local governments, African American (AA) communities see to be more vulnerable as emerging data show disproportionate rates of infection and mortality among AAs across the nation. OBJECTIVES: In a sample of AA church members, to conduct a rapid community assessment during the early phase of the coronavirus disease 2019 pandemic. METHODS: Our community-based participatory research team, partnering with the local AA church community and including trained lay health workers, conducted the assessment via telephone and online. RESULTS: Although most participants reported high confidence regarding recommendations for physical distancing, more than 60% reported elevated anxiety and stress, and 10% indicated that they needed more information about staying healthy and safe during the pandemic. CONCLUSIONS: Community-based participatory research with lay health workers is an effective method to implement a community needs assessment, problem-solve with community members, and build community health infrastructure during a public health crisis.

The Impact of Psychosocial Stress from Life Trauma and Racial Discrimination on Epigenetic Aging-A Systematic Review.

PURPOSE: The purpose of this review was to explore the effects of psychosocial stress from life trauma and racial discrimination on epigenetic aging. DESIGN: A systematic review of the last 10 years was conducted using four databases: PubMed/MEDLINE, Web of Science, PsychInfo, and CINAHL. METHODS: Articles were identified using the following terms: ([(DNA methylation) AND (epigenetic clock)] OR [(DNA methylation) AND (epigenetic age)]) AND (discrimination OR trauma)). Original research articles published in English measuring life trauma, post-traumatic stress, experience of discrimination, and epigenetic clocks or aging were analyzed using PRISMA guidelines. RESULTS: Ten articles met inclusion criteria. The study sample size ranged from 96 to 1163 and most study populations had a mean age under 50 and included predominantly White male participants. One study identified accelerated epigenetic aging associated with discrimination using Hannum's clock; 33% of studies evaluating life trauma reported epigenetic age acceleration using GrimAge or Horvath's clock; 25% of studies evaluating childhood trauma reported epigenetic age acceleration using Horvath's clock; and 71% of studies assessing post-traumatic stress observed epigenetic age acceleration with all clocks, while one study reported deceleration using Horvath's clock. CONCLUSIONS: The experiences of life trauma, post-traumatic stress, and discrimination may be associated with accelerated epigenetic aging that can be consistently detected using different epigenetic clocks. Additional studies inclusive of diverse populations and other psychosocial stressors are needed. RELEVANCE: Nursing scholars and other health scientists who utilize epigenetic age acceleration to assess health risks may need to consider including psychosocial stressors in their studies as covariates.

Development and testing of a biobanking acceptability scale: A multistage effort to add a biobank to an existing longitudinal study.

BACKGROUND: More biobanks linked to demographic, phenotypic, and clinical data are needed to advance multiple sclerosis (MS) research; however, little is known about biobanking attitudes among persons with MS, broadly, as well as willingness of participants in an existing longitudinal study to donate biospecimens, specifically. METHODS: To assess biobanking attitudes in a cohort of MS patients in an ongoing longitudinal study, a new Biobanking Acceptability Scale (BAS) was developed, its reliability and predictive validity tested, and factors that influenced biobanking intent as well as behavior were explored. Analysis included descriptive statistics, factor analysis, Cronbach's α, and Pearson's bivariate correlation coefficients. RESULTS: In 2018, 227 participants completed the 10-item BAS. Biobanking attitudes were generally positive (BAS total score, M = 38.8 out of 50; SD = 6.7), and most participants expressed willingness to donate hair (87%), saliva (85%), and/or blood (72%). In 2019, 143 participants consented to biobanking and were mailed supplies; 110 individuals provided at least one biospecimen, resulting in 110 saliva samples and 89 hair samples. The 10-item BAS displayed good internal consistency (α = 0.81). Demographic and clinical variables were not significantly associated with BAS score nor actual donation. Total BAS score was related to consent (r = 0.36, p < .001) and to actual donation of hair or saliva samples (r = 0.24, p < .01). CONCLUSION: Overall, the participants had positive attitudes toward biobanking; the scale should be assessed in more diverse samples. The BAS predicted biobanking consent, and thus may be a useful measure to identify individuals most likely to donate biospecimens and/or identify potential barriers to biobanking that can be addressed through study design.

Health Promotion, Functional Abilities, and Quality of Life Before and During COVID-19 in People With Multiple Sclerosis.

BACKGROUND: Because multiple sclerosis (MS) is an autoimmune disease and many individuals with MS take disease-modifying drugs that suppress immune response, serious concerns have been expressed about the potential effect of COVID-19 on those with this chronic condition. OBJECTIVES: The purpose of this research was to utilize the most recent 5 years of data from an ongoing longitudinal study of health promotion and quality of life (QoL) among people with long-standing MS to investigate changes across time in functional limitations, health promotion, and health-related QoL. METHODS: Participants are mailed an annual survey to complete about their health promotion, depressive symptoms, health status, social support, MS-related functional limitations, and QoL. Differences across time were analyzed with repeated measures of analysis of variances and planned contrasts. RESULTS: In 2021, the 141 participants had a mean age of 69 years and had been diagnosed with MS for 34 years, on average. Most had attended college, were married/partnered women, and reported adequate economic resources. Thirty-seven percent reported they were in poor to fair health. Physical activity and health responsibility scores decreased significantly during 2020-2021 compared with 2017-2019. Significant changes in depressive symptoms, social support, and functional limitation scores followed a different pattern, with the largest changes occurring between 2018 and 2019. QoL and other health promotion scores did not change significantly across time. DISCUSSION: The relatively small changes in health indicators revealed here suggest that older people with long-standing MS may have generally been able to maintain their health promotion, functional abilities, and QoL from before to during the COVID-19 pandemic. However, nurses and other providers should support them to resume their physical activity and regular provider contact as COVID-19 restrictions are eased. The patterns observed here demonstrate the importance of examining changes across an extended period, rather than simply looking at 1 year before and 1 year after a major event, such as COVID-19. These findings can help nurses understand how to help their patients with chronic health conditions maximize their health as they move forward.

Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review.

BACKGROUND: Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. METHODOLOGY: A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms "vaginal microbiome", "pregnancy", and "16S rRNA sequencing". Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. RESULTS: Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. CONCLUSION: Considerable differences in study design and data formatting methods may contribute to underrepresentation of GBS, and other known pathogens, in existing vaginal microbiome literature. Previous studies have identified considerable variation in methodology across vaginal microbiome studies. This study adds to this body of work because in addition to laboratory or statistical methods, how results and data are shared (e.g., only analyzing genus level data or 20 most abundant microbes), may hinder reproducibility and limit our understanding of the influence of less abundant microbes. Sharing detailed methods, analysis code, and raw data may improve reproducibility and ability to more accurately compare microbial communities across studies.

Novice nurses' sleep disturbance trajectories within the first 2 years of work and actual turnover: A prospective longitudinal study.

BACKGROUND: Novice nurses experience radical changes in their sleep-wake cycle and sleep difficulties after exposure to a rotating shift work schedule. The link between workplace hardship and employee turnover may be dependent on factors at the individual level, e.g., individual health. Nurses with sleep disturbance are more vulnerable to stressful stimuli and lack resilience at work compared with those without sleep disturbance. OBJECTIVES: To classify novice nurses according to sleep disturbance trajectories during the first 2 years of work, to compare turnover rates according to trajectory classification, and to compare levels of sleep disturbance between stayers and leavers within each trajectory class. DESIGN: Prospective longitudinal design. SETTINGS: A tertiary hospital in Seoul, South Korea. PARTICIPANTS: A total of 465 newly graduated nurses who started work between September 2014 and December 2015. METHODS: Data were collected 6 times within the first 2 years of work (on the first day of orientation before ward placement, at 6 weeks after starting work, and at 6, 12, 18, and 24 months of work). Sleep disturbance was assessed using the General Sleep Disturbance Scale. Turnover information was retrieved from the hospital's administrative data system to determine whether anyone had left the hospital at each data collection point. Unconditional latent growth curve analysis was performed to identify latent classes of trajectories of sleep disturbance among novice nurses during the first 2 years of work. RESULTS: The 2-year trajectories of sleep disturbance were classified into two distinct groups: the high symptomatic group (Class 1: 57.4%) and the low symptomatic group (Class 2: 42.6%). In comparison with Class 2, Class 1 consistently showed a higher turnover in each period. In Class 1, leavers who left the hospital at the next measurement point tended to report more severe sleep disturbance at prior measurements. This pattern was also observed for the overall sample. However, in Class 2, an inconsistent pattern between stayers and leavers was observed. CONCLUSIONS: This study identified two distinct classes of sleep disturbance among novice nurses during the first 2 years of work. Given that many nurses experience sleep problems at pre-employment and during the early career period, a comprehensive approach to address this issue should be implemented in nursing schools and hospitals. The basic nursing curriculum should include self-care management strategies for sleep difficulties to ensure retention at work. At-risk nurses should receive organizational support and early monitoring to prevent the adverse effects of poor sleep.

The Influence of Discrimination and Coping Style on Blood Pressure Among Black/African American Women in the InterGEN Study.

Purpose: Although research has explored the effects of racism on mental health, few studies have investigated the effects of racism on physical health. In this study, we examined the influence of racial discrimination and race-related stress and coping on blood pressure within a cohort of Black/African American women. Methods: This was a secondary data analysis of 226 Black/African American women from the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure study. Experiences of racial discrimination and coping, measured by the Experiences of Discrimination scale and the Race-Related Events Scale, were analyzed in relation to systolic blood pressure (SBP) and diastolic blood pressure (DBP). Multiple linear regression was used to explore the interaction effect of coping and discrimination on blood pressure for both scales. Results: Age and elevated body mass index were associated with increased SBP and DBP, and low income was associated with increased DBP. Among individuals who reported no personal experience of discrimination, more active coping strategies were associated with higher DBP. There was no evidence of a relationship between type of coping strategies used and blood pressure among individuals who did report experiences of discrimination. Conclusion: Differences in coping strategy in response to racism were not found to have a significant moderating effect on DBP in Black/African American women.

Pre-employment health lifestyle profiles and actual turnover among newly graduated nurses: A descriptive and prospective longitudinal study.

BACKGROUND: Newly graduated nurses' pre-employment health lifestyles play particularly important roles in their smooth adaptation to and retention in clinical nursing; however, the longitudinal relationship between pre-employment health lifestyles and work outcomes, such as turnover, remains underexamined. To identify the health lifestyle profiles of specific populations of interest, recent studies have employed multifaceted approaches using health behaviors and/or statuses. OBJECTIVES: To identify the pre-employment health lifestyle profiles of newly graduated nurses, and to examine the longitudinal relationships between health lifestyle profiles and actual turnover. DESIGN: Descriptive and prospective longitudinal study design. SETTINGS: One tertiary hospital in Seoul, South Korea. PARTICIPANTS: A total of 464 newly graduated nurses who started work between September 2014 and December 2015. METHODS: The outcome was actual turnover-whether participants had resigned from the organization and the days they worked up to December 31, 2017. We measured eight health lifestyle variables on the first day of orientation before ward placement (i.e., at baseline): quantity and quality of sleep, eating three meals a day, having a regular diet, alcohol consumption, moderate exercise, depression, and self-rated health. We employed latent class analysis to identify the health lifestyle profiles of new nurses, and used Cox proportional hazards regression to examine the longitudinal relationships between health lifestyle profiles and actual turnover. RESULTS: We classified newly graduated nurses' pre-employment health lifestyle profiles into two groups: unhealthy lifestyle (15.6%) and discordant (84.4%). Compared with the new nurses in the discordant group, those in the unhealthy lifestyle group had significantly higher probabilities of resigning (HR = 2.38, 95% CIs of HR = 1.62-3.50); this relationship remained significant after adjusting for perceived job stress at six weeks of work (HR = 2.26, 95% CIs of HR = 1.50-3.39). CONCLUSIONS: This study identified significant differences in the patterns of newly graduated nurses' pre-employment health lifestyles; our analysis showed that classification in the unhealthy lifestyle group was a turnover risk factor. Given that new nurses' health lifestyles affect work outcomes, hospitals should implement organizational and educational initiatives to encourage healthy lifestyles. In considering pre-employment health lifestyle profiles, hospitals should also monitor novice nurses' adaptation and wellness. Nursing education should include strategies to enhance nursing students' own health. Further extensive longitudinal studies should seek to identify the health lifestyle profiles of heterogeneous nurse populations.

Shift-work nurses' work environments and health-promoting behaviours in relation to sleep disturbance: A cross-sectional secondary data analysis.

AIMS AND OBJECTIVES: To examine the association of nursing work environments and health-promoting behaviours with shift-work nurses' sleep disturbance. BACKGROUND: Shift-work nurses reportedly have sleep problems, which affect their sleep quality and quantity. Given the high risk of developing performance decrements and medication errors in sleep-disturbed nurses, factors related to sleep disturbance among shift-work nurses should be investigated. DESIGN: A cross-sectional secondary data analysis. METHODS: Our study analysed data from 339 nurses who had been involved in rotating shift work including night shifts for more than 6 months. To examine associations of nursing work environments and health-promoting behaviours with sleep disturbance, multiple linear regression models were generated. This study is reported in accordance with the STrengthening the Reporting of OBservational studies in Epidemiology guideline. RESULTS: Nurses with more collegial relations with physicians were significantly less likely to have high levels of sleep disturbance (B = -4.01, p = 0.04). Those with higher levels of sleep disturbance were significantly more likely to report less stress management (B = -9.56, p < 0.01) and higher health responsibility (B = 9.30, p < 0.01). CONCLUSIONS: To alleviate shift-work nurses' sleep disturbance, organisational supports for collaborative relations with physician and increased healthcare accessibility are needed. Individual nurses should develop healthy lifestyles to reduce occupational stress and alleviate sleep disorders. RELEVANCE TO CLINICAL PRACTICE: To improve shift-work nurses' sleep, collegial relations with physicians and healthy lifestyles should be promoted.