Comparing Published Gut Microbiome Taxonomic Data Across Multinational Studies.

BACKGROUND: Nurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design and hypothesis generation. OBJECTIVES: This article aims to present and define important analysis considerations in microbiome study planning and to identify genera shared across studies despite methodological differences. This methods article will highlight a workflow that the nurse scientist can use to combine and evaluate taxonomy tables for microbiome study or research proposal planning. METHODS: We compiled taxonomy tables from 13 published gut microbiome studies that had used Ion Torrent sequencing technology. We searched for studies that had amplified multiple hypervariable (V) regions of the 16S rRNA gene when sequencing the bacteria from healthy gut samples. RESULTS: We obtained 15 taxonomy tables from the 13 studies, comprised of samples from four continents and eight V regions. Methodology among studies was highly variable, including differences in V regions amplified, geographic location, and population demographics. Nevertheless, of the 354 total genera identified from the 15 data sets, 25 were shared in all V regions and the four continents. When relative abundance differences across the V regions were compared, Dorea and Roseburia were statistically different. Taxonomy tables from Asian subjects had increased average abundances of Prevotella and lowered abundances of Bacteroides compared with the European, North American, and South American study subjects. DISCUSSION: Evaluating taxonomy tables from previously published literature is essential for study planning. The genera found from different V regions and continents highlight geography and V region as important variables to consider in microbiome study design. The 25 shared genera across the various studies may represent genera commonly found in healthy gut microbiomes. Understanding the factors that may affect the results from a variety of microbiome studies will allow nurse scientists to plan research proposals in an informed manner. This work presents a valuable framework for future cross-study comparisons conducted across the globe.

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity.

Many patients with alcohol use disorder (AUD) consume alcohol chronically and in large amounts that alter intestinal microbiota, damage the gastrointestinal tract, and thereby injure other organs via malabsorption and intestinal inflammation. We hypothesized that alcohol consumption and subsequent abstinence would change the gut microbiome in adults admitted to a treatment program. Stool and oral specimens, diet data, gastrointestinal assessment scores, anxiety, depression measures and drinking amounts were collected longitudinally for up to 4 weeks in 22 newly abstinent inpatients with AUD who were dichotomized as less heavy drinkers (LHD, <10 drinks/d) and very heavy drinkers (VHD, 10 or more drinks/d). Next-generation 16 S rRNA gene sequencing was performed to measure the gut and oral microbiome at up to ten time points/subject and LHD and VHD were compared for change in principal components, Shannon diversity index and specific genera. The first three principal components explained 46.7% of the variance in gut microbiome diversity across time and all study subjects, indicating the change in gut microbiome following abstinence. The first time point was an outlier in three-dimensional principal component space versus all other time points. The gut microbiota in LHD and VHD were significantly dissimilar in change from day 1 to day 5 (p = .03) and from day 1 to week 3 (p = .02). The VHD drinking group displayed greater change from baseline. The Shannon diversity index of the gut microbiome changed significantly during abstinence in five participants. In both groups, the Shannon diversity was lower in the oral microbiome than gut. Ten total genera were shared between oral and stool in the AUD participants. These data were compared with healthy controls from the Human Microbiome Project to investigate the concept of a core microbiome. Rapid changes in gut microbiome following abstinence from alcohol suggest resilience of the gut microbiome in AUD and reflects the benefits of refraining from the highest levels of alcohol and potential benefits of abstinence.

A systematic approach for studying the signs and symptoms of fever in adult patients: the fever assessment tool (FAST).

BACKGROUND: Although body temperature is one of four key vital signs routinely monitored and treated in clinical practice, relatively little is known about the symptoms associated with febrile states. The purpose of this study was to assess the validity, reliability and feasibility of the Fever Assessment Tool (FAST) in an acute care research setting. METHODS: Qualitative: To assess content validity and finalize the FAST instrument, 12 adults from an inpatient medical-surgical unit at the National Institutes of Health (NIH) Clinical Center participated in cognitive interviews within approximately 12 h of a febrile state (tympanic temperature ≥ 38° Celsius). Quantitative: To test reliability, validity and feasibility, 56 new adult inpatients completed the 21-item FAST. RESULTS: The cognitive interviews clarified and validated the content of the final 21-item FAST. Fifty-six patients completed the FAST from two to 133 times during routine vital sign assessment, yielding 1,699 temperature time points. Thirty-four percent of the patients (N = 19) experienced fever at one or more time points, with a total of 125 febrile time points. Kuder-Richardson 20 (KR-20) reliability of the FAST was 0.70. Four nonspecific symptom categories, Tired or Run-Down (12), Sleepy (13), Weak or Lacking Energy (11), and Thirsty (9) were among the most frequently reported symptoms in all participants. Using Generalized Estimating Equations (GEE), the odds of reporting eight symptoms, Warm (4), Sweating (5), Thirsty (9), General Body Aches (10), Weak or Lacking Energy (11), Tired or Run Down (12) and Difficulty Breathing (17), were increased when patients had a fever (Fever Now), compared to the two other subgroups-patients who had a fever, but not at that particular time point, (Fever Not Now) and patients who never had a fever (Fever Never). Many, but not all, of the comparisons were significant in both groups. CONCLUSION: Results suggest the FAST is reliable, valid and easy to administer. In addition to symptoms usually associated with fever (e.g. feeling warm), symptoms such as Difficulty Breathing (17) were identified with fever. Further study in a larger, more diverse patient population is warranted. TRIAL REGISTRATION: Clinical Trials Number: NCT01287143 (January 2011).

The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science.

BACKGROUND: As more is understood regarding the human microbiome, it is increasingly important for nurse scientists and healthcare practitioners to analyze these microbial communities and their role in health and disease. 16S rRNA sequencing is a key methodology in identifying these bacterial populations that has recently transitioned from use primarily in research to having increased utility in clinical settings. OBJECTIVES: The objectives of this review are to (a) describe 16S rRNA sequencing and its role in answering research questions important to nursing science; (b) provide an overview of the oral, lung, and gut microbiomes and relevant research; and (c) identify future implications for microbiome research and 16S sequencing in translational nursing science. DISCUSSION: Sequencing using the 16S rRNA gene has revolutionized research and allowed scientists to easily and reliably characterize complex bacterial communities. This type of research has recently entered the clinical setting, one of the best examples involving the use of 16S sequencing to identify resistant pathogens, thereby improving the accuracy of bacterial identification in infection control. Clinical microbiota research and related requisite methods are of particular relevance to nurse scientists-individuals uniquely positioned to utilize these techniques in future studies in clinical settings.

Factors Influencing Nurses' Use of Hazardous Drug Safe-Handling Precautions.

PURPOSE/OBJECTIVES: To identify factors associated with oncology nurses' use of hazardous drug (HD) safe-handling precautions in inpatient clinical research units.
. DESIGN: Descriptive, cross-sectional.
. SETTING: The National Institutes of Health Clinical Center in Bethesda, Maryland.
. SAMPLE: 115 RNs working on high-volume HD administration units. 
. METHODS: Survey data were collected online using the Hazardous Drug Handling Questionnaire. Data were analyzed using descriptive statistics and multiple regression analysis.
. MAIN RESEARCH VARIABLES: Exposure knowledge, self-efficacy, barriers to personal protective equipment use, perceived risk, conflict of interest, interpersonal influences, workplace safety climate, and total mean HD precaution use.
. FINDINGS: Participants demonstrated high exposure knowledge, self-efficacy, perceived risk, interpersonal influences, and workplace safety climate. Participants demonstrated moderate barriers and conflict of interest. Total mean HD precaution use proved highest during HD administration and lowest for handling excreta at 48 hours. Average patients per day significantly influenced total HD precaution. CONCLUSIONS: Despite high exposure knowledge, barriers to personal protective equipment use and conflict of interest may contribute to reduced adoption of personal protective practices among oncology nurses.
. IMPLICATIONS FOR NURSING: Hospital and unit-specific factors captured by the predictor variables could contribute to institutional HD policy.

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples.

OBJECTIVES: There is much speculation on which hypervariable region provides the highest bacterial specificity in 16S rRNA sequencing. The optimum solution to prevent bias and to obtain a comprehensive view of complex bacterial communities would be to sequence the entire 16S rRNA gene; however, this is not possible with second generation standard library design and short-read next-generation sequencing technology. METHODS: This paper examines a new process using seven hypervariable or V regions of the 16S rRNA (six amplicons: V2, V3, V4, V6-7, V8, and V9) processed simultaneously on the Ion Torrent Personal Genome Machine (Life Technologies, Grand Island, NY). Four mock samples were amplified using the 16S Ion Metagenomics Kit™ (Life Technologies) and their sequencing data is subjected to a novel analytical pipeline. RESULTS: Results are presented at family and genus level. The Kullback-Leibler divergence (DKL), a measure of the departure of the computed from the nominal bacterial distribution in the mock samples, was used to infer which region performed best at the family and genus levels. Three different hypervariable regions, V2, V4, and V6-7, produced the lowest divergence compared to the known mock sample. The V9 region gave the highest (worst) average DKL while the V4 gave the lowest (best) average DKL. In addition to having a high DKL, the V9 region in both the forward and reverse directions performed the worst finding only 17% and 53% of the known family level and 12% and 47% of the genus level bacteria, while results from the forward and reverse V4 region identified all 17 family level bacteria. CONCLUSIONS: The results of our analysis have shown that our sequencing methods using 6 hypervariable regions of the 16S rRNA and subsequent analysis is valid. This method also allowed for the assessment of how well each of the variable regions might perform simultaneously. Our findings will provide the basis for future work intended to assess microbial abundance at different time points throughout a clinical protocol.

Beyond intuition: patient fever symptom experience.

CONTEXT: Fever is an important sign of inflammation recognized by health care practitioners and family caregivers. However, few empirical data obtained directly from patients exist to support many of the long-standing assumptions about the symptoms of fever. Many of the literature-cited symptoms, including chills, diaphoresis, and malaise, have limited scientific bases, yet they often represent a major justification for antipyretic administration. OBJECTIVES: To describe the patient experience of fever symptoms for the preliminary development of a fever assessment questionnaire. METHODS: Qualitative interviews were conducted with 28 inpatients, the majority (86%) with cancer diagnoses, who had a recorded temperature of ≥38°C within approximately 12 hours before the interview. A semi-structured interview guide was used to elicit patient fever experiences. Thematic analyses were conducted by three independent research team members, and the data were verified through two rounds of consensus building. RESULTS: Eleven themes emerged. The participants reported experiences of feeling cold, weakness, warmth, sweating, nonspecific bodily sensations, gastrointestinal symptoms, headaches, emotional changes, achiness, respiratory symptoms, and vivid dreams/hallucinations. CONCLUSION: Our data not only confirm long-standing symptoms of fever but also suggest new symptoms and a level of variability and complexity not captured by the existing fever literature. Greater knowledge of patients' fever experiences will guide more accurate assessment of symptoms associated with fever and the impact of antipyretic treatments on patient symptoms in this common condition. Results from this study are contributing to the content validity of a future instrument that will evaluate patient outcomes related to fever interventions.

A characterization of the oral microbiome in allogeneic stem cell transplant patients.

BACKGROUND: The mouth is a complex biological structure inhabited by diverse bacterial communities. The purpose of this study is to describe the effects of allogeneic stem cell transplantation on the oral microbiota and to examine differences among those patients who acquired respiratory complications after transplantation. METHODOLOGY/PRINCIPAL FINDINGS: All patients were consented at the National Institutes of Health, Clinical Center. Bacterial DNA was analyzed from patients' oral specimens using the Human Oral Microbe Identification Microarray. The specimens were collected from four oral sites in 45 allogeneic transplantation patients. Specimens were collected at baseline prior to transplantation, after transplantation at the nadir of the neutrophil count and after myeloid engraftment. If respiratory signs and symptoms developed, additional specimens were obtained. Patients were followed for 100 days post transplantation. Eleven patients' specimens were subjected to further statistical analysis. Many common bacterial genera, such as Streptococcus, Veillonella, Gemella, Granulicatella and Camplyobacter were identified as being present before and after transplantation. Five of 11 patients developed respiratory complications following transplantation and there was preliminary evidence that the oral microbiome changed in their oral specimens. Cluster analysis and principal component analysis revealed this change in the oral microbiota. CONCLUSIONS/SIGNIFICANCE: After allogeneic transplantation, the oral bacterial community's response to a new immune system was not apparent and many of the most common core oral taxa remained unaffected. However, the oral microbiome was affected in patients who developed respiratory signs and symptoms after transplantation. The association related to the change in the oral microbiota and respiratory complications after transplantation will be validated by future studies using high throughput molecular methods.

Effects of systematic oral care in critically ill patients: a multicenter study.

BACKGROUND: No standard oral assessment tools are available for determining frequency of oral care in critical care patients, and the method of providing oral care is controversial. OBJECTIVES: To examine the effects of a systematic program of oral care on oral assessment scores in critically ill intubated and nonintubated, patients. METHODS: Clinical data were collected 3 times during critical care admissions before and after institution of a systematic program of oral care in 3 different medical centers. The oral care education program consisted of instruction from a dentist or dental hygienist and a clear procedure outlining systematic oral care. The Beck Oral Assessment Scale and the mucosal-plaque score were used to assess the oral cavity. Data were analyzed by using linear mixed modeling with controls for severity of illness. RESULTS: Scores on the Beck Scale differed significantly (F = 4.79, P = .01) in the pattern of scores across the 3 days and between the control group (before oral education) and the systematic oral care group. Unlike the control group, the treatment group had decreasing scores on the Beck Scale from day 1 to day 5. The mucosal-plaque score and the Beck Scale scores had strong correlations throughout the study; the highest correlation was on day 5 (r = 0.798, P < .001, n = 43). CONCLUSIONS: Oral assessment scores improved after nurses implemented a protocol for systematic oral care. Use of the Beck Scale and the mucosal-plaque score could standardize oral assessment and guide nurses in providing oral interventions.

Evidence to support tooth brushing in critically ill patients.

Tooth brushing in critically ill patients has been advocated by many as a standard of care despite the limited evidence to support this practice. Attention has been focused on oral care as the evidence accumulates to support an association between the bacteria in the oral microbiome and those respiratory pathogens that cause pneumonia. It is plausible to assume that respiratory pathogens originating in the oral cavity are aspirated into the lungs, causing infection. A recent study of the effects of a powered toothbrush on the incidence of ventilator-associated pneumonia was stopped early because of a lack of effect in the treatment group. This review summarizes the evidence that supports the effectiveness of tooth brushing in critically ill adults and children receiving mechanical ventilation. Possible reasons for the lack of benefit of tooth brushing demonstrated in clinical trials are discussed. Recommendations for future trials in critically ill patients are suggested. With increased emphasis being placed on oral care, the evidence that supports this intervention must be evaluated carefully.