Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study.

BACKGROUND: Hospital-acquired and ventilator-associated-pneumonia (HAP/VAP) are one of the most prevalent health-care associated infections in the intensive care unit (ICU). Culture-independent methods were therefore developed to provide faster route to diagnosis and treatment. Among these, metagenomic next-generation sequencing (mNGS) has shown considerable promise. METHODS: This proof-of-concept study describes the technical feasibility and evaluates the clinical validity of the mNGS for the detection and characterization of the etiologic agents causing hospital-acquired and ventilator-associated pneumonia. We performed a prospective study of all patients with HAP/VAP hospitalized in our intensive care unit for whom a bronchoalveolar lavage (BAL) was performed between July 2017 and November 2018. We compared BAL fluid culture and mNGS results of these patients. RESULTS: A total of 32 BAL fluids were fully analyzed. Of these, 22 (69%) were positive by culture and all pathogens identified were also reported by mNGS. Among the culture-positive BAL samples, additional bacterial species were revealed by mNGS for 12 patients, raising the issue of their pathogenic role (colonization versus coinfection). Among BALF with culture-negative test, 5 were positive in mNGS test. CONCLUSIONS: This study revealed concordant results for pneumonia panel pathogens between mNGS and culture-positive tests and identified additional pathogens potentially implicated in pneumonia without etiologic diagnosis by culture. mNGS has emerged as a promising methodology for infectious disease diagnoses to support conventional methods. Prospective studies with real-time mNGS are warranted to examine the impact on antimicrobial decision-making and clinical outcome.

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome.

The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.

Positive Schemas: Replication, Associations With Negative Schemas, and the Dark Triad.

The purpose of the current study was to replicate the factor structure of the 14 positive schemas identified in the earlier study by Louis et al. (2018). Using confirmatory factor analysis (CFA), and Multi-group CFA, the 14 positive schemas were found to be robust across four new non-clinical English-speaking community samples - USA (n = 396), South Africa (n = 390), Nigeria (n = 364), and India (n = 306). Further, results from CFA, and chi square tests showed that positive and negative schemas were independent but related constructs, and that they do not reflect bipolarity. Using hierarchical regression and Pearson's correlations the negative schemas of Entitlement, Approval Seeking and Mistrust, and the positive schema of Empathic Consideration were found to be associated positively and negatively respectively with Machiavellianism, narcissism, and psychopathy of the Dark Triad scale in all four worldwide samples. Implications of this finding in Schema Therapy treatment were discussed.

Moral Distress Amongst District Leaders: Intensity, Dilemmas, and Coping Mechanisms in the Context of Covid-19.

Purpose: This study examines the sources and intensity of moral distress among school district leaders during the first full school year of the Covid-19 pandemic and investigates their coping mechanisms for addressing issues that create moral dilemmas for them. Design and Evidence: We draw on semi-structured interviews with 26 school district leaders across 13 school districts in the Northwestern United States. Brief summaries detailing themes in each interview were prepared. Magnitude coding was used to understand the intensity of district leaders' feelings of distress. Open coding and axial coding allowed us to categorize the origins/sources of distress and the approaches/strategies district leaders used to reduce feelings of moral distress. Findings: Reported moral distress ranged from none to moderate but manageable amounts. Three types of problems were described as morally distressing: political problems with the community or unions, staff problems including staff stress, staff resistance, and collaboration amongst staff members, and an inability to meet student needs due to resource, policy, or community/family constraints. Leaders' coping mechanisms included social responses such as team building, but also drew on individual virtues such as persistence and patience. Implications: Within the ranks of district leaders, the extent to which leaders frame their challenges in a moral frame is varied. A sizable group articulated challenges with implications for moral action in primarily technical or political terms. If district leaders engage unevenly with the moral tradeoffs of their decisions, they risk adopting an overly managerialist frame.

Development and Validation of the Young Parenting Inventory (YPI-R3) for Measuring Past Deviant and Normal Variations in Parenting.

Most measures of past parenting patterns have a restricted range of about two to three negative parenting constructs. The Young Parenting Inventory (YPI-R2) provides a more nuanced framework that measures a fuller spectrum of these negative parenting patterns and, therefore, holds the potential of being a more useful guide to parents and caretakers. The YPI-R2 is made up of six validated subscales. An additional four were identified but were not sufficiently robust to be included. The purpose of this study is to determine if these four scales can be strengthened through the development of additional items and be empirically validated. Using non-clinical, English-speaking community samples from Singapore (n = 592, 628) and Malaysia (n = 222, 229), these revised scales were tested using multiple exploratory factor analyses with fathers and mothers rated separately. After further scale refinement, the final model, which consisted of 10 subscales and 41 items, was then subjected to confirmatory factor analysis using 4 other non-clinical international samples with separate ratings for fathers and mothers-USA (n = 259, 281), South Africa (n = 318, 372), Nigeria (n = 328, 344) and India (n = 277, 289). The results show that the YPI-R3 with 10 subscales is a robust and cross-culturally acceptable model. Correlations and hierarchical multiple regression analyses showed that the YPI-R3 has good convergent validity and predictive capabilities with measures of psychopathology, personality traits, emotional distress, negative schemas and other distal measures of functioning in everyday life-gratitude, humor and satisfaction with life.

The Development of the Love and Respect Marriage Scale.

The constructs of love and respect have been known to be essential ingredients contributing positively to marital satisfaction, but to-date they have mostly been measured using separate scales. However, given the overlap between both constructs this study set out, using self-report methodologies, to develop a comprehensive scale which measures both love and respect known as The Love and Respect Marriage Scale. Using a nonclinical community Singapore sample (n = 400), an initial item pool was developed, and through exploratory factor analysis, a robust factor structure emerged that consisted of eight subscales and 46 items. This factor structure was shown to be a consistent and cross-culturally acceptable model using samples from USA, n = 396, South Africa, n = 390, Nigeria, n = 364, and India, n = 306. Good reliability values were achieved. Construct, convergent, divergent, and incremental validity were also demonstrated as comparisons were made with shorter established marriage scales. Implications and advantages of a longer marital scale were discussed.Supplemental data for this article is available online at https://doi.org/10.1080/0092623X.2021.1963362 .

The Good Enough Parenting early intervention schema therapy based program: Participant experience.

BACKGROUND AND OBJECTIVES: Schema therapy (ST) has become a mainstream therapy for the treatment of psychopathology and has been validated through a series of large scale, international randomized control trials. Among other things, schema therapy emphasizes the meeting of core emotional needs in children by primary caregivers as these unmet needs continue to adversely affect their lives into adulthood. An early intervention parenting program has been developed to help parents meet these core emotional needs in order to prevent the development of psychopathology in the first place. The program, Good Enough Parenting, is equally focused on reducing problems and strengthening parenting practices, regardless of where the child is on the "disordered to well-being continuum". This study aims to explore "patient experience" by users of this program. Best clinical research guidelines advocate that participants should be used as collaborators rather than pure recipients; this process should predate large scale trials. DESIGN: An exploratory qualitative study with 55 parent-participants of Good Enough Parenting was conducted. METHODS: One-to-one interviews were conducted with participants, using critical incident technique and guided by semi-structured interview schedule, to explore their experiences with the program. Transcripts were then analyzed using thematic analysis. RESULTS: Coding showed a high degree of inter-rater reliability (kappa value of 0.78). The themes that emerged were Cultivating Awareness of Parents' Own Schemas, Cultivating Intentionality, Working through Developmental Issues, Responses to Challenges at Home, Performing Multiple Roles, and the Learning Process. Participants overwhelmingly reported satisfaction within these key themes. CONCLUSIONS: The results support the development of the program and the choice of "participant reported outcome measures" for use in subsequent randomized controlled trials.

Characterization and analytical validation of a new antigenic rapid diagnostic test for Ebola virus disease detection.

Hemorrhagic fever outbreaks are difficult to diagnose and control in part because of a lack of low-cost and easily accessible diagnostic structures in countries where etiologic agents are present. Furthermore, initial clinical symptoms are common and shared with other endemic diseases such as malaria or typhoid fever. Current molecular diagnostic methods such as polymerase chain reaction require trained personnel and laboratory infrastructure, hindering diagnostics at the point of need, particularly in outbreak settings. Therefore, rapid diagnostic tests such as lateral flow can be broadly deployed and are typically well-suited to rapidly diagnose hemorrhagic fever viruses, such as Ebola virus. Early detection and control of Ebola outbreaks require simple, easy-to-use assays that can detect very low amount of virus in blood. Here, we developed and characterized an immunoassay test based on immunochromatography coupled to silver amplification technology to detect the secreted glycoprotein of EBOV. The glycoprotein is among the first viral proteins to be detected in blood. This strategy aims at identifying infected patients early following onset of symptoms by detecting low amount of sGP protein in blood samples. The limit of detection achieved by this sGP-targeted kit is 2.2 x 104 genome copies/ml in plasma as assayed in a monkey analytical cohort. Clinical performance evaluation showed a specificity of 100% and a sensitivity of 85.7% when evaluated with plasma samples from healthy controls and patients infected with Zaire Ebola virus from Macenta, Guinea. This rapid and accurate diagnostic test could therefore be used in endemic countries for early detection of infected individuals in point of care settings. Moreover, it could also support efficient clinical triage in hospitals or clinical centers and thus reducing transmission rates to prevent and better manage future severe outbreaks.

Data withholding and the next generation of scientists: results of a national survey.

PURPOSE: To provide the first national data on the nature, extent, and consequences of withholding among life science trainees. METHOD: In 2003, the authors surveyed 1,077 second-year doctoral students and postdoctoral fellows in life sciences at 50 U.S. universities, with a comparison group of trainees in computer science and chemical engineering. The study variables examined trainees' exposure to and the consequences of data withholding. RESULTS: Two hundred forty-six trainees (23.0%) reported that they had asked for and been denied access to information, data, materials, or programming associated with published research and 221 (20.6%) to unpublished research. Eighty-five trainees (7.9%) reported that they had denied another academic scientist's request(s) related to their own published research. Five hundred thirty-three trainees (50.8%) reported that withholding had had a negative effect on the progress of their research, 508 (48.5%) on the rate of discovery in their lab/research group, 472 (45.0%) on the quality of their relationships with academic scientists, 346 (33.0%) on the quality of their education, and 299 (28.5%) on the level of communication in their lab/research group. Trainees denied access to research were significantly more likely to report that data withholding had had a negative effect on several aspects of the educational experience. CONCLUSIONS: Data withholding had demonstrated negative effects on trainees. The life sciences, more so than chemical engineering or computer science, will have to address this issue among its trainees. Failure to do so could result in delayed research, inefficient training, and a culture of withholding among future life scientists.