Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023.

BackgroundThe COVID-19 pandemic was largely driven by genetic mutations of SARS-CoV-2, leading in some instances to enhanced infectiousness of the virus or its capacity to evade the host immune system. To closely monitor SARS-CoV-2 evolution and resulting variants at genomic-level, an innovative pipeline termed SARSeq was developed in Austria.AimWe discuss technical aspects of the SARSeq pipeline, describe its performance and present noteworthy results it enabled during the pandemic in Austria.MethodsThe SARSeq pipeline was set up as a collaboration between private and public clinical diagnostic laboratories, a public health agency, and an academic institution. Representative SARS-CoV-2 positive specimens from each of the nine Austrian provinces were obtained from SARS-CoV-2 testing laboratories and processed centrally in an academic setting for S-gene sequencing and analysis.ResultsSARS-CoV-2 sequences from up to 2,880 cases weekly resulted in 222,784 characterised case samples in January 2021-March 2023. Consequently, Austria delivered the fourth densest genomic surveillance worldwide in a very resource-efficient manner. While most SARS-CoV-2 variants during the study showed comparable kinetic behaviour in all of Austria, some, like Beta, had a more focused spread. This highlighted multifaceted aspects of local population-level acquired immunity. The nationwide surveillance system enabled reliable nowcasting. Measured early growth kinetics of variants were predictive of later incidence peaks.ConclusionWith low automation, labour, and cost requirements, SARSeq is adaptable to monitor other pathogens and advantageous even for resource-limited countries. This multiplexed genomic surveillance system has potential as a rapid response tool for future emerging threats.

Preparing Planarian Cells for High-Content Fluorescence Microscopy Using RNA in Situ Hybridization and Immunocytochemistry.

High-content fluorescence microscopy combines the efficiency of high-throughput techniques with the ability to extract quantitative information from biological systems. Here we describe a modular collection of assays adapted for fixed planarian cells that enable multiplexed measurements of biomarkers in microwell plates. These include protocols for RNA fluorescent in situ hybridization (RNA FISH) as well as immunocytochemical protocols for quantifying proliferating cells targeting phosphorylated histone H3 as well as 5-bromo-2'-deoxyuridine (BrdU) incorporated into the nuclear DNA. The assays are compatible with planarians of virtually any size, as the tissue is disaggregated into a single-cell suspension before fixation and staining. By sharing many reagents with established planarian whole-mount staining protocols, preparation of samples for high-content microscopy adoption requires little additional investment.

Body size-dependent energy storage causes Kleiber's law scaling of the metabolic rate in planarians.

Kleiber's law, or the 3/4 -power law scaling of the metabolic rate with body mass, is considered one of the few quantitative laws in biology, yet its physiological basis remains unknown. Here, we report Kleiber's law scaling in the planarian Schmidtea mediterranea. Its reversible and life history-independent changes in adult body mass over 3 orders of magnitude reveal that Kleiber's law does not emerge from the size-dependent decrease in cellular metabolic rate, but from a size-dependent increase in mass per cell. Through a combination of experiment and theoretical analysis of the organismal energy balance, we further show that the mass allometry is caused by body size dependent energy storage. Our results reveal the physiological origins of Kleiber's law in planarians and have general implications for understanding a fundamental scaling law in biology.

[Specimen labelling: A complex process with a high error rate]. / Etikettierung von Laborröhrchen: ein komplexer Prozess mit hoher Fehleranfälligkeit.

Errors associated with the labelling of laboratory specimens repeatedly occur in health facilities and are often described in Critical Incident Reporting Systems (CIRS). The analysis of these error reports and the complexity of the specimen collection process pose major challenges for responsible health care professionals. To examine which errors occur in the labelling of laboratory specimens, and what leads to their detection, the error reports of 42 Swiss hospitals within the Critical Incident Reporting & Reaching NETwork (CIRRNET) were systematically analysed. METHOD: Within the scope of a reporting month in the year 2016, 42 hospitals were asked to pay particular attention to the issue of mislabelled laboratory specimens, to report these errors in the local CIRS system, and to forward the information to the CIRRNET database. In addition, using a systematic keyword search, a search for old error reports on the mislabelling of laboratory specimens was conducted in the CIRRNET database and the results extracted. 227 error reports were finally included in the analysis. All these error reports were analysed systematically and by content, and the problem areas described in these reports allocated to newly defined categories. The systematic analysis included: the time of error detection, the problem area described, the length of time between error occurrence and error detection, as well as possible safety barriers. RESULTS: The majority (52 %) of labelling errors of laboratory specimens are detected in the laboratory, 21.1 % on the hospital ward before the specimens are sent to the laboratory to be processed, and a further 24.7 % at a very late stage when test results are associated with the patient on the ward. The analysis of the problem areas described showed that patient identification (7.9 %) was a key issue. The most frequent errors occurred in connection with the labelling of laboratory test tubes (45.4 %) and analysis forms or requisition slips (33 %). Numerous errors went undetected throughout the entire process, i.e. right up until the moment when the test result was finally assigned to the patient. The analysis also provided information about possible safety barriers for future prevention of laboratory specimen mislabelling. CONCLUSIONS: A content-analysis approach is essential to the evaluation of error reports as it is the only way to identify all the problems of laboratory specimen mislabelling described. Furthermore, a deductive approach also facilitates the identification of possible safety barriers. The findings provide valuable information for mislabelling prevention approaches that is not otherwise available. Further analysis of error reports from Critical Incident Reporting Systems is necessary in order to gain more experience with the methodical approach and to draw conclusions as to whether the complex process of analysing each individual error report yields information that is more useful than the analysis of the error reports of an identified problem area.

Chief physicians' attitudes towards early warning score systems in Switzerland: Results of a cross-sectional survey.

RATIONALE, AIMS AND OBJECTIVES: Early warning score systems (EWS-S) have been shown to be valuable tools to recognize otherwise unnoticed clinical deterioration (CDET) of patients. They have been associated with fewer unplanned transfers to the intensive care unit (UTICU) and lower in-hospital mortality. Little is known about their current usage in Switzerland and about the attitudes towards such tools among chief physicians. We aimed to assess the use of EWS-S in Switzerland and the attitudes of chief physicians towards EWS-S depending on previously experienced CDET followed by UTICU, reanimation, or death. METHODS: Chief physicians of medical and surgical departments from all acute care hospitals in Switzerland were asked to participate within a project that aims to develop recommendations for the use of EWS-S in Switzerland (n = 118). The explorative study assessed perceived CDET, which led to UTICU, reanimation, or death of a patient, the knowledge and usage about different EWS-S and attitudes towards EWS-S in a written questionnaire. Means and percentages were used, and differences were assessed with independent t tests, chi-square, or Fisher exact test, as appropriate. RESULTS: Adverse events based on CDET were reported frequently, and awareness among chief physicians was high. Less than half of the chief physicians knew tools that systematically assess CDET with one-fifth of responders reporting using tools at their department. Previous experiences of UTICU, reanimation, or death after due to CDET were associated with more positive attitudes towards EWS-S. CONCLUSIONS: Adverse events based on CDET of patients are frequent and the awareness of this problem is high among chief physicians. Positive attitudes were more common with previous experiences of adverse events due to CDET. Our results strengthen the argumentation that the recommendation and future implementation of EWS-S in Switzerland would be meaningful.

Transcriptional regulators form diverse groups with context-dependent regulatory functions.

One of the most important questions in biology is how transcription factors (TFs) and cofactors control enhancer function and thus gene expression. Enhancer activation usually requires combinations of several TFs, indicating that TFs function synergistically and combinatorially. However, while TF binding has been extensively studied, little is known about how combinations of TFs and cofactors control enhancer function once they are bound. It is typically unclear which TFs participate in combinatorial enhancer activation, whether different TFs form functionally distinct groups, or if certain TFs might substitute for each other in defined enhancer contexts. Here we assess the potential regulatory contributions of TFs and cofactors to combinatorial enhancer control with enhancer complementation assays. We recruited GAL4-DNA-binding-domain fusions of 812 Drosophila TFs and cofactors to 24 enhancer contexts and measured enhancer activities by 82,752 luciferase assays in S2 cells. Most factors were functional in at least one context, yet their contributions differed between contexts and varied from repression to activation (up to 289-fold) for individual factors. Based on functional similarities across contexts, we define 15 groups of TFs that differ in developmental functions and protein sequence features. Similar TFs can substitute for each other, enabling enhancer re-engineering by exchanging TF motifs, and TF-cofactor pairs cooperate during enhancer control and interact physically. Overall, we show that activators and repressors can have diverse regulatory functions that typically depend on the enhancer context. The systematic functional characterization of TFs and cofactors should further our understanding of combinatorial enhancer control and gene regulation.

Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specificity to certain enhancers. This is conceivable, as various core promoter sequence elements are differentially distributed between genes of different functions, including elements that are predominantly found at either developmentally regulated or at housekeeping genes. Here we show that thousands of enhancers in Drosophila melanogaster S2 and ovarian somatic cells (OSCs) exhibit a marked specificity to one of two core promoters--one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor--and confirm the existence of these two classes for five additional core promoters from genes with diverse functions. Housekeeping enhancers are active across the two cell types, while developmental enhancers exhibit strong cell-type specificity. Both enhancer classes differ in their genomic distribution, the functions of neighbouring genes, and the core promoter elements of these neighbouring genes. In addition, we identify two transcription factors--Dref and Trl--that bind and activate housekeeping versus developmental enhancers, respectively. Our results provide evidence for a sequence-encoded enhancer-core-promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.

A vignette study to examine health care professionals' attitudes towards patient involvement in error prevention.

BACKGROUND: Various authorities recommend the participation of patients in promoting patient safety, but little is known about health care professionals' (HCPs') attitudes towards patients' involvement in safety-related behaviours. OBJECTIVE: To investigate how HCPs evaluate patients' behaviours and HCP responses to patient involvement in the behaviour, relative to different aspects of the patient, the involved HCP and the potential error. DESIGN: Cross-sectional fractional factorial survey with seven factors embedded in two error scenarios (missed hand hygiene, medication error). Each survey included two randomized vignettes that described the potential error, a patient's reaction to that error and the HCP response to the patient. SETTING: Twelve hospitals in Switzerland. PARTICIPANTS: A total of 1141 HCPs (response rate 45%). MEASUREMENTS: Approval of patients' behaviour, HCP response to the patient, anticipated effects on the patient-HCP relationship, HCPs' support for being asked the question, affective response to the vignettes. Outcomes were measured on 7-point scales. RESULTS: Approval of patients' safety-related interventions was generally high and largely affected by patients' behaviour and correct identification of error. Anticipated effects on the patient-HCP relationship were much less positive, little correlated with approval of patients' behaviour and were mainly determined by the HCP response to intervening patients. HCPs expressed more favourable attitudes towards patients intervening about a medication error than about hand sanitation. CONCLUSIONS: This study provides the first insights into predictors of HCPs' attitudes towards patient engagement in safety. Future research is however required to assess the generalizability of the findings into practice before training can be designed to address critical issues.

Effects of an educational patient safety campaign on patients' safety behaviours and adverse events.

Rationale, aims and objectives The study aims to investigate the effects of a patient safety advisory on patients' risk perceptions, perceived behavioural control, performance of safety behaviours and experience of adverse incidents. Method Quasi-experimental intervention study with non-equivalent group comparison was used. Patients admitted to the surgical department of a Swiss large non-university hospital were included. Patients in the intervention group received a safety advisory at their first clinical encounter. Outcomes were assessed using a questionnaire at discharge. Odds ratios for control versus intervention group were calculated. Regression analysis was used to model the effects of the intervention and safety behaviours on the experience of safety incidents. Results Two hundred eighteen patients in the control and 202 in the intervention group completed the survey (75 and 77% response rates, respectively). Patients in the intervention group were less likely to feel poorly informed about medical errors (OR = 0.55, P = 0.043). There were 73.1% in the intervention and 84.3% in the control group who underestimated the risk for infection (OR = 0.51, CI 0.31-0.84, P = 0.009). Perceived behavioural control was lower in the control group (meanCon = 3.2, meanInt = 3.5, P = 0.010). Performance of safety-related behaviours was unaffected by the intervention. Patients in the intervention group were less likely to experience any safety-related incident or unsafe situation (OR for intervention group = 0.57, CI 0.38-0.87, P = 0.009). There were no differences in concerns for errors during hospitalization. There were 96% of patients (intervention) who would recommend other patients to read the advisory. Conclusions The results suggest that the safety advisory decreases experiences of adverse events and unsafe situations. It renders awareness and perceived behavioural control without increasing concerns for safety and can thus serve as a useful instrument for communication about safety between health care workers and patients.

'New perspectives on well-known issues': patients' experiences and perceptions of safety in Swiss hospitals.

Patients' reports of safety-related events and perceptions of safety can be a valuable source for hospitals. Patients of eight acute care hospitals in Switzerland were surveyed for safety-related events and concerns for safety. In workshops with hospitals areas for improvement were analyzed and priorities for change identified. To evaluate the benefit of the approach, semi-structured interviews were conducted with hospital risk managers. 3,983 patients returned the survey (55% response rate). 21.4% reported at least one definite safety event, and the mean number of 'definite' incidents per patient was 0.31 (95% CI=0.29 to 0.34). 3.2% were very concerned and 14.7% were somewhat concerned about medical errors and safety. Having experienced a safety-related event, younger age, length of stay, poor health and a poor education increased the probability of reporting concerns. With some exceptions, results confirmed the hospitals' a priori expectations regarding the strengths and weaknesses of their institutions. Risk managers emphasized the usability of results for their work and the special value of referring to the patient's perspective at their home institutions. A considerable fraction of patients subjectively experiences safety-related events and is concerned about safety. Patient-generated data introduced a new quality into the discussion of safety issues within hospitals, and some expected that patients' experiences and concerns could affect patient volumes. Though the study is limited by the short time horizon and the lack of follow-up, the results suggest that the described approach is feasible and can serve as a supplemental tool for risk identification and management.

Patients' and healthcare workers' perceptions of a patient safety advisory.

OBJECTIVE: To assess patients' and healthcare workers' (hcw) attitudes and experiences with a patient safety advisory, to investigate predictors for patients' safety-related behaviors and determinants for staff support for the advisory. DESIGN: Cross-sectional surveys of patients (n= 1053) and hcw (n= 275). SETTING: Three Swiss hospitals. PARTICIPANTS: Patients who received the safety advisory and hcw caring for these patients. INTERVENTION: Patient safety advisory disseminated to patients at the study hospitals. MAIN OUTCOME MEASURES: Attitudes towards and experiences with the advisory. Hcw support for the intervention and patients' intentions to apply the recommendations were modelled using regression analyses. RESULTS: Patients (95%) and hcw (78%) agreed that hospitals should educate patients how to prevent errors. Hcw and patients' evaluations of the safety advisory were positive and followed a similar pattern. Patients' intentions to engage in safety were significantly predicted by behavioral control, subjective norms, attitudes, safety behaviors during hospitalization and experiences with taking action. Hcw support for the campaign was predicted by rating of the advisory (Odds ratio (OR) 3.4, confidence interval (CI) 1.8-6.1, P< 0.001), the belief that it prevents errors (OR 1.7, CI 1.2-2.5, P= 0.007), perceived increased vigilance of patients (OR 1.9, CI 1.1-3.3, P= 0.034) and experience of unpleasant situations (OR 0.6, CI 0.4-1.0, P= 0.035). CONCLUSIONS: The safety advisory was well accepted by patients and hcw. To be successful, the advisory should be accompanied by measures that target norms and barriers in patients, and support staff in dealing with difficult situations.