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This study describes the hybrid genome assemblies of four Shiga toxin-producing Escherichia coli strains isolated from the recto-anal junction of slaughter-age Irish sheep. In silico serotyping and genome analysis determined that each of the strains harbored a Shiga-toxin subtype, a complete locus of enterocyte effacement, and a rare O-island 122., Competing Interests: The authors declare no conflict of interest.

Innovation in the education and training of healthcare staff is required to support complementary approaches to learning from patient safety and everyday events in healthcare. Debriefing is a commonly used learning tool in healthcare education but not in clinical practice. Little is known about how to implement debriefing as an approach to safety learning across a health system. After action review (AAR) is a debriefing approach designed to help groups come to a shared mental model about what happened, why it happened and to identify learning and improvement. This paper describes a digital-based implementation strategy adapted to the Irish healthcare system to promote AAR uptake. The digital strategy aims to assist implementation of national level incident management policies and was collaboratively developed by the RCSI University of Medicine and Health Sciences and the National Quality and Patient Safety Directorate of the Health Service Executive. During the COVID-19 pandemic, a well-established in-person AAR training programme was disrupted and this led to the development of a series of open access videos on AAR facilitation skills (which accompany the online version of this paper). These provide: (1) an introduction to the AAR facilitation process; (2) a simulation of a facilitated formal AAR; (3) techniques for handling challenging situations that may arise in an AAR and a (4) reflection on the benefits of the AAR process. These have the potential to be used widely to support learning from patient safety and everyday events including excellent care., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Introduction : Interventions designed to improve safety culture in hospitals foster organisational environments that prevent patient safety events and support organisational and staff learning when events do occur. A safety culture supports the required health workforce behaviours and norms that enable safe patient care, and the well-being of patients and staff. The impact of safety culture interventions on staff perceptions of safety culture and patient outcomes has been established. To-date, however, there is no common understanding of what staff outcomes are associated with interventions to improve safety culture and what staff outcomes should be measured. Objectives : The study seeks to examine the effect of safety culture interventions on staff in hospital settings, globally. Methods and Analysis : A mixed methods systematic review will be conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Searches will be conducted using the electronic databases of MEDLINE, EMBASE, CINAHL, Health Business Elite, and Scopus. Returns will be screened in Covidence according to inclusion and exclusion criteria. The mixed-methods appraisal tool (MMAT) will be used as a quality assessment tool. The Cochrane Collaboration's tool for assessing risk of bias in randomised trials and non-randomised studies of interventions will be employed to verify bias. Synthesis will follow the Joanna Briggs Institute methodological guidance for mixed methods reviews, which recommends a convergent approach to synthesis and integration. Discussion : This systematic review will contribute to the international evidence on how interventions to improve safety culture may support staff outcomes and how such interventions may be appropriately designed and implemented., Competing Interests: No competing interests were disclosed., (Copyright: © 2022 Finn M et al.)

The diagnostic protocol currently used globally to identify Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is RT-qPCR. The spread of these infections and the epidemiological imperative to describe variation across the virus genome have highlighted the importance of sequencing. SARS-CoV-2 rapid antigen diagnostic tests (RADTs) are designed to detect viral nucleocapsid protein with positive results suggestive of the presence of replicating virus and potential infectivity. In this study, we developed a protocol for recovering SARS-CoV-2 RNA from "spent" RADT devices of sufficient quality that can be used directly for whole virus genome sequencing. The experimental protocol included the spiking of RADTs at different concentrations with viable SARS-CoV-2 variant Alpha (lineage B.1.1.7), lysis for direct use or storage. The lysed suspensions were used for RNA extraction and RT-qPCR. In parallel, we also tested the stability of the viral RNA in the RADTs and the RNA extracted from the RADTs was used as a template for tiling-PCR and whole virus genome sequencing. RNA recovered from RADTs spiked with SARS-CoV-2 was detected through RT-qPCR with C t values suitable for sequencing and the recovery from RADTs was confirmed after 7 days of storage at both 4 and 20°C. The genomic sequences obtained at each time-point aligned to the strain used for the spiking, demonstrating that sufficient SARS-CoV-2 viral genome can be readily recovered from positive-RADT devices in which the virus has been safely inactivated and genomically conserved. This protocol was applied to obtain whole virus genome sequence from RADTs ran in the field where the omicron variant was detected. The study demonstrated that viral particles of SARS-CoV-2 suitable for whole virus genome sequencing can be recovered from positive spent RADTs, extending their diagnostic utility, as a risk management tool and for epidemiology studies. In large deployment of the RADTs, positive devices could be safely stored and used as a template for sequencing allowing the rapid identification of circulating variants and to trace the source and spread of outbreaks within communities and guaranteeing public health., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Macori, Russell, Barry, McCarthy, Koolman, Wall, Sammin, Mulcahy and Fanning.)

Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by the formation of nodules, abscesses, and fistulae at intertriginous sites. The skin-gut axis is an area of emerging research in inflammatory skin disease and is a potential contributory factor to the pathogenesis of HS. A total of 59 patients with HS provided fecal samples and nasal and skin swabs of affected sites for analysis. A total of 30 healthy controls provided fecal samples, and 20 healthy controls provided nasal and skin swabs. We performed bacterial 16S ribosomal RNA gene amplicon sequencing on total DNA derived from the samples. Microbiome alpha diversity was significantly lower in the fecal, skin, and nasal samples of individuals with HS, which may be secondary to disease biology or related to antibiotic usage. Ruminococcus gnavus was more abundant in the fecal microbiome of individuals with HS, which is also reported in Crohn's disease, suggesting comorbidity due to shared gut microbiota alterations. Finegoldia magna was overabundant in HS skin samples relative to that in the healthy controls. It is possible that local inflammation is driven by F. magna by promoting the formation of neutrophil extracellular traps. These alterations in both the gut and skin microbiome in HS warrant further exploration, and therapeutic strategies, including fecal microbiota transplant or bacteriotherapy, could be of benefit., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Shiga toxin-producing Escherichia coli (STEC) organisms are a diverse group of pathogenic bacteria capable of causing serious human illness, and serogroups O157 and O26 are frequently implicated in human disease. Ruminant hosts are the primary STEC reservoir, and small ruminants are important contributors to STEC transmission. This study investigated the prevalence, serotypes, and shedding dynamics of STEC, including the supershedding of serogroups O157 and O26, in Irish sheep. Recto-anal mucosal swab samples ( n  = 840) were collected over 24 months from two ovine slaughtering facilities. Samples were plated on selective agars and were quantitatively and qualitatively assessed via real-time PCR (RT-PCR) for Shiga toxin prevalence and serogroup. A subset of STEC isolates ( n  = 199) were selected for whole-genome sequencing and analyzed in silico . In total, 704/840 (83.8%) swab samples were Shiga toxin positive following RT-PCR screening, and 363/704 (51.6%) animals were subsequently culture positive for STEC. Five animals were shedding STEC O157, and three of these were identified as supershedders. No STEC O26 was isolated. Post hoc statistical analysis showed that younger animals are more likely to harbor STEC and that STEC carriage is most prevalent during the summer months. Following sequencing, 178/199 genomes were confirmed as STEC. Thirty-five different serotypes were identified, 15 of which were not yet reported for sheep. Serotype O91:H14 was the most frequently reported. Eight Shiga toxin gene variants were reported, two stx 1 and six stx 2 , and three novel Shiga-toxin subunit combinations were observed. Variant stx 1c was the most prevalent, while many strains also harbored stx 2b . IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) bacteria are foodborne, zoonotic pathogens of significant public health concern. All STEC organisms harbor stx , a critical virulence determinant, but it is not expressed in most serotypes. Sheep shed the pathogen via fecal excretion and are increasingly recognized as important contributors to the dissemination of STEC. In this study, we have found that there is high prevalence of STEC circulating within sheep and that prevalence is related to animal age and seasonality. Further, sheep harbor a variety of non-O157 STEC, whose prevalence and contribution to human disease have been underinvestigated for many years. A variety of Stx variants were also observed, some of which are of high clinical importance.

Background: After Action Review is a form of facilitated team learning and review of events. The methodology originated in the United States Army and forms part of the Incident Management Framework in the Irish Health Services. After Action Review has been hypothesized to improve safety culture and the effect of patient safety events on staff (second victim experience) in health care settings. Yet little direct evidence exists to support this and its implementation has not been studied., Aim: To investigate the effect of After Action Review on safety culture and second victim experience and to examine After Action Review implementation in a hospital setting., Methods: A mixed methods study will be conducted at an Irish hospital. To assess the effect on safety culture and second victim experience, hospital staff will complete surveys before and twelve months after the introduction of After Action Review to the hospital (Hospital Survey on Safety Culture 2.0 and Second Victim Experience and Support Tool). Approximately one in twelve staff will be trained as After Action Review Facilitators using a simulation based training programme. Six months after the After Action Review training, focus groups will be conducted with a stratified random sample of the trained facilitators. These will explore enablers and barriers to implementation using the Theoretical Domains Framework. At twelve months, information will be collected from the trained facilitators and the hospital to establish the quality and resource implications of implementing After Action Review., Discussion: The results of the study will directly inform local hospital decision-making and national and international approaches to incorporating After Action Review in hospitals and other healthcare settings., Competing Interests: The authors have declared that no competing interests exist.

Objectives: To profile the aims and characteristics of quality improvement (QI) initiatives conducted in Ireland, to review the quality of their reporting and to assess outcomes and costs., Design: Scoping review., Data Sources: Systematic searches were conducted in PubMed, Web of Science, Embase, Google Scholar, Lenus and rian.ie. Two researchers independently screened abstracts (n=379) and separately reviewed 43 studies identified for inclusion using a 70-item critique tool. The tool was based on the Quality Improvement Minimum Quality Criteria Set (QI-MQCS), an appraisal instrument for QI intervention publications, and health economics reporting criteria. After reaching consensus, the final dataset was analysed using descriptive statistics. To support interpretations, findings were presented at a national stakeholder workshop., Eligibility Criteria: QI studies implemented and evaluated in Ireland and published between January 2015 and April 2020., Results: The 43 studies represented various QI interventions. Most studies were peer-reviewed publications (n=37), conducted in hospitals (n=38). Studies mainly aimed to improve the 'effectiveness' (65%), 'efficiency' (53%), 'timeliness' (47%) and 'safety' (44%) of care. Fewer aimed to improve 'patient-centredness' (30%), 'value for money' (23%) or 'staff well-being' (9%). No study aimed to increase 'equity'. Seventy per cent of studies described 14 of 16 QI-MQCS dimensions. Least often studies reported the 'penetration/reach' of an initiative and only 35% reported health outcomes. While 53% of studies expressed awareness of costs, only eight provided at least one quantifiable figure for costs or savings. No studies assessed the cost-effectiveness of the QI., Conclusion: Irish QI studies included in our review demonstrate varied aims and high reporting standards. Strategies are needed to support greater stimulation and dissemination of QI beyond the hospital sector and awareness of equity issues as QI work. Systematic measurement and reporting of costs and outcomes can be facilitated by integrating principles of health economics in QI education and guidelines., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Shiga-toxin producing Escherichia coli (STEC) are zoonotic foodborne pathogens that are capable of causing serious human illness. Ovine ruminants are recognized as an important source of STEC and a notable contributor to contamination within the food industry. This review examined the prevalence of STEC in the ovine food production chain from farm-to-fork, reporting carriage in sheep herds, during abattoir processing, and in raw and ready-to-eat meats and meat products. Factors affecting the prevalence of STEC, including seasonality and animal age, were also examined. A relative prevalence can be obtained by calculating the mean prevalence observed over multiple surveys, weighted by sample number. A relative mean prevalence was obtained for STEC O157 and all STEC serogroups at multiple points along the ovine production chain by using suitable published surveys. A relative mean prevalence (and range) for STEC O157 was calculated: for feces 4.4% (0.2-28.1%), fleece 7.6% (0.8-12.8%), carcass 2.1% (0.2-9.8%), and raw ovine meat 1.9% (0.2-6.3%). For all STEC independent of serotype, a relative mean prevalence was calculated: for feces 33.3% (0.9-90.0%), carcass 58.7% (2.0-81.6%), and raw ovine meat 15.4% (2.7-35.5%). The prevalence of STEC in ovine fleece was reported in only one earlier survey, which recorded a prevalence of 86.2%. Animal age was reported to affect shedding in many surveys, with younger animals typically reported as having a higher prevalence of the pathogen. The prevalence of STEC decreases significantly along the ovine production chain after the application of postharvest interventions. Ovine products pose a small risk of potential STEC contamination to the food supply chain.

Background: The density and phenotype of tumour-associated macrophages have been linked with prognosis in a range of solid tumours. While there is strong preclinical evidence that tumour-associated macrophages promote aspects of tumour progression, it can be challenging to infer clinical activity from surface markers and ex vivo behaviour. We investigated the association of macrophage infiltration with prognosis and functional changes in the tumour microenvironment in primary human melanoma., Methods: Fifty-seven formalin-fixed, paraffin-embedded primary melanomas were analysed by immunohistochemical analysis of CD68, CD163, inducible nitric oxide synthase (iNOS) and arginase expression. RNA sequencing was performed on serial sections of 20 of the stained tumours to determine the influence of macrophage infiltration on gene expression., Results: CD68 + cells are a functionally active subset of macrophages that are associated with increased iNOS and arginase staining and altered gene expression. In comparison, while there is a greater accumulation of CD163 + macrophages in larger tumours, these cells are comparatively inactive, with no association with the level of iNOS or arginase staining, and no effect on gene expression within the tumour. The infiltration of either subset of macrophages did not correlate to overall survival., Conclusions: Thus, melanomas contain distinct macrophage populations with diverse phenotypes, but with no observable prognostic role.

Objective: Although frontline clinicians are crucial in implementing and spreading innovations, their engagement in quality improvement remains suboptimal. Our goal was to identify facilitators and barriers to the development and engagement of clinicians in quality improvement., Design: A 25-item questionnaire informed by theoretical frameworks was developed, tested and disseminated by email., Settings: Members and fellows of the International Society for Quality in Healthcare., Participants: 1010 eligible participants (380 fellows and 647 members)., Interventions: None., Main Outcome Measures: Self-efficacy and effectiveness in conducting and leading quality improvement activities., Results: We received 212 responses from 50 countries, a response rate of 21%. Dedicated time for quality improvement, mentorship and coaching and a professional quality improvement network were significantly related to higher self-efficacy. Factors enhancing effectiveness were dedicated time for quality improvement, multidisciplinary improvement teams, professional development in quality improvement, ability to select areas for improvement and organizational values and culture. Inadequate time, mentorship, organizational support and access to professional development resources were key barriers. Personal strengths contributing to effectiveness were the ability to identify problems that need to be fixed, reflecting on and learning from experiences and facilitating sharing of ideas. Key quality improvement implementation challenges were adopting new payment models, demonstrating the business case for quality and safety and building a culture of accountability and transparency., Conclusions: Our findings highlight areas that organizations and professional development programs should focus on to promote clinician development and engagement in quality improvement. Barriers related to training, time, mentorship, organizational support and implementation must be concurrently addressed to augment the effectiveness of other approaches., (© The Author(s) 2020. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Molecular methods may reveal the presence of pathogens in samples through the detection of specific target gene(s) associated with microorganisms, but often, the subsequent cultural isolation of the pathogen is not possible. This discrepancy may be related to low concentration of the cells, presence of dead cells, competitive microflora, injured cells and cells in a viable but non-culturable state, free DNA and the presence of free bacteriophages which can carry the target gene causing the PCR-positive/culture-negative results. Shiga-toxigenic Escherichia coli (STEC) was used as a model for studying this phenomenon, based on the phage-encoded cytotoxins genes (Stx family) as the detection target in samples through real-time qPCR. Stx phages can be integrated in the STEC chromosome or can be isolated as free particles in the environment. In this study, a combination of PCR with culturing was used for investigating the presence of the stx1 and stx2 genes in 155 ovine recto-anal junction swab samples (method (a)-PCR). Samples which were PCR-positive and culture-negative were subjected to additional analyses including detection of dead STEC cells (method (b)-PCR-PMA dye assay), presence of Stx phages (method (c)-plaque assays) and inducible integrated phages (method (d)-phage induction). Method (a) showed that even though 121 samples gave a PCR-positive result (78%), only 68 samples yielded a culturable isolate (43.9%). Among the 53 (34.2%) PCR-positive/culture-negative samples, 21 (39.6%) samples were shown to have STEC dead cells only, eight (15.1%) had a combination of dead cells and inducible stx phage, while two samples (3.8%) had a combination of dead cells, inducible phage and free stx phage, and a further two samples had Stx1 free phages only (3.8%). It was thus possible to reduce the samples with no explanation to 20 (37.7% of 53 samples), representing a further step towards an improved understanding of the STEC PCR-positive/culture-negative phenomenon.

A quantitative PCR method is described for the detection and quantification of E. coli O157 and O26 in sheep recto-anal junction swabs. The method incorporated a short enrichment step (5 h) and the use of a developed standard calibration curve relating the real time PCR cycle threshold (Ct) values to the initial concentration of pathogen in the sheep sample., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Purpose: This article seeks to explore ways in which one can share and spread best practice, that have the potential for transformational change. It describes the cultural and behavioural mindset that is needed to make this happen., Design/methodology/approach: The overall approach is aimed at documenting the essential features of a best practice, giving pointers to relevant experts in that practice, deducing general guidelines, diffusing basic knowledge, and using subject-matter experts to apply and adapt the practices in a new context., Findings: Best practice resources require to be actively promoted, otherwise one may end up with databases and people that are under-used and not fulfilling their potential. One should resist the temptation to focus on explicit knowledge; databases of best practices are insufficient. Databases point to examples and people, but it is through people that deep knowledge is transferred., Originality/value: The information provided in this article is the viewpoint of the authors, who are experts in the field. Hopefully, their views will give the potential for transformational change.