International multicenter evaluation of the DiversiLab bacterial typing system for Escherichia coli and Klebsiella spp.

Successful multidrug-resistant clones are increasing in prevalence globally, which makes the ability to identify these clones urgent. However, adequate, easy-to-perform, and reproducible typing methods are lacking. We investigated whether DiversiLab (DL), an automated repetitive-sequence-based PCR bacterial typing system (bioMérieux), is suitable for comparing isolates analyzed at different geographic centers. A total of 39 Escherichia coli and 39 Klebsiella species isolates previously typed by the coordinating center were analyzed. Pulsed-field gel electrophoresis (PFGE) confirmed the presence of one cluster of 6 isolates, three clusters of 3 isolates, and three clusters of 2 isolates for each set of isolates. DL analysis was performed in 11 centers in six different countries using the same protocol. The DL profiles of 425 E. coli and 422 Klebsiella spp. were obtained. The DL system showed a lower discriminatory power for E. coli than did PFGE. The local DL data showed a low concordance, as indicated by the adjusted Rand and Wallace coefficients (0.132 to 0.740 and 0.070 to 1.0 [E. coli] and 0.091 to 0.864 and 0.056 to 1.0 [Klebsiella spp.], respectively). The central analysis showed a significantly improved concordance (0.473 to 1.0 and 0.290 to 1.0 [E. coli] and 0.513 to 0.965 and 0.425 to 1.0 [Klebsiella spp.], respectively). The misclassifications of profiles for individual isolates were mainly due to inconsistent amplification, which was most likely due to variations in the quality and amounts of the isolated DNA used for amplification. Despite local variations, the DL system has the potential to indicate the occurrence of clonal outbreaks in an international setting, provided there is strict adherence to standardized, reproducible DNA isolation methods and analysis protocols, all supported by a central database for profile comparisons

Spintronics: Fundamentals and applications

Spintronics, or spin electronics, involves the study of active control and manipulation of spin degrees of freedom in solid-state systems. This article reviews the current status of this subject, including both recent advances and well-established results. The primary focus is on the basic physical principles underlying the generation of carrier spin polarization, spin dynamics, and spin-polarized transport in semiconductors and metals. Spin transport differs from charge transport in that spin is a nonconserved quantity in solids due to spin-orbit and hyperfine coupling. The authors discuss in detail spin decoherence mechanisms in metals and semiconductors. Various theories of spin injection and spin-polarized transport are applied to hybrid structures relevant to spin-based devices and fundamental studies of materials properties. Experimental work is reviewed with the emphasis on projected applications, in which external electric and magnetic fields and illumination by light will be used to control spin and charge dynamics to create new functionalities not feasible or ineffective with conventional electronics.Comment: invited review, 36 figures, 900+ references; minor stylistic changes from the published versio

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

Motivation: Predicting RNA–RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA–RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA–RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting

BACKGROUND: Tracing of SARS-CoV-2 transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction of viral transmission networks by integration of molecular epidemiology into classical contact tracing. METHODS: In collaboration with local public health authorities, we set up an integrated system of genomic surveillance in an urban setting, combining a) viral surveillance sequencing, b) genetically based identification of infection clusters in the population, c) integration of public health authority contact tracing data, and d) a user-friendly dashboard application as a central data analysis platform. RESULTS: Application of the integrated system from August to December 2020 enabled a characterization of viral population structure, analysis of four outbreaks at a maximum care hospital, and genetically based identification of five putative population infection clusters, all of which were confirmed by contact tracing. The system contributed to the development of improved hospital infection control and prevention measures and enabled the identification of previously unrecognized transmission chains, involving a martial arts gym and establishing a link between the hospital to the local population. CONCLUSIONS: Integrated systems of genomic surveillance could contribute to the monitoring and, potentially, improved management of SARS-CoV-2 transmission in the population

A new 28Si single crystal: counting the atoms for the new kilogram definition

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Compliance-Bewertung im Umgang mit peripheren Venenkathetern auf Normalstationen eines Universitätsklinikums

Objective: The risk of peripheral venous catheter (PVC) infections in inpatients is often underestimated, even if it is lower than that for central venous catheters. Guidelines for the prevention of PVC-associated infections describe the evidence-based management of PVCs. The aims of this study were the development of standardized methods for compliance assessment regarding PVC management and the evaluation of self-reported knowledge and implementations among healthcare providers regarding PVC care.Method: We developed a checklist based on the recommendation of the Commission of Hospital Hygiene and Infection Prevention at the Robert Koch Institute (KRINKO) Berlin for the standardized evaluation of PVC management. The following parameters were collected and evaluated: condition of the puncture site, condition of the bandage, presence of an extension set, presence of a plug, and documentation. The checklist was applied in 14 normal wards in 2019. After feedback of the ward staff on the results, it was applied again in 2020 in the same wards. For retrospective data analysis, we used a newly developed PVC-quality index. After the second evaluation in 2020, we carried out an anonymous survey among the healthcare providers.Results: The evaluation of 627 indwelling PVCs showed a significant increase in compliance related to the presence of an extension set (p=0.049) and documentation (p<0.001) in the 2nd year. The quality index increased in 12 out of 14 wards. The participants of the survey were aware of the in-house standard "Prevention of vascular catheter-associated infections", with a mean score of 4.98 on a Likert scale (1=not aware, 7=completely aware). The main barrier to implementation of the preventive measures was the time factor. Survey participants were more aware of PVC placement than PVC care.Conclusion: The PVC quality index is a valuable tool for the assessment of compliance regarding PVC management in daily practice. Feedback from the ward staff on the results of compliance assessment improves PVC management, but the outcome is very heterogeneous.Zielsetzung: Das Infektionsrisiko von peripheren Venenkathetern (PVK) bei stationären Patienten wird, auch wenn es niedriger ist als das von zentralen Venenkathetern, häufig unterschätzt. Leitlinien zur Prävention von PVK-assoziierten Infektionen beinhalten Evidenz-basierte Maßnahmen zur Anlage, Pflege und Nutzung von liegenden PVK. Ziel dieser Studie war, ein Verfahren zur standardisierten Bewertung der Compliance im Umgang mit liegenden PVK zu entwickeln und zu testen. Außerdem sollte eine Selbsteinschätzung des Personals zu Kenntnis und Umsetzung der Präventionsmaßnahmen erhoben werden.Methode: Basierend auf den KRINKO-Empfehlungen wurde eine Checkliste zur standardisierten Bewertung der Umsetzung von Präventionsmaßnahmen bei liegenden PVK entwickelt. Folgende Parameter wurden erhoben und bewertet: Zustand der Punktionsstelle, Zustand des Verbands, Vorhandensein eines Extensionssets, Verschluss, Nutzung und Dokumentation der Maßnahmen. Die Checkliste wurde erstmals im Jahr 2019 auf 14 Normalstationen angewendet und nach Feedback der Ergebnisse erneut im Jahr 2020 auf denselben Stationen eingesetzt. Mithilfe eines neu entwickelten PVK-Qualitätsindex erfolgte ein retrospektiver Vergleich. Nach der 2. Bewertung wurde eine anonyme Mitarbeiterbefragung mittels Fragebogen durchgeführt.Ergebnisse: Bei der Bewertung von 627 liegenden PVK zeigte sich eine signifikante Steigerung der Compliance bezogen auf das Vorhandensein eines Extensionssets (p=0,049) und die Dokumentation (p<0,001) im 2. Jahr. Der Qualitätsindex ist auf 12 der 14 beobachteten Stationen gestiegen. Die Bekanntheit einzelner Maßnahmen des hausinternen Standards "Prävention gefäßkatheterassoziierter Infektionen" wurde mit dem Mittelwert 4,98 von 7 auf einer Likert-Skala angegeben; als einziges Hindernis in der Umsetzung konnte der Faktor Zeit identifiziert werden. Maßnahmen bei PVK-Anlage waren zu einem höheren Anteil bekannt als Maßnahmen der PVK-Pflege. Fazit: Der PVK-Qualitätsindex ist erfolgreich angewendet worden und ist geeignet, die PVK-bezogene Compliance standardisiert zu erheben. Feedback der Compliance im Umgang mit PVK hat diese verbessert, aber der Effekt ist sehr heterogen