Distribution-Free Bounds for Serial Correlation Coefficients in Heteroskedastic Symmetric Time Series

We consider the problem of testing whether the observations X1, · · ·, Xn of a time series are independent with unspecified (possibly nonidentical) distributions symmetric about a common known median. Various bounds on the distributions of serial correlation coefficients are proposed: exponential bounds, Eaton-type bounds, Chebyshev bounds and Berry-Esséen-Zolotarev bounds. The bounds are exact in finite samples, distribution-free and easy to compute. The performance of the bounds is evaluated and compared with traditional serial dependence tests in a simulation experiment. The procedures proposed are applied to U.S. data on interest rates (commercial paper rate). Nous étudions le problème qui consiste à tester lâhypothèse que des observations X1, · · ·, Xn dâune série chronologique sont indépendantes avec des distributions non spécifiées (possiblement non identiques) symétriques autour dâune médiane connue. Nous proposons plusieurs bornes sur les distributions des coefficients dâautocorrélation : bornes exponen-tielles, bornes de type Eaton, bornes de Chebyshev et bornes de Berry-Esséen-Zolotarev. Les bornes sont exactes dans les échantillons finis, non paramétriques et faciles à calculer. Nous évaluons par simulation la performance des bornes et comparons celle-ci à celle de tests dâautocorrélation traditionnels. Les procédures proposées sont appliquées à des données de taux dâintérêt américaines (âcommercial paper rateâ).autocorrelation; serial dependence; nonparametric test; distribution-free test; heterogeneity; heteroskedasticity; symmetric distribution; robustness; exact test; bound; exponential bound; large deviations; Chebyshev inequality; Berry-Esséen; interest rates, autocorrelation; serial dependence; nonparametric test; distribution-free test; heterogeneity; heteroskedasticity; symmetric distribution; robustness; exact test; bound; exponential bound; large deviations; Chebyshev inequality; Berry-Esséen; interest rates

Methicillin-Resistant Staphylococcus aureus ST398 in Swine Farm Personnel, Belgium

We assessed methicillin-resistant Staphylococcus aureus (MRSA) in persons on 49 swine farms in Belgium. Surveys showed that 48 (37.8%) persons carried MRSA ST398 and 1 (0.8%) had concurrent skin infection. Risk factors for carriage were MRSA carriage by pigs, regular contact with pigs and companion animals, and use of protective clothing

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Background: Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results: We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions: Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Background Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification

Next-generation sequencing: what are the needs in routine clinical microbiology? A survey among clinicians involved in infectious diseases practice

BackgroundThe translation of Next-Generation Sequencing (NGS) from research to clinical microbiology is increasing rapidly, but its integration into routine clinical care struggles to catch-up. A challenge for clinical laboratories is that the substantial investments made in the required technologies and resources must meet both current and forthcoming needs.MethodsTo get a clinical perspective of these needs, we have sent a survey to infectious diseases clinicians of five hospitals, covering the following topics: NGS knowledge, expected syndromes and patients foreseen to benefit from NGS, and expected impact on antimicrobial prescription.ResultsAccording to clinicians, benefits of NGS are mostly expected in neurological and respiratory infections diagnostics.ConclusionA better dialog between microbiologists and clinicians about hopes and limits of NGS in microbiology may help identifying key investments needed for clinical laboratories, today and tomorrow

Struggle with a gap between intensive care units and general wards

Nursing critically ill patients includes planning and performing safe discharges from Intensive Care Units (ICU) to the general wards. The aim of this study was to obtain a deeper understanding of the main concern in the ICU transitional process—the care before, during, and after the transfer of ICU patients. Interviews were conducted with 35 Swedish nurses and analysed according to grounded theory. The main concern was the nurses' “struggling with a gap.” The “gap” was caused by differences in the altered level of care and contributed to difficulties for nurses encountering an overlap during the transitional care. The categories: sheltering, seeking organizational intertwining and striving for control are related to the core category and were used to generate a theory. The nurses sought improved collaboration, and employed patient-centred routines. They wanted access to necessary tools; they relayed or questioned their own competence and sought assurance of the patients' ability to be transferred. If the nurses felt a loss of control, lack of intertwining and lack of collaboration, they sheltered their patients and themselves. Intertwining was more difficult to perform, but actually even more important to do. With knowledge about ICU transitional care, collaboration, routines, and with an organization that provides an educational environment, the process could be improved

MRSA surveillance programmes worldwide : moving towards a harmonised international approach

Multinational surveillance programmes for methicillin-resistant Staphylococcus aureus (MRSA) are dependent on national structures for data collection. This study aimed to capture the diversity of national MRSA surveillance programmes and to propose a framework for harmonisation of MRSA surveillance. The International Society of Antimicrobial Chemotherapy (ISAC) MRSA Working Group conducted a structured survey on MRSA surveillance programmes and organised a webinar to discuss the programmes’ strengths and challenges as well as guidelines for harmonisation. Completed surveys represented 24 MRSA surveillance programmes in 16 countries. Several countries reported separate epidemiological and microbiological surveillance. Informing clinicians and national policy-makers were the most common purposes of surveillance. Surveillance of bloodstream infections (BSIs) was present in all programmes. Other invasive infections were often included. Three countries reported active surveillance of MRSA carriage. Method- ology and reporting of antimicrobial susceptibility, virulence factors, molecular genotyping and epidemiological metadata varied greatly. Current MRSA surveillance programmes rely upon heterogeneous data collection systems, which hampers international epidemiological monitoring and research. To harmonise MRSA surveillance, we suggest improving the integration of microbiological and epidemiological data, implementation of central biobanks for MRSA isolate collection, and inclusion of a representative sample of skin and soft-tissue infection cases in addition to all BSI cases.peer-reviewe

External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories

Objective: This first pilot on external quality assessment (EQA) of SARS-CoV-2 whole genome sequencing, initiated by the ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) and Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing.Methods: Ten samples with varying viral loads were sent out to 15 clinical laboratories who had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centres were compared on were identification of 1) SNPs and indels, 2) Pango lineages, and 3) clusters between samples.Results: The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to varying depth (up to 100-fold difference across centres). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignment. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data.Conclusions: The pilot EQA was an overall success. It was able to show the high quality of participating labs and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.</p

Phylogenetic Analysis of Staphylococcus aureus CC398 Reveals a Sub-Lineage Epidemiologically Associated with Infections in Horses

In the early 2000s, a particular MRSA clonal complex (CC398) was found mainly in pigs and pig farmers in Europe. Since then, CC398 has been detected among a wide variety of animal species worldwide. We investigated the population structure of CC398 through mutation discovery at 97 genetic housekeeping loci, which are distributed along the CC398 chromosome within 195 CC398 isolates, collected from various countries and host species, including humans. Most of the isolates in this collection were received from collaborating microbiologists, who had preserved them over years. We discovered 96 bi-allelic polymorphisms, and phylogenetic analyses revealed that an epidemic sub-clone within CC398 (dubbed 'clade (C)') has spread within and between equine hospitals, where it causes nosocomial infections in horses and colonises the personnel. While clade (C) was strongly associated with S. aureus from horses in veterinary-care settings (p = 2 × 10(-7)), it remained extremely rare among S. aureus isolates from human infections

Finding the Pace of the Learning Practice of Purposeful Organising.

The purpose with this paper is to understand how the creation of a new purposeful organising within the public sector developed by exploring the nature of the learning practice that was deployed in an empirical case. Five patterns of actions were found in the empirical material that served different purposes in relation to the rhythm of the learning practice. The patterns of actions are in this paper called navigating, planning, communicatinganddocumenting.These four were recurring and synchronized in time through a fifth, overarching pattern of actions called pacing. The paper contributes to the understanding of learning in organising by expanding our knowledge of how patterns of actions are synchronized temporally in a learning practice