Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit

Background: Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak. Methods: Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools. Results: The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters. Conclusion: The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates

To fail an asylum seeker: time, space and legal events

This is the final version. Available on open access from SAGE Publications via the DOI in this recordLegal geographers have recently highlighted the importance of attending to the interaction of time and space to understand law and its enactment. We build on these efforts to examine the spatiotemporal influences over the processes by which asylum claim determination procedures in Western industrialised countries seek to reconstruct past events for the purposes of deciding refugee claims. Two ‘common-sense’ beliefs underpin this reconstruction: that the occurrences leading to a fear of persecution can be isolated, and that the ‘truth’ of an asylum claim is objectively independent from the process of uncovering it. We critically interrogate these assumptions by conceptualising the fears of people seeking asylum as ‘events’ (Deleuze, 2004). Basing our argument on first-hand accounts of asylum interviews and asylum appeals derived from 41 interviews with former asylum seekers conducted in 2014 and 2015, we explore the folding together of asylum ‘truths’ and the spatiotemporal processes by which they are arrived at, arguing that refused asylum seekers are not simply detected by the process – they are produced by it.Economic and Social Research Council (ESRC)European Research Counci

Genome Sequencing of Xanthomonas vasicola Pathovar vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharide Synthesis, Type-IV Pilus and Type-III Secretion Effectors

This is the final version. Available on open access from MDPI via the DOI in this recordXanthomonas vasicola pathovar vasculorum (Xvv) is the bacterial agent causing gumming disease in sugarcane. Here, we compare complete genome sequences for five isolates of Xvv originating from sugarcane and one from maize. This identified two distinct types of lipopolysaccharide synthesis gene clusters among Xvv isolates: one is similar to that of Xanthomonas axonopodis pathovar citri (Xac) and is probably the ancestral type, while the other is similar to those of the sugarcane-inhabiting species, Xanthomonas sacchari. Four of six Xvv isolates harboured sequences similar to the Xac plasmid, pXAC47, and showed a distinct Type-IV pilus (T4P) sequence type, whereas the T4P locus of the other two isolates resembled that of the closely related banana pathogen, Xanthomonas campestris pathovar musacearum (Xcm). The Xvv isolate from maize has lost a gene encoding a homologue of the virulence effector, xopAF, which was present in all five of the sugarcane isolates, while xopL contained a premature stop codon in four out of six isolates. These findings shed new light on evolutionary events since the divergence of Xvv and Xcm, as well as further elucidating the relationships between the two closely related pathogens.This study was supported in part by the National Agriculture Research Organisation, Uganda, under the MSI/World Bank grant 2009

Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing

Microarray and next-generation sequencing techniques which allow whole genome analysis of chromatin structure and sequence-specific protein binding are revolutionizing our view of chromosome architecture and function. However, many current methods in this field rely on biochemical purification of highly specific fractions of DNA prepared from chromatin digested with either micrococcal nuclease or DNaseI and are restricted in the parameters they can measure. Here, we show that a broad size-range of genomic DNA species, produced by partial micrococcal nuclease digestion of chromatin, can be sequenced using paired-end mode next-generation technology. The paired sequence reads, rather than DNA molecules, can then be size-selected and mapped as particle classes to the target genome. Using budding yeast as a model, we show that this approach reveals position and structural information for a spectrum of nuclease resistant complexes ranging from transcription factor-bound DNA elements up to mono- and poly-nucleosomes. We illustrate the utility of this approach in visualizing the MNase digestion landscape of protein-coding gene transcriptional start sites, and demonstrate a comparative analysis which probes the function of the chromatin-remodelling transcription factor Cbf1p

The tribunal atmosphere: on qualitative barriers to access to justice

This the final version. Available on open access from Elsevier via the DOI in this recordVulnerable groups’ direct experiences and impressions of British courts and tribunals have often been overlooked by politicians and policy makers (JUSTICE, 2019). This paper takes a geographical, empirical approach to access to justice to respond to these concerns, paying attention to the atmosphere of First Tier Immigration and Asylum Tribunal hearings to explore the qualitative aspects of (in)access to justice during asylum appeals. It draws on 41 interviews with former appellants and 390 observations of hearings in the First tier immigration and asylum tribunal to unpack the lived experiences of tribunal users and to identify three ways in which the atmosphere in tribunals can constitute a barrier to access to justice. First, asylum appellants are frequently profoundly disorientated upon arrival at the tribunal. Second, appellants become distrustful of the courtroom when they cannot see it as independent of the state. Third they often experience the courtroom procedures and the interactions that take place as disrespectful, inhibiting their participation. These insights demonstrate how the concept of ‘atmosphere’ can illuminate legal debates in valuable ways. Additionally we argue that legal policy making must find better ways to take vulnerable litigants’ experiences into account.Economic and Social Research Council (ESRC)European Commissio

De novo genome assembly of the meadow brown butterfly, Maniola jurtina

This is the final version. Available on open access from the Genetics Society of America via the DOI in this record. Data availability: The raw sequencing data and genome assembly have been deposited at the NCBI SRA database under the BioProject PRJNA498046 and genome accession number VMKL00000000. Blast results, annotation and proteome associated with this manuscript are available at https://zenodo.org/record/3352197. Scripts used for the analysis of genomic data are available at: https://github.com/kumarsaurabh20/Maniola_jurtina_genome_sequencing. Supplemental material available at FigShare: https://doi.org/10.25387/g3.11594187Meadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology. To meet this aim, a clear description of genotype is required. Here we present the draft genome sequence of M. jurtina to serve as a founding genetic resource for this species. Seven libraries were constructed using pooled DNA from five wild caught spotted females and sequenced using Illumina, PacBio RSII and MinION technology. A novel hybrid assembly approach was employed to generate a final assembly with an N50 of 214 kb (longest scaffold 2.9 Mb). The sequence assembly described here predicts a gene count of 36,294 and includes variants and gene duplicates from five genotypes. Core BUSCO (Benchmarking Universal Single-Copy Orthologs) gene sets of Arthropoda and Insecta recovered 90.5% and 88.7% complete and single-copy genes respectively. Comparisons with 17 other Lepidopteran species placed 86.5% of the assembled genes in orthogroups. Our results provide the first high-quality draft genome and annotation of the butterfly M. jurtina.European Research Council (ERC)Natural Environment Research Council (NERC)Leverhulme TrustRoyal SocietyUniversity of Exete

Quality-of-life analysis of pembrolizumab vs brentuximab vedotin for relapsed/refractory classical Hodgkin lymphoma

KEYNOTE-204 (NCT02684292) demonstrated a progression-free survival advantage for pembrolizumab over brentuximab vedotin (BV) in patients who had relapsed or refractory classical Hodgkin lymphoma (R/R cHL) following, or who were ineligible for, autologous stem cell transplantation (ASCT). Health-related quality of life (HRQoL), measured by patient-reported outcomes (PROs) from KEYNOTE-204, are reported from patients who received ≥1 dose of study treatment and completed ≥1 PRO assessment. The EORTC QoL Questionnaire Core 30 (QLQ-C30) and EuroQoL EQ-5D were administered at baseline, every 6 weeks until week 24, and every 12 weeks thereafter. Prespecified end points included least squares mean (LSM) changes from baseline to week 24 and time to true deterioration (TTD; ≥10-point decline from baseline). Comparisons were evaluated using 2-sided P values uncontrolled for multiplicity. High compliance at baseline (.90%) and through week 24 (.80%) was demonstrated across treatment groups (PRO analysis set: Pembrolizumab, n = 146; BV, n = 150). The EORTC QLQ-C30 global health status (GHS)/ quality of life (QoL) score improved from baseline to week 24 on pembrolizumab and worsened on BV and demonstrated significant LSM differences at 24 weeks (GHS/QoL: 8.60 [95% confidence interval, 3.89-13.31]; P = .0004). Significant improvements were observed in each QLQ-C30 domain except emotional and cognitive functioning. Compared with BV, pembrolizumab prolonged TTD for GHS/QoL (hazard ratio, 0.40 [95% CI, 0.22-0.74]; P = .003) and each QLQ-C30 domain except cognitive functioning. In conclusion, pembrolizumab demonstrated overall improvements in PROs of HRQoL measures over BV in the KEYNOTE-204 study. These data and previously reported efficacy results support pembrolizumab as the preferred treatment option for patients with R/R cHL who are ineligible for or experience relapse after ASCT

Comments on the continuing widespread and unnecessary use of a defective emission equation in field emission related literature

Field electron emission (FE) has relevance in many different technological contexts. However, many related technological papers use a physically defective elementary FE equation for local emission current density (LECD). This equation takes the tunneling barrier as exactly triangular, as in the original FE theory of 90 years ago. More than 60 years ago, it was shown that the so-called Schottky-Nordheim (SN) barrier, which includes an image-potential-energy term (that models exchange-and-correlation effects) is better physics. For a metal-like emitter with work-function 4.5 eV, the SN-barrier-related Murphy-Good FE equation predicts LECD values that are higher than the elementary equation values by a large factor, often between around 250 and around 500. By failing to mention/apply this 60-year-old established science, or to inform readers of the large errors associated with the elementary equation, many papers (aided by defective reviewing) spread a new kind of "pathological science", and create a modern research-integrity problem. The present paper aims to enhance author and reviewer awareness by summarizing relevant aspects of FE theory, by explicitly identifying the misjudgment in the original 1928 Fowler-Nordheim paper, by explicitly calculating the size of the resulting error, and by showing in detail why most FE theoreticians regard the 1950s modifications as better physics. Suggestions are made, about nomenclature and about citation practice, that may help to diminish misunderstandings.Comment: Submitted for publication; in v2 a correction to historical information (with no numerical consequences) has been made in Appendix

What’s missing from legal geography and materialist studies of law? Absence and the assembling of asylum appeal hearings in Europe

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: Due to the ethical and legally sensitive nature of the research, ethnographic notes taken in court could not be made openly available. Appellant interviewees were not asked for their permission to share their interview transcripts in an online open archive because of concerns that they could misunderstand what was being asked for, or feel obliged to agree but subsequently feel less able to conduct free conversation in research interviews as a result, thereby negatively impacting on the quality of the data generated. Additional details relating to, and data resulting from, to a survey taken during observations of British asylum appeals between 2013 and 2016 are available from the UK Data Archive (persistent identifier: 10.5255/UKDA-SN-852032).There is an absence of absence in legal geography and materialist studies of the law. Drawing on a multi‐sited ethnography of European asylum appeal hearings, this paper illustrates the importance of absences for a fully‐fledged materiality of legal events. We show how absent materials impact hearings, that non‐attending participants profoundly influence them, and that even when participants are physically present, they are often simultaneously absent in other, psychological registers. In so doing we demonstrate the importance and productivity of thinking not only about law's omnipresence but also the absences that shape the way law is experienced and practiced. We show that attending to the distribution of absence and presence at legal hearings is a way to critically engage with legal performance.Economic and Social Research Council (ESRC)European Research Council (ERC

Molecular mechanisms of toxicity of silver nanoparticles in zebrafish embryos.

addresses: Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK. [email protected]: Journal Article; Research Support, Non-U.S. Gov'tThis is an open access article that is freely available in ORE or from the publisher's web site. http://pubs.acs.org/doi/abs/10.1021/es401758d. Please cite the published version© 2013 American Chemical SocietySupporting Information: Further details on the methodology and results for the characterization of the silver particles used for the exposures, mortality curves, sequencing analysis, and a number of supporting figures and tables. This material is available free of charge via the Internet at http://pubs.acs.org.Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk-, and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24 h of exposure, but with a recovery at 48 h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24 h, but not at 48 h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.Natural Environment Research Council (NERC)NERC Biomolecular Analysis FacilityUK Environment AgencySystems Biology Seed fund, University of Exete