Optimised human stool sample collection for multi-omic microbiota analysis

To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and – 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately – 80 °C frozen) sample and should be prioritised for human stool microbiome studie

Comparative genomics of Campylobacter concisus:Analysis of clinical strains reveals genome diversity and pathogenic potential

We thank members of the GI Research Team for discussions and advice. The authors thank Brennan Martin and the Centre for Genome Enabled Biology and Medicine for Illumina sequencing and useful discussions. This work was supported by a Fulbright Scholarship to G.L.H., an NHS Grampian Endowment grant fund to I.M. and G.L.H., a CSO clinical academic fellowship to R.H. (CAF/08/01). R.H. is supported by an NHS Research Scotland Career Researcher Fellowship. This work was generously supported by the Catherine McEwan Foundation. Sequence deposition The C. concisus raw sequencing reads and genome assemblies are freely available from the EMBL-EBI ENA under the study Accession PRJEB22351.Peer reviewedPublisher PD

Novel Campylobacter concisus lipooligosaccharide is a determinant of inflammatory potential and virulence

This work was supported in part by Department of Veterans Affairs Merit Review award BX000727 (to G.A.J.). The authors also acknowledge National Institutes of Health National Center for Research Resources Shared Instrumentation Grant S10 RR029446 (to H. E. Witkowska) for acquisition of the Synapt G2 high definition mass spectrometer, which is located at the University of California, San Francisco Sandler-Moore Mass Spectrometry Core Facility and supported by the Sandler Family Foundation, the Gordon and Betty Moore Foundation, National Institutes of Health/National Cancer Institute Cancer Center Support Grant P30 CA082103, and the Canary Foundation. G.A.J. is a recipient of the Senior Research Career Scientist award from the Department of Veterans Affairs. R.H. is funded by a Career Researcher Fellowship from NHS Research Scotland. The BISCUIT study was funded by a Clinical Academic Training Fellowship from the Chief Scientist Office (CAF/08/01). This is paper number 116 from the Center for Immunochemistry. The contents of this article do not represent the views of the Department of Veterans Affairs or the United States Government. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. K.B. acknowledges funding from the Child Health Research Charitable Incorporated Organisation and the Bogue Fellowship for travel. The authors declare that they have no conflicts of interest with the contents of this article.Peer reviewe

A miniaturized 4 K platform for superconducting infrared photon counting detectors

We report on a miniaturized platform for superconducting infrared photon counting detectors. We have implemented a fibre-coupled superconducting nanowire single photon detector in a Stirling/Joule–Thomson platform with a base temperature of 4.2 K. We have verified a cooling power of 4 mW at 4.7 K. We report 20% system detection efficiency at 1310 nm wavelength at a dark count rate of 1 kHz. We have carried out compelling application demonstrations in single photon depth metrology and singlet oxygen luminescence detection

Comparative genomics of Campylobacter concisus : Analysis of clinical strains reveals genome diversity and pathogenic potential

We thank members of the GI Research Team for discussions and advice. The authors thank Brennan Martin and the Centre for Genome Enabled Biology and Medicine for Illumina sequencing and useful discussions. This work was supported by a Fulbright Scholarship to G.L.H., an NHS Grampian Endowment grant fund to I.M. and G.L.H., a CSO clinical academic fellowship to R.H. (CAF/08/01). R.H. is supported by an NHS Research Scotland Career Researcher Fellowship. This work was generously supported by the Catherine McEwan Foundation. Sequence deposition The C. concisus raw sequencing reads and genome assemblies are freely available from the EMBL-EBI ENA under the study Accession PRJEB22351.Peer reviewedPublisher PD

Building a Methodological Foundation for Impactful Urban Planetary Health Science.

Anthropogenic environmental change will heavily impact cities, yet associated health risks will depend significantly on decisions made by urban leaders across a wide range of non-health sectors, including transport, energy, housing, basic urban services, and others. A subset of planetary health researchers focus on understanding the urban health impacts of global environmental change, and how these vary globally and within cities. Such researchers increasingly adopt collaborative transdisciplinary approaches to engage policy-makers, private citizens, and other actors in identifying and evaluating potential policy solutions that will reduce environmental impacts in ways that simultaneously promote health, equity, and/or local economies-in other words, maximising 'co-benefits'. This report presents observations from a participatory workshop focused on challenges and opportunities for urban planetary health research. The workshop, held at the 16th International Conference on Urban Health (ICUH) in Xiamen, China, in November 2019, brought together 49 participants and covered topics related to collaboration, data, and research impact. It featured research projects funded by the Wellcome Trust's Our Planet Our Health (OPOH) programme. This report aims to concisely summarise and disseminate participants' collective contributions to current methodological practice in urban planetary health research

Comparative genomics and genome biology of Campylobacter showae

We thank the Garrett and Huttenhower laboratories for useful discussions. This work was supported by a Fulbright Scholarship to GH, an NHS Grampian Endowment grant fund to I.M. and G.H., a CSO clinical academic fellowship to R.H. (CAF/08/01). RH is supported by an NHS Research Scotland Career Researcher Fellowship. NIH NIDDK grant R24DK110499 to CH, and NSF grant DBI-1053486 to CH.Peer reviewedPublisher PD

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine