Operationalising factors that explain the emergence of infectious diseases : A case study of the human campylobacteriosis epidemic

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The risk of inflammatory bowel disease in patients with axial spondyloarthritis treated with biologic agents : BSRBR-AS and meta-analysis

Funding: The BSRBR-AS is supported by the British Society for Rheumatology and they have received funds for the registry from Pfizer, AbbVie and UCB. These companies have no input in determining the topics for analysis or work involved in undertaking it but do receive an advance copy of the manuscript on which they may make comments. ACKNOWLEDGEMENTS: The original idea for the study was suggested by John Mansfield and discussed with Lesley Kay (both Newcastle upon Tyne Hospitals NHS Foundation Trust). All authors discussed and contributed to designing this study and the analysis plan, which was undertaken by RLB and (updated and) overseen by OR, LED and GJM. Results were reviewed by all authors. GJM, RLB, OR and LED all contributed to drafting the manuscript which was critically reviewed by all authors. RLB undertook this work while a visiting student based at the University of Aberdeen from Ludwig-Maximilians Universität (Munich).Peer reviewedPostprin

Mining whole genome sequence data to efficiently attribute individuals to source populations

Acknowledgements: The Campylobacter work in this project was supported by Food Standards Scotland project FSS00017 and the Scottish Government (Rural and Environment Science and Analytical Services Division) project A13559368.Peer reviewedPublisher PD

Determining factors related to poor quality of life in patients with axial spondyloarthritis : results from the British Society for Rheumatology Biologics Register (BSRBR-AS)

The BSRBR-AS is funded by the British Society for Rheumatology who have received funding for this from Pfizer, AbbVie and UCB. These companies receive advance copies of manuscripts for comments, but made none in relation to this manuscript.Peer reviewedPublisher PD

The role of metrology in axSpA : does it provide unique information in assessing patients and predicting outcome? Results from the BSRBR-AS registry

ACKNOWLEDGMENTS We thank the staff who contributed to running the BSRBR-AS register and we also thank the recruiting staff at the clinical centers, details of which are available at: www.abdn.ac.uk/bsrbr-as.Peer reviewedPostprin

Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods : activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis

We would like to thank all the persons and institutes that have provided the project with isolates and accompanying information. Without them, this project would not have been possible. Lin Cathrine T. Brandal, Norwegian Institute of Public Health, Norway Julio Vázquez Moreno and Raquel Abad Torreblanca, Instituto de Salud Carlos III, Spain Marc Lecuit, Institut Pasteur, France Alexandre Leclercq, Institut Pasteur, France Iva Hristova, National Center of Infectious and Parasitic Diseases, Bulgaria Marija Trkov, National Laboratory of Health, Environment and Food, Slovenia Cecilia Jernberg, Public Health Agency of Sweden, Sweden Ariane Pietzka, Austrian Agency for Health and Food Safety, Austria Eelco Franz and Ingrid Friesema, RIVM, The Netherlands Carlo Spanu, University of Sassari Sardinia Ifip, French Institute for Pig and Pork Industry, Maisons-Alfort, France All the NRLs for providing the isolates from the EU baseline study Special thanks to Sylvain Brisse and Alexandra Moura, Institut Pasteur, France, for providing cgMLST data. The authors would also like to thank the EFSA staff members: Maria Teresa da Silva Felicio, Beatriz Guerra, Ernesto Lìebana and Valentina Rizzi as well as the members of the Working Group on Listeria monocytogenes contamination of ready-to-eat foods: Kostas Koutsoumanis, Roland Lindqvist, Moez Sanaa, Panagiotis Skandamis, Niko Speybroek, Johanna Takkinen and Martin Wagner for the support, revisions and suggestions during the development of the present procurement activity and report.Publisher PD

Evolution of an Agriculture-Associated Disease Causing Campylobacter coli Clade: Evidence from National Surveillance Data in Scotland

The common zoonotic pathogen Campylobacter coli is an important cause of bacterial gastroenteritis worldwide but its evolution is incompletely understood. Using multilocus sequence type (MLST) data of 7 housekeeping genes from a national survey of Campylobacter in Scotland (2005/6), and a combined population genetic-phylogenetics approach, we investigated the evolutionary history of C. coli. Genealogical reconstruction of isolates from clinical infection, farm animals and the environment, revealed a three-clade genetic structure. The majority of farm animal, and all disease causing genotypes belonged to a single clade (clade 1) which had comparatively low synonymous sequence diversity, little deep branching genetic structure, and a higher number of shared alleles providing evidence of recent clonal decent. Calibration of the rate of molecular evolution, based on within-species genetic variation, estimated a more rapid rate of evolution than in traditional estimates. This placed the divergence of the clades at less than 2500 years ago, consistent with the introduction of an agricultural niche having had an effect upon the evolution of the C. coli clades. Attribution of clinical isolate genotypes to source, using an asymmetric island model, confirmed that strains from chicken and ruminants, and not pigs or turkeys, are the principal source of human C. coli infection. Taken together these analyses are consistent with an evolutionary scenario describing the emergence of agriculture-associated C. coli lineage that is an important human pathogen

LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe

Funding information This work was funded by EFSA, contract number C/EFSA/BIOCONTAM/2014/01-CT 1 on “Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis’, EFSA-Q-2014-00 026. Acknowledgements A. P., T. D. and K. G. are affiliated to the National Institute for Health Research – Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England, in collaboration with the University of East Anglia, the University of Oxford and the Quadram Institute. A. P., T. D. and K. G. are based at Public Health England. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England.Peer reviewedPublisher PD

Elucidating the aetiology of human Campylobacter coli infections

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Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7

This work was supported by: Scotland by Food Standards Scotland [Grant Number FS102029] and University of Aberdeen; New Zealand, Institute of Environmental Science and Research; Canada, the Public Health Agency of Canada; United States, United States Department of AgriculturePeer reviewedPostprin