Salmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa

Autor: Siân V. Owen, de Pinna E, Hinton Jcd., Nicholas A. Feasey, Lukeki Kaindama, Rowe Wpm, C. Lane, Philip M. Ashton, Lesley Larkin, Satheesh Nair, Claire Jenkins, Timothy J. Dallman

The ST313 sequence type of Salmonella enterica serovar Typhimurium causes invasive non-typhoidal salmonellosis amongst immunocompromised people in sub-Saharan Africa (sSA). Previously, two distinct phylogenetic lineages of ST313 have been described w

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1ae0b4cc005f9b59ed73a2d613b11645
https://doi.org/10.1101/139576

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

Autor: Nicholls SM; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Poplawski R; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Bull MJ; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Underwood A; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Chapman M; Health Data Research UK Cambridge, Wellcome Genome Campus, Hinxton, UK., Abu-Dahab K; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Taylor B; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Colquhoun RM; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Rowe WPM; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Jackson B; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Hill V; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., O'Toole Á; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Rey S; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Southgate J; School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK., Amato R; Wellcome Sanger Institute, Hinxton, UK., Livett R; Wellcome Sanger Institute, Hinxton, UK., Gonçalves S; Wellcome Sanger Institute, Hinxton, UK., Harrison EM; Wellcome Sanger Institute, Hinxton, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK., Peacock SJ; Department of Medicine, University of Cambridge, Cambridge, UK., Aanensen DM; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Rambaut A; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Connor TR; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.; School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK.; Quadram Institute, Norwich, UK., Loman NJ; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK. n.j.loman@bham.ac.uk.

Publikováno v: Genome biology [Genome Biol] 2021 Jul 01; Vol. 22 (1), pp. 196. Date of Electronic Publication: 2021 Jul 01.

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa.

Autor: Pulford CV; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Perez-Sepulveda BM; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Canals R; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Bevington JA; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Bengtsson RJ; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Wenner N; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Rodwell EV; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Kumwenda B; University of Malawi, College of Medicine, Blantyre, Malawi., Zhu X; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Bennett RJ; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Stenhouse GE; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Malaka De Silva P; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Webster HJ; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Bengoechea JA; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK., Dumigan A; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK., Tran-Dien A; Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France., Prakash R; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi., Banda HC; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi., Alufandika L; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi., Mautanga MP; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi., Bowers-Barnard A; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Beliavskaia AY; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Predeus AV; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Rowe WPM; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Darby AC; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Hall N; Earlham Institute, Norwich Research Park, Norwich, UK., Weill FX; Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France., Gordon MA; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi., Feasey NA; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi., Baker KS; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK., Hinton JCD; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK. jay.hinton@liverpool.ac.uk.

Publikováno v: Nature microbiology [Nat Microbiol] 2021 Mar; Vol. 6 (3), pp. 327-338. Date of Electronic Publication: 2020 Dec 21.

When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data.

Autor: Rowe WPM; Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK. w.rowe@bham.ac.uk.; Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, WA4 4AD, UK. w.rowe@bham.ac.uk.

Publikováno v: Genome biology [Genome Biol] 2019 Sep 13; Vol. 20 (1), pp. 199. Date of Electronic Publication: 2019 Sep 13.

Indexed variation graphs for efficient and accurate resistome profiling.

Autor: Rowe WPM; Institute of Integrative Biology, The University of Liverpool, Liverpool, UK.; Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK., Winn MD; Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2018 Nov 01; Vol. 34 (21), pp. 3601-3608.