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Quraishi M, Acharjee A, Beggs A, Horniblow R, Tselepis C, Gkoutos G, Ghosh S, Rossiter A, Loman N, van Schaik W, Withers D, Walters J, Hirschfield G, Iqbal T.
Journal of Crohn’s and Colitis 2020, Issue7
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Insight into Molecular Epidemiology, Antimicrobial Resistance, and Virulence Genes of Extensively Drug-Resistant Acinetobacter baumannii in Thailand
Kongthai P, Thummeepak R, Leungtongkam U, Pooarlai R, Kitti T, Thanwisai A, Chantratita N, Millard A, Sitthisak S.
Microbial Drug Resistance 2020
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Applied and Environmental Microbiology 2020, Issue20
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A genome-wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate degradation and phosphate transport systems
Turner A, Yasir M, Bastkowski S, Telatin A, Page A, Charles I, Webber M.
Journal of Antimicrobial Chemotherapy 2020, Issue11
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Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology
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Gut 2020, Issue7
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The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses
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Computational and Structural Biotechnology Journal 2020
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Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications
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Bioinformatics 2020, Issue6
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Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali
Senghore M, Diarra B, Gehre F, Otu J, Worwui A, Muhammad A, Kwambana-Adams B, Kay G, Sanogo M, Baya B, Orsega S, Doumbia S, Diallo S, de Jong B, Pallen M, Antonio M.
Scientific Reports 2020, Issue1
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Microbial Genomics 2020, Issue9
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The Next Million Names for Archaea and Bacteria
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Trends in Microbiology 2020
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Current Research in Biotechnology 2020
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Donor plasmids for phenotypically neutral chromosomal gene insertions in Enterobacteriaceae
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Microbiology 2020, Issue12
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Gene duplication drives genome expansion in Thaumarchaeota
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Horizontal Gene Transfer and Silver Nanoparticles Production in a New Marinomonas Strain Isolated From the Antarctic Psychrophilic Ciliate Euplotes Focardii
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The COVID-19 Genomics UK (COG-UK)
Lancet Microbe 2020
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Mechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases
Scott McDougall, Laura Clausen, Hye Jeong Ha, Isobel Gibson, Mark Bryan, Nazreen Hadjirin, Elizabeth Lay, Claire Raisen, Xiaoliang Ba, Olivier Restif, Julian Parkhill, Mark A.Holmes
Veterinary Microbiology, Volume 242, March 2020, 108592
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Genome sequence and characterisation of coliphage vB_Eco_SLUR29
Ibrahim Besler, Pavelas Sazinas, Christian Harrison, Lucy Gannon, Tamsin Redgwell, Slawomir Michniewski, Steven P. Hooton, Jon L. Hobman, Andrew Millard
PHAGE, ahead of print. Published Online: 7 Jan 2020
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Genome Biol. 2020 Feb 12;21(1):34. doi: 10.1186/s13059-020-1947-1.
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A Novel Inducible Prophage from Burkholderia Vietnamiensis G4 is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia
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Viruses 2020, 12(6), 601
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Methanogenic Granules Are Replicated, Whole Microbial Communities With Reproducible Responses To Environmental Cues
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A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture
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Population analysis of Legionella pneumophila reveals the basis of resistance to complement-mediated killing
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Metagenomics Strain Resolution on Assembly Graphs
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Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages
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Duplications drive diversity in Bordetella pertussis on an underestimated scale
Jonathan S. Abrahams, Michael R. Weigand, Natalie Ring, Iain MacArthur, Scott Peng, Margaret M. Williams, Barrett Bready, Anthony P. Catalano, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Jay M. Sage, Stefan Bagby, M. Lucia Tondella, Andrew R. Gorringe, Andrew Preston
bioRxiv 2020.02.06.937284; doi: https://doi.org/10.1101/2020.02.06.937284
De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning
Within-Host Diversity and Vertical Transmission of Group B Streptococcus Among Mother-infant Dyads in The Gambia
Ebenezer Foster-Nyarko, Madikay Senghore, Brenda A. Kwambana-Adams, Nabil-Fareed Alikhan, Anuradha Ravi, James Jafali, Kaddijatou Jawneh, Amara Jah, Maimuna Jarju, Fatima Ceesay, Sainabou Bojang, Archibald Worwui, Aderonke Odutola, Ezra Ogundare, Mark J. Pallen, Martin Ota, Martin Antonio
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The landscape of coadaptation in Vibrio parahaemolyticus
Yujun Cui, Chao Yang, Hongling Qiu, Hui Wang, Ruifu Yang, Daniel Falush
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AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments
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bioRxiv 593624; doi: https://doi.org/10.1101/593624
Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel
Florent Lassalle, Philippe Veber, Elita Jauneikaite, Xavier Didelot
bioRxiv: 586495; doi: https://doi.org/10.1101/586495
Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing
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Kathryn E. Holt, Florent Lassalle, Kelly L. Wyres, Ryan Wick, Rafał J. Mostowy
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Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics
Riding the wave of genomics, to investigate aquatic coliphage diversity and activity
Antibiotics select for novel pathways of resistance in biofilms
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bioRxiv 605212;doi: https://doi.org/10.1101/605212
Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments
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bioRxiv 690347; doi: https://doi.org/10.1101/690347
De Novo Growth of Methanogenic Granules Indicates a Biofilm Life-Cycle with Complex Ecology
Health assessment of the cleaner fish ballan wrasse Labrus bergylta from the British south-west coast.
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Recent mixing of Vibrio parahaemolyticus populations.
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Draft Genome Sequence of a New Pseudomonas sp. Strain, ef1, Associated with the Psychrophilic Antarctic Ciliate Euplotes focardii.
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Microb Genom. 2019 Sep;5(9). doi: 10.1099/mgen.0.000293. Epub 2019 Sep 11.
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Gigascience. 2019 Oct 1;8(10). pii: giz119.
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Ben Pascoe, Lisa K. Williams, Jessica K. Calland, Guillaume Méric, Matthew D. Hitchings, Myles Dyer, Joseph Ryder, Sophie Shaw, Bruno S. Lopes, Cosmin Chintoan-Uta, Elaine Allan, Ana Vidal, Catherine Fearnley, Paul Everest, Justin A. Pachebat, Tristan A. Cogan, Mark P. Stevens, Thomas J. Humphrey, Thomas S. Wilkinson, Alison J. Cody, Frances M. Colles, Keith A. Jolley, Martin C. J. Maiden, Norval Strachan, Bruce M. Pearson, Dennis Linton, Brendan W. Wren, Julian Parkhill, David J. Kelly, Arnoud H. M. van Vliet, Ken J. Forbes, Samuel K. Sheppard
Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000279. Epub 2019 Jul 16.
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Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens.
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Appl Environ Microbiol. 2019 Aug 14;85(17). pii: e00853-19. doi: 10.1128/AEM.00853-19. Print 2019 Sep 1.
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Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages.
Espadinha D, Sobral RG, Mendes CI, Méric G, Sheppard SK, Carriço JA, de Lencastre H, Miragaia M.
Front Microbiol. 2019 Aug 27;10:1971. doi: 10.3389/fmicb.2019.01971. eCollection 2019.
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Early Colonization of Weathered Polyethylene by Distinct Bacteria in Marine Coastal Seawater.
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The future of NGS (Next Generation Sequencing) analysis in testing food authenticity.
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Future Generation Computer Systems, Volume 94, May 2019, Pages 802-810.
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Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria.
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Nat Microbiol. 2019 Jun;4(6):996-1005. doi: 10.1038/s41564-019-0383-z. Epub 2019 Mar 4.
Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans.
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Ultra-deep, long-read nanopore sequencing of mock microbial community standards.
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Gigascience. 2019 May 1;8(5). pii: giz043. doi: 10.1093/gigascience/giz043.
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Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments.
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Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination.
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Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease.
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Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition.
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An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
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Reply to ‘Errors in long-read assemblies can critically affect protein prediction’.
Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M.
Nat Biotechnol. 2019 Feb;37(2):127-128. doi: 10.1038/s41587-018-0005-y. No abstract available.
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Metagenomics of the Viral Community in Three Cattle Slurry Samples.
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Prevalence of faecal carriage of extended-spectrum β-lactamase (ESBL)-producing Escherichia coliin veterinary hospital staff and students.
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Riding the wave of genomics to investigate aquatic coliphage diversity and activity.
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The consistent differential expression of genetic pathways following exposure of an industrial Pseudomonas aeruginosa strain to preservatives and a laundry detergent formulation.
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Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.
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Convergent amino acid signatures in polyphyletic Campylobacter jejuni sub-populations suggest human niche tropism
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Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria
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Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells.
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Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O’Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.
Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13.
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Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease.
Kirk KF, Méric G, Nielsen HL, Pascoe B, Sheppard SK, Thorlacius-Ussing O, Nielsen H.
Sci Rep. 2018 Jan 30;8(1):1902. doi: 10.1038/s41598-018-20135-4.
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Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil.
Rossi GAM, Silva HO, Aguilar CEG, Rochetti AL, Pascoe B, Méric G, Mourkas E, Hitchings MD, Mathias LA, de Azevedo Ruiz VL, Fukumasu H, Sheppard SK, Vidal AMC.
FEMS Microbiol Lett. 2018 Feb 1;365(3). doi: 10.1093/femsle/fnx283.
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Nanopore sequencing and assembly of a human genome with ultra-long reads.
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O’Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.
Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.
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Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319.
Azevedo Antunes C, Richardson EJ, Quick J, Fuentes-Utrilla P, Isom GL, Goodall EC, Möller J, Hoskisson PA, Mattos-Guaraldi AL, Cunningham AF, Loman NJ, Sangal V, Burkovski A, Henderson IR.
Genome Announc. 2018 Feb 1;6(5). pii: e01566-17. doi: 10.1128/genomeA.01566-17.
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RADpainter and fineRADstructure: Population Inference from RADseq Data.
Malinsky M, Trucchi E, Lawson DJ, Falush D.
Mol Biol Evol. 2018 May 1;35(5):1284-1290. doi: 10.1093/molbev/msy023.
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Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015.
Pini A, Zomahoun D, Duraffour S, Derrough T, Charles M, Quick J, Loman N, Cowley L, Leno M, Ouedraogo N, Thiam O, Hernández-Romieu A, Iko A, Keita H, Konate D, Soumah AA, Bouchouar E, Ileka-Priouzeau S, Keita S, Diallo B, Cisse F, Jansa J, Carroll M, Günther S, Severi E, Formenty P.
Euro Surveill. 2018 Mar;23(12). doi: 10.2807/1560-7917.ES.2018.23.12.17-00140.
PMID: 29589579
Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.
Joyce A, Ijaz UZ, Nzeteu C, Vaughan A, Shirran SL, Botting CH, Quince C, O’Flaherty V, Abram F.
Front Microbiol. 2018 Mar 21;9:540. doi: 10.3389/fmicb.2018.00540. eCollection 2018.
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Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.
Nat Microbiol. 2018 Jul;3(7):804-813. doi: 10.1038/s41564-018-0176-9. Epub 2018 Jun 11. Erratum in: Nat Microbiol. 2018 Aug;3(8):963.
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Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA.
Yokoyama M, Stevens E, Laabei M, Bacon L, Heesom K, Bayliss S, Ooi N, O’Neill AJ, Murray E, Williams P, Lubben A, Reeksting S, Meric G, Pascoe B, Sheppard SK, Recker M, Hurst LD, Massey RC.
Genome Biol. 2018 Jul 18;19(1):94. doi: 10.1186/s13059-018-1469-2.
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Trends in fluoroquinolone resistance in Campylobacter.
Sproston EL, Wimalarathna HML, Sheppard SK.
Microb Genom. 2018 Jan;4(8). doi: 10.1099/mgen.0.000198. Epub 2018 Jul 19.
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High Resolution Whole Genome Multilocus Sequence Typing (wgMLST) Schemes for Salmonella enterica Weltevreden Epidemiologic Investigations.
Pakpoom Tadee, Phacharaporn Boonkhot, Matthew Hitchings, Ben Pascoe, Samuel Sheppard, Prapas Patchanee.
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Genomic epidemiology of clinical Campylobacter spp. at a single health trust site.
Dunn SJ, Pascoe B, Turton J, Fleming V, Diggle M, Sheppard SK, McNally A, Manning G.
Microb Genom. 2018 Oct;4(10). doi: 10.1099/mgen.0.000227. Epub 2018 Oct 11.
PMID: 30307843
Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.
Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M.
Curr Biol. 2018 Aug 6;28(15):2420-2428.e10. doi: 10.1016/j.cub.2018.05.058. Epub 2018 Jul 19.
PMID: 30033331
Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry.
Bayliss SC, Verner-Jeffreys DW, Ryder D, Suarez R, Ramirez R, Romero J, Pascoe B, Sheppard SK, Godoy M, Feil EJ.
Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000201. Epub 2018 Jul 24.
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A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk.
Berthenet E, Yahara K, Thorell K, Pascoe B, Meric G, Mikhail JM, Engstrand L, Enroth H, Burette A, Megraud F, Varon C, Atherton JC, Smith S, Wilkinson TS, Hitchings MD, Falush D, Sheppard SK.
BMC Biol. 2018 Aug 2;16(1):84. doi: 10.1186/s12915-018-0550-3.
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A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots.
Lawson DJ, van Dorp L, Falush D.
Nat Commun. 2018 Aug 14;9(1):3258. doi: 10.1038/s41467-018-05257-7.
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Genomic and epidemiological monitoring of yellow fever virus transmission potential.
Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG.
Science. 2018 Aug 31;361(6405):894-899. doi: 10.1126/science.aat7115. Epub 2018 Aug 23.
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Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.
Ring N, Abrahams JS, Jain M, Olsen H, Preston A, Bagby S.
Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000234. Epub 2018 Nov 21.
PMID: 30461375
Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.
Méric G, Mageiros L, Pensar J, Laabei M, Yahara K, Pascoe B, Kittiwan N, Tadee P, Post V, Lamble S, Bowden R, Bray JE, Morgenstern M, Jolley KA, Maiden MCJ, Feil EJ, Didelot X, Miragaia M, de Lencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK.
Nat Commun. 2018 Nov 28;9(1):5034. doi: 10.1038/s41467-018-07368-7.
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Bacterial Flagellins: Does Size Matter?
Thomson NM, Rossmann FM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ.
Trends Microbiol. 2017 Dec 16. pii: S0966-842X(17)30259-7. doi:10.1016/j.tim.2017.11.010. Review.
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Ebola Virus Persistence in Breast Milk After No Reported Illness: A Likely Source of Virus Transmission From Mother to Child.
Sissoko D, Keïta M, Diallo B, Aliabadi N, Fitter DL, Dahl BA, Akoi Bore J, Raymond Koundouno F, Singethan K, Meisel S, Enkirch T, Mazzarelli A, Amburgey V, Faye O, Alpha Sall A, Magassouba N, Carroll MW, Anglaret X, Malvy D, Formenty P, Bruce Aylward R, Keïta S, Harouna Djingarey M, Loman NJ, Günther S, Duraffour S.
Clin Infect Dis. 2017 Feb 15;64(4):513-516. doi: 10.1093/cid/ciw793.
PMID: 27940938
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.
Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.
PMID: 28967888
Autonomous Discovery and Management in Virtual Container Clusters
Joshua Higgins, Violeta Holmes, Colin Venters
The Computer Journal, Volume 60, Issue 2, February 2017, Pages 240–252, https://doi.org/10.1093/comjnl/bxw102
Bioinformatics for NGS-based metagenomics and the application to biogas research.
Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J.
J Biotechnol. 2017 Nov 10;261:10-23. doi: 10.1016/j.jbiotec.2017.08.012. Epub 2017 Aug 18.
PMID: 28823476
Virus genomes reveal factors that spread and sustained the Ebola epidemic.
Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.
Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.
PMID: 28405027
Haemagglutinin and neuraminidase sequencing delineate nosocomial influenza outbreaks with accuracy equivalent to whole genome sequencing.
Houghton R, Ellis J, Galiano M, Clark TW, Wyllie S.
J Infect. 2017 Apr;74(4):377-384. doi: 10.1016/j.jinf.2016.12.015. Epub 2017 Jan 16.
PMID: 28104386
Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria.
Senghore M, Otu J, Witney A, Gehre F, Doughty EL, Kay GL, Butcher P, Salako K, Kehinde A, Onyejepu N, Idigbe E, Corrah T, de Jong B, Pallen MJ, Antonio M.
PLoS One. 2017 Sep 19;12(9):e0184510.
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PMID:28926571
An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.
Card RM, Cawthraw SA, Nunez-Garcia J, Ellis RJ, Kay G, Pallen MJ, Woodward MJ, Anjum MF.
MBio. 2017 Jul 18;8(4). pii: e00777-17.
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PMID:28720731
The Gut Microbiota and the Hepatologist: Will Our Bugs Prove to be the Missing Link?
Pallen MJ, Quraishi MN.
Dig Dis. 2017;35(4):377-383. doi: 10.1159/000456590. Epub 2017 May 3. Review.
PMID:28468018
Identification of the anti-mycobacterial functional properties of piperidinol derivatives.
Guy CS, Tichauer E, Kay GL, Phillips DJ, Bailey TL, Harrison J, Furze CM, Millard AD, Gibson MI, Pallen MJ, Fullam E.
Br J Pharmacol. 2017 Jul;174(14):2183-2193. doi: 10.1111/bph.13744. Epub 2017 Mar 23.
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The Enigmatic Esx Proteins: Looking Beyond Mycobacteria.
Unnikrishnan M, Constantinidou C, Palmer T, Pallen MJ.
Trends Microbiol. 2017 Mar;25(3):192-204. doi: 10.1016/j.tim.2016.11.004. Epub 2016 Nov 25. Review.
PMID: 27894646
Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus.
Murray S, Pascoe B, Méric G, Mageiros L, Yahara K, Hitchings MD, Friedmann Y, Wilkinson TS, Gormley FJ, Mack D, Bray JE, Lamble S, Bowden R, Jolley KA, Maiden MCJ, Wendlandt S, Schwarz S, Corander J, Fitzgerald JR, Sheppard SK.
Genome Biol Evol. 2017 Apr 1;9(4):830-842. doi: 10.1093/gbe/evx037.
PMID: 28338786
Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins.
Vale FF, Nunes A, Oleastro M, Gomes JP, Sampaio DA, Rocha R, Vítor JM, Engstrand L, Pascoe B, Berthenet E, Sheppard SK, Hitchings MD, Mégraud F, Vadivelu J, Lehours P.
Sci Rep. 2017 Feb 16;7:42471. doi: 10.1038/srep42471.
PMID: 28205536
Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.
Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D.
PLoS Genet. 2017 Feb 23;13(2):e1006546. doi: 10.1371/journal.pgen.1006546. eCollection 2017 Feb. Erratum in: PLoS Genet. 2017 Apr 14;13(4):e1006730.
PMID: 28231283
Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027, Originally Isolated from an Outer Ear Infection.
Jayal A, Johns BE, Purdy KJ, Maddocks SE.
Genome Announc. 2017 Nov 30;5(48). pii: e01397-17. doi: 10.1128/genomeA.01397-17.
PMID: 29192089
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR.
Microb Genom. 2017 Sep 4;3(10):e000131. doi: 10.1099/mgen.0.000131. eCollection 2017 Oct.
PMID: 29177089
Comparison of classical multi-locus sequence typing software for next-generation sequencing data.
Page AJ, Alikhan NF, Carleton HA, Seemann T, Keane JA, Katz LS.
Microb Genom. 2017 Jul 4;3(8):e000124. doi: 10.1099/mgen.0.000124. eCollection 2017 Aug. Review.
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Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species.
Thorpe HA, Bayliss SC, Hurst LD, Feil EJ.
Genetics. 2017 May;206(1):363-376. doi: 10.1534/genetics.116.195784. Epub 2017 Mar 9.
PMID: 28280056
Bioreactor scalability: laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactors
Connelly, Stephanie, Shin, Seung G., Dillon, Robert J., Ijaz, Umer Z., Quince, Christopher, Sloan, William T. and Collins, Gavin
Front Microbiol. 2017 May 1;8:664. doi:10.3389/fmicb.2017.00664
PMID: 28507535
DESMAN: a new tool for de novo extraction of strains from metagenomes
Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G. and Eren, A. M.
Genome Biol. 2017 Sep 21;18(1):181. doi:10.1186/s13059-017-1309-9
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Shotgun metagenomics, from sampling to analysis
Quince, C, Walker, AW, Simpson, JT, Loman, NJ & Segata, N
Nat Biotechnol. 2017 Sep 12;35(9):833-844 . doi: 10.1038/nbt.3935
PMID: 28898207
Comparative Genomics of Bacteriophage of the Genus Seuratvirus
Pavelas Sazinas Tamsin Redgwell Branko Rihtman Aurelija Grigonyte Slawomir Michniewski David J Scanlan Jon Hobman Andrew Millard
Genome Biol Evol. 2018 Jan 1;10(1):72-76. doi: 10.1093/gbe/evx275
PMID: 29272407
The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred
Umer Zeeshan Ijaz, Christopher Quince, Laura Hanske, Nick Loman, Szymon T. Calus, Martin Bertz, Christine A. Edwards, Daniel R. Gaya, Richard Hansen, Paraic McGrogan, Richard K. Russell, Konstantinos Gerasimidis
PLoS One. 2017 Feb 21;12(2):e0172605. doi: 10.1371/journal.pone.0172605
PMID: 28222161
Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes
Florez-Cuadrado D, Ugarte-Ruiz M, Meric G, Quesada A, Porrero MC, Pascoe B, Sáez-Llorente JL, Orozco GL, Domínguez L and Sheppard SK
Front Microbiol. 2017 Nov 15;8:2240. doi: 10.3389/fmicb.2017.02240
PMID: 29187841
Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
Koji Yahara, Guillaume Méric, Aidan J. Taylor, Stefan P. W. de Vries, Susan Murray, Ben Pascoe, Leonardos Mageiros, Alicia Torralbo, Ana Vidal, Anne Ridley, Sho Komukai, Helen Wimalarathna, Alison J. Cody, Frances M. Colles, Noel McCarthy, David Harris, James E. Bray, Keith A. Jolley, Martin C. J. Maiden, Stephen D. Bentley, Julian Parkhill, Christopher D. Bayliss, Andrew Grant, Duncan Maskell, Xavier Didelot, David J. Kelly, Samuel K. Sheppard
Environ Microbiol. 2017 Jan;19(1):361-380. doi: 10.1111/1462-2920.13628
PMID: 27883255
Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape
Diane Esson, Srishti Gupta, David Bailey, Paul Wigley, Amy Wedley, Alison E. Mather, Guillaume Méric, Pietro Mastroeni, Samuel K. Sheppard, Nicholas R. Thomson, Julian Parkhill, Duncan J. Maskell, Graham Christie, Andrew J. Grant
Microb Pathog. 2017 Mar;104:202-211. doi: 10.1016/j.micpath.2017.01.042
PMID: 28131954
Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex
Loveridge EJ, Jones C, Bull MJ, Moody SC, Kahl MW, Khan Z, Neilson L, Tomeva M, Adams SE, Wood AC, Rodriguez-Martin D, Pinel I, Parkhill J, Mahenthiralingam E, Crosby J.
J Bacteriol. 2017 Jun 13;199(13). doi: 10.1128/JB.00125-17.
PMID: 28439036
Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1
Owen SV, Wenner N, Canals R, Makumi A, Hammarlöf DL, Gordon MA, Aertsen A, Feasey NA and Hinton JCD
Front Microbiol. 2017 Feb 23;8:235. doi: 10.3389/fmicb.2017.00235.
PMID: 28280485
Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
Amandine Thépault Guillaume Méric, Katell Rivoal, Ben Pascoe, Leonardos Mageiros, Fabrice Touzain, Valérie Rose, Véronique Béven, Marianne Chemaly, and Samuel K. Sheppard
Appl Environ Microbiol. 2017 Mar 17;83(7). pii: e03085-16. doi: 10.1128/AEM.03085-16.
PMID: 28115376
Draft Genome Sequence of Bacteriophage vB_Eco_swan01
Michniewski S, Redgwell T, Scanlan DJ, Millard AD
Send to
Genome Announc. 2017 Jul 13;5(28). pii: e00501-17. doi: 10.1128/genomeA.00501-17.
PMID: 28705961
Genomic variation and evolution of Vibrio parahaemolyticus ST36 over the course of a transcontinental epidemic expansion
Martinez-Urtaza J, van Aerle R, Abanto M, Haendiges J, Myers RA, Trinanes J, Baker-Austin C, Gonzalez-Escalona N
MBio. 2017 Nov 14;8(6). pii: e01425-17. doi: 10.1128/mBio.01425-17.
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First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador.
Márquez S, Carrera J, Pullan ST, Lewandowski K, Paz V, Loman N, Quick J, Bonsall D, Powell R, Thézé J, Pybus OG, Klenerman P, Eisenberg J, Coloma J, Carroll MW, Trueba G, Logue CH.
Genome Announc. 2017 Feb 23;5(8). pii: e01673-16. doi: 10.1128/genomeA.01673-16.
PMID: 28232448
Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections.
Dearlove BL, Cody AJ, Pascoe B, Méric G, Wilson DJ, Sheppard SK.ISME J. 2016 Mar;10(3):721-9. doi: 10.1038/ismej.2015.149. Epub 2015 Aug 25.
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CGAT: a model for immersive personalized training in computational genomics.
Sims D, Ponting CP, Heger A.
Brief Funct Genomics. 2016 Jan;15(1):32-7. doi: 10.1093/bfgp/elv021. Epub 2015 May 16.
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The Landscape of Realized Homologous Recombination in Pathogenic Bacteria.
Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MC, Sheppard SK, Falush D.
Mol Biol Evol. 2016 Feb;33(2):456-71. doi: 10.1093/molbev/msv237. Epub 2015 Oct 29.
PMID: 26516092
Mobile real-time surveillance of Zika virus in Brazil.
Faria NR1, Sabino EC2, Nunes MR3,4, Alcantara LC5, Loman NJ6, Pybus OG1.
Genome Med. 2016 Sep 29;8(1):97. DOI: 10.1186/s13073-016-0356-2
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Sugar addiction: the state of the science.
Westwater ML, Fletcher PC, Ziauddeen H.
Eur J Nutr. 2016 Nov;55(Suppl 2):55-69. doi: 10.1007/s00394-016-1229-6. Epub 2016 Jul 2.
PMID: 27372453
Draft Genome Sequences of Three Novel Clostridium Isolates from Northern Iraq.
Rashid SR, Clokie MR, Millard AD.
Genome Announc. 2016 Feb 25;4(1). pii: e00033-16. doi: 10.1128/genomeA.00033-16.
PMID: 26950326
Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes.
Rihtman B, Meaden S, Clokie MR, Koskella B, Millard AD.
PeerJ. 2016 Jun 1;4:e2055. doi: 10.7717/peerj.2055. eCollection 2016.
PMID: 27280068
Mobile real-time surveillance of Zika virus in Brazil.
Faria NR, Sabino EC, Nunes MR, Alcantara LC, Loman NJ, Pybus OG.
Genome Med. 2016 Sep 29;8(1):97.
PMID: 27683027
From Escherich to the Escherichia coli genome.
Méric G, Hitchings MD, Pascoe B, Sheppard SK.
Lancet Infect Dis. 2016 Jun;16(6):634-636. doi: 10.1016/S1473-3099(16)30066-4.
Seqenv: linking sequences to environments through text mining.
Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E.
PeerJ. 2016 Dec 20;4:e2690. doi: 10.7717/peerj.2690. eCollection 2016.
PMID: 28028456
Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations.
Pascoe B, Méric G, Yahara K, Wimalarathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MCJ, McCarthy ND, Didelot X, Parker CT, Sheppard SK.
Mol Ecol. 2017 Sep;26(17):4497-4508. doi: 10.1111/mec.14176. Epub 2017 Jun 19.
PMID: 28493321
Genomic variations leading to alterations in cell morphology of Campylobacter spp.
Esson D, Mather AE, Scanlan E, Gupta S, de Vries SP, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, Mastroeni P, Sheppard SK, Christie G, Thomson NR, Parkhill J, Maskell DJ, Grant AJ.
Sci Rep. 2016 Dec 2;6:38303. doi: 10.1038/srep38303.
PMID: 27910897
Genomic epidemiology reveals multiple introductions of Zika virus into the United States.
Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG.
Nature. 2017 Jun 15;546(7658):401-405. doi: 10.1038/nature22400. Epub 2017 May 24.
PMID: 28538723
Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG.
Nature. 2017 Jun 15;546(7658):406-410. doi: 10.1038/nature22401. Epub 2017 May 24.
PMID: 28538727
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ.
Nat Protoc. 2017 Jun;12(6):1261-1276. doi: 10.1038/nprot.2017.066. Epub 2017 May 24.
PMID: 28538739
Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain.
Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF, Squire D, Cunningham AF, Cole JA, Loman N, Henderson IR.
Microb Genom. 2017 Mar 23;3(3):mgen000106. doi: 10.1099/mgen.0.000106. eCollection 2017 Mar.
PMID: 28663823
Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach.
Fonseca VG, Sinniger F, Gaspar JM, Quince C, Creer S, Power DM, Peck LS, Clark MS.
Sci Rep. 2017 Jul 21;7(1):6094. doi: 10.1038/s41598-017-06687-x.
PMID: 28733608
Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing.
McMurray CL, Hardy KJ, Calus ST, Loman NJ, Hawkey PM.
Microbiome. 2016 Dec 2;4(1):63.
PMID: 27912796
Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter.
Woodcock DJ, Krusche P, Strachan NJC, Forbes KJ, Cohan FM, Méric G, Sheppard SK.
Sci Rep. 2017 Aug 29;7(1):9650. doi: 10.1038/s41598-017-09483-9.
PMID: 28851932
Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens.
Monteil CL, Yahara K, Studholme DJ, Mageiros L, Méric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK.
Microb Genom. 2016 Oct 21;2(10):e000089. doi: 10.1099/mgen.0.000089. eCollection 2016 Oct.
PMID: 28348830
Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.
McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO, Corander J.
PLoS Genet. 2016 Sep 12;12(9):e1006280. doi: 10.1371/journal.pgen.1006280. eCollection 2016 Sep.
PMID: 27618184
Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance.
Yan X, Li Z, Chlebowicz MA, Tao X, Ni M, Hu Y, Li Z, Grundmann H, Murray S, Pascoe B, Sheppard SK, Bo X, van Dijl JM, Du P, Zhang M, You Y, Yu X, Meng F, Wang S, Zhang J.
Int J Med Microbiol. 2016 Dec;306(8):722-729. doi: 10.1016/j.ijmm.2016.08.001. Epub 2016 Aug 10.
PMID: 27528592
What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.
Connor TR, Owen SV, Langridge G, Connell S, Nair S, Reuter S, Dallman TJ, Corander J, Tabing KC, Le Hello S, Fookes M, Doublet B, Zhou Z, Feltwell T, Ellington MJ, Herrera S, Gilmour M, Cloeckaert A, Achtman M, Parkhill J, Wain J, De Pinna E, Weill FX, Peters T, Thomson N.
MBio. 2016 Aug 23;7(4). pii: e00527-16. doi: 10.1128/mBio.00527-16.
PMID: 27555304
Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides.
Culebro A, Revez J, Pascoe B, Friedmann Y, Hitchings MD, Stupak J, Sheppard SK, Li J, Rossi M.
J Bacteriol. 2016 Sep 22;198(20):2829-40. doi: 10.1128/JB.00347-16. Print 2016 Oct 15.
PMID: 27481928
Bayesian identification of bacterial strains from sequencing data.
Sankar A, Malone B, Bayliss SC, Pascoe B, Méric G, Hitchings MD, Sheppard SK, Feil EJ, Corander J, Honkela A.
Microb Genom. 2016 Aug 25;2(8):e000075. doi: 10.1099/mgen.0.000075. eCollection 2016 Aug.
PMID: 28348870
Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages.
Gilbert MJ, Miller WG, Yee E, Zomer AL, van der Graaf-van Bloois L, Fitzgerald C, Forbes KJ, Méric G, Sheppard SK, Wagenaar JA, Duim B.
Genome Biol Evol. 2016 Jul 2;8(6):2006-19. doi: 10.1093/gbe/evw146.
PMID: 27333878
Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle.
Mainda G, Lupolova N, Sikakwa L, Bessell PR, Muma JB, Hoyle DV, McAteer SP, Gibbs K, Williams NJ, Sheppard SK, La Ragione RM, Cordoni G, Argyle SA, Wagner S, Chase-Topping ME, Dallman TJ, Stevens MP, Bronsvoort BM, Gally DL.
Sci Rep. 2016 May 25;6:26589. doi: 10.1038/srep26589.
PMID: 27220895
Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.
Ray JL, Althammer J, Skaar KS, Simonelli P, Larsen A, Stoecker D, Sazhin A, Ijaz UZ, Quince C, Nejstgaard JC, Frischer M, Pohnert G, Troedsson C.
Mol Ecol. 2016 Nov;25(21):5585-5602. doi: 10.1111/mec.13844. Epub 2016 Oct 20.
PMID: 27662431
Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days.
Diallo B, Sissoko D, Loman NJ, Bah HA, Bah H, Worrell MC, Conde LS, Sacko R, Mesfin S, Loua A, Kalonda JK, Erondu NA, Dahl BA, Handrick S, Goodfellow I, Meredith LW, Cotten M, Jah U, Guetiya Wadoum RE, Rollin P, Magassouba N, Malvy D, Anglaret X, Carroll MW, Aylward RB, Djingarey MH, Diarra A, Formenty P, Keïta S, Günther S, Rambaut A, Duraffour S.
Clin Infect Dis. 2016 Nov 15;63(10):1353-1356. Epub 2016 Sep 1.
PMID: 27585800
Draft Genome Sequence of the Bacteriophage vB_Eco_slurp01.
Sazinas P, Smith C, Suhaimi A, Hobman JL, Dodd CE, Millard AD.
Genome Announc. 2016 Nov 17;4(6). pii: e01111-16. doi: 10.1128/genomeA.01111-16.
PMID: 27856574
VSEARCH: a versatile open source tool for metagenomics.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F.
PeerJ. 2016 Oct 18;4:e2584. eCollection 2016.
PMID: 27781170
The effect of DNA extraction methodology on gut microbiota research applications.
Gerasimidis K, Bertz M, Quince C, Brunner K, Bruce A, Combet E, Calus S, Loman N, Ijaz UZ.
BMC Res Notes. 2016 Jul 26;9:365. doi: 10.1186/s13104-016-2171-7.
PMID: 27456340
Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.
Senghore M, Bayliss SC, Kwambana-Adams BA, Foster-Nyarko E, Manneh J, Dione M, Badji H, Ebruke C, Doughty EL, Thorpe HA, Jasinska AJ, Schmitt CA, Cramer JD, Turner TR, Weinstock G, Freimer NB, Pallen MJ, Feil EJ, Antonio M.
Appl Environ Microbiol. 2016 Sep 16;82(19):5910-7. doi: 10.1128/AEM.01496-16. Print 2016 Oct 1.
PMID: 27474712
Challenges in microbial ecology: building predictive understanding of community function and dynamics.
Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS.
ISME J. 2016 Nov;10(11):2557-2568. doi: 10.1038/ismej.2016.45. Epub 2016 Mar 29. Review.
PMID: 27022995
Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015.
Keita M, Duraffour S, Loman NJ, Rambaut A, Diallo B, Magassouba N, Carroll MW, Quick J, Sall AA, Glynn JR, Formenty P, Subissi L, Faye O.
Emerg Infect Dis. 2016 Dec;22(12):2149-2152. doi: 10.3201/eid2212.160847.
PMID: 27869596
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.
Schirmer M, D’Amore R, Ijaz UZ, Hall N, Quince C.
BMC Bioinformatics. 2016 Mar 11;17:125. doi: 10.1186/s12859-016-0976-y.
PMID: 26968756
Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters.
Haig SJ, Gauchotte-Lindsay C, Collins G, Quince C.
Environ Sci Technol. 2016 Mar 15;50(6):3101-10. doi: 10.1021/acs.est.5b05027. Epub 2016 Mar 3.
PMID: 26895622
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.
Torondel B, Ensink JH, Gundogdu O, Ijaz UZ, Parkhill J, Abdelahi F, Nguyen VA, Sudgen S, Gibson W, Walker AW, Quince C.
Microb Biotechnol. 2016 Mar;9(2):209-23. doi: 10.1111/1751-7915.12334. Epub 2016 Feb 15.
PMID: 26875588
Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples.
Harris LG, Murray S, Pascoe B, Bray J, Meric G, Mageiros L, Wilkinson TS, Jeeves R, Rohde H, Schwarz S, de Lencastre H, Miragaia M, Rolo J, Bowden R, Jolley KA, Maiden MC, Mack D, Sheppard SK.
PLoS One. 2016 Mar 15;11(3):e0151240. doi: 10.1371/journal.pone.0151240. eCollection 2016. Erratum in: PLoS One. 2016;11(4):e0154510. Magerios, Leonardos [corrected to Mageiros, Leonardos].
PMID: 26978068
Comparative Genomics Study of Staphylococcus epidermidis Isolates from Orthopedic-Device-Related Infections Correlated with Patient Outcome.
Post V, Harris LG, Morgenstern M, Mageiros L, Hitchings MD, Méric G, Pascoe B, Sheppard SK, Richards RG, Moriarty TF.
J Clin Microbiol. 2017 Oct;55(10):3089-3103. doi: 10.1128/JCM.00881-17. Epub 2017 Aug 9.
PMID: 28794175
Inhibiting mycobacterial tryptophan synthase by targeting the inter-subunit interface.
Abrahams KA, Cox JAG, Fütterer K, Rullas J, Ortega-Muro F, Loman NJ, Moynihan PJ, Pérez-Herrán E, Jiménez E, Esquivias J, Barros D, Ballell L, Alemparte C, Besra GS.
Sci Rep. 2017 Aug 25;7(1):9430. doi: 10.1038/s41598-017-09642-y.
PMID: 28842600
Real-time, portable genome sequencing for Ebola surveillance.
Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JH, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sanchez A, Carter LL, Doerrbecker J, Enkirch T, Dorival IGG, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallash E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Trina R, Bello A, Sall AA, Faye O, Faye O, Magassouba N, Williams CV, Amburgey V, Winona L, Davis E, Gerlach J, Washington F, Monteil V, Jourdain M, Bererd M, Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P, Turner D, Pollakis G, Hiscox JA, Matthews DA, O’Shea MK, Johnston AM, Wilson D, Hutley E, Smit E, Di Caro A, Woelfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keita S, Rambaut A, Formenty P, Gunther S, Carroll MW.
Nature. 2016 Feb 11;530(7589):228-232. doi: 10.1038/nature16996. Epub 2016 Feb 3.
PMID: 26840485
Biochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target.
Gurcha SS, Usha V, Cox JA, Fütterer K, Abrahams KA, Bhatt A, Alderwick LJ, Reynolds RC, Loman NJ, Nataraj V, Alemparte C, Barros D, Lloyd AJ, Ballell L, Hobrath JV, Besra GS.
PLoS One. 2014 Nov 19;9(11):e113568. doi: 10.1371/journal.pone.0113568. eCollection 2014.
PMID: 25409504
Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011.
Knetsch CW, Connor TR, Mutreja A, van Dorp SM, Sanders IM, Browne HP, Harris D, Lipman L, Keessen EC, Corver J, Kuijper EJ, Lawley TD.
Euro Surveill. 2014 Nov 13;19(45):20954.
PMID: 25411691
Max Perutz and the Structure of Hemoglobin.
Steensma DP, Shampo MA, Kyle RA.
Mayo Clin Proc. 2015 Aug;90(8):e89. doi: 10.1016/j.mayocp.2015.04.026.
PMID: 26250737
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR.
Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196. Epub 2014 Nov 20.
PMID: 25414349
Characterization of plasmids in extensively drug-resistant acinetobacter strains isolated in India and Pakistan.
Jones LS, Carvalho MJ, Toleman MA, White PL, Connor TR, Mushtaq A, Weeks JL, Kumarasamy KK, Raven KE, Török ME, Peacock SJ, Howe RA, Walsh TR.
Antimicrob Agents Chemother. 2015 Feb;59(2):923-9. doi: 10.1128/AAC.03242-14. Epub 2014 Nov 24.
PMID: 25421466
Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex.
Morley L, McNally A, Paszkiewicz K, Corander J, Méric G, Sheppard SK, Blom J, Manning G.
Appl Environ Microbiol. 2015 Jun;81(11):3641-7. doi: 10.1128/AEM.00546-15. Epub 2015 Mar 20.
PMID: 25795671
Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.
Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MC, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK.
Genome Biol Evol. 2015 Apr 16;7(5):1313-28. doi: 10.1093/gbe/evv066.
PMID: 25888688
Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis.
Facey PD, Méric G, Hitchings MD, Pachebat JA, Hegarty MJ, Chen X, Morgan LV, Hoeppner JE, Whitten MM, Kirk WD, Dyson PJ, Sheppard SK, Del Sol R.
Genome Biol Evol. 2015 Jul 15;7(8):2188-202. doi: 10.1093/gbe/evv136.
PMID: 26185096
Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.
Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I, Dias da Silveira W, Semmler T, Wieler LH, Jenkins C, Cravioto A, Faruque SM, Parkhill J, Wook Kim D, Keddy KH, Thomson NR.
Elife. 2015 Aug 4;4:e07335. doi: 10.7554/eLife.07335.
PMID: 26238191
Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni.
Pascoe B, Méric G, Murray S, Yahara K, Mageiros L, Bowen R, Jones NH, Jeeves RE, Lappin-Scott HM, Asakura H, Sheppard SK.
Environ Microbiol. 2015 Nov;17(11):4779-89. doi: 10.1111/1462-2920.13051. Epub 2015 Oct 14.
PMID: 26373338
Twenty years of bacterial genome sequencing.
Loman NJ, Pallen MJ.
Nat Rev Microbiol. 2015 Dec;13(12):787-94. doi: 10.1038/nrmicro3565. Epub 2015 Nov 9. Review.
PMID: 26548914
Draft Genome Sequences of 14 Escherichia coli Phages Isolated from Cattle Slurry.
Smith R, O’Hara M, Hobman JL, Millard AD.
Genome Announc. 2015 Dec 31;3(6). pii: e01364-15. doi: 10.1128/genomeA.01364-15.
PMID: 26722010
Gesing S, Connor TR and Ian Taylor. Genomics and Biological Big Data: Facing Current and Future Challenges around Data and Software Sharing and Reproducibility. 2015 Nov. arXiv:1511.02689
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.
D’Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N.
BMC Genomics. 2016 Jan 14;17:55. doi: 10.1186/s12864-015-2194-9.
PMID: 26763898
Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition.
Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K.
Am J Gastroenterol. 2015 Dec;110(12):1718-29; quiz 1730. doi: 10.1038/ajg.2015.357. Epub 2015 Nov 3.
PMID: 26526081
The relationship between microbial community evenness and function in slow sand filters.
Haig SJ, Quince C, Davies RL, Dorea CC, Collins G.
MBio. 2015 Oct 13;6(5):e00729-15. doi: 10.1128/mBio.00729-15.
PMID: 26463159
Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.
Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C.
ISME J. 2016 Jan;10(1):85-96. doi: 10.1038/ismej.2015.101. Epub 2015 Jul 3.
PMID: 26140533
Harris, K., T.L. Parsons, U.Z. Ijaz, L. Lahti, I. Holmes, and C. Quince, 2015. Linking statistical and ecological theory: Hubbell’s unified neutral theory of biodiversity as a hierarchical Dirichlet process. Proceedings of the IEEE: doi: 10.1109/JPROC.2015.2428213.
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW.
BMC Biol. 2014 Nov 12;12:87. doi: 10.1186/s12915-014-0087-z.
PMID: 25387460
Binning metagenomic contigs by coverage and composition.
Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.
Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.
PMID: 25218180
A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.
Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M.
Genome Med. 2014 Nov 15;6(11):101. doi: 10.1186/s13073-014-0101-7. eCollection 2014.
PMID: 25484920
Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing.
Quick J, Cumley N, Wearn CM, Niebel M, Constantinidou C, Thomas CM, Pallen MJ, Moiemen NS, Bamford A, Oppenheim B, Loman NJ.
BMJ Open. 2014 Nov 4;4(11):e006278. doi: 10.1136/bmjopen-2014-006278.
PMID: 25371418
Microbiomes and metagenomes: window on the past, promises for the future Midlands Molecular Microbiology meeting Nottingham September 2015
Genomics and metagenomics in medical microbiology: opportunities and challenges BMFZ meeting Düsseldorf November 2015
Implementing a nationwide cyber infrastructure for microbiology: CLIMB UCISA Infrastructure Group Meeting Oxford October 2015
Bioinformatics showcase Applied Bioinformatics and Public Health Microbiology Cambridge May 2015
CLIMB Balti and Bioinformatics Birmingham May 2014
For a list of past training events please follow see our training page