Assessing and removing the effect of unwanted technical variations in microbiome data by Muhamad Fachrul, Guillaume Méric, Michael Inouye, Sünje Johanna Pamp, Agus Salim

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Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli. by Laura J Searle, Guillaume Méric, Ida Porcelli, Samuel K Sheppard, Sacha Lucchini

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A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter. by Guillaume Méric, Koji Yahara, Leonardos Mageiros, Ben Pascoe, Martin C J Maiden, Keith A Jolley, Samuel K Sheppard

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Trycycler: consensus long-read assemblies for bacterial genomes by Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt

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Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes by Diego Florez-Cuadrado, María Ugarte-Ruiz, Guillaume Meric, Alberto Quesada, M. C. Porrero, Ben Pascoe, Jose L. Sáez-Llorente, Gema L. Orozco, Lucas Domínguez, Lucas Domínguez, Samuel K. Sheppard

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The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species by Clara Atterby, Evangelos Mourkas, Evangelos Mourkas, Guillaume Méric, Ben Pascoe, Ben Pascoe, Helen Wang, Jonas Waldenström, Samuel K. Sheppard, Samuel K. Sheppard, Björn Olsen, Josef D. Järhult, Patrik Ellström

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Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages by Diana Espadinha, Diana Espadinha, Rita G. Sobral, Catarina Inês Mendes, Guillaume Méric, Samuel K. Sheppard, Samuel K. Sheppard, João A. Carriço, Hermínia de Lencastre, Hermínia de Lencastre, Maria Miragaia

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High-resolution sweep metagenomics using fast probabilistic inference [version 2; peer review: 2 approved] by Tommi Mäklin, Teemu Kallonen, Sophia David, Christine J. Boinett, Ben Pascoe, Guillaume Méric, David M. Aanensen, Edward J. Feil, Stephen Baker, Julian Parkhill, Samuel K. Sheppard, Jukka Corander, Antti Honkela

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Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity by Keira Tucker, Leonardos Mageiros, Alno Carstens, Ludwig Bröcker, Edward Archer, Katrin Smith, Evangelos Mourkas, Ben Pascoe, Daan Nel, Guillaume Meric, Samuel K. Sheppard, Barbara Kasprzyk-Hordern, Marelize Botes, Edward J. Feil, Gideon Wolfaardt

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Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA by Maho Yokoyama, Emily Stevens, Maisem Laabei, Leann Bacon, Kate Heesom, Sion Bayliss, Nicola Ooi, Alex J. O’Neill, Ewan Murray, Paul Williams, Anneke Lubben, Shaun Reeksting, Guillaume Meric, Ben Pascoe, Samuel K. Sheppard, Mario Recker, Laurence D. Hurst, Ruth C. Massey

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Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. by Ben Pascoe, Francesca Schiaffino, Susan Murray, Guillaume Méric, Sion C Bayliss, Matthew D Hitchings, Evangelos Mourkas, Jessica K Calland, Rosa Burga, Pablo Peñataro Yori, Keith A Jolley, Kerry K Cooper, Craig T Parker, Maribel Paredes Olortegui, Margaret N Kosek, Samuel K Sheppard

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Correction: Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples. by Llinos G Harris, Susan Murray, Ben Pascoe, James Bray, Guillaume Meric, Leonardos Mageiros, Thomas S Wilkinson, Rose Jeeves, Holger Rohde, Stefan Schwarz, Herminia de Lencastre, Maria Miragaia, Joana Rolo, Rory Bowden, Keith A Jolley, Martin C J Maiden, Dietrich Mack, Samuel K Sheppard

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Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples. by Llinos G Harris, Susan Murray, Ben Pascoe, James Bray, Guillaume Meric, Leonardos Mageiros, Thomas S Wilkinson, Rose Jeeves, Holger Rohde, Stefan Schwarz, Herminia de Lencastre, Maria Miragaia, Joana Rolo, Rory Bowden, Keith A Jolley, Martin C J Maiden, Dietrich Mack, Samuel K Sheppard

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Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter by Evangelos Mourkas, Koji Yahara, Sion C Bayliss, Jessica K Calland, Håkan Johansson, Leonardos Mageiros, Zilia Y Muñoz-Ramirez, Grant Futcher, Guillaume Méric, Matthew D Hitchings, Santiago Sandoval-Motta, Javier Torres, Keith A Jolley, Martin CJ Maiden, Patrik Ellström, Jonas Waldenström, Ben Pascoe, Samuel K Sheppard

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Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli by Leonardos Mageiros, Guillaume Méric, Sion C. Bayliss, Johan Pensar, Ben Pascoe, Evangelos Mourkas, Jessica K. Calland, Koji Yahara, Susan Murray, Thomas S. Wilkinson, Lisa K. Williams, Matthew D. Hitchings, Jonathan Porter, Kirsty Kemmett, Edward J. Feil, Keith A. Jolley, Nicola J. Williams, Jukka Corander, Samuel K. Sheppard

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Genome evolution and the emergence of pathogenicity in avian Escherichia coli by Leonardos Mageiros, Guillaume Méric, Sion C. Bayliss, Johan Pensar, Ben Pascoe, Evangelos Mourkas, Jessica K. Calland, Koji Yahara, Susan Murray, Thomas S. Wilkinson, Lisa K. Williams, Matthew D. Hitchings, Jonathan Porter, Kirsty Kemmett, Edward J. Feil, Keith A. Jolley, Nicola J. Williams, Jukka Corander, Samuel K. Sheppard

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Taxonomic signatures of cause-specific mortality risk in human gut microbiome by Aaro Salosensaari, Ville Laitinen, Aki S. Havulinna, Guillaume Meric, Susan Cheng, Markus Perola, Liisa Valsta, Georg Alfthan, Michael Inouye, Jeramie D. Watrous, Tao Long, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory C. Humphrey, Jon G. Sanders, Mohit Jain, Pekka Jousilahti, Veikko Salomaa, Rob Knight, Leo Lahti, Teemu Niiranen

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Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis by Guillaume Méric, Leonardos Mageiros, Johan Pensar, Maisem Laabei, Koji Yahara, Ben Pascoe, Nattinee Kittiwan, Phacharaporn Tadee, Virginia Post, Sarah Lamble, Rory Bowden, James E. Bray, Mario Morgenstern, Keith A. Jolley, Martin C. J. Maiden, Edward J. Feil, Xavier Didelot, Maria Miragaia, Herminia de Lencastre, T. Fintan Moriarty, Holger Rohde, Ruth Massey, Dietrich Mack, Jukka Corander, Samuel K. Sheppard

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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy by Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight

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