EpiCollect+: linking smartphones to web applications for complex data collection projects [v1; ref status: indexed, http://f1000r.es/3vk] by David M. Aanensen, Derek M. Huntley, Mirko Menegazzo, Chris I. Powell, Brian G. Spratt

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EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection. by David M Aanensen, Derek M Huntley, Edward J Feil, Fada'a al-Own, Brian G Spratt

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Genomic Epidemiology of CC30 Methicillin-Resistant Staphylococcus aureus Strains from Argentina Reveals Four Major Clades with Distinctive Genetic Features by Sabrina Di Gregorio, María Sol Haim, Jesús Vielma Vallenilla, Victoria Cohen, Lucía Rago, Lucía Gulone, David M. Aanensen, Silvia Argimón, Marta Mollerach

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Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis. by Hajo Grundmann, David M Aanensen, Cees C van den Wijngaard, Brian G Spratt, Dag Harmsen, Alexander W Friedrich, European Staphylococcal Reference Laboratory Working Group

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Diversification of Colonization Factors in a Multidrug-Resistant <named-content content-type="genus-species">Escherichia coli</named-content> Lineage Evolving under Negative Freque... by Alan McNally, Teemu Kallonen, Christopher Connor, Khalil Abudahab, David M. Aanensen, Carolyne Horner, Sharon J. Peacock, Julian Parkhill, Nicholas J. Croucher, Jukka Corander

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Multilocus sequence typing and further genetic characterization of the enigmatic pathogen, Staphylococcus hominis. by Liangfen Zhang, Jonathan C Thomas, Maria Miragaia, Ons Bouchami, Fernando Chaves, Pedro A d'Azevedo, David M Aanensen, Herminia de Lencastre, Barry M Gray, D Ashley Robinson

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Mapping the global emergence of Batrachochytrium dendrobatidis, the amphibian chytrid fungus. by Deanna H Olson, David M Aanensen, Kathryn L Ronnenberg, Christopher I Powell, Susan F Walker, Jon Bielby, Trenton W J Garner, George Weaver, Bd Mapping Group, Matthew C Fisher

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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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Novel multidrug-resistant sublineages of Staphylococcus aureus clonal complex 22 discovered in India by Monica I. Abrudan, Varun Shamanna, Akshatha Prasanna, Anthony Underwood, Silvia Argimón, Geetha Nagaraj, Sabrina Di Gregorio, Vandana Govindan, Ashwini Vasanth, Sravani Dharmavaram, Mihir Kekre, David M. Aanensen, K. L. Ravikumar

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Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments by Jose F. Delgado-Blas, Cristina M. Ovejero, Sophia David, Natalia Montero, William Calero-Caceres, M. Pilar Garcillan-Barcia, Fernando de la Cruz, Maite Muniesa, David M. Aanensen, Bruno Gonzalez-Zorn

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Comparison of two multilocus sequence based genotyping schemes for Leptospira species. by Ahmed Ahmed, Janjira Thaipadungpanit, Siriphan Boonsilp, Vanaporn Wuthiekanun, Kishore Nalam, Brian G Spratt, David M Aanensen, Lee D Smythe, Niyaz Ahmed, Edward J Feil, Rudy A Hartskeerl, Sharon J Peacock

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Genomic Analysis and Comparison of Two Gonorrhea Outbreaks by Xavier Didelot, Janina Dordel, Lilith K. Whittles, Caitlin Collins, Nicole Bilek, Cynthia J. Bishop, Peter J. White, David M. Aanensen, Julian Parkhill, Stephen D. Bentley, Brian G. Spratt, Simon R. Harris

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Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae. by Sophia David, Joshua L C Wong, Julia Sanchez-Garrido, Hok-Sau Kwong, Wen Wen Low, Fabio Morecchiato, Tommaso Giani, Gian Maria Rossolini, Stephen J Brett, Abigail Clements, Konstantinos Beis, David M Aanensen, Gad Frankel

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Genomic epidemiology describes introduction and outbreaks of antifungal drug-resistant Candida auris by Dana Kappel, Hugh Gifford, Amelie Brackin, Alireza Abdolrasouli, David W. Eyre, Katie Jeffery, Silke Schlenz, David M. Aanensen, Colin S. Brown, Andrew Borman, Elizabeth Johnson, Alison Holmes, Darius Armstrong-James, Matthew C. Fisher, Johanna Rhodes

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Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. by Stephen D Bentley, David M Aanensen, Angeliki Mavroidi, David Saunders, Ester Rabbinowitsch, Matthew Collins, Kathy Donohoe, David Harris, Lee Murphy, Michael A Quail, Gabby Samuel, Ian C Skovsted, Margit Staum Kaltoft, Bart Barrell, Peter R Reeves, Julian Parkhill, Brian G Spratt

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High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020 by Erkison Ewomazino Odih, Anderson O. Oaikhena, Anthony Underwood, Yaovi Mahuton Gildas Hounmanou, Oyinlola O. Oduyebo, Abayomi Fadeyi, Aaron O. Aboderin, Veronica O. Ogunleye, Silvia Argimón, Vitus Nnaemeka Akpunonu, Phillip O. Oshun, Abiodun Egwuenu, Tochi J. Okwor, Chikwe Ihekweazu, David M. Aanensen, Anders Dalsgaard, Iruka N. Okeke

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A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch by Leonor Sánchez-Busó, Corin A. Yeats, Benjamin Taylor, Richard J. Goater, Anthony Underwood, Khalil Abudahab, Silvia Argimón, Kevin C. Ma, Tatum D. Mortimer, Daniel Golparian, Michelle J. Cole, Yonatan H. Grad, Irene Martin, Brian H. Raphael, William M. Shafer, Katy Town, Teodora Wi, Simon R. Harris, Magnus Unemo, David M. Aanensen

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A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species. by Siriphan Boonsilp, Janjira Thaipadungpanit, Premjit Amornchai, Vanaporn Wuthiekanun, Mark S Bailey, Matthew T G Holden, Cuicai Zhang, Xiugao Jiang, Nobuo Koizumi, Kyle Taylor, Renee Galloway, Alex R Hoffmaster, Scott Craig, Lee D Smythe, Rudy A Hartskeerl, Nicholas P Day, Narisara Chantratita, Edward J Feil, David M Aanensen, Brian G Spratt, Sharon J Peacock

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Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria. by Odion O Ikhimiukor, Anderson O Oaikhena, Ayorinde O Afolayan, Abayomi Fadeyi, Aderemi Kehinde, Veronica O Ogunleye, Aaron O Aboderin, Oyinlola O Oduyebo, Charles J Elikwu, Erkison Ewomazino Odih, Ifeoluwa Komolafe, Silvia Argimón, Abiodun Egwuenu, Ini Adebiyi, Oluwadamilola A Sadare, Tochi Okwor, Mihir Kekre, Anthony Underwood, Chikwe Ihekweazu, David M Aanensen, Iruka N Okeke

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Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive <named-content content-type="genus-species">Staphylococcus aureus</nam... by David M. Aanensen, Edward J. Feil, Matthew T. G. Holden, Janina Dordel, Corin A. Yeats, Artemij Fedosejev, Richard Goater, Santiago Castillo-Ramírez, Jukka Corander, Caroline Colijn, Monika A. Chlebowicz, Leo Schouls, Max Heck, Gerlinde Pluister, Raymond Ruimy, Gunnar Kahlmeter, Jenny Åhman, Erika Matuschek, Alexander W. Friedrich, Julian Parkhill, Stephen D. Bentley, Brian G. Spratt, Hajo Grundmann

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