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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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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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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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 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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Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines by Silvia Argimón, Melissa A. L. Masim, June M. Gayeta, Marietta L. Lagrada, Polle K. V. Macaranas, Victoria Cohen, Marilyn T. Limas, Holly O. Espiritu, Janziel C. Palarca, Jeremiah Chilam, Manuel C. Jamoralin, Alfred S. Villamin, Janice B. Borlasa, Agnettah M. Olorosa, Lara F. T. Hernandez, Karis D. Boehme, Benjamin Jeffrey, Khalil Abudahab, Charmian M. Hufano, Sonia B. Sia, John Stelling, Matthew T. G. Holden, David M. Aanensen, Celia C. Carlos

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Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap by Iruka N Okeke, Ben Taylor, Celia Carlos, Nicole Wheeler, Marietta Lagrada, Polle K. Macaranas, Agnettah M. Olorosa, June Gayeta, Melissa Ana Masim, Elmer M. Herrera, David M Aanensen, Khalil Abudahab, Monica Abrudan, Silvia Argimon, Harry Harste, Mihir Kekre, Ali Molloy, Dawn Muddyman, Anneke Schmider, Anthony Underwood, María del Pilar Donado Godoy, Johan Fabian Bernal Morales, Alejandra Arevalo, Maria Fernanda Valencia Guerrero, Erik Cristopher Dustin Osma Castro, Anderson O. Oaikhena, Ayorinde Oluwatobiloba Afolayan, Jolaade J Ajiboye, Ravikumar K. L., Geetha Nagaraj, Varun Shammana, Vandana Govindan, Akshata Prabhu, Darmavaram Sravani, Shincy M. R., Rajitha G. V., Carolin Vegvari, John Stelling

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The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa by Se Eun Park, Duy Thanh Pham, Christine Boinett, Vanessa K. Wong, Gi Deok Pak, Ursula Panzner, Ligia Maria Cruz Espinoza, Vera von Kalckreuth, Justin Im, Heidi Schütt-Gerowitt, John A. Crump, Robert F. Breiman, Yaw Adu-Sarkodie, Ellis Owusu-Dabo, Raphaël Rakotozandrindrainy, Abdramane Bassiahi Soura, Abraham Aseffa, Nagla Gasmelseed, Karen H. Keddy, Jürgen May, Amy Gassama Sow, Peter Aaby, Holly M. Biggs, Julian T. Hertz, Joel M. Montgomery, Leonard Cosmas, Beatrice Olack, Barry Fields, Nimako Sarpong, Tsiriniaina Jean Luco Razafindrabe, Tiana Mirana Raminosoa, Leon Parfait Kabore, Emmanuel Sampo, Mekonnen Teferi, Biruk Yeshitela, Muna Ahmed El Tayeb, Arvinda Sooka, Christian G. Meyer, Ralf Krumkamp, Denise Myriam Dekker, Anna Jaeger, Sven Poppert, Adama Tall, Aissatou Niang, Morten Bjerregaard-Andersen, Sandra Valborg Løfberg, Hye Jin Seo, Hyon Jin Jeon, Jessica Fung Deerin, Jinkyung Park, Frank Konings, Mohammad Ali, John D. Clemens, Peter Hughes, Juliet Nsimire Sendagala, Tobias Vudriko, Robert Downing, Usman N. Ikumapayi, Grant A. Mackenzie, Stephen Obaro, Silvia Argimon, David M. Aanensen, Andrew Page, Jacqueline A. Keane, Sebastian Duchene, Zoe Dyson, Kathryn E. Holt, Gordon Dougan, Florian Marks, Stephen Baker

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Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes by Megan E Carey, Zoe A Dyson, Danielle J Ingle, Afreenish Amir, Mabel K Aworh, Marie Anne Chattaway, Ka Lip Chew, John A Crump, Nicholas A Feasey, Benjamin P Howden, Karen H Keddy, Mailis Maes, Christopher M Parry, Sandra Van Puyvelde, Hattie E Webb, Ayorinde Oluwatobiloba Afolayan, Anna P Alexander, Shalini Anandan, Jason R Andrews, Philip M Ashton, Buddha Basnyat, Ashish Bavdekar, Isaac I Bogoch, John D Clemens, Kesia Esther da Silva, Anuradha De, Joep de Ligt, Paula Lucia Diaz Guevara, Christiane Dolecek, Shanta Dutta, Marthie M Ehlers, Louise Francois Watkins, Denise O Garrett, Gauri Godbole, Melita A Gordon, Andrew R Greenhill, Chelsey Griffin, Madhu Gupta, Rene S Hendriksen, Robert S Heyderman, Yogesh Hooda, Juan Carlos Hormazabal, Odion O Ikhimiukor, Junaid Iqbal, Jobin John Jacob, Claire Jenkins, Dasaratha Ramaiah Jinka, Jacob John, Gagandeep Kang, Abdoulie Kanteh, Arti Kapil, Abhilasha Karkey, Samuel Kariuki, Robert A Kingsley, Roshine Mary Koshy, AC Lauer, Myron M Levine, Ravikumar Kadahalli Lingegowda, Stephen P Luby, Grant Austin Mackenzie, Tapfumanei Mashe, Chisomo Msefula, Ankur Mutreja, Geetha Nagaraj, Savitha Nagaraj, Satheesh Nair, Take K Naseri, Susana Nimarota-Brown, Elisabeth Njamkepo, Iruka N Okeke, Sulochana Putli Bai Perumal, Andrew J Pollard, Agila Kumari Pragasam, Firdausi Qadri, Farah N Qamar, Sadia Isfat Ara Rahman, Savitra Devi Rambocus, David A Rasko, Pallab Ray, Roy Robins-Browne, Temsunaro Rongsen-Chandola, Jean Pierre Rutanga, Samir K Saha, Senjuti Saha, Karnika Saigal, Mohammad Saiful Islam Sajib, Jessica C Seidman, Jivan Shakya, Varun Shamanna, Jayanthi Shastri, Rajeev Shrestha, Sonia Sia, Michael J Sikorski, Ashita Singh, Anthony M Smith, Kaitlin A Tagg, Dipesh Tamrakar, Arif Mohammed Tanmoy, Maria Thomas, Mathew S Thomas, Robert Thomsen, Nicholas R Thomson, Siaosi Tupua, Krista Vaidya, Mary Valcanis, Balaji Veeraraghavan, François-Xavier Weill, Jackie Wright, Gordon Dougan, Silvia Argimón, Jacqueline A Keane, David M Aanensen, Stephen Baker, Kathryn E Holt, Global Typhoid Genomics Consortium Group Authorship

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