Ecosyste.ms: Papers

10.1099/mgen.0.000225

Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny
Cited by: 20
Author(s): Cameron J. Reid, Matthew Z. DeMaere, Steven P. Djordjevic
Software Mentions: 14
Published: almost 6 years ago

10.1099/mgen.0.000499

A comprehensive and high-quality collection of Escherichia coli genomes and their genes
Cited by: 32
Author(s): Gal Horesh, Grace A. Blackwell, Gerry Tonkin‐Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Software Mentions: 12
Published: almost 4 years ago

10.1099/mgen.0.000131

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Cited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: about 7 years ago

10.1099/mgen.0.000190

Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections
Cited by: 32
Author(s): Cosmika Goswami, Stephen Fox, Matthew T. G. Holden, Martin Connor, Alistair Leanord, Thomas J. Evans
Software Mentions: 5
Published: over 6 years ago

10.1099/mgen.0.000456

Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone
Cited by: 14
Author(s): Eleonora Tassinari, Matt Bawn, Gaëtan Thilliez, Oliver J. Charity, Luke Acton, Mark Kirkwood, Liljana Petrovska, Timothy J. Dallman, Catherine M. Burgess, Neil Hall, Geraldine Duffy, Robert A. Kingsley
Software Mentions: 4
Published: about 4 years ago

10.1099/mgen.0.000205

Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages
Cited by: 37
Author(s): Koji Yahara, Shuichi Nakayama, Ken Shimuta, Ken-ichi Lee, Masatomo Morita, Takuya Kawahata, Toshiro Kuroki, Yuko Watanabe, Hitomi Ohya, Mitsuru Yasuda, Takashi Deguchi, Xavier Didelot, Makoto Ohnishi
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-019-1785-1

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center
Cited by: 21
Author(s): Matthew J. Ellington, Eva Heinz, Alexander M. Wailan, Matthew J. Dorman, Marcus C. de Goffau, Amy K. Cain, Sonal P. Henson, Nicholas Gleadall, Christine J. Boinett, Gordon Dougan, Nicholas M. Brown, Neil Woodford, Julian Parkhill, M. Estée Török, Sharon J. Peacock, Nicholas R. Thomson
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000297

Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids
Cited by: 16
Author(s): Raymond Kiu, Shabhonam Caim, Anaïs Painset, Derek Pickard, Craig Swift, Gordon Dougan, Alison E. Mather, Corinne Amar, Lindsay J. Hall
Software Mentions: 4
Published: about 5 years ago

10.1099/mgen.0.000335

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study
Cited by: 56
Author(s): Ronan Doyle, Denise M O’Sullivan, Sean Aller, Sebastian Bruchmann, Taane G. Clark, Andreu Coello Pelegrin, Martin Cormican, Ernest Diez Benavente, Matthew J. Ellington, Elaine McGrath, Yair Motro, Thi Phuong Thuy Nguyen, Jody Phelan, Liam Shaw, Richard Stabler, Alex van Belkum, Lucy van Dorp, Neil Woodford, Jacob Moran-Gilad, Jim F. Huggett, Kathryn Harris
Software Mentions: 4
Published: almost 5 years ago

10.1099/mgen.0.000355

Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico
Cited by: 5
Author(s): Enzo Guerrero-Araya, Claudio Meneses, Eduardo Castro-Nallar, Ana M Guzmán D, Manuel Álvarez-Lobos, Carlos Quesada-Gómez, Daniel Paredes-Sabja, César Rodríguez
Software Mentions: 3
Published: over 4 years ago

10.1099/mgen.0.000124

Comparison of classical multi-locus sequence typing software for next-generation sequencing data
Cited by: 27
Author(s): Andrew J. Page, Nabil-Fareed Alikhan, Heather Carleton, Torsten Seemann, Jacqueline A. Keane, Lee S. Katz
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-38943-7

Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1
Cited by: 40
Author(s): Eva Heinz, Hasan Ejaz, Josefin Bartholdson Scott, Nancy Wang, Shruti Gujaran, Derek Pickard, Jonathan J. Wilksch, Hanwei Cao, Ikramul Haq, Gordon Dougan, Richard A. Strugnell
Software Mentions: 1
Published: almost 6 years ago

10.1099/mgen.0.000119

Pre-vaccine serotype composition within a lineage signposts its serotype replacement – a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK
Cited by: 21
Author(s): Rebecca A. Gladstone, Vanessa T. Devine, Jessica Jones, David W. Cleary, Johanna M.C. Jefferies, Stephen D. Bentley, Saul N Faust, Stuart C. Clarke
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0008440

High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya
Cited by: 35
Author(s): Samuel Kariuki, Cecilia Mbae, Sandra Van Puyvelde, Robert Onsare, Susan Kavai, Celestine Wairimu, Ronald Ngetich, John D. Clemens, Gordon Dougan
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-018-5018-x

Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre
Cited by: 15
Author(s): Bryan A. Wee, Anna Tai, L. Sherrard, Nouri L. Ben Zakour, Kirt R. Hanks, Timothy J. Kidd, Kay A. Ramsay, Iain L. Lamont, David M. Whiley, Scott C. Bell, Scott A. Beatson
Software Mentions: 1
Published: over 6 years ago