pypi: snippy | Projects | 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: over 5 years ago

10.1099/mgen.0.000503

Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Cited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: almost 4 years ago

10.1186/s13059-021-02473-1

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Cited by: 20
Author(s): Rachel Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal
Software Mentions: 10
Published: about 3 years ago

10.1099/mgen.0.000511

Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Cited by: 12
Author(s): Matthew P. Moore, Iain L. Lamont, David Williams, Steve Paterson, Iréna Kukavica-Ibrulj, Nicholas P. Tucker, D. Kenna, Jane F. Turton, Julie Jeukens, Luca Freschi, Bryan A. Wee, Nicholas J. Loman, Stephen Holden, Susan Manzoor, Peter M. Hawkey, Kevin W Southern, Martin Walshaw, Roger C. Levesque, Joanne L. Fothergill, Craig Winstanley
Software Mentions: 9
Published: over 3 years ago

10.1099/mgen.0.000491

Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes
Cited by: 10
Author(s): Stefanie Lüth, Carlus Deneke, Sylvia Kleta, Sascha Al Dahouk
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pbio.3001276

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae
Cited by: 37
Author(s): Matthieu Haudiquet, Amandine Nucci, Olaya Rendueles, Eduardo P. C. Rocha
Software Mentions: 9
Published: over 3 years ago

10.1186/s40168-021-01140-8

Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
Cited by: 18
Author(s): Olga María Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Fortin, Ben Shapiro
Software Mentions: 8
Published: about 3 years ago

10.3389/fmicb.2020.00103

Resistance Evolution Against Antimicrobial Peptides in Staphylococcus aureus Alters Pharmacodynamics Beyond the MIC
Cited by: 40
Author(s): Baydaa El Shazely, Guozhi Yu, Paul R. Johnston, Jens Rolff
Software Mentions: 8
Published: almost 5 years ago

10.3390/pathogens10080988

Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021
Cited by: 11
Author(s): Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Christiano Perin, Alexandre Horn, Camila Peter, Gabriela Bettella Cybis, Patrícia Aline Gröhs Ferrareze, Liane Nanci Rotta, Flavio Cadegiani, Ricardo Ariel Zimerman, Claudia Elizabeth Thompson
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.ppat.1009418

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity
Cited by: 10
Author(s): Cédric Lood, Charlotte Peeters, Quentin Lamy-Besnier, Jeroen Wagemans, Daniël De Vos, Marijke Proesmans, Jean‐Paul Pirnay, Fedoua Echahidi, Denis Piérard, M Thimmesch, Anca Boeras, Katrien Lagrou, Evelien De Canck, Elke De Wachter, Vera van Noort, Rob Lavigne, Peter Vandamme
Software Mentions: 7
Published: over 3 years ago

10.1128/mSphere.00535-21

A Comprehensive Map of Mycobacterium tuberculosis Complex Regions of Difference
Cited by: 11
Author(s): Dmitry Bespiatykh, Julia Bespyatykh, Igor Mokrousov, Egor Shitikov
Software Mentions: 6
Published: about 3 years ago

10.3389/fpubh.2019.00241

Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation
Cited by: 28
Author(s): Helena M. B. Seth-Smith, Ferdinando Bonfiglio, Aline Cuénod, Josiane Reist, Adrian Egli, Daniel Wüthrich
Software Mentions: 5
Published: about 5 years ago

10.1186/s13073-020-00751-4

Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
Cited by: 98
Author(s): Mao Xiao, Xiaoqing Liu, Jingkai Ji, Min Li, Jiandong Li, Lin Yang, Wanying Sun, Peng Ren, Guifang Yang, Jincun Zhao, Tianzhu Liang, Huahui Ren, Cheng Tian, Zhong Huang, Wenchen Song, Yanqun Wang, Ziqing Deng, Yongqiang Zhao, Zhihua Ou, Daxi Wang, Jielun Cai, Xinyi Cheng, Taiqing Feng, Honglong Wu, Yanping Gong, Huanming Yang, Jian Wang, Xun Xu, Shida Zhu, Fang Chen, Yanyan Zhang, Weijun Chen, Yimin Li, Junhua Li
Software Mentions: 5
Published: over 4 years ago

10.3389/fcimb.2021.667327

Development and Characterization of High-Throughput Caenorhabditis elegans – Enterococcus faecium Infection Model
Cited by: 4
Author(s): Alexey V. Revtovich, Elissa Tjahjono, Kavindra V. Singh, Blake Hanson, Barbara E. Murray, Natalia V. Kirienko
Software Mentions: 5
Published: over 3 years ago

10.1099/mgen.0.000266

Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors
Cited by: 18
Author(s): Eva Heinz, Richard Brindle, Andrina Morgan-McCalla, Keisha Peters, Nicholas R. Thomson
Software Mentions: 4
Published: over 5 years ago

10.1093/ve/veaa012

Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
Cited by: 13
Author(s): Florent Lassalle, Mathew A. Beale, Tehmina Bharucha, Charlotte A. Williams, Rachel Williams, Juliana Cudini, Richard A. Goldstein, Tanzina Haque, Daniel P. Depledge, Judith Breuer
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-020-07232-3

CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution
Cited by: 2
Author(s): Juan Maldonado, Antony T. Vincent, Martin Chenal, Frédéric J. Veyrier
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-019-5833-8

Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups
Cited by: 26
Author(s): Claudia Hemsley, Paul O’Neill, Angela Essex-Lopresti, Isobel H. Norville, Tim Atkins, Richard W. Titball
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-33593-7

Genomics of experimental adaptation of Staphylococcus aureus to a natural combination of insect antimicrobial peptides
Cited by: 22
Author(s): Olga Makarova, Paul R. Johnston, Alexandro Rodríguez‐Rojas, Baydaa El Shazely, Javier Moreno-Morales, Jens Rolff
Software Mentions: 3
Published: about 6 years ago

10.1186/s13073-020-00814-6

A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition
Cited by: 69
Author(s): Stefan E. Heiden, Nils–Olaf Hübner, Jürgen A. Bohnert, Claus–Dieter Heidecke, Axel Krämer, Veronika Balau, Wolfgang Gierer, Stephan Schaefer, Tim Eckmanns, Sören Gatermann, Elias Eger, Sebastian Guenther, Karsten Becker, Katharina Schaufler
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pntd.0008105

Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus
Cited by: 16
Author(s): Robert Kozak, Russell S. Fraser, Mia J Biondi, Anna Majer, Sarah J. Medina, Bryan D. Griffin, Darwyn Kobasa, Patrick J. Stapleton, Chantel Urfano, Giorgi Babuadze, Kym Antonation, Lisa Fernando, Stephanie A. Booth, Brandon N. Lillie, Gary P. Kobinger
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008649

Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress
Cited by: 49
Author(s): Alexandro Rodríguez‐Rojas, Joshua Jay Kim, Paul R. Johnston, Olga Makarova, Murat Eravci, Christoph Weise, Regine Hengge, Jens Rolff
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.10121

The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake
Cited by: 8
Author(s): Idowu B. Olawoye, Simon D. W. Frost, Christian Happi
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pbio.3000805

Combining antibiotics with antivirulence compounds can have synergistic effects and reverse selection for antibiotic resistance in Pseudomonas aeruginosa
Cited by: 62
Author(s): Chiara Rezzoagli, Martina Archetti, Ingrid Mignot, Michael Baumgärtner, Rolf Kümmerli
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms9051022

Genomics and Virulence of Klebsiella pneumoniae Kpnu95 ST1412 Harboring a Novel Incf Plasmid Encoding Blactx-M-15 and Qnrs1 Causing Community Urinary Tract Infection
Cited by: 3
Author(s): Ayala Gancz, Kira Kondratyeva, Dorit Cohen-Eli, Shiri Navon-Venezia
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2020.01430

A Hopeful Sea-Monster: A Very Large Homologous Recombination Event Impacting the Core Genome of the Marine Pathogen Vibrio anguillarum
Cited by: 6
Author(s): Nicola M. Coyle, Kerry L. Bartie, Sion C. Bayliss, Michaël Bekaert, Alexandra Adams, Stuart McMillan, David W. Verner–Jeffreys, Andrew P. Desbois, Edward J. Feil
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.01699

Genomic and Phenotypic Analysis of an ESBL-Producing E. coli ST1159 Clonal Lineage From Wild Birds in Mongolia
Cited by: 7
Author(s): Peter Schierack, Stefan E. Heiden, Muhammad Moman Khan, Lena Nikolaus, Rafał Kolenda, Michael Stubbe, Davaa Lkhagvasuren, Stefan Rödiger, Sebastian Guenther, Katharina Schaufler
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.47606

Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment
Cited by: 21
Author(s): L. Baker, Lindsay L Freed, Cole G. Easson, Jose V. Lopez, Danté B. Fenolio, Tracey Sutton, Spencer V. Nyholm, Tory A. Hendry
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2020.585374

Phylogenomic Analysis of Campylobacter fetus Reveals a Clonal Structure of Insertion Element ISCfe1 Positive Genomes
Cited by: 4
Author(s): Mostafa Y. Abdel-Glil, Helmut Hotzel, Herbert Tomaso, Jörg Linde
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1008850

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
Cited by: 37
Author(s): Matt Bawn, Nabil-Fareed Alikhan, Gaëtan Thilliez, Mark Kirkwood, Nicole E. Wheeler, Liljana Petrovska, Timothy J. Dallman, Evelien M. Adriaenssens, Neil Hall, Robert A. Kingsley
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms8121851

Analysis of Complete Genome Sequence of Acinetobacter baumannii Strain ATCC 19606 Reveals Novel Mobile Genetic Elements and Novel Prophage
Cited by: 13
Author(s): Mohammad Hamidian, Lucía Blasco, Lauren N Tillman, Joyce To, María Tomás, Garry Myers
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.53886

Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
Cited by: 68
Author(s): Daniel R. Evans, M. Patrick Griffith, Alexander Sundermann, Kathleen A. Shutt, Melissa Saul, Mustapha M. Mustapha, Jane W. Marsh, Vaughn S. Cooper, Lee H. Harrison, Daria Van Tyne
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-021-07708-w

Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil
Cited by: 23
Author(s): Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Amanda de Menezes Mayer, Gabriela Bettella Cybis, Carla Andretta Moreira Neves, Patrícia Aline Gröhs Ferrareze, Meriane Demoliner, Paula Rodrigues de Almeida, Juliana Schons Gularte, Alana Witt Hansen, Matheus Nunes Weber, Juliane Deise Fleck, Ricardo Ariel Zimerman, Lívia Kmetzsch, Fernando Rosado Spilki, Claudia Elizabeth Thompson
Software Mentions: 2
Published: over 3 years ago

10.1186/s12866-021-02124-2

Identification and elimination of genomic regions irrelevant for magnetosome biosynthesis by large-scale deletion in Magnetospirillum gryphiswaldense
Cited by: 7
Author(s): Theresa Zwiener, Frank Mickoleit, Marina Dziuba, Christian Rückert, Tobias Busche, Jörn Kalinowski, Damien Faivre, René Uebe, Dirk Schüler
Software Mentions: 2
Published: over 3 years ago

10.1186/s12866-021-02203-4

Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms
Cited by: 8
Author(s): Ming C. Hao, Wanli Ma, Xiutao Dong, Xiaofeng Li, Fang Cheng, Yujiao Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/s12934-021-01517-2

Towards a 'chassis' for bacterial magnetosome biosynthesis: genome streamlining of Magnetospirillum gryphiswaldense by multiple deletions
Cited by: 15
Author(s): Theresa Zwiener, Marina Dziuba, Frank Mickoleit, Christian Rückert, Tobias Busche, Jörn Kalinowski, René Uebe, Dirk Schüler
Software Mentions: 2
Published: almost 4 years ago

10.1099/mgen.0.000279

Domestication of Campylobacter jejuni NCTC 11168
Cited by: 21
Author(s): Ben Pascoe, Lisa Williams, Jessica K. Calland, Guillaume Méric, Matthew D. Hitchings, Myles Dyer, Joseph Ryder, Sophie Shaw, Bruno Silvester Lopes, Cosmin Chintoan-Uta, Elaine Allan, Ana Maria Centola Vidal, Catherine Fearnley, Paul Everest, Justin A. Pachebat, Tristan A Cogan, Mark P. Stevens, T. J. Humphrey, Thomas S. Wilkinson, Alison J. Cody, Frances M. Colles, Keith A. Jolley, Martin C. J. Maiden, Norval James Colin 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
Software Mentions: 2
Published: over 5 years ago

10.1099/mgen.0.000295

Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids
Cited by: 26
Author(s): Cameron J. Reid, Jessica McKinnon, Steven P. Djordjevic
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms9071345

Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany
Cited by: 1
Author(s): Stefan E. Heiden, Katharina Sydow, Stephan Schaefer, I. Klempien, Veronika Balau, Péter Bauer, Nils–Olaf Hübner, Katharina Schaufler
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9091911

What WGS Reveals about Salmonella enterica subsp. enterica in Wildlife in Germany
Cited by: 8
Author(s): Laura Uelze, Angelina Bloch, Maria Blettner, Mirjam Grobbel, Carlus Deneke, Matthias Fischer, Burkhard Malorny, Michael Pietsch, Sandra Simon, István Szabó, Simon H. Tausch, Jennie Fischer
Software Mentions: 2
Published: about 3 years ago

10.3390/pathogens10060759

Whole-Genome Sequencing for Tracing the Genetic Diversity of Brucella abortus and Brucella melitensis Isolated from Livestock in Egypt
Cited by: 14
Author(s): Aman Ullah Khan, Falk Melzer, Ashraf E. Sayour, Waleed S. Shell, Jörg Linde, Mostafa Y. Abdel-Glil, Sherif Abdel Ghafar Elsayed El-Soally, Mandy C. Elschner, Hossam E. M. Sayour, Eman S. Ramadan, Shereen Aziz Mohamed, Ashraf Hendam, Rania I. Ismail, Lubna F. Farahat, Uwe Roesler, Heinrich Neubauer, Hosny El-Adawy
Software Mentions: 2
Published: over 3 years ago

10.3389/fcimb.2019.00014

Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection
Cited by: 11
Author(s): Kristine M. Wylie, Todd Wylie, Patrick Minx, David A. Rosen
Software Mentions: 2
Published: almost 6 years ago

10.3389/fevo.2021.630207

Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish
Cited by: 8
Author(s): Alison L. Gould, Allison Fritts-Penniman, Ana Gaisiner
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2020.01591

Mobility of β-Lactam Resistance Under Bacterial Co-infection and Ampicillin Treatment in a Mouse Model
Cited by: 5
Author(s): Alexander Laskey, Marie Ottenbrite, John Devenish, Mingsong Kang, Mirjana Savic, Susan A. Nadin-Davis, John Chmara, Min Lin, James A. Robertson, Kyrylo Bessonov, Simone Gurnik, Kira Liu, John H. E. Nash, Andrew Scott, Edward Topp, Jiewen Guan
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2021.662575

Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda
Cited by: 13
Author(s): Elias Eger, Stefan E. Heiden, Katja Korolew, Claude Bayingana, Jules Ndoli, Augustin Sendegeya, Jean Bosco Gahutu, Mathis S. E. Kurz, Frank P. Mockenhaupt, Julia Müller, Stefan Simm, Katharina Schaufler
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.633467

Isopropoxy Benzene Guanidine Kills Staphylococcus aureus Without Detectable Resistance
Cited by: 6
Author(s): Xiufeng Zhang, Wenguang Xiong, Xianfeng Peng, Yixing Lu, Jie Hao, Zhanfen Qin, Zhenling Zeng
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.631845

Staphylococcus aureus ST59: Concurrent but Separate Evolution of North American and East Asian Lineages
Cited by: 7
Author(s): Jo-Ann McClure, Sahreena Lakhundi, Amani Niazy, George Dong, Osahon Obasuyi, Paul M. Gordon, Sidong Chen, John Conly, Kunyan Zhang
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.701265

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis
Cited by: 9
Author(s): Xiaolei Su, Yinghua Guo, Tingzheng Fang, Xuege Jiang, Dapeng Wang, Diangeng Li, Po Bai, Zhang Bin, Junfeng Wang, Changting Liu
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.ppat.1009209

Enhanced biofilm and extracellular matrix production by chronic carriage versus acute isolates of Salmonella Typhi
Cited by: 7
Author(s): Aishwarya Devaraj, Juan F. González, Bradley Eichar, Gaëtan Thilliez, Robert A. Kingsley, Stephen Baker, Marc W. Allard, Lauren O. Bakaletz, John S. Gunn, Steven D. Goodman
Software Mentions: 2
Published: almost 4 years ago

10.1098/rspb.2020.2876

Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella
Cited by: 16
Author(s): Amandine Nucci, Eduardo P. C. Rocha, Olaya Rendueles
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-47740-1

Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada
Cited by: 17
Author(s): Patrick J. Stapleton, Alireza Eshaghi, Chi Yon Seo, Sarah E. Wilson, Tara Harris, Shelley L. Deeks, Shelly Bolotin, Lee W. Goneau, Jonathan B. Gubbay, Samir N. Patel
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.00640-18

Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells
Cited by: 144
Author(s): Frédéric Goormaghtigh, Nathan Fraikin, Marta Putrinš, Thibaut Hallaert, Vasili Hauryliuk, Abel García-Pino, Andreas Sjödin, Sergo Kasvandik, Klas I. Udekwu, Tanel Tenson, Niilo Kaldalu, Laurence Van Melderen
Software Mentions: 2
Published: over 6 years ago

10.1128/mBio.00465-20

Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump
Cited by: 48
Author(s): Elizabeth Grimsey, Chiara Fais, Robert L. Marshall, Vito Ricci, Maria Laura Ciusa, Jack Stone, Alasdair Ivens, Giuliano Malloci, Paolo Ruggerone, Attilio Vittorio Vargiu, Laura J. V. Piddock
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-021-07738-4

Genome-wide association studies reveal candidate genes associated to bacteraemia caused by ST93-IV CA-MRSA
Cited by: 0
Author(s): Stanley Pang, Denise A Daley, Shafi Sahibzada, Shakeel Mowlaboccus, Marc Stegger, Geoffrey W. Coombs
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-86243-w

Salmonella nomenclature in the genomic era: a time for change
Cited by: 21
Author(s): Marie Anne Chattaway, Gemma Langridge, John Wain
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2017.00603

Analysis of the Listeria monocytogenes Population Structure among Isolates from 1931 to 2015 in Australia
Cited by: 31
Author(s): Amy V. Jennison, Jesse J. Masson, Ning Fang, Rikki Graham, Mark Bradbury, Narelle Fegan, Kari S. Gobius, Trudy Graham, Christine J D Guglielmino, Janelle Brown, Edward M. Fox
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-95285-z

Evidence of an epidemic spread of KPC-producing Enterobacterales in Czech hospitals
Cited by: 10
Author(s): Lucie Kraftova, Marc Finianos, Vendula Študentová, Kateřina Chudějová, Vladislav Jakubů, Helena Žemličková, Costas C. Papagiannitsis, Ibrahim Bitar, Jaroslav Hrabák
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.03098

Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements
Cited by: 10
Author(s): Veronica M. Jarocki, Cameron J. Reid, Toni A. Chapman, Steven P. Djordjevic
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0229863

Genome–scale approach to study the genetic relatedness among Brucella melitensis strains
Cited by: 12
Author(s): Ana Pelerito, Baltazar Nunes, Maria Sofia Núncio, João Paulo Gomes
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1009829

Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages
Cited by: 9
Author(s): Jessica K. Calland, Ben Pascoe, Sion C. Bayliss, Evangelos Mourkas, Elvire Berthenet, Harry A. Thorpe, Matthew D. Hitchings, Edward J. Feil, Jukka Corander, Martin J. Blaser, Daniel Falush, Samuel K. Sheppard
Software Mentions: 1
Published: about 3 years ago

10.3390/pathogens10030331

Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma
Cited by: 4
Author(s): Montserrat Palau, Núria Piqué, María José Ramírez‐Lázaro, Sergio Lario, Xavier Calvet Calvo, David Miñana-Galbis
Software Mentions: 1
Published: over 3 years ago

10.3390/pathogens10070817

How Bacteria Change after Exposure to Silver Nanoformulations: Analysis of the Genome and Outer Membrane Proteome
Cited by: 0
Author(s): Anna Kędziora, Mateusz Speruda, Maciej Wernecki, Barbara Dudek, Katarzyna Kapczyńska, Eva Krzyżewska, Jacek Rybka, Gabriela Bugla-Płoskońska
Software Mentions: 1
Published: over 3 years ago

10.1093/jacamr/dlab112

Two carbapenem-resistant ST1:ST231:KL1:OCL1Acinetobacter baumanniistrains recovered in Tehran, Iran, carry AbaR31 in the chromosome and AbaR4 and TnaphA6in a RepAci6 plasmid
Cited by: 5
Author(s): Masoumeh Douraghi, Parisa Aris, Joyce To, Garry Myers, Mohammad Hamidian
Software Mentions: 1
Published: over 3 years ago

10.3390/microorganisms8121945

Physiological Response of Corynebacterium glutamicum to Indole
Cited by: 16
Author(s): Tatjana Walter, Kareen H. Veldmann, Susanne Götker, Tobias Busche, Christian Rückert, Arman Beyraghdar Kashkooli, Jannik Paulus, Katarina Cankar, Volker F. Wendisch
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13567-020-00834-5

First European report of Francisella tularensis subsp. holarctica isolation from a domestic cat
Cited by: 4
Author(s): Sonja Kittl, Thierry Francey, Isabelle Brodard, Francesco C. Origgi, Stéphanie Borel, Marie-Pierre Ryser-Degiorgis, Ariane Schweighauser, Joerg Jores
Software Mentions: 1
Published: about 4 years ago

10.1128/mBio.02831-19

The O-Antigen Epitope Governs Susceptibility to Colistin in Salmonella enterica
Cited by: 18
Author(s): Vito Ricci, Dexian Zhang, Christopher Teale, Laura J. V. Piddock
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms7100388

Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections
Cited by: 1
Author(s): Weihua Huang, Guiqing Wang, Changhong Yin, Donald Chen, Abhay Dhand, Melissa Chanza, Nevenka Dimitrova, John T. Fallon
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2021.651488

Re-evaluation of a Neonatal Mouse Model of Infection With Enterotoxigenic Escherichia coli
Cited by: 1
Author(s): Carla Carroll, Dianna M Hocking, Kristy Azzopardi, Judyta Praszkier, Vicki Bennett-Wood, Kaylani Almeida, Danielle J. Ingle, Sarah L. Baines, Marija Tauschek, Roy M. Robins‐Browne
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2017.01906

Methicillin Resistant Staphylococcus aureus Transmission in a Ghanaian Burn Unit: The Importance of Active Surveillance in Resource-Limited Settings
Cited by: 10
Author(s): Nana Ama Amissah, Andrew H. Buultjens, Anthony Ablordey, Lieke van Dam, Opoku-Ware Ampomah, Sarah L. Baines, Dieter Bulach, Caitlin S. Tetteh, Isaac Prah, Tjip S. van der Werf, Alexander Friedrich, Torsten Seemann, Jan Maarten van Dijl, Ymkje Stienstra, Timothy P. Stinear, John W. A. Rossen
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2021.636788

The Surge of Hypervirulent ST398 MRSA Lineage With Higher Biofilm-Forming Ability Is a Critical Threat to Clinics
Cited by: 13
Author(s): Huiying Lü, Lin Zhao, Yuanguo Si, Ying Jin, Yanan Wang, Tianming Li, Yingxin Dai, Qian Huang, Xiaowei Ma, Lei He
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.611246

Within-Host Microevolution of Pseudomonas aeruginosa Urinary Isolates: A Seven-Patient Longitudinal Genomic and Phenotypic Study
Cited by: 9
Author(s): Agnès Cottalorda, Marie Leoz, Sandrine Dahyot, François Gravey, Maxime Grand, Thomas Froidure, Fabien Aujoulat, Simon Le Hello, Estelle Jumas‐Bilak, Martine Pestel-Caron
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2018.02568

The Occurence of Colistin-Resistant Hypervirulent Klebsiellapneumoniae in China
Cited by: 33
Author(s): Yang Lü, Yu Feng, Alan McNally, Zhiyong Zong
Software Mentions: 1
Published: about 6 years ago

10.2807/1560-7917.ES.2020.25.16.1900457

Two multi-fragment recombination events resulted in the β-lactam-resistant serotype 11A-ST6521 related to Spain9V-ST156 pneumococcal clone spreading in south-western Europe, 2008 to 2016
Cited by: 13
Author(s): Aida González-Díaz, Miguel P. Machado, Jordi Càmara, José Yuste, Emmanuelle Varon, Mirian Domenech, María Del Grosso, José María Marimón, Emilia Cercenado, Nieves Larrosa, María Dolores Quesada, Dionísia Fontanals, Assiya El-Mniai, Meritxell Cubero, João André Carriço, Sara Martí, Mário Ramirez, Carmen Ardanuy
Software Mentions: 1
Published: over 4 years ago

10.1186/s12866-021-02293-0

Increased gene expression and copy number of mutated blaKPC lead to high-level ceftazidime/avibactam resistance in Klebsiella pneumoniae
Cited by: 10
Author(s): Lingxiao Sun, Haibo Li, Qi Wang, Yingmei Liu, Bin Cao
Software Mentions: 1
Published: over 3 years ago

10.1007/s10096-017-2905-z

Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections
Cited by: 19
Author(s): Florian Tagini, B. Aubert, Nicolas Troillet, Trestan Pillonel, G. Praz, Pierre Alex Crisinel, Guy Prod’hom, Sandra Asner, Gilbert Greub
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-020-79621-3

Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population
Cited by: 2
Author(s): Syeda A. Hadi, Ida Viktoria Kolte, Evan P. Brenner, Eunice Atsuko Totumi Cunha, Vera Simonsen, Lucilaine Ferrazoli, Daniel Antunes Maciel Villela, Reinaldo Souza-Santos, Janani Ravi, Srinand Sreevatsan, Paulo Cesar Basta
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2021.604031

Multidrug-Resistant (MDR) Klebsiella variicola Strains Isolated in a Brazilian Hospital Belong to New Clones
Cited by: 7
Author(s): Tatiana Amabile de Campos, Felipe Marques de Almeida, Ana Paula Cardoso Almeida, Rafael Nakamura-Silva, Mariana de Oliveira Silva, Isabela Felix Alencar de Sousa, Louise Cerdeira, Nilton Lincopán, George J. Pappas, André Pitondo-Silva
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: snippy

Papers Mentioning snippy 77