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ArticlesPeer ReviewedFull Text
Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates
Author / Creator:Benulič, Katarina ; Pirš, Mateja ; Couto, Natacha ; Chlebowicz, Monika ; Rossen, John W A ; Zorec, Tomaž Mark ; Seme, Katja ; Poljak, Mario ; Lejko Zupanc, Tatjana ; Ružić-Sabljić, Eva ; Cerar, Tjaša
Publisher:United States: Public Library of Science
Journal title:PloS one, 2020-04, Vol.15 (4), p.e0231503-e0231503
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Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium
Author / Creator:Lisotto, Paola ; Raangs, Erwin C ; Couto, Natacha ; Rosema, Sigrid ; Lokate, MariÃ«tte ; Zhou, Xuewei ; Friedrich, Alexander W ; Rossen, John W. A ; Harmsen, Hermie J. M ; Bathoorn, Erik ; Chlebowicz-Fliss, Monika A
Publisher:London: BioMed Central Ltd
Journal title:BMC genomics, 2021-10, Vol.22 (1), p.1-758, Article 758
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Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
Author / Creator:Schuele, Leonard ; Cassidy, Hayley ; Lizarazo, Erley ; Strutzberg-Minder, Katrin ; Schuetze, Sabine ; Loebert, Sandra ; Lambrecht, Claudia ; Harlizius, Juergen ; Friedrich, Alex W ; Peter, Silke ; Niesters, Hubert G M ; Rossen, John W A ; Couto, Natacha
Publisher:Switzerland: MDPI AG
Journal title:Viruses, 2020-11, Vol.12 (12), p.1358
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ArticlesPeer ReviewedFull Text
Towards unified reporting of genome sequencing results in clinical microbiology
Author / Creator:Mutschler, Eugenio ; Roloff, Tim ; Neves, Aitana ; Vangstein Aamot, Hege ; Rodriguez-Sanchez, Belén ; Ramirez, Mario ; Rossen, John ; Couto, Natacha ; Novais, Ângela ; Howden, Benjamin P ; Brisse, Sylvain ; Reuter, Sandra ; Nolte, Oliver ; Egli, Adrian ; Seth-Smith, Helena M B
Publisher:United States: PeerJ. Ltd
Journal title:PeerJ (San Francisco, CA), 2024-08, Vol.12, p.e17673, Article e17673
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Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity
Author / Creator:Raineri, Elisa J M ; Maaß, Sandra ; Wang, Min ; Brushett, Siobhan ; Palma Medina, Laura M ; Sampol Escandell, Neus ; Altulea, Dania ; Raangs, Erwin ; de Jong, Anne ; Vera Murguia, Elias ; Feil, Edward J ; Friedrich, Alex W ; Buist, Girbe ; Becher, Dörte ; García-Cobos, Silvia ; Couto, Natacha ; van Dijl, Jan Maarten
Publisher:England: BioMed Central
Journal title:Microbiome, 2022-12, Vol.10 (1), p.239-239, Article 239
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The Diversity, Resistance Profiles and Plasmid Content of Klebsiella spp. Recovered from Dairy Farms Located around Three Cities in Pakistan
Author / Creator:Habib, Samia ; Gibbon, Marjorie J ; Couto, Natacha ; Kakar, Khadija ; Habib, Safia ; Samad, Abdul ; Munir, Asim ; Fatima, Fariha ; Mohsin, Mashkoor ; Feil, Edward J
Publisher:Switzerland: MDPI AG
Journal title:Antibiotics (Basel), 2023-03, Vol.12 (3), p.539
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Author Correction: Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens
Author / Creator:Couto, Natacha ; Schuele, Leonard ; Raangs, Erwin C. ; Machado, Miguel P. ; Mendes, Catarina I. ; Jesus, Tiago F. ; Chlebowicz, Monika ; Rosema, Sigrid ; Ramirez, Mário ; Carriço, João A. ; Autenrieth, Ingo B. ; Friedrich, Alex W. ; Peter, Silke ; Rossen, John W.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2019-04, Vol.9 (1), p.6406-6406, Article 6406
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Complete Genome Sequences of Two Methicillin-Resistant Staphylococcus haemolyticus Isolates of Multilocus Sequence Type 25, First Detected by Shotgun Metagenomics
Author / Creator:Couto Natacha ; Chlebowicz, Monika A ; Raangs, Erwin C ; Friedrich, Alex W ; Rossen, John W
Publisher:Washington: American Society for Microbiology
Journal title:Microbiology resource announcements, 2018-04, Vol.6 (14)
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Detection of Legionella Anisa in Water from Hospital Dental Chair Units and Molecular Characterization by Whole-Genome Sequencing
Author / Creator:Fleres, Giuseppe ; Couto, Natacha ; Lokate, Mariette ; van der Sluis, Luc W M ; Ginevra, Christophe ; Jarraud, Sophie ; Deurenberg, Ruud H ; Rossen, John W ; García-Cobos, Silvia ; Friedrich, Alex W
Publisher:Switzerland: MDPI AG
Journal title:Microorganisms (Basel), 2018-07, Vol.6 (3), p.71
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Determining the Virulence Properties of Escherichia coli ST131 Containing Bacteriocin-Encoding Plasmids Using Short- and Long-Read Sequencing and Comparing Them with Those of Other E. coli Lineages
Author / Creator:da Cruz Campos, Ana Carolina ; Cavallo, Francis M ; L Andrade, Nathália ; van Dijl, Jan Maarten ; Couto, Natacha ; Zrimec, Jan ; Lo Ten Foe, Jerome R ; P Rosa, Ana C ; V Damasco, Paulo ; Friedrich, Alex W ; Chlebowicz-Flissikowska, Monika A ; Rossen, John W A
Publisher:Switzerland: MDPI AG
Journal title:Microorganisms (Basel), 2019-11, Vol.7 (11), p.534
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ArticlesPeer ReviewedFull Text
Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae
Author / Creator:David, Sophia ; Cohen, Victoria ; Reuter, Sandra ; Sheppar, Anna E. ; Giani, Tommaso ; Parkhill, Julian ; Rossolini, Gian Maria ; Feil, Edward J. ; Grundman, Hajo ; Aanensen, David M.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2020-10, Vol.117 (40), p.25043-25054
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ArticlesPeer ReviewedFull Text
Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens
Author / Creator:Couto, Natacha ; Schuele, Leonard ; Raangs, Erwin C. ; Machado, Miguel P. ; Mendes, Catarina I. ; Jesus, Tiago F. ; Chlebowicz, Monika ; Rosema, Sigrid ; Ramirez, Mário ; Carriço, João A. ; Autenrieth, Ingo B. ; Friedrich, Alex W. ; Peter, Silke ; Rossen, John W.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2018-09, Vol.8 (1), p.13767-13, Article 13767
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ArticlesPeer ReviewedFull Text
A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings
Author / Creator:Thorpe, Harry A. ; Booton, Ross ; Kallonen, Teemu ; Gibbon, Marjorie J. ; Couto, Natacha ; Passet, Virginie ; López-Fernández, Sebastián ; Rodrigues, Carla ; Matthews, Louise ; Mitchell, Sonia ; Reeve, Richard ; David, Sophia ; Merla, Cristina ; Corbella, Marta ; Ferrari, Carolina ; Comandatore, Francesco ; Marone, Piero ; Brisse, Sylvain ; Sassera, Davide ; Corander, Jukka ; Feil, Edward J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature microbiology, 2022-12, Vol.7 (12), p.2054-2067
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Genetic Relatedness, Antimicrobial and Biocide Susceptibility Comparative Analysis of Methicillin-Resistant and -Susceptible Staphylococcus pseudintermedius from Portugal
Author / Creator:Couto, Natacha ; Belas, Adriana ; Couto, Isabel ; Perreten, Vincent ; Pomba, Constança
Publisher:United States: Mary Ann Liebert, Inc
Journal title:Microbial drug resistance (Larchmont, N.Y.), 2014-08, Vol.20 (4), p.364-371
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ArticlesPeer ReviewedFull Text
627. Molecular Epidemiology of Daptomycin-resistant Staphylococcus aureus Causing Bloodstream Infections
Author / Creator:Gudipati, Smitha ; Perri, Mary ; Couto, Natacha ; Herc, Erica ; Zervos, Marcus
Publisher:Oxford: Oxford University Press
Journal title:Open forum infectious diseases, 2019-10, Vol.6 (Supplement_2), p.S291-S291
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ArticlesPeer ReviewedFull Text
Prevalence, species distribution and antimicrobial resistance patterns of methicillin-resistant staphylococci in Lithuanian pet animals
Author / Creator:Ruzauskas, Modestas ; Couto, Natacha ; Kerziene, Sigita ; Siugzdiniene, Rita ; Klimiene, Irena ; Virgailis, Marius ; Pomba, Constança
Publisher:England: BioMed Central Ltd
Journal title:Acta veterinaria scandinavica, 2015-06, Vol.57 (1), p.27-27, Article 27
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ArticlesPeer ReviewedFull Text
The Diversity, Resistance Profiles and Plasmid Content of IKlebsiella/I spp. Recovered from Dairy Farms Located around Three Cities in Pakistan
Author / Creator:Habib, Samia ; Gibbon, Marjorie J ; Couto, Natacha ; Kakar, Khadija ; Habib, Safia ; Samad, Abdul ; Munir, Asim ; Fatima, Fariha ; Mohsin, Mashkoor ; Feil, Edward J
Publisher:MDPI AG
Journal title:Antibiotics (Basel), 2023-03, Vol.12 (3)
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ArticlesPeer ReviewedFull Text
Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing
Author / Creator:Cassidy, Hayley ; Schuele, Leonard ; Lizarazo-Forero, Erley ; Couto, Natacha ; Rossen, John W A ; Friedrich, Alex W ; van Leer-Buter, Coretta ; Niesters, Hubert G M
Publisher:UK: Oxford University Press
Journal title:Virus evolution, 2022, Vol.8 (1), p.veab109-veab109
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ArticlesPeer ReviewedFull Text
Methicillin-resistant coagulase-negative Staphylococcus spp. prevalence in Lithuanian dogs: a cross-sectional study/Presjecno istrazivanje prevalencije koagulaza negativnih izolata safilokoka, otporni...
Author / Creator:Ruzauskas, Modestas ; Couto, Natacha ; Siugzdiniene, Rita ; Klimiene, Irena ; Virgailis, Marius ; Vaskeviciute, Lina ; Mockeliunas, Raimundas ; Pomba, Constanca
Publisher:Sveuciliste U Zagrebu
Journal title:Veterinarski arhiv, 2015-03, Vol.85 (2), p.175
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ReportsFull Text
Towards unified reporting of genome sequencing results in clinical microbiology
Author / Creator:Mutschler, Eugenio ; Roloff, Tim ; Neves, Aitana ; Vangstein Aamot, Hege ; Rodriguez-Sanchez, Belén ; Ramirez, Mario ; Rossen, John ; Couto, Natacha ; Novais, Ângela ; Howden, Benjamin P ; Brisse, Sylvain ; Reuter, Sandra ; Nolte, Oliver ; Egli, Adrian ; Seth-Smith, Helena M. B ; ,
Publisher:PeerJ. Ltd
Journal title:PeerJ, 2024, Vol.12, p.e17673
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Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates

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Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium

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Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples

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Towards unified reporting of genome sequencing results in clinical microbiology

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Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity

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The Diversity, Resistance Profiles and Plasmid Content of Klebsiella spp. Recovered from Dairy Farms Located around Three Cities in Pakistan

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Author Correction: Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

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Complete Genome Sequences of Two Methicillin-Resistant Staphylococcus haemolyticus Isolates of Multilocus Sequence Type 25, First Detected by Shotgun Metagenomics

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Detection of Legionella Anisa in Water from Hospital Dental Chair Units and Molecular Characterization by Whole-Genome Sequencing

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Determining the Virulence Properties of Escherichia coli ST131 Containing Bacteriocin-Encoding Plasmids Using Short- and Long-Read Sequencing and Comparing Them with Those of Other E. coli Lineages

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Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae

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Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

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A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

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Genetic Relatedness, Antimicrobial and Biocide Susceptibility Comparative Analysis of Methicillin-Resistant and -Susceptible Staphylococcus pseudintermedius from Portugal

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627. Molecular Epidemiology of Daptomycin-resistant Staphylococcus aureus Causing Bloodstream Infections

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Prevalence, species distribution and antimicrobial resistance patterns of methicillin-resistant staphylococci in Lithuanian pet animals

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The Diversity, Resistance Profiles and Plasmid Content of IKlebsiella/I spp. Recovered from Dairy Farms Located around Three Cities in Pakistan

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Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing

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Methicillin-resistant coagulase-negative Staphylococcus spp. prevalence in Lithuanian dogs: a cross-sectional study/Presjecno istrazivanje prevalencije koagulaza negativnih izolata safilokoka, otporni...

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Towards unified reporting of genome sequencing results in clinical microbiology

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