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608 results on '"Willems, Rob J."'

2. Colonization of vancomycin-resistant Enterococcus faecium in human-derived colonic epithelium: Unraveling the transcriptional dynamics of host-enterococcal interactions

Author

Stege, Paul B, primary, Beekman, Jeffrey M, additional, Hendrickx, Antoni P A, additional, van Eijk, Laura, additional, Rogers, Malbert R C, additional, Suen, Sylvia W F, additional, Vonk, Annelotte M, additional, Willems, Rob J L, additional, and Paganelli, Fernanda L, additional

Published
2024
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5. PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli.

Author

MMB Research line 2, Infection & Immunity, Paganini, Julian A, Kerkvliet, Jesse J, Vader, Lisa, Plantinga, Nienke L, Meneses, Rodrigo, Corander, Jukka, Willems, Rob J L, Arredondo-Alonso, Sergio, Schürch, Anita C, MMB Research line 2, Infection & Immunity, Paganini, Julian A, Kerkvliet, Jesse J, Vader, Lisa, Plantinga, Nienke L, Meneses, Rodrigo, Corander, Jukka, Willems, Rob J L, Arredondo-Alonso, Sergio, and Schürch, Anita C

Published
2024

6. Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

Author

IRAS OH Epidemiology Microbial Agents, IRAS – One Health Microbial, Kerkvliet, Jesse J., Bossers, Alex, Kers, Jannigje G., Meneses, Rodrigo, Willems, Rob J L, Schürch, Anita C., IRAS OH Epidemiology Microbial Agents, IRAS – One Health Microbial, Kerkvliet, Jesse J., Bossers, Alex, Kers, Jannigje G., Meneses, Rodrigo, Willems, Rob J L, and Schürch, Anita C.

Published
2024

7. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Author

Pöntinen, Anna K., Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R., Novais, Carla, Gladstone, Rebecca A., Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A., Jamrozy, Dorota, Bentley, Stephen D., Lanza, Val F., Torres, Carmen, Peixe, Luisa, Coque, Teresa M., Parkhill, Julian, Schürch, Anita C., Willems, Rob J. L., and Corander, Jukka

Published
2021
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10. The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection

Author

Chaguza, Chrispin, primary, Pöntinen, Anna K., additional, Top, Janetta, additional, Arredondo-Alonso, Sergio, additional, Freitas, Ana R., additional, Novais, Carla, additional, Torres, Carmen, additional, Bentley, Stephen D., additional, Peixe, Luisa, additional, Coque, Teresa M., additional, Willems, Rob J. L., additional, and Corander, Jukka, additional

Published
2023
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11. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition

Author

Stege, Paul B., primary, Hordijk, Joost, additional, Sandholt, Arnar K. S., additional, Zomer, Aldert L., additional, Viveen, Marco C., additional, Rogers, Malbert R. C., additional, Salomons, Moniek, additional, Wagenaar, Jaap A., additional, Mughini-Gras, Lapo, additional, Willems, Rob J. L., additional, and Paganelli, Fernanda L., additional

Published
2023
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12. Prediction of the intestinal resistome by a three-dimensional structure-based method

Author

Ruppé, Etienne, Ghozlane, Amine, Tap, Julien, Pons, Nicolas, Alvarez, Anne-Sophie, Maziers, Nicolas, Cuesta, Trinidad, Hernando-Amado, Sara, Clares, Irene, Martínez, Jose Luís, Coque, Teresa M., Baquero, Fernando, Lanza, Val F., Máiz, Luis, Goulenok, Tiphaine, de Lastours, Victoire, Amor, Nawal, Fantin, Bruno, Wieder, Ingrid, Andremont, Antoine, van Schaik, Willem, Rogers, Malbert, Zhang, Xinglin, Willems, Rob J. L., de Brevern, Alexandre G., Batto, Jean-Michel, Blottière, Hervé M., Léonard, Pierre, Léjard, Véronique, Letur, Aline, Levenez, Florence, Weiszer, Kevin, Haimet, Florence, Doré, Joël, Kennedy, Sean P., and Ehrlich, S. Dusko

Published
2019
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13. Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone

Author

Boralli, Camila Maria dos Santos, primary, Paganini, Julian Andres, additional, Meneses, Rodrigo Silva, additional, Mata, Camila Pacheco Silveira Martins da, additional, Leite, Edna Marilea Meireles, additional, Schürch, Anita C., additional, Paganelli, Fernanda L., additional, Willems, Rob J. L., additional, and Camargo, Ilana Lopes Baratella Cunha, additional

Published
2023
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16. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition

Author

Infectious Diseases and Immunology, IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., IRAS – One Health Microbial, Infectious Diseases and Immunology - KLIF, Stege, Paul B, Hordijk, Joost, Sandholt, Arnar K S, Zomer, Aldert L, Viveen, Marco C, Rogers, Malbert R C, Salomons, Moniek, Wagenaar, Jaap A, Mughini-Gras, Lapo, Willems, Rob J L, Paganelli, Fernanda L, Infectious Diseases and Immunology, IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., IRAS – One Health Microbial, Infectious Diseases and Immunology - KLIF, Stege, Paul B, Hordijk, Joost, Sandholt, Arnar K S, Zomer, Aldert L, Viveen, Marco C, Rogers, Malbert R C, Salomons, Moniek, Wagenaar, Jaap A, Mughini-Gras, Lapo, Willems, Rob J L, and Paganelli, Fernanda L

Published
2023

20. Interventions to reduce colonisation and transmission of antimicrobial-resistant bacteria in intensive care units: an interrupted time series study and cluster randomised trial

Author

Derde, Lennie P G, Cooper, Ben S, Goossens, Herman, Malhotra-Kumar, Surbhi, Willems, Rob J L, Gniadkowski, Marek, Hryniewicz, Waleria, Empel, Joanna, Dautzenberg, Mirjam J D, Annane, Djillali, Aragão, Irene, Chalfine, Annie, Dumpis, Uga, Esteves, Francisco, Giamarellou, Helen, Muzlovic, Igor, Nardi, Giuseppe, Petrikkos, George L, Tomic, Viktorija, Martí, Antonio Torres, Stammet, Pascal, Brun-Buisson, Christian, and Bonten, Marc J M

Published
2014
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21. Characterization of bla KPC-2 and bla NDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone.

Author

Boralli, Camila Maria dos Santos, Paganini, Julian Andres, Meneses, Rodrigo Silva, Mata, Camila Pacheco Silveira Martins da, Leite, Edna Marilea Meireles, Schürch, Anita C., Paganelli, Fernanda L., Willems, Rob J. L., and Camargo, Ilana Lopes Baratella Cunha

Subjects
KLEBSIELLA pneumoniae, ESCHERICHIA coli, MOLECULAR cloning, PULSED-field gel electrophoresis, PLASMIDS, WHOLE genome sequencing
Abstract

The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids' transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem. [ABSTRACT FROM AUTHOR]

Published
2023
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24. The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis

Author

van Hal, Sebastiaan J, primary, Willems, Rob J L, additional, Gouliouris, Theodore, additional, Ballard, Susan A, additional, Coque, Teresa M, additional, Hammerum, Anette M, additional, Hegstad, Kristin, additional, Pinholt, Mette, additional, Howden, Benjamin P, additional, Malhotra-Kumar, Surbhi, additional, Werner, Guido, additional, Yanagihara, Katsunori, additional, Earl, Ashlee M, additional, Raven, Katherine E, additional, Corander, Jukka, additional, and Bowden, Rory, additional

Published
2022
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33. Erratum for Janssen et al., “Evolution of Colistin Resistance in the Klebsiella pneumoniae Complex Follows Multiple Evolutionary Trajectories with Variable Effects on Fitness and Virulence Characteristics”

Author

Janssen, Axel B., primary, Doorduijn, Dennis J., additional, Mills, Grant, additional, Rogers, Malbert R. C., additional, Bonten, Marc J. M., additional, Rooijakkers, Suzan H. M., additional, Willems, Rob J. L., additional, Bengoechea, Jose A., additional, and van Schaik, Willem, additional

Published
2021
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34. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Author

MMB Research line 2, Infection & Immunity, Pöntinen, Anna K, Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R, Novais, Carla, Gladstone, Rebecca A, Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A, Jamrozy, Dorota, Bentley, Stephen D, Lanza, Val F, Torres, Carmen, Peixe, Luisa, Coque, Teresa M, Parkhill, Julian, Schürch, Anita C, Willems, Rob J L, Corander, Jukka, MMB Research line 2, Infection & Immunity, Pöntinen, Anna K, Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R, Novais, Carla, Gladstone, Rebecca A, Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A, Jamrozy, Dorota, Bentley, Stephen D, Lanza, Val F, Torres, Carmen, Peixe, Luisa, Coque, Teresa M, Parkhill, Julian, Schürch, Anita C, Willems, Rob J L, and Corander, Jukka

Published
2021

35. Evolution of colistin resistance in the Klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics

Author

MMB Research line 2, MMB Research line 1, Infection & Immunity, MMB Research Algemeen, MMB, Epi Infectieziekten, JC onderzoeksprogramma Infectieziekten, Janssen, Axel B, Doorduijn, Dennis J, Mills, Grant, Rogers, Malbert R C, Bonten, Marc J M, Rooijakkers, Suzan H M, Willems, Rob J L, Bengoechea, Jose A, van Schaik, Willem, MMB Research line 2, MMB Research line 1, Infection & Immunity, MMB Research Algemeen, MMB, Epi Infectieziekten, JC onderzoeksprogramma Infectieziekten, Janssen, Axel B, Doorduijn, Dennis J, Mills, Grant, Rogers, Malbert R C, Bonten, Marc J M, Rooijakkers, Suzan H M, Willems, Rob J L, Bengoechea, Jose A, and van Schaik, Willem

Published
2021

39. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Author

van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, Kluytmans, Jan A J W, van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, and Kluytmans, Jan A J W

Published
2020

40. gplas: a comprehensive tool for plasmid analysis using short-read graphs

Author

Sub Mathematical Modeling, Mathematical Modeling, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, Schürch, Anita C, Sub Mathematical Modeling, Mathematical Modeling, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, and Schürch, Anita C

Published
2020

41. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli

Author

Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Rosendahl Huber, Axel, van Hoeck, Arne, Wood, Henry M, Nomburg, Jason, Gurjao, Carino, Manders, Freek, Dalmasso, Guillaume, Stege, Paul B, Paganelli, Fernanda L, Geurts, Maarten H, Beumer, Joep, Mizutani, Tomohiro, Miao, Yi, van der Linden, Reinier, van der Elst, Stefan, Garcia, K Christopher, Top, Janetta, Willems, Rob J L, Giannakis, Marios, Bonnet, Richard, Quirke, Phil, Meyerson, Matthew, Cuppen, Edwin, van Boxtel, Ruben, Clevers, Hans, Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Rosendahl Huber, Axel, van Hoeck, Arne, Wood, Henry M, Nomburg, Jason, Gurjao, Carino, Manders, Freek, Dalmasso, Guillaume, Stege, Paul B, Paganelli, Fernanda L, Geurts, Maarten H, Beumer, Joep, Mizutani, Tomohiro, Miao, Yi, van der Linden, Reinier, van der Elst, Stefan, Garcia, K Christopher, Top, Janetta, Willems, Rob J L, Giannakis, Marios, Bonnet, Richard, Quirke, Phil, Meyerson, Matthew, Cuppen, Edwin, van Boxtel, Ruben, and Clevers, Hans

Abstract

Various species of the intestinal microbiota have been associated with the development of colorectal cancer1,2, but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin3. This compound is believed to alkylate DNA on adenine residues4,5 and induces double-strand breaks in cultured cells3. Here we expose human intestinal organoids to genotoxic pks+ E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in colorectal cancer. Our study describes a distinct mutational signature in colorectal cancer and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.

Published
2020

42. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Child Health, MMB Research line 2, Epi Infectieziekten, MMB, van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, Kluytmans, Jan A J W, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Child Health, MMB Research line 2, Epi Infectieziekten, MMB, van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, and Kluytmans, Jan A J W

Published
2020

43. Microevolution of acquired colistin resistance in Enterobacteriaceae from ICU patients receiving selective decontamination of the digestive tract

Author

MMB Research line 2, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Epi Infectieziekten, MMB, Janssen, Axel B, van Hout, Denise, Bonten, Marc J M, Willems, Rob J L, van Schaik, Willem, MMB Research line 2, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Epi Infectieziekten, MMB, Janssen, Axel B, van Hout, Denise, Bonten, Marc J M, Willems, Rob J L, and van Schaik, Willem

Published
2020

44. Evolution of Colistin Resistance in the Klebsiella pneumoniae Complex Follows Multiple Evolutionary Trajectories with Variable Effects on Fitness and Virulence Characteristics

Author

Janssen, Axel B., primary, Doorduijn, Dennis J., additional, Mills, Grant, additional, Rogers, Malbert R. C., additional, Bonten, Marc J. M., additional, Rooijakkers, Suzan H. M., additional, Willems, Rob J. L., additional, Bengoechea, Jose A., additional, and van Schaik, Willem, additional

Published
2020
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48. Vancomycin-resistant Enterococcus faecium (VREF) from Norwegian poultry cluster with VREF from poultry from the United Kingdom and the Netherlands in an amplified fragment length polymorphism genogroup

Author

Borgen, Katrine, Wasteson, Yngvild, Kruse, Hilde, and Willems, Rob J. L.

Subjects
Microbiological research -- Analysis, Vancomycin -- Physiological aspects, Drug resistance in microorganisms -- Research, Enterococcus -- Genetic aspects, Genetic polymorphisms -- Research, Genomes -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on the vancomycin-resistant Enterococcus faecium isolates. The genetic relationship between these isolates and vancomycin-susceptible E. faecium isolates from Norwegian poultry has been investigated and the results are reported.

Published
2002

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