On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data

por Arredondo-Alonso, Sergio, Willems, Rob J., van Schaik, Willem, Schürch, Anita C.
Publicado 2017

Conditionally essential genes for survival during starvation in Enterococcus faecium E745

por de Maat, Vincent, Arredondo-Alonso, Sergio, Willems, Rob J. L., van Schaik, Willem
Publicado 2020

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals

por Arredondo-Alonso, Sergio, Top, Janetta, Corander, Jukka, Willems, Rob J. L., Schürch, Anita C.
Publicado 2021

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

por Paganini, Julian A., Plantinga, Nienke L., Arredondo-Alonso, Sergio, Willems, Rob J. L., Schürch, Anita C.
Publicado 2021

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

por Tonkin-Hill, Gerry, Gladstone, Rebecca A., Pöntinen, Anna K., Arredondo-Alonso, Sergio, Bentley, Stephen D., Corander, Jukka
Publicado 2023

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

por Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, Schürch, Anita C
Publicado 2020

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium

por Top, Janetta, Arredondo-Alonso, Sergio, Schürch, Anita C., Puranen, Santeri, Pesonen, Maiju, Pensar, Johan, Willems, Rob J. L., Corander, Jukka
Publicado 2020

A high-throughput multiplexing and selection strategy to complete bacterial genomes

por Arredondo-Alonso, Sergio, Pöntinen, Anna K, Cléon, François, Gladstone, Rebecca A, Schürch, Anita C, Johnsen, Pål J, Samuelsen, Ørjan, Corander, Jukka
Publicado 2021

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

por Arredondo-Alonso, Sergio, Rogers, Malbert R. C., Braat, Johanna C., Verschuuren, Tess D., Top, Janetta, Corander, Jukka, Willems, Rob J. L., Schürch, Anita C.
Publicado 2018

Corrigendum: mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

por Arredondo-Alonso, Sergio, Rogers, Malbert R. C., Braat, Johanna C., Verschuuren, Tess D., Top, Janetta, Corander, Jukka, Willems, Rob J. L., Schürch, Anita C.
Publicado 2019

Mge-cluster: a reference-free approach for typing bacterial plasmids

por Arredondo-Alonso, Sergio, Gladstone, Rebecca A, Pöntinen, Anna K, Gama, João A, Schürch, Anita C, Lanza, Val F, Johnsen, Pål Jarle, Samuelsen, Ørjan, Tonkin-Hill, Gerry, Corander, Jukka
Publicado 2023

Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal...

por Verschuuren, T D, van Hout, D, Arredondo-Alonso, S, Fluit, A C, Reuland, E A, Top, J, Schürch, A C, Bosch, T, Bonten, M J M, Kluytmans, J A J W, Willems, R J L
Publicado 2021

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

por Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J. C., Rogers, M. R. C., van Schaik, W., Kaski, S., Willems, R. J. L., Corander, J., Schürch, A. C.
Publicado 2020

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

por 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
Publicado 2021

Evolutionary and functional history of the Escherichia coli K1 capsule

por Arredondo-Alonso, Sergio, Blundell-Hunter, George, Fu, Zuyi, Gladstone, Rebecca A., Fillol-Salom, Alfred, Loraine, Jessica, Cloutman-Green, Elaine, Johnsen, Pål J., Samuelsen, Ørjan, Pöntinen, Anna K., Cléon, François, Chavez-Bueno, Susana, De la Cruz, Miguel A., Ares, Miguel A., Vongsouvath, Manivanh, Chmielarczyk, Agnieszka, Horner, Carolyne, Klein, Nigel, McNally, Alan, Reis, Joice N., Penadés, José R., Thomson, Nicholas R., Corander, Jukka, Taylor, Peter W., McCarthy, Alex J.
Publicado 2023