Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut

Marta Rozwandowicz; Manal AbuOun; Patricia Alba; Muna F. Anjum; Magdalena Zając; Michael S.M. Brouwer; Stefan Börjesson; Manuela Caniça; Virginia Carfora; Elena L. Diaconu; Benoît Doublet; Daisy Gates; Jens-Andre Hammerl; Henrik Hasman; Thomas H.A. Haverkamp; Antoni P.A. Hendrickx; Oskar K. Lindsjö; Vera Manageiro; Soleveig S. Mo; Mattias Myrenås; Kristina Rizzardi; Jannice Schau Slettemeås; Marianne Sunde; Engeline van Duijkeren; Angela H.A.M. van Hoek; Kees T. Veldman; Arkadiusz Bomba; Emma Nord; Pieter-Jan Ceyssens; Joost Hordijk

doi:10.1099/mgen.0.001535

Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut

Marta Rozwandowicz
, Manal AbuOun
, Patricia Alba
, Muna F. Anjum
, Magdalena Zając
, Michael S.M. Brouwer
, Stefan Börjesson
, Manuela Caniça
, Virginia Carfora
, Elena L. Diaconu
, Benoît Doublet
, Daisy Gates
, Jens-Andre Hammerl
, Henrik Hasman
, Thomas H.A. Haverkamp
, Antoni P.A. Hendrickx
, Oskar K. Lindsjö
, Vera Manageiro
, Soleveig S. Mo
, Mattias Myrenås

Kristina Rizzardi, Jannice Schau Slettemeås, Marianne Sunde, Engeline van Duijkeren, Angela H.A.M. van Hoek, Kees T. Veldman, Arkadiusz Bomba, Emma Nord, Pieter-Jan Ceyssens, Joost Hordijk

School of Health Sciences, Örebro University, Örebro, Sweden
extern
Animal and Plant Health Agency (APHA), Weybridge, UK
Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri” (IZSLT), Rome, Italy
National Veterinary Research Institute (PIWET), Pulawy, Poland
Swedish Veterinary Agency (SVA), Uppsala, Sweden
National Institute of Health Doctor Ricardo Jorge (INSA), Lisboa, Portugal
INRAE, Université de Tours, ISP, F-37380, Nouzilly, France
German Federal Institute for Risk Assessment (BfR), Berlin, Germany
Statens Serum Institut (SSI), Copenhagen, Denmark
Norwegian Veterinary Institute (NVI), Ås, Norway
National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
Public Health Agency of Sweden (FOHM), Solna, Sweden
Wageningen Bioveterinary Research (WBVR), part of Wageningen University and Research, Lelystad, The Netherlands
Unit of Human Bacterial Diseases, Sciensano, Elsene, Belgium

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

This manuscript presents the phylogeny and conservation of IncK2 plasmids in Europe. It also provides insights into genetic traits responsible for IncK2 plasmids and its Escherichia coli host adaptation to the chicken gut. Fifty-eight E. coli isolates from nine European countries were sequenced using Illumina and Nanopore technology. Genetic analyses were performed to determine the relatedness of IncK2 plasmids and their E. coli hosts from poultry (80% of the total) and other sources. To analyse genetic traits associated with E. coli and IncK2 plasmid from chicken origin, a genome-wide association study (GWAS) was performed. The phylogenetic analysis of IncK2 plasmids revealed conservation across sources and countries of isolation. GWAS revealed multiple genes associated with IncK2 plasmids or its E. coli host from chicken origin. The predicted functions of these genes can indicate a selective advantage in the chicken gut, and that IncK2 plasmids are adapted to the physiological environment of the chicken gut.

Original language	English
Article number	001535
Journal	Microbial genomics
Volume	12
Issue number	3
DOIs	https://doi.org/10.1099/mgen.0.001535
Publication status	Published - 13 Mar 2026
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2026 National Institute for Public Health and the Environment. All rights reserved.

Funding

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 773830. M.F.A. received co-funding from the Veterinary Medicines Directorate, UK, project VM0533. For NVI, co-funding was received from the Norwegian Research Council. Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri (IZSLT), Italy, was also partially supported by the European Union funding from the NextGeneration EU-MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases (Project No. PE00000007, INF-ACT, PE13 INF-ACT, Node 3 and Node 4). Research at the National Veterinary Research Institute (PIWet), Poland, was also partially supported by the Polish Ministry of Education and Science from the funds for science in the years 2018–2022 allocated for the implementation of a co-financed international project.

Funders	Funder number
Istituto Zooprofilattico Sperimentale del Lazio e della Toscana
INF-ACT
Norges Forskningsråd
Państwowy Instytut Weterynaryjny - Państwowy Instytut Badawczy
Ministerstwo Edukacji i Nauki
PIWet
Horizon 2020 Framework Programme	773830
Veterinary Medicines Directorate	VM0533
European Commission	PE00000007

Keywords

IncK2
genome-wide association study (GWAS)
plasmid
whole-genome sequencing

Access to Document

10.1099/mgen.0.001535Licence: CC BY

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001535

Cite this

Rozwandowicz, M., AbuOun, M., Alba, P., Anjum, M. F., Zając, M., Brouwer, M. S. M., Börjesson, S., Caniça, M., Carfora, V., Diaconu, E. L., Doublet, B., Gates, D., Hammerl, J.-A., Hasman, H., Haverkamp, T. H. A., Hendrickx, A. P. A., Lindsjö, O. K., Manageiro, V., Mo, S. S., ... Hordijk, J. (2026). Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut. Microbial genomics, 12(3), Article 001535. https://doi.org/10.1099/mgen.0.001535

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title = "Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut",

abstract = "This manuscript presents the phylogeny and conservation of IncK2 plasmids in Europe. It also provides insights into genetic traits responsible for IncK2 plasmids and its Escherichia coli host adaptation to the chicken gut. Fifty-eight E. coli isolates from nine European countries were sequenced using Illumina and Nanopore technology. Genetic analyses were performed to determine the relatedness of IncK2 plasmids and their E. coli hosts from poultry (80\% of the total) and other sources. To analyse genetic traits associated with E. coli and IncK2 plasmid from chicken origin, a genome-wide association study (GWAS) was performed. The phylogenetic analysis of IncK2 plasmids revealed conservation across sources and countries of isolation. GWAS revealed multiple genes associated with IncK2 plasmids or its E. coli host from chicken origin. The predicted functions of these genes can indicate a selective advantage in the chicken gut, and that IncK2 plasmids are adapted to the physiological environment of the chicken gut.",

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Rozwandowicz, M, AbuOun, M, Alba, P, Anjum, MF, Zając, M, Brouwer, MSM, Börjesson, S, Caniça, M, Carfora, V, Diaconu, EL, Doublet, B, Gates, D, Hammerl, J-A, Hasman, H, Haverkamp, THA, Hendrickx, APA, Lindsjö, OK, Manageiro, V, Mo, SS, Myrenås, M, Rizzardi, K, Schau Slettemeås, J, Sunde, M, van Duijkeren, E, van Hoek, AHAM, Veldman, KT, Bomba, A, Nord, E, Ceyssens, P-J & Hordijk, J 2026, 'Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut', Microbial genomics, vol. 12, no. 3, 001535. https://doi.org/10.1099/mgen.0.001535

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AU - Rozwandowicz, Marta

AU - AbuOun, Manal

AU - Alba, Patricia

AU - Anjum, Muna F.

AU - Zając, Magdalena

AU - Brouwer, Michael S.M.

AU - Börjesson, Stefan

AU - Caniça, Manuela

AU - Carfora, Virginia

AU - Diaconu, Elena L.

AU - Doublet, Benoît

AU - Gates, Daisy

AU - Hammerl, Jens-Andre

AU - Hasman, Henrik

AU - Haverkamp, Thomas H.A.

AU - Hendrickx, Antoni P.A.

AU - Lindsjö, Oskar K.

AU - Manageiro, Vera

AU - Mo, Soleveig S.

AU - Myrenås, Mattias

AU - Rizzardi, Kristina

AU - Schau Slettemeås, Jannice

AU - Sunde, Marianne

AU - van Duijkeren, Engeline

AU - van Hoek, Angela H.A.M.

AU - Veldman, Kees T.

AU - Bomba, Arkadiusz

AU - Nord, Emma

AU - Ceyssens, Pieter-Jan

AU - Hordijk, Joost

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AB - This manuscript presents the phylogeny and conservation of IncK2 plasmids in Europe. It also provides insights into genetic traits responsible for IncK2 plasmids and its Escherichia coli host adaptation to the chicken gut. Fifty-eight E. coli isolates from nine European countries were sequenced using Illumina and Nanopore technology. Genetic analyses were performed to determine the relatedness of IncK2 plasmids and their E. coli hosts from poultry (80% of the total) and other sources. To analyse genetic traits associated with E. coli and IncK2 plasmid from chicken origin, a genome-wide association study (GWAS) was performed. The phylogenetic analysis of IncK2 plasmids revealed conservation across sources and countries of isolation. GWAS revealed multiple genes associated with IncK2 plasmids or its E. coli host from chicken origin. The predicted functions of these genes can indicate a selective advantage in the chicken gut, and that IncK2 plasmids are adapted to the physiological environment of the chicken gut.

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KW - genome-wide association study (GWAS)

KW - plasmid

KW - whole-genome sequencing

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DO - 10.1099/mgen.0.001535

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SN - 2057-5858

VL - 12

JO - Microbial genomics

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M1 - 001535

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Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut

Abstract

Bibliographical note

Funding

Keywords

Access to Document

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