Genomic characterization and sub-clustering of Escherichia coli clonal complex 38 reveal host associated genetic markers

Louise Roer, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark. loro@ssi.dk.
Astrid Rasmussen, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Frank Hansen, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Lars E. Christoffersen, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Raphael Sieber, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Flemming Scheutz, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Rene S. Hendriksen, Reseach group Global Capacity building, National Food Institute, Technical University of Denmark, Kgs, Lyngby, Denmark.
Brian D. Johnston, Minneapolis Veterans Affairs Health Care System, Minneapolis, MN, USA.
James R. Johnson, Minneapolis Veterans Affairs Health Care System, Minneapolis, MN, USA.
Barbara J. Holzknecht, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Lillian Søes, Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.
Kristian Schønning, Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
Dennis B. Holmgaard, Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark.
Ulrik S. Justesen, Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.
Claus Østergaard, Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark.
Turid S. Søndergaard, Department of Clinical Microbiology, Sønderjylland Hospital, Aabenraa, Denmark.
Marc T. Nielsen, Department of Clinical Diagnostics, Esbjerg and Grindsted Hospital, Esbjerg, Denmark.
Mikala Wang, Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark.
Hans L. Nielsen, Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.
Sam Abraham, European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mobile Elements and Plasmids (ESGMAP), Basel, Switzerland.
Daniel E. Park, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
Maliha Aziz, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
Lance B. Price, European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mobile Elements and Plasmids (ESGMAP), Basel, Switzerland.
Anette M. Hammerum, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Henrik Hasman, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Marc Stegger, European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mobile Elements and Plasmids (ESGMAP), Basel, Switzerland.

Document Type

Journal Article

Publication Date

1-26-2026

Journal

Communications medicine

DOI

10.1038/s43856-026-01402-2

Abstract

BACKGROUND: Escherichia coli clonal complex 38 (CC38) is a genetically diverse lineage increasingly linked to antimicrobial resistance and extraintestinal infections in humans. Despite its clinical and epidemiological relevance, its population structure, zoonotic potential, and ecological associations remain poorly understood. METHODS: We analyzed 242 human E. coli CC38 bloodstream isolates collected through Danish national surveillance, 83 isolates from food and production animals, and 2313 international genomes to investigate host associations and transmission dynamics. Phylogenetic reconstruction, Bayesian host prediction based on mobile genetic elements, and statistical testing of plasmid-host associations were used to delineate population structure and identify potential host-associated markers. RESULTS: Here we show that Danish CC38 isolates belong to multiple sub-lineages, with no evidence of foodborne outbreaks and limited hospital transmission. Bayesian host prediction supports a poultry origin for several distinct human sub-lineages. Global analyses of 2638 genomes reveal two major clusters: a poultry-associated Cluster I and a predominantly human-associated Cluster II, which subdivides into eight sub-lineages with distinct host, resistance, and virulence profiles. Two small plasmids, ColRNAI and Col(MG828), are strongly enriched in poultry and livestock isolates but largely absent from human-associated sub-clusters, indicating their value as host-associated genetic markers. CONCLUSIONS: Our findings refine the phylogenetic structure of E. coli CC38 and identify plasmid markers that may enhance genomic surveillance of zoonotic transmission. These results highlight the importance of a One Health approach to monitor antimicrobial resistance across human, food, and animal reservoirs. Together, these insights support data-driven One Health surveillance and intervention strategies.

Department

Environmental and Occupational Health

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