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

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.