Abstract
The bacterial accessory genome, comprised of plasmids, phages, and other mobile elements, underpins the adaptability of bacterial populations. Pangenome (core and accessory) analysis of pathogens can reveal epidemiological relatedness missed by using core-genome methods alone. Employing a k-mer-based Jaccard Index approach to compute pangenome relatedness, we explore the population structure and epidemiology of Salmonella enterica serotype Hadar (Hadar), an emerging zoonotic pathogen in the United States (U.S.) linked to both commercial and backyard poultry. A total of 3384 U.S. Hadar genomes collected between 1990 and 2023 are analyzed here. Hadar populations underwent substantial shifts between 2019 and 2020 in the U.S., driven by the expansion of a lineage carrying a previously uncommon prophage-like element. Phylogenetic and pangenomic relatedness, coupled with epidemiological data, suggest this lineage emerged from extant populations circulating in commercial poultry, with subsequent dissemination into backyard poultry environments. We demonstrate the utility of pangenomic approaches for mapping vertical and horizontal diversity and informing complex dynamics of zoonotic bacterial pathogens.
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Data availability
The authors declare that all genomic data supporting the findings of this study are publicly available through NCBI and Enterobase using accession numbers listed within the paper and its supplementary information files available through Figshare. Epidemiological data is available within supplementary information files. Some human patient information collected as part of routine public health surveillance or through supplementary standardized questionnaires are not publicly available due to data privacy laws; deidentified data are available on request by contacting pulsenet@cdc.gov, per data sharing policies. Source data are provided with this paper.
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Acknowledgements
The authors would like to acknowledge state and local public health departments and laboratories for isolation and sequencing of Hadar genomes included in this analysis. The authors thank FDA colleagues Olgica Ceric, Beilei Ge, Claudine Kabera, as well as University of Minnesota Professor Timothy Johnson, for their valuable expertise. This work was supported by the Centers for Disease Control and Prevention (Contract No. 75D30123P18303 to FdlC). This work was also supported by the Spanish Ministry of Science and Innovation MCIN/AEI/10.13039/501100011033 (PID2020-117923GB-I00 to FdlC and MPGB). The views expressed in this article are those of the authors and do not necessarily reflect the official policy of the Agencies within the U.S. Department of Health and Human Services (CDC, FDA) and the U.S. Department of Agriculture (FSIS, APHIS), or the U.S. Government. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Health and Human Services or the U.S. Department of Agriculture.
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K.A.T., A.P.C., H.E.W., G.S.S., M.K.S., K.B., M.P.G.B. and F.dlC.–Conceptualization. K.A.T., A.P.C., H.E.W., G.S.S., Z.E., M.L., J.Y.K., M.S., C.L., B.H., B.R.M.S., D.M., S.M., K.M., J.H., J.M.W., J.M.B. and K.B.–Data collection. K.A.T., A.P.C., H.E.W., G.S.S., M.S., C.L., B.H., B.R.M.S., K.B. and U.D.–Data curation. K.A.T., A.P.C., H.E.W., M.K.S., S.R.S., M.P.G.B. and Fdl.C.–Methodology. K.A.T., A.P.C., H.E.W., M.K.S., S.R.S., and M.P.G.B.–Analysis. K.A.T., A.P.C., H.E.W., M.K.S., S.R.S., M.P.G.B. and Fdl.C.–Visualization. K.A.T., A.P.C., H.E.W., G.S.S., K.B., M.P.G.B. and Fdl.C.– Writing - original draft. K.A.T., A.P.C., H.E.W., G.S.S., Z.E., M.L., J.Y.K., M.S., G.T., C.L., B.H., B.R.M.S., M.K.S., D.M., S.M., K.M., J.H., J.M.W., C.S., J.M.B., S.S., K.B., J.P.F., U.D., S.R.S., M.P.G.B. and Fdl.C.–Writing - review and editing. All authors read and approved the final manuscript.
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Tagg, K.A., Peñil-Celis, A., Webb, H.E. et al. Pangenome dynamics and population structure of the zoonotic pathogen Salmonella enterica serotype Hadar. Nat Commun (2026). https://doi.org/10.1038/s41467-025-68026-3
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DOI: https://doi.org/10.1038/s41467-025-68026-3
