Evidence map›Paper›PMID 41578138›Full record

ArticleNature communications2026

Pangenome dynamics and population structure of the zoonotic pathogen Salmonella enterica serotype Hadar.

Kaitlin A Tagg, Arancha Peñil-Celis, Hattie E Webb, G Sean Stapleton, Zachary Ellison, Molly Leeper, Justin Y Kim, Mustafa Simmons, Glenn Tillman, Cong Li and 17 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

27 authors.

Kaitlin A Tagg *Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Arancha Peñil-Celis *Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas-Universidad de Cantabria, Santander, Spain. arancha.penil@unican.es.ORCID http://orcid.org/0000-0003-2295-1563
Hattie E WebbDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA. hwebb@cdc.gov.ORCID http://orcid.org/0000-0002-1190-7930
G Sean StapletonDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Zachary EllisonDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.ORCID http://orcid.org/0009-0001-5585-878X
Molly LeeperDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Justin Y KimDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Mustafa SimmonsFood Safety and Inspection Service, United States Department of Agriculture, Washington D.C, USA.
Glenn TillmanFood Safety and Inspection Service, United States Department of Agriculture, Washington D.C, USA.
Cong LiCenter for Veterinary Medicine, United States Food and Drug Administration, Laurel, USA.
Beth HarrisNational Animal Health Laboratory Network, Animal and Plant Health Inspection Services, U.S. Department of Agriculture, Ames, USA.
Brenda R Morningstar-ShawNational Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, USA.
Molly K SteeleDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Daniel MallalColorado Department of Public Health and Environment, Glendale, USA.
Shannon MatzingerColorado Department of Public Health and Environment, Glendale, USA.ORCID http://orcid.org/0000-0001-7910-4600
Kathy ManionMontana Public Health Laboratory, Helena, USA.
John HergertUtah Public Health Laboratory, Taylorsville, USA.
Jennifer M WagnerUtah Public Health Laboratory, Taylorsville, USA.ORCID http://orcid.org/0000-0002-3548-5904
Colin SchwensohnDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Joshua M BrandenburgDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Sheryl ShawFood Safety and Inspection Service, United States Department of Agriculture, Washington D.C, USA.
Katharine BenedictDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Jason P FolsterDivision of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
Uday DessaiFood Safety and Inspection Service, United States Department of Agriculture, Washington D.C, USA.ORCID http://orcid.org/0000-0001-6244-4633
Santiago Redondo-SalvoInstituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas-Universidad de Cantabria, Santander, Spain.ORCID http://orcid.org/0000-0003-0089-6030
M Pilar Garcillan-BarciaInstituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas-Universidad de Cantabria, Santander, Spain.ORCID http://orcid.org/0000-0001-7058-5428
Fernando de la CruzInstituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas-Universidad de Cantabria, Santander, Spain.ORCID http://orcid.org/0000-0003-4758-6857

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Genome, BacterialSalmonella entericaSalmonella Infections, AnimalZoonosesAnimalsPhylogenyPoultryPoultry DiseasesProphagesSerogroupUnited States

Identifiers

PMID41578138
PMCPMC12868874

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.