<b>Shifting Perspective: </b><b><i>Helicobacter pylori</i></b><b> Plasmids Exhibit Unique Epidemiological and Genomic Features, Unlike other Stomach Bacteria, with Implications for Patient Pathology and Antimicrobial Resistance</b>
Creators: name: Alfaray, Ricky Indra
name: Saruuljavkhlan, Batsaikhan
name: Fauzia, Kartika Afrida
name: Torres, Roberto C
name: Tourrette, Elise
name: Thorell, Kaisa
name: Matsumoto, Takashi
name: Akada, Junko
name: Kryukov, Kirill A.
name: Nurkolis, Fahrul
name: Dewayani, Astri
name: Falush, Daniel
name: Miftahussurur, Muhammad
name: Yamaoka, Yoshio
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 320203
subject: Clinical microbiology
classificationCode: 310509
subject: Genomics
classificationCode: 310701
subject: Bacteriology
classificationCode: 420299
subject: Epidemiology not elsewhere classified

description: This dataset is open to provide detailed information about the study on <i>H. pylori</i> plasmids. The dataset contains supplementary materials and analysis resources essential for understanding the role of plasmids in <i>H. pylori </i>biology, antimicrobial resistance, and pathogenicity.<b>Supplemental Data</b><br>Appendix1_Supplementary_Information<br>This file includes supplementary tables and figures referenced in the main manuscript. It covers epidemiological data, genomic features of <i>H. pylori</i> plasmids, and clinical implications. These materials provide a deeper understanding of plasmid-associated phenomena in <i>H. pylori</i> populations.<br>Appendix2-H_pylori_Plasmid_WGS_and_Quality_Metadata<br>This dataset contains global metadata of <i>H. pylori </i>plasmid whole-genome sequencing (WGS) samples. It includes detailed quality evaluations (e.g., QUAST results), highlighting genomic accuracy, completeness, and assembly statistics. The data ensures robust genomic analysis of <i>H. pylori</i> plasmids.<br>Appendix3-Global_H.pylori_Genome_Metadata<br>Global sequence metadata for <i>H. pylori</i> strains, including strain accession numbers and source details. This dataset supports investigations of plasmid influence on <i>H. pylori</i> genomic characteristics.<br>Appendix4-Global_AST_or_AMR_Plasmid_Dataset<br>This dataset provides antimicrobial susceptibility profiles of <i>H. pylor</i>i strains carrying plasmids. It includes clinical metadata from multiple countries, enabling analyses of how plasmids contribute to antimicrobial resistance (AMR) phenotypes in <i>H. pylor</i>i.<br>Appendix5-Global_DSP_Plasmid_Dataset<br>Clinical metadata of patients with <i>H. pylori </i>infection, detailing diagnostic and pathological profiles. This dataset supports exploration of plasmid contributions to <i>H. pylori </i>pathogenicity and host-pathogen dynamics.<br>Appendix6-Stomach_Plasmid_Genome_Metadata<br>Global sequence metadata for plasmids from stomach-associated bacterial species, offering comparative insights into the ecological and genetic roles of plasmids in the stomach environment.<br>Appendix7-Global_Plasmid_Identification_Metadata<br>Metadata and clustering analysis results related to <i>H. pylor</i><i>i</i> plasmids. This dataset highlights plasmid distribution, genetic diversity, and classification, as well as species identification and lifestyle predictions of plasmids.<br>Appendix8-Plasmid_Annotation_Metadata<br>Genomic annotations of<i> H. pylori</i> plasmids generated using tools like RAST and Prokka. This dataset includes detailed information on gene functions, structural components, and other genomic elements, supporting investigations into plasmid biology and potential roles in pathogenesis.<br><b>Analysis Information</b>This section includes R scripts and bootstrap datasets used for statistical and significance analysis. The provided resources ensure reproducibility and transparency in plasmid-associated investigations.<br><b>Sequence Files of Plasmids</b>All identified plasmid sequences are provided as FASTA files. The file names correspond to the strain names of <i>H. pylori </i>from which the plasmids were identified. Additional information about each strain, including metadata and related analysis, can be found in the supplementary materials.<i>Note: </i>Additional files containing detailed plasmid element sequences or annotations are available upon request. Please contact the corresponding author for access or further inquiries.<br><b>Contact for Further Information</b>For additional details, contact: Prof. Yoshio Yamaoka, MD, PhD; Faculty of Medicine, Oita University, Japan<br>Email: yyamaoka@oita-u.ac.jp<br>Thank you very much.<br><br>Kind regards,authors