PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

Plasmids*/genetics ; Gene Transfer, Horizontal* ; Virulence Factors*/genetics ; Bacteria*/genetics ; Bacteria*/drug effects ; Drug Resistance, Bacterial*/genetics; Humans ; Databases, Genetic ; Genome, Bacterial

Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the 'One Health' approach, it is crucial to control the spread of plasmids carrying such genes. To achieve this, a comprehensive characterization of plasmids in pathogens is essential. Here we present the Plasmids in Pathogens Database (PIPdb), a pioneering resource that includes 792 964 plasmid segment clusters (PSCs) derived from 1 009 571 assembled genomes across 450 pathogenic species from 110 genera. To our knowledge, PIPdb is the first database specifically dedicated to plasmids in pathogenic bacteria, offering detailed multi-dimensional metadata such as collection date, geographical origin, ecosystem, host taxonomy, and habitat. PIPdb also provides extensive functional annotations, including plasmid type, insertion sequences, integron, oriT, relaxase, T4CP, virulence factors genes, heavy metal resistance genes and antibiotic resistance genes. The database features a user-friendly interface that facilitates studies on plasmids across diverse host taxa, habitats, and ecosystems, with a focus on those carrying antimicrobial resistance genes (ARGs). We have integrated online tools for plasmid identification and annotation from assembled genomes. Additionally, PIPdb includes a risk-scoring system for identifying potentially high-risk plasmids. The PIPdb web interface is accessible at https://nmdc.cn/pipdb.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

2021YFF0703805 National Key Research and Development Program of China; XDB0830000 Chinese Academy of Sciences; 2022YFC2602301 National Key Research and Development Program of China; 22193064 National Natural Science Foundation of China; SRPG22007 Self-supporting Program of Guangzhou National Laboratory

0 (Virulence Factors)

Date Created: 20241026 Date Completed: 20250108 Latest Revision: 20250116

20250117

PMC11701594

10.1093/nar/gkae952

39460620