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Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli
Published on: March 24, 2023
PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and
Qianhui Zhu1,2, Qi Chen1,3, Shenghan Gao1,2
1Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Abstract:
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.
Insights
The Plasmids in Pathogens Database (PIPdb) is a new resource for studying plasmids in pathogenic bacteria. It helps track genes for antibiotic resistance and virulence, crucial for a
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Plasmids are mobile genetic elements that can carry resistance and virulence genes, facilitating their spread among pathogens.
- Controlling plasmid dissemination is vital for public health under the 'One Health' initiative.
- Comprehensive characterization of plasmids in pathogens is essential for effective control strategies.
Purpose of the Study:
- To introduce the Plasmids in Pathogens Database (PIPdb), a novel resource for comprehensive plasmid analysis.
- To provide a centralized platform for detailed metadata and functional annotations of plasmids from pathogenic bacteria.
- To facilitate research on plasmid epidemiology, evolution, and the spread of antimicrobial resistance genes (ARGs).
Main Methods:
- Curated a large dataset of 792,964 plasmid segment clusters (PSCs) from 1,009,571 assembled genomes.
- Collected multi-dimensional metadata including geographical origin, host taxonomy, and habitat.
- Performed extensive functional annotations for plasmid types, ARGs, virulence factors, and mobile genetic elements.
Main Results:
- PIPdb is the first database dedicated to plasmids in pathogenic bacteria.
- The database contains detailed information on plasmids from 450 species across 110 genera.
- Includes user-friendly tools for plasmid identification, annotation, and risk assessment.
Conclusions:
- PIPdb serves as a pioneering resource for understanding plasmid dynamics in pathogens.
- Facilitates research on the spread of ARGs and virulence factors.
- Supports a 'One Health' approach by enabling better characterization and control of high-risk plasmids.
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