In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Open accessAbstract
In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae . These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from www.pubmlst.org and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of Salmonella enterica serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49 S . Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens.
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- Authors
- Carattoli, A., Zankari, E., García-Fernández, A., Voldby Larsen, M., Lund, O., Villa, L., Møller Aarestrup, F., & Hasman, H.
- Affiliations
- Istituto Superiore di Sanità (IT)
- Technical University of Denmark (DK)
- Danish Technical University, Center for Biological Sequence Analysis, Department of Systems Biology, Lyngby, Denmark
- Danish Technical University, National Food Institute, Division for Epidemiology and Microbial Genomics, Lyngby, Denmark
- Venue
- Antimicrobial Agents and Chemotherapy
- Publisher
- American Society for Microbiology
- Published
- 2014-07
- Volume
- 58
- Issue
- 7
- Pages
- 3895-3903
- ISSN
- 0066-4804 (ISSN-L)
- 1098-6596
- PMC
- PMC4068535
- OpenAlex
- W2143325926
- Semantic Scholar
- 0651de08ebb8b02f39da45f5098f18b575ef7273
- Cited by
- 4,877
- References
- 35
- Citations by year
- 2026: 594 · 2025: 632 · 2024: 596 · 2023: 561 · 2022: 593 · 2021: 544 · 2020: 466 · 2019: 317 · 2018: 243 · 2017: 173 · 2016: 109 · 2015: 38 · 2014: 8 · 2012: 2
- FWCI
- 50.00
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Antimicrobial Agents and Chemotherapy (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Life Sciences › Agricultural and Biological Sciences › Food Science › Salmonella and Campylobacter epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Keywords
- plasmid detection, plasmid typing, Enterobacteriaceae, Salmonella typhimurium, plasmid replicons, antimicrobial resistance, multidrug-resistant bacteria, web-based tool, plasmid database, draft genome sequence
- MeSH terms
- Computer Simulation, Enterobacteriaceae, Plasmids, Replicon, Reproducibility of Results, Genome, Bacterial, Internet, Drug Resistance, Bacterial, Databases, Genetic, Multilocus Sequence Typing
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