In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

By A. Carattoli, E. Zankari, A. García-Fernández, Mette Voldby Larsen, Ole Lund, L. Villa, Frank Møller Aarestrup, Henrik Hasman. Antimicrobial Agents and Chemotherapy, 2014

4,096 citations recorded by the source corpus.

Subfields: Food Science, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/0651de08ebb8b02f39da45f5098f18b575ef7273

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In Food Science

1. James Robertson
2. John H. E. Nash
3. Alla L. Lapidus
4. Mark B. Schultz
5. Kathryn E. Holt

In Molecular Biology

1. Kathryn E. Holt
2. John H. E. Nash
3. James Robertson
4. Alla L. Lapidus
5. Dmitry Antipov
6. Andreas Keller
7. Christina Backes
8. Valentina Galata

In Plant Science

1. John H. E. Nash
2. James Robertson
3. Kathryn E. Holt
4. Simon R. Harris
5. Andrew J. Page
6. Dmitry Antipov
7. Julian Parkhill
8. Pavel A. Pevzner

Citations in the corpus

• PLSDB: a resource of complete bacterial plasmids (2018, methodology): “Using PlasmidFinder 5452 records (39.5”
• MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies (2018, methodology): “Numerous typing schemes have been developed for plasmids [7, 11, 13] but replicon typing has served as the standard method for categorizing plasmids based on the DNA sequences responsible for replication of the plasmid [4, 7, 11, 14].”
• plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data (2016, methodology): “Carattoli et al. (2014) developed PlasmidFinder software for detecting and classifying variants of known plasmids based on their similarity with plasmids present in plasmid databases. However, PlasmidFinder is unable to identify novel plasmids that have no significant similarities to known plasmids.”
• PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures (2018, methodology): “Another simple approach is implemented in the PlasmidFinder (25), which is a web-based program aimed at identifying plasmid replicons in bacterial genome assemblies.”
• ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads (2017, methodology): “ARG-ANNOT, CARD, PlasmidFinder, ResFinder, VFDB, and the SRST2 version of ARG-ANNOT are currently available.”
• Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health (2015, background): “Gene databases analyzed were AMR alleles [ARG-Annot (70)], plasmid replicons [PlasmidFinder (59)], and virulence andwzi alleles [K.”