PLSDB: advancing a comprehensive database of bacterial plasmids

Abstract

Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.

Diversity and distribution of Type VI Secretion System gene clusters in bacterial plasmids

“…Finally, in dozens of these T6SS-harboring plasmids we identified genes mainly associated with chromosomes, such as rRNA, and this, added to the fact that most of them are megabases in size (~ 60% of the Mb size group had rRNA genes vs ~ 4% of the Kb size group), raised the question of whether they were in fact plasmids or another type of replicon. Recently, Schmartz et al (2022) 26 analyzed putative plasmids in terms of the presence of ribosomal genes to identify mislabelled sequences. Thus, some sequences initially considered in our study were filtered.…”

“…A total of 30,660 replicons, classified as plasmids, were obtained from the NCBI Refseq database ( https://www.ncbi.nlm.nih.gov/genome/browse/#!/plasmids/ ) in Sep-2021, and encompassed more than 20 bacterial phyla (Table S6 ). Since some NCBI sequences tagged as plasmids are mislabeled chromosomal sequences, we removed from our dataset those sequences that were not present in the PLSDB 26 , a curated database of bacterial plasmids fed from the NCBI nucleotide database. Some replicons of some genera presented sizes in megabases (e.g., Ralstonia solanacearum strain RS10 plasmid unnamed with ~ 2 Mb; Rhizobium phaseoli strain BS3 plasmid pBS3d with ~ 1.1 Mb).…”

Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis

“… Closest relatives were identified using the NCBI BLASTN suite and the megablast algorithm against the nr/nt database (Jan 16th 2022) The hits shown were selected by sorting the best 100 hits by first accession length (ascending), then percent identity (descending) and finally query cover (descending) The top three hits were selected. Plasmid replicon type was determined using PLSDB [ 39 ] …”

“…Further, the Kleborate (v2.0.0) tool was used to investigate potential Klebsiella -related virulence traits [ 38 ]. The PLSDB was used to identify plasmid replicon types [ 39 ] and BLASTN was used to identify closely related plasmids. To this end, the whole plasmid sequence was used as a query in a BLASTN (megablast) [ 40 ] search against NCBI nr/nr and the results sorted according to accession length (ascending), percent identity (descending) and finally query cover (descending).…”

Tools of the trade: plasmid repositories and standardized plasmid manipulation for molecular and synthetic biology

“…Indeed, the number of naturally occurring bacterial plasmids continues to grow rapidly with the advancement of new sequencing technologies. Currently, there are more than 34 000 bacterial plasmids listed in the NCBI Reference Sequence (RefSeq) database; which represents an almost twofold increase within the 2020–2021 period (Schmartz et al ., 2021 ). Plasmids vary enormously in size, DNA topology (e.g.…”