Linear plasmids in Klebsiella and other Enterobacteriaceae

Hawkey, Jane; Cottingham, Hugh; Tokolyi, Alex; Wick, Ryan R.; Judd, Louise M.; Cerdeira, Louise; Garcia, Doroti de Oliveira; Wyres, Kelly L.; Holt, Kathryn E.

doi:10.1099/mgen.0.000807

Cited by 4 publications

(2 citation statements)

References 54 publications

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“…Although we were unable to determine the exact terminal sequences of their genomes, a terminal inverted sequence of at least 490 bp was identified. Moreover, the two plasmids showed >90 % nucleotide sequence identity with the linear plasmids previously identified in Klebsiella and other Enterobacteriaceae [ 37 ].…”

Section: Resultsmentioning

confidence: 95%

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Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes

Nagano,

Taniguchi,

Ono

et al. 2023

Microbial Genomics

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Plasmids play important roles in bacterial genome diversification. In the Serratia marcescens complex (SMC), a notable contribution of plasmids to genome diversification was also suggested by our recent analysis of >600 draft genomes. As accurate analyses of plasmids in draft genomes are difficult, in this study we analysed 142 closed genomes covering the entire complex, 67 of which were obtained in this study, and identified 132 plasmids (1.9–244.4 kb in length) in 77 strains. While the average numbers of plasmids in clinical and non-clinical strains showed no significant difference, strains belonging to clade 2 (one of the two hospital-adapted lineages) contained more plasmids than the others. Pangenome analysis revealed that of the 28 954 genes identified, 12.8 % were plasmid-specific, and 1.4 % were present in plasmids or chromosomes depending on the strain. In the latter group, while transposon-related genes were most prevalent (31.4 % of the function-predicted genes), genes related to antimicrobial resistance and heavy metal resistance accounted for a notable proportion (22.7 %). Mash distance-based clustering separated the 132 plasmids into 23 clusters and 50 singletons. Most clusters/singletons showed notably different GC contents compared to those of host chromosomes, suggesting their recent or relatively recent appearance in the SMC. Among the 23 clusters, 17 were found in only clinical or only non-clinical strains, suggesting the possible preference of their distribution on the environmental niches of host strains. Regarding the host strain phylogeny, 16 clusters were distributed in two or more clades, suggesting their interclade transmission. Moreover, for many plasmids, highly homologous plasmids were found in other species, indicating the broadness of their potential host ranges, beyond the genus, family, order, class or even phylum level. Importantly, highly homologous plasmids were most frequently found in Klebsiella pneumoniae and other species in the family Enterobacteriaceae , suggesting that this family, particularly K. pneumoniae , is the main source for plasmid exchanges with the SMC. These results highlight the power of closed genome-based analysis in the investigation of plasmids and provide important insights into the nature of plasmids distributed in the SMC.

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Section: Resultsmentioning

confidence: 95%

“…Among the 24 untypeable plasmids, 13 were small plasmids (1.9-5.1 kb), but the remaining 11 ranged from 13.9 to 139.9 kb in size. They included the two linear plasmids, which probably use a 5′ terminus-binding protein as a primer for replication [37,38]. The MOB types of 112 plasmids were determined by MOB-Typer.…”

Section: Replicon and Mob Types Of Plasmidsmentioning

confidence: 99%

Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes

Nagano,

Taniguchi,

Ono

et al. 2023

Microbial Genomics

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Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing

Suzuki

Hashimoto

Hirabayashi

et al. 2023

Methods in Molecular Biology

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Plassembler: an automated bacterial plasmid assembly tool

et al. 2023

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Summary With recent advances in sequencing technologies, it is now possible to obtain near-perfect complete bacterial chromosome assemblies cheaply and efficiently by combining a long-read-first assembly approach with short-read polishing. However, existing methods for assembling bacterial plasmids from long-read-first assemblies often misassemble or even miss bacterial plasmids entirely and accordingly require manual curation. Plassembler was developed to provide a tool that automatically assembles and outputs bacterial plasmids using a hybrid assembly approach. It achieves increased accuracy and computational efficiency compared to the existing gold standard tool Unicycler by removing chromosomal reads from the input read sets using a mapping approach. Availability Plassembler is implemented in Python and is installable as a bioconda package using ‘conda install -c bioconda plassembler’. The source code is available on GitHub at https://github.com/gbouras13/plassembler. The full benchmarking pipeline can be found at https://github.com/gbouras13/plassembler_simulation_benchmarking, while the benchmarking input FASTQ and output files can be found at https://doi.org/10.5281/zenodo.7996690. Supplementary information Supplementary data are available at Bioinformatics online.

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Linear plasmids in Klebsiella and other Enterobacteriaceae

Abstract: Linear plasmids are extrachromosomal DNA elements that have been found in a small number of bacterial species. To date, the only linear plasmids described in the family Enterobacteriaceae belong to Salmonella , first found in Salmonella enterica Typhi.… Show more

Cited by 4 publications

References 54 publications

Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes

Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes

Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing

Plassembler: an automated bacterial plasmid assembly tool

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