Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes Article Swipe
Débora Satie Nagano
,
Itsuki Taniguchi
,
Tomoyuki Ono
,
Keiji Nakamura
,
Yasuhiro Gotoh
,
Tetsuya Hayashi
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1099/mgen.0.001135
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1099/mgen.0.001135
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.
Related Topics
Concepts
Plasmid
Biology
Genome
Genetics
Transposable element
Serratia marcescens
Horizontal gene transfer
Gene
Clade
Phylogenetics
Escherichia coli
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1099/mgen.0.001135
- OA Status
- gold
- Cited By
- 5
- References
- 45
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4388697893
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4388697893Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1099/mgen.0.001135Digital Object Identifier
- Title
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Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomesWork title
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articleOpenAlex work type
- Language
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enPrimary language
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2023Year of publication
- Publication date
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2023-11-15Full publication date if available
- Authors
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Débora Satie Nagano, Itsuki Taniguchi, Tomoyuki Ono, Keiji Nakamura, Yasuhiro Gotoh, Tetsuya HayashiList of authors in order
- Landing page
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https://doi.org/10.1099/mgen.0.001135Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.1099/mgen.0.001135Direct OA link when available
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Plasmid, Biology, Genome, Genetics, Transposable element, Serratia marcescens, Horizontal gene transfer, Gene, Clade, Phylogenetics, Escherichia coliTop concepts (fields/topics) attached by OpenAlex
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5Total citation count in OpenAlex
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2025: 3, 2024: 2Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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