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Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y, Katsura K, Kurokawa K, Oshima K, Hattori M, Parkhill J, Sebaihia M, Coulthurst SJ, Gotoh N, Thomson NR, Ewbank JJ, Hayashi T - Genome Biol Evol (2014)

Bottom Line: Naturally, it is found in many environmental niches, and is capable of infecting plants and animals.We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species.Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Research Organization, University of Miyazaki, JapanPresent address: Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Japan.

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Comparison of the gene contents of SM39 and Db11. (A) Venn diagram showing the numbers of conserved and strain-specific CDSs. (B) COG category-based functional analysis of each group of CDSs, the conserved and strain-specific CDSs. J: translation, ribosomal structure, and biogenesis; K: transcription; L: replication, recombination, and repair; D: cell cycle control, cell division chromosome partitioning; V: defense mechanisms; O: posttranslational modification, protein turnover, and chaperones; T: signal transduction mechanisms; M: cell wall/membrane/envelope biogenesis; U: intracellular trafficking, secretion, and vesicular transport; N: Cell motility; C: energy production and conversion; G: carbohydrate transport and metabolism; E: amino acid transport and metabolism; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; I: lipid transport and metabolism; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; R: general function prediction only; S: function unknown. (C) Conservation of each group of CDSs in four strains of other Serratia species (S. proteamaculans 568, S. odorifera DSM4582, S. plymuthica 4Rx13, and S. plymuthica AS9).
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evu160-F2: Comparison of the gene contents of SM39 and Db11. (A) Venn diagram showing the numbers of conserved and strain-specific CDSs. (B) COG category-based functional analysis of each group of CDSs, the conserved and strain-specific CDSs. J: translation, ribosomal structure, and biogenesis; K: transcription; L: replication, recombination, and repair; D: cell cycle control, cell division chromosome partitioning; V: defense mechanisms; O: posttranslational modification, protein turnover, and chaperones; T: signal transduction mechanisms; M: cell wall/membrane/envelope biogenesis; U: intracellular trafficking, secretion, and vesicular transport; N: Cell motility; C: energy production and conversion; G: carbohydrate transport and metabolism; E: amino acid transport and metabolism; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; I: lipid transport and metabolism; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; R: general function prediction only; S: function unknown. (C) Conservation of each group of CDSs in four strains of other Serratia species (S. proteamaculans 568, S. odorifera DSM4582, S. plymuthica 4Rx13, and S. plymuthica AS9).

Mentions: To extend the analysis of unique and shared genes between the two strains, we performed a clustering analysis of the SM39 and Db11 CDSs using an all-against-all BLASTP approach (outlined in supplementary fig. S1, Supplementary Material online). This showed that 3,970 genes (or gene families) were conserved in both strains with additional 860 SM39-specific and 728 Db11-specific genes (fig. 2A). Functional classification of these genes based on the Cluster of Orthologous Groups (COG) categories indicated that genes belonging to “category L (replication, recombination, and repair)” and “category V (defense mechanisms)” are more highly represented in SM39 than in Db11 (fig. 2B). These differences are largely attributable to the presence of more genes associated with lateral gene transfer in SM39 such as insertion sequence (IS) transposases and integrases (category L), and genes for restriction-modification systems and multidrug transport systems (category V). For example, SM39 carries a higher variety and number of IS elements: 18 compared with the 5 carried by Db11 (table 1). These IS elements were classified into 11 distinct types, nine of which represent novel IS elements. Eight types were found in SM39 and four in Db11, with only ISSe5 being shared by both isolates (supplementary table S3, Supplementary Material online). More prophages were also found in SM39 (seven) than in Db11 (only two), with none of the prophages and other integrative elements being shared by the two strains (table 1 and supplementary table S4, Supplementary Material online).Fig. 2.—


Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y, Katsura K, Kurokawa K, Oshima K, Hattori M, Parkhill J, Sebaihia M, Coulthurst SJ, Gotoh N, Thomson NR, Ewbank JJ, Hayashi T - Genome Biol Evol (2014)

Comparison of the gene contents of SM39 and Db11. (A) Venn diagram showing the numbers of conserved and strain-specific CDSs. (B) COG category-based functional analysis of each group of CDSs, the conserved and strain-specific CDSs. J: translation, ribosomal structure, and biogenesis; K: transcription; L: replication, recombination, and repair; D: cell cycle control, cell division chromosome partitioning; V: defense mechanisms; O: posttranslational modification, protein turnover, and chaperones; T: signal transduction mechanisms; M: cell wall/membrane/envelope biogenesis; U: intracellular trafficking, secretion, and vesicular transport; N: Cell motility; C: energy production and conversion; G: carbohydrate transport and metabolism; E: amino acid transport and metabolism; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; I: lipid transport and metabolism; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; R: general function prediction only; S: function unknown. (C) Conservation of each group of CDSs in four strains of other Serratia species (S. proteamaculans 568, S. odorifera DSM4582, S. plymuthica 4Rx13, and S. plymuthica AS9).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4231636&req=5

evu160-F2: Comparison of the gene contents of SM39 and Db11. (A) Venn diagram showing the numbers of conserved and strain-specific CDSs. (B) COG category-based functional analysis of each group of CDSs, the conserved and strain-specific CDSs. J: translation, ribosomal structure, and biogenesis; K: transcription; L: replication, recombination, and repair; D: cell cycle control, cell division chromosome partitioning; V: defense mechanisms; O: posttranslational modification, protein turnover, and chaperones; T: signal transduction mechanisms; M: cell wall/membrane/envelope biogenesis; U: intracellular trafficking, secretion, and vesicular transport; N: Cell motility; C: energy production and conversion; G: carbohydrate transport and metabolism; E: amino acid transport and metabolism; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; I: lipid transport and metabolism; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; R: general function prediction only; S: function unknown. (C) Conservation of each group of CDSs in four strains of other Serratia species (S. proteamaculans 568, S. odorifera DSM4582, S. plymuthica 4Rx13, and S. plymuthica AS9).
Mentions: To extend the analysis of unique and shared genes between the two strains, we performed a clustering analysis of the SM39 and Db11 CDSs using an all-against-all BLASTP approach (outlined in supplementary fig. S1, Supplementary Material online). This showed that 3,970 genes (or gene families) were conserved in both strains with additional 860 SM39-specific and 728 Db11-specific genes (fig. 2A). Functional classification of these genes based on the Cluster of Orthologous Groups (COG) categories indicated that genes belonging to “category L (replication, recombination, and repair)” and “category V (defense mechanisms)” are more highly represented in SM39 than in Db11 (fig. 2B). These differences are largely attributable to the presence of more genes associated with lateral gene transfer in SM39 such as insertion sequence (IS) transposases and integrases (category L), and genes for restriction-modification systems and multidrug transport systems (category V). For example, SM39 carries a higher variety and number of IS elements: 18 compared with the 5 carried by Db11 (table 1). These IS elements were classified into 11 distinct types, nine of which represent novel IS elements. Eight types were found in SM39 and four in Db11, with only ISSe5 being shared by both isolates (supplementary table S3, Supplementary Material online). More prophages were also found in SM39 (seven) than in Db11 (only two), with none of the prophages and other integrative elements being shared by the two strains (table 1 and supplementary table S4, Supplementary Material online).Fig. 2.—

Bottom Line: Naturally, it is found in many environmental niches, and is capable of infecting plants and animals.We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species.Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Research Organization, University of Miyazaki, JapanPresent address: Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Japan.

Show MeSH
Related in: MedlinePlus