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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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The chromosomes of Serratia marcescens strains SM39 and Db11. (A) Circular maps of the SM39 and Db11 chromosomes. From the outside in, the first circle shows the nucleotide sequence positions (in Mb), and the second circle shows the locations of strain-specific regions of ≥5 kb (purple: prophages and integrative elements; red: others) with an indication of their features and/or encoded products/functions (PP, prophages; IE, integrative elements; EPS, exopolysaccharide biosynthesis). The third and fourth circles show CDSs transcribed clockwise and anticlockwise, respectively (yellow: CDSs conserved in both strains, blue: CDSs specific to one strain), the fifth circle the rRNA operons, the sixth circle the G+C content, and the seventh circle the GC skew. (B) Dot plot presentation of DNA sequence homologies between the chromosomes. Locations of ori and seven rRNA operons (rrn1–rrn7) are indicated.
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evu160-F1: The chromosomes of Serratia marcescens strains SM39 and Db11. (A) Circular maps of the SM39 and Db11 chromosomes. From the outside in, the first circle shows the nucleotide sequence positions (in Mb), and the second circle shows the locations of strain-specific regions of ≥5 kb (purple: prophages and integrative elements; red: others) with an indication of their features and/or encoded products/functions (PP, prophages; IE, integrative elements; EPS, exopolysaccharide biosynthesis). The third and fourth circles show CDSs transcribed clockwise and anticlockwise, respectively (yellow: CDSs conserved in both strains, blue: CDSs specific to one strain), the fifth circle the rRNA operons, the sixth circle the G+C content, and the seventh circle the GC skew. (B) Dot plot presentation of DNA sequence homologies between the chromosomes. Locations of ori and seven rRNA operons (rrn1–rrn7) are indicated.

Mentions: The chromosomes of SM39 and Db11 are similar in size, 5,225,577 and 5,113,802 bp, respectively, and gene number (table 1 and fig. 1A). SM39 carries two plasmids, pSMC1 (41,517 bp) and pSMC2 (58,929 bp). No extrachromosomal elements were found in Db11. Overall, the chromosomes of the two strains are highly conserved and essentially collinear, except for a large inversion of the oriC region flanked by rRNA operons (fig. 1B). Surprisingly for members of the same species, the ANI between the conserved genomic regions of the two strains (4,391 kb) is only 95.1%. This can be compared with a figure of 97.0% for the ANI between two distantly related members of E. coli, strains K-12 and E2348/69. Despite this, the 16S rRNA genes of the two strains show 99.4% sequence identity, consistent with DB11 and SM39 being members of the same species (Kim et al. 2014; see also supplementary fig. S3, Supplementary Material online). Further with a criterion of ≤90% nucleotide sequence identity and ≥5 kb length, we identified 44 genomic regions specific to SM39, totaling 628 kb (12% of the genome), and 39 specific regions (447 kb or 8.7% of the genome) for Db11 (fig. 1A; see also supplementary tables S1 and S2, Supplementary Material online). The relatively low ANI value for the two S. marcescens strains and the considerable amount of isolate-specific sequences may reflect the diversity of niches that this species can occupy.Fig. 1.—


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)

The chromosomes of Serratia marcescens strains SM39 and Db11. (A) Circular maps of the SM39 and Db11 chromosomes. From the outside in, the first circle shows the nucleotide sequence positions (in Mb), and the second circle shows the locations of strain-specific regions of ≥5 kb (purple: prophages and integrative elements; red: others) with an indication of their features and/or encoded products/functions (PP, prophages; IE, integrative elements; EPS, exopolysaccharide biosynthesis). The third and fourth circles show CDSs transcribed clockwise and anticlockwise, respectively (yellow: CDSs conserved in both strains, blue: CDSs specific to one strain), the fifth circle the rRNA operons, the sixth circle the G+C content, and the seventh circle the GC skew. (B) Dot plot presentation of DNA sequence homologies between the chromosomes. Locations of ori and seven rRNA operons (rrn1–rrn7) are indicated.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4231636&req=5

evu160-F1: The chromosomes of Serratia marcescens strains SM39 and Db11. (A) Circular maps of the SM39 and Db11 chromosomes. From the outside in, the first circle shows the nucleotide sequence positions (in Mb), and the second circle shows the locations of strain-specific regions of ≥5 kb (purple: prophages and integrative elements; red: others) with an indication of their features and/or encoded products/functions (PP, prophages; IE, integrative elements; EPS, exopolysaccharide biosynthesis). The third and fourth circles show CDSs transcribed clockwise and anticlockwise, respectively (yellow: CDSs conserved in both strains, blue: CDSs specific to one strain), the fifth circle the rRNA operons, the sixth circle the G+C content, and the seventh circle the GC skew. (B) Dot plot presentation of DNA sequence homologies between the chromosomes. Locations of ori and seven rRNA operons (rrn1–rrn7) are indicated.
Mentions: The chromosomes of SM39 and Db11 are similar in size, 5,225,577 and 5,113,802 bp, respectively, and gene number (table 1 and fig. 1A). SM39 carries two plasmids, pSMC1 (41,517 bp) and pSMC2 (58,929 bp). No extrachromosomal elements were found in Db11. Overall, the chromosomes of the two strains are highly conserved and essentially collinear, except for a large inversion of the oriC region flanked by rRNA operons (fig. 1B). Surprisingly for members of the same species, the ANI between the conserved genomic regions of the two strains (4,391 kb) is only 95.1%. This can be compared with a figure of 97.0% for the ANI between two distantly related members of E. coli, strains K-12 and E2348/69. Despite this, the 16S rRNA genes of the two strains show 99.4% sequence identity, consistent with DB11 and SM39 being members of the same species (Kim et al. 2014; see also supplementary fig. S3, Supplementary Material online). Further with a criterion of ≤90% nucleotide sequence identity and ≥5 kb length, we identified 44 genomic regions specific to SM39, totaling 628 kb (12% of the genome), and 39 specific regions (447 kb or 8.7% of the genome) for Db11 (fig. 1A; see also supplementary tables S1 and S2, Supplementary Material online). The relatively low ANI value for the two S. marcescens strains and the considerable amount of isolate-specific sequences may reflect the diversity of niches that this species can occupy.Fig. 1.—

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