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Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water.

Schwartz T, Armant O, Bretschneider N, Hahn A, Kirchen S, Seifert M, Dötsch A - Microb Biotechnol (2014)

Bottom Line: The expression of resistance genes, genetic mobile elements in PA49 was independent from the water matrix.Consistently, the antibiotic sensitive strain PA30 did not show any difference in expression of the intrinsic resistance determinants and genetic mobile elements.However, changes in environmental milieus resulted in rather unspecific transcriptional responses than selected and stimuli-specific gene regulation.

View Article: PubMed Central - PubMed

Affiliation: Institute of Functional Interfaces (IFG), Campus North, Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany.

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Related in: MedlinePlus

Coverage of genomic reference sequences by the newly assembled genomes. The reference sequences that were used for the hybrid de novo assembly are displayed on the outer circles (diagram to the right) with an additional display of the accessory elements alone (missing the PAO1 chromosome, diagram to the left). Regions that are covered by the contigs of strains PA30 and PA49 or overlap with the chromosome of another reference strain PA14 are highlighted by coloured areas in the concentric inner circles as specified by the color legend.
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fig01: Coverage of genomic reference sequences by the newly assembled genomes. The reference sequences that were used for the hybrid de novo assembly are displayed on the outer circles (diagram to the right) with an additional display of the accessory elements alone (missing the PAO1 chromosome, diagram to the left). Regions that are covered by the contigs of strains PA30 and PA49 or overlap with the chromosome of another reference strain PA14 are highlighted by coloured areas in the concentric inner circles as specified by the color legend.

Mentions: An alignment of the contigs with P. aeruginosa reference strain PAO1 showed a huge overlap of 95.8% for PA30 and 96.4% for PA49 (Fig. 1; Table S2), reflecting the highly conserved character of the P. aeruginosa core genome. Comparing the contigs with the genome islands that were used in the alignment process revealed a distinct pattern of accessory genomic elements for the two strains covering large fractions of the various genomic islands (Fig. 1; Table S2). Strain PA30 contains full length or near-full length sequences of PAGI-5 to PAGI-11, larger fractions of PAGI-1 and PAGI-2 and several regions of PAGI-3, whereas only insignificant fractions of the remaining genomic elements occurred. In case of the multi-resistant strain PA49, all genomic islands except the smaller PAGI-9 to PAGI-11 were covered at varying percentages (Table S2). The scattered distribution of regions within the genomic islands that actually showed homology with PA49 contigs may be partially explained by incomplete sequence assembly. However, the fact that both the contigs and the genomic island reference sequences contained a large amount of non-overlapping regions (data not shown) suggests that at least in some cases, the accessory elements found in PA30 and PA49 only partially contain sequences that are homologous to the genomic islands and also include a substantial amount of new and previously uncharacterized sequences.


Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water.

Schwartz T, Armant O, Bretschneider N, Hahn A, Kirchen S, Seifert M, Dötsch A - Microb Biotechnol (2014)

Coverage of genomic reference sequences by the newly assembled genomes. The reference sequences that were used for the hybrid de novo assembly are displayed on the outer circles (diagram to the right) with an additional display of the accessory elements alone (missing the PAO1 chromosome, diagram to the left). Regions that are covered by the contigs of strains PA30 and PA49 or overlap with the chromosome of another reference strain PA14 are highlighted by coloured areas in the concentric inner circles as specified by the color legend.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321378&req=5

fig01: Coverage of genomic reference sequences by the newly assembled genomes. The reference sequences that were used for the hybrid de novo assembly are displayed on the outer circles (diagram to the right) with an additional display of the accessory elements alone (missing the PAO1 chromosome, diagram to the left). Regions that are covered by the contigs of strains PA30 and PA49 or overlap with the chromosome of another reference strain PA14 are highlighted by coloured areas in the concentric inner circles as specified by the color legend.
Mentions: An alignment of the contigs with P. aeruginosa reference strain PAO1 showed a huge overlap of 95.8% for PA30 and 96.4% for PA49 (Fig. 1; Table S2), reflecting the highly conserved character of the P. aeruginosa core genome. Comparing the contigs with the genome islands that were used in the alignment process revealed a distinct pattern of accessory genomic elements for the two strains covering large fractions of the various genomic islands (Fig. 1; Table S2). Strain PA30 contains full length or near-full length sequences of PAGI-5 to PAGI-11, larger fractions of PAGI-1 and PAGI-2 and several regions of PAGI-3, whereas only insignificant fractions of the remaining genomic elements occurred. In case of the multi-resistant strain PA49, all genomic islands except the smaller PAGI-9 to PAGI-11 were covered at varying percentages (Table S2). The scattered distribution of regions within the genomic islands that actually showed homology with PA49 contigs may be partially explained by incomplete sequence assembly. However, the fact that both the contigs and the genomic island reference sequences contained a large amount of non-overlapping regions (data not shown) suggests that at least in some cases, the accessory elements found in PA30 and PA49 only partially contain sequences that are homologous to the genomic islands and also include a substantial amount of new and previously uncharacterized sequences.

Bottom Line: The expression of resistance genes, genetic mobile elements in PA49 was independent from the water matrix.Consistently, the antibiotic sensitive strain PA30 did not show any difference in expression of the intrinsic resistance determinants and genetic mobile elements.However, changes in environmental milieus resulted in rather unspecific transcriptional responses than selected and stimuli-specific gene regulation.

View Article: PubMed Central - PubMed

Affiliation: Institute of Functional Interfaces (IFG), Campus North, Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany.

Show MeSH
Related in: MedlinePlus