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Journal of Microbiological Methods, 2011, 84, 283-289.

Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites

J. Zhang, J. Jurriaan van Aartsen, X. Jiang, Y. Shao, C. Tai, X. He, Z. Tan, Z. Deng, S. Jia*, K. Rajakumar and H.Y. Ou*

 Link to PubMed
Klebsiella pneumoniae is an important bacterial pathogen of man that is commonly associated with opportunistic and hospital-associated infections. Increasing levels of multiple-antibiotic resistance associated with this species pose a major emerging clinical problem. This organism also occurs naturally in other diverse environments, including the soil. Consistent with its varied lifestyle and membership of the Enterobacteriaceae family, K. pneumoniae genomes exhibit highly plastic architecture comprising a core genome backbone interspersed with numerous and varied alien genomic islands. In this study the size of the presently known K. pneumoniae pan-genome gene pool was estimated through analysis of complete sequences of three chromosomes and 31 plasmids belonging to K. pneumoniae strains. In addition, using a PCR-based strategy the genomic content of eight tRNA/tmRNA gene sites that serve as DNA insertion hotspots were investigated in 28 diverse environmental and clinical strains of K. pneumoniae. Sequencing and characterization of five newly identified horizontally-acquired tmRNA-associated islands further expanded the archived K. pneumoniae gene pool to a total of 7648 unique gene members. Large-scale investigation of the content of tRNA/tmRNA hotspots will be useful to identify and/or survey accessory sequences dispersed amongst hundreds to thousands of members of many key bacterial species.

Fig. 1. Determination of the known K. pneumoniae gene pool as represented within three fully sequenced chromosomes, 31 plasmids and five tmRNA-borne islands identified in this study
Fig. 2. tRIP-PCR matrix results for eight tRNA/tmRNA gene hotspots in 28 environmental (green) and clinical (black) strains of K. pneumoniae.
Fig. 3. Comparative schematic maps of tmRNA-associated islands in seven K. pneumoniae strains and one Salmonella enterica strain.


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