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The pheV Phenylalanine tRNA Gene in Klebsiella pneumoniae Clinical Isolates Is an Integration Hotspot for Possible Niche-Adaptation Genomic Islands

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Abstract

Horizontally acquired genomic islands may allow bacteria to conquer and colonize previously uncharted niches. Four Klebsiella pneumoniae tRNA gene insertion hotspots (arg6, asn34, met56, and pheV) in 101 clinical isolates derived from blood, sputum, wound, bile or urine specimens were screened by long-range PCR for the presence or absence of integrated islands. The pheV phenylalanine tRNA gene was the most frequently occupied site and harbored at least three entirely distinct types of islands: (1) KpGI-1, a 3.7 kb island coding for four proteins, three of which showed high similarity to two hypothetical proteins and a Gcn5-related N-acetyltransferase in Salmonella enterica, (2) KpGI-2, a 6.4 kb island coding for five proteins including a truncated phage-like integrase, two helicase-related proteins, and a homolog of the functionally elusive Fic protein, and (3) KpGI-3, a 12.6 kb island which carried seven fimbriae-related genes, first identified in MGH78578. Consistent with the niche-adaptation hypothesis, KpGI-1-like islands which coded for the putative acetyltransferase were significantly over-represented in sputum isolates as compared to urine (P < 0.001), blood (P < 0.05) or bile (P < 0.05) derived isolates. Despite the unique nature of KpGI-2, likely homologs of orf5_KpGI-2 that coded for Fic were also found at undefined locations in six other clinical isolates, though none possessed the other KpGI-2 genes. We propose that the pheV-associated islands described in this study may contribute to fine tuning and adaptation of K. pneumoniae strains toward preferred infection and/or colonization pathways.

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Acknowledgments

This work was supported by grants from the 863 program, Ministry of Science and Technology of China (2006AA02Z328), the Shanghai Medical Key Discipline, National Natural Science Foundation of China (30672503, 30700013/C010103), Clinical-Base Conjunct Medicine Research Foundation of China (JC07-20), Shanghai Rising-Star Program (Q7A14028), Royal Society–National Natural Science Foundation of China International Joint Program (KR/ZD; 2007/R3) and Medisearch, Leicestershire (KR). Nan Chen was supported by Graduate Student Innovation Foundation of Fudan University; JJvA was supported by an Anniversary PhD Scholarship from the University of Leicester.

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Authors and Affiliations

  1. Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, 12 Central Urumqi Road, Shanghai, 200040, People’s Republic of China

    Nan Chen, XiaoFei Jiang, Min Li, ZeHua Yang, QuHao Wei, XiaoYun Chen & Yuan Lu

  2. Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, People’s Republic of China

    Hong-Yu Ou, Xinyi He & Zixin Deng

  3. Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester, LE1 9HN, UK

    Jon Jurriaan van Aartsen & Kumar Rajakumar

  4. Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, LE1 5WW, UK

    Kumar Rajakumar

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  1. Nan Chen
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  2. Hong-Yu Ou
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  3. Jon Jurriaan van Aartsen
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  4. XiaoFei Jiang
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  5. Min Li
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  12. Yuan Lu
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Correspondence to Yuan Lu.

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Nan Chen and Hong-Yu Ou contributed equally to this work.

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Chen, N., Ou, HY., van Aartsen, J.J. et al. The pheV Phenylalanine tRNA Gene in Klebsiella pneumoniae Clinical Isolates Is an Integration Hotspot for Possible Niche-Adaptation Genomic Islands. Curr Microbiol 60, 210–216 (2010). https://doi.org/10.1007/s00284-009-9526-4

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  • DOI: https://doi.org/10.1007/s00284-009-9526-4

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