Analysis of the 16S-23S rRNA Gene Internal Transcribed Spacer Region in Klebsiella Species

doi:10.1128/JCM.00927-08

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Journal of Clinical Microbiology, November 2008, p. 3555-3563, Vol. 46, No. 11
0095-1137/08/$08.00+0 doi:10.1128/JCM.00927-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Analysis of the 16S–23S rRNA Gene Internal Transcribed Spacer Region in Klebsiella Species

Min Wang,¹^,2^,3^,4^, Boyang Cao,¹^,2^,3^,4^, Qunfang Yu,¹^,2^,3^,4 Lei Liu,¹^,2^,3^,4 Qili Gao,⁶ Lei Wang,¹^,2^,3^,4^,5 and Lu Feng¹^,2^,3^,4^,5^*

TEDA School of Biological Sciences and Biotechnology, Nankai University,¹ Tianjin Key Laboratory of Microbial Functional Genomics,³ Tianjin Research Center for Functional Genomics and Biochips,⁴ Tianjin Biochip Corporation, 23 HongDa Street,⁵ Tianjin Entry-Exit Inspection and Quarantine Bureau, 8 ZhaoFa Residential Quarter, the Second Street, TEDA, Tianjin 300457,⁶ Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300071, China²

Received 14 May 2008/ Returned for modification 22 July 2008/ Accepted 19 August 2008

The 16S-23S rRNA gene internal transcribed spacer (ITS) regionsof Klebsiella spp., including Klebsiella pneumoniae subsp. pneumoniae,Klebsiella pneumoniae subsp. ozaenae, Klebsiella pneumoniaesubsp. rhinoscleromatis, Klebsiella oxytoca, Klebsiella planticola,Klebsiella terrigena, and Klebsiella ornithinolytica, were characterized,and the feasibility of using ITS sequences to discriminate Klebsiellaspecies and subspecies was explored. A total of 336 ITS sequencesfrom 21 representative strains and 11 clinical isolates of Klebsiellawere sequenced and analyzed. Three distinct ITS types—ITS^none(without tRNA genes), ITS^glu [with a tRNA^{Glu (UUC)} gene], andITS^ile+ala [with tRNA^{Ile (GAU)} and tRNA^{Ala (UGC)} genes]—weredetected in all species except for K. pneumoniae subsp. rhinoscleromatis,which has only ITS^glu and ITS^ile+ala. The presence of ITS^nonein Enterobacteriaceae had never been reported before. Both thelength and the sequence of each ITS type are highly conservedwithin the species, with identity levels from 0.961 to 1.000for ITS^none, from 0.967 to 1.000 for ITS^glu, and from 0.968to 1.000 for ITS^ile+ala. Interspecies sequence identities rangefrom 0.775 to 0.989 for ITS^none, from 0.798 to 0.997 for ITS^glu,and from 0.712 to 0.985 for ITS^ile+ala. Regions with significantinterspecies variations but low intraspecies polymorphisms wereidentified; these may be targeted in the design of probes forthe identification of Klebsiella to the species level. Phylogeneticanalysis based on ITS regions reveals the relationships amongKlebsiella species similarly to that based on 16S rRNA genes.

* Corresponding author. Mailing address: TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 HongDa Street, TEDA, Tianjin 300457, China. Phone: 86-22-66229592. Fax: 86-22-66229596. E-mail: fenglu63{at}nankai.edu.cn

Published ahead of print on 27 August 2008.

M.W. and B.C. contributed equally to this report.

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