Next Article 
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

ABSTRACT
The 16S-23S rRNA gene internal transcribed spacer (ITS) regions
of
Klebsiella spp., including
Klebsiella pneumoniae subsp.
pneumoniae, Klebsiella pneumoniae subsp.
ozaenae, Klebsiella pneumoniae subsp.
rhinoscleromatis, Klebsiella oxytoca, Klebsiella planticola, Klebsiella terrigena, and
Klebsiella ornithinolytica, were characterized,
and the feasibility of using ITS sequences to discriminate
Klebsiella species and subspecies was explored. A total of 336 ITS sequences
from 21 representative strains and 11 clinical isolates of
Klebsiella were sequenced and analyzed. Three distinct ITS types—ITS
none (without tRNA genes), ITS
glu [with a tRNA
Glu (UUC) gene], and
ITS
ile+ala [with tRNA
Ile (GAU) and tRNA
Ala (UGC) genes]—were
detected in all species except for
K. pneumoniae subsp.
rhinoscleromatis,
which has only ITS
glu and ITS
ile+ala. The presence of ITS
none in
Enterobacteriaceae had never been reported before. Both the
length and the sequence of each ITS type are highly conserved
within the species, with identity levels from 0.961 to 1.000
for ITS
none, from 0.967 to 1.000 for ITS
glu, and from 0.968
to 1.000 for ITS
ile+ala. Interspecies sequence identities range
from 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 significant
interspecies variations but low intraspecies polymorphisms were
identified; these may be targeted in the design of probes for
the identification of
Klebsiella to the species level. Phylogenetic
analysis based on ITS regions reveals the relationships among
Klebsiella species similarly to that based on 16S rRNA genes.

INTRODUCTION
The genus
Klebsiella is generally classified into seven species
and subspecies, including
Klebsiella pneumoniae subsp.
pneumoniae, Klebsiella pneumoniae subsp.
ozaenae, Klebsiella pneumoniae subsp.
rhinoscleromatis, Klebsiella oxytoca, Klebsiella planticola, Klebsiella terrigena, and
Klebsiella ornithinolytica (
30,
40).
Pathogenic
Klebsiella strains belonging to
K. pneumoniae subsp.
pneumoniae and
K. oxytoca are known to cause hospital-acquired
infections such as septicemia, pneumonia, and urinary tract
and soft tissue infections (
35,
36,
39). As a cause of nosocomial
infection due to gram-negative bacteria,
Klebsiella ranks next
to
Escherichia coli, accounting for 8% of endemic hospital infections
and 3% of epidemic outbreaks (
3,
41). Recently, strains of
K. planticola and
K. terrigena, initially regarded as "environmental"
isolates, were also isolated from human clinical specimens and
animals (
6,
42). Meanwhile, the appearance of multiresistant
strains among clinical
Klebsiella isolates, especially those
producing extended-spectrum beta-lactamases (ESBLs), which show
resistance to extended-spectrum cephalosporins, has been increasing
over the past several years (
10,
31). Frequencies as high as
40% have been reported in some regions, and the available data
suggest a further increase in the incidence of ESBL-producing
isolates (
10,
23,
31,
34). Therefore, nosocomial-infection surveillance
is necessary in order to collect data that can be used in the
prevention and control of
Klebsiella infection (
8,
20).
In clinical microbiology laboratories, Klebsiella strains are currently identified by using automated instruments based on classical biochemical tests such as the Vitek and API systems. Identification to the species level is often difficult, because some of the species share similar biochemical profiles (11, 26). For example, K. planticola and K. terrigena are generally misidentified as K. pneumoniae subsp. pneumoniae or K. oxytoca in most automated-instrument identification systems (42). Also, K. pneumoniae subsp. pneumoniae and K. oxytoca cannot be differentiated by classical phenotypic approaches (5, 21, 28). However, a recent study by Hansen et al. suggested that it is possible to differentiate K. pneumoniae subsp. pneumoniae from K. oxytoca with 18 biochemical tests (16). A number of DNA-based methods for the detection of pathogenic Klebsiella spp. have been developed, including PCR and restriction fragment length polymorphism analysis based on the gyrA gene (18), fluorescent in situ hybridization and real-time PCR based on the 16S rRNA gene (19), and fluorescent in situ hybridization based on the ESBL gene for detection of ESBL-producing K. pneumoniae subsp. pneumoniae (31).
The rRNA genes (16S, 23S, and 5S) are ideal candidates for bacterial identification and evolutionary studies, because they are highly conserved within the species (15). The major disadvantage of these sequences is that the "variable" regions are not sensitive enough to allow clear differentiation of closely related microorganisms (32). The 16S-23S rRNA gene internal transcribed spacer (ITS) sequence, which is not subject to the same selective pressure as the rRNA genes and consequently has a 10-times-greater evolution rate, appears to be able to overcome the apparent limitation of rRNA genes (2, 14). Sequence and length polymorphisms found in the ITS are increasingly being used as tools for bacterial species and subspecies identification (17, 27, 29, 37), typing (25, 37), and evolutionary studies (1, 12, 33). Gürtler et al. reported that ITS sequence analysis is complementary to the 16S rRNA gene for phylogenetic analysis (13). A PCR method based on ITS sequences has been developed for the detection and identification of K. pneumoniae subsp. pneumoniae (22, 24). Information related to ITS regions in Klebsiella is still lacking, with only 1 ITS sequence from K. oxytoca and 21 ITS sequences from nine K. pneumoniae subsp. pneumoniae strains available in GenBank.
In this study, we sequenced 336 ITS sequences from 21 representative strains and 11 clinical isolates covering all seven Klebsiella species and subspecies. Three distinct ITS types—ITSnone (without tRNA genes), ITSglu [with the tRNAGlu (UUC) gene], and ITSile+ala [with tRNAIle (GAU) and tRNAAla (UGC) genes]—were detected. The sequence and length polymorphisms of the ITS regions were analyzed. Phylogenetic analyses based on ITS regions were also carried out. This is the first detailed assessment of ITS regions in the genus Klebsiella. Sequences in the ITS regions with significant interspecies variations and low intraspecies polymorphisms may be targeted to develop probes for the identification of Klebsiella strains to the species or subspecies level.

MATERIALS AND METHODS
Bacterial strains and cultivation conditions.
The
Klebsiella strains used in this study are listed in Table
1. All strains were grown in LB medium at 37°C overnight
with shaking.
DNA isolation.
Genomic DNA from each strain was extracted from 1.0 ml of the
overnight culture (approximately 10
9 CFU) using the Tiangen
DNA extraction kit (Tiangen Biotech Co., Ltd., China) according
to the manufacturer's protocol.
Amplification of ITS regions.
Primers wl-5793 (5'-TGT ACA CAC CGC CCG TC-3') and wl-5794 (5'-GGT ACT TAG ATG TTT CAG TTC-3'), designed based on the most conserved sequences at the end of the 16S rRNA gene and at the beginning of the 23S rRNA gene in Klebsiella, respectively, were used to amplify ITS regions from all Klebsiella strains. The PCR mixture used contained 1x PCR buffer (50 mM KCl, 10 mM Tris-HCl [pH 8.3]), 2.5 mM MgCl2, 200 µM deoxynucleoside triphosphate, 1.0 U Taq DNA polymerase (TaKaRa Biotechnology [Dalian] Co. Ltd., China), 10 nM each primer, and 100 ng of the DNA template in a final volume of 50 µl. PCR conditions were as follows: initial denaturation at 95°C for 5 min; 35 cycles of 94°C for 30 s, 50°C for 30 s, and 72°C for 1 min; and a final extension at 72°C for 5 min. An aliquot (2 µl) of PCR products was run in an agarose gel to check for amplified fragments.
Cloning and sequencing.
PCR amplicons were cloned into the pGEM-T Easy vector (Promega, MA) and transformed into Escherichia coli DH5-
. Transformants, indicated by white colonies on an ampicillin plate containing isopropyl-β-D-thiogalactopyranoside (IPTG) and 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-Gal), were selected randomly. Plasmid DNA was isolated by the conventional alkaline-lysis method, digested with EcoRI, and visualized on agarose gels to confirm the insertion. The presence of the correct insert was verified by sequencing using an ABI 3730 automated DNA sequencer (Applied Biosystems). Seven to 16 transformants per strain were examined in order to reveal all possible amplicons.
Sequence analysis.
Multiple-sequence alignment of ITS sequences was carried out with the CLUSTAL W program (http://www.ebi.ac.uk/clustalw/). The identity level was calculated using BioEdit software (http://www.mbio.ncsu.edu/BioEdit/page2.html). Phylogenetic trees were constructed using the neighbor-joining method and plotted with the Molecular Evolutionary Genetics Analysis (MEGA) software package (version 3.1; http://www.megasoftware.net). Bootstrap analysis was carried out based on 1,000 replicates.
Nucleotide sequence accession numbers.
Klebsiella ITS sequences were submitted to GenBank under accession numbers EU623084 to EU623419.

RESULTS
Amplification of the ITS.
To design the primers for the PCR amplification of
Klebsiella ITS regions, all the available 16S and 23S rRNA gene sequences
of the genus in the the Ribosomal Data Project (
http://rdp.cme.msu.edu/)
and NCBI (
http://www.ncbi.nlm.nih.gov/) databases, including
102 16S rRNA gene sequences and 31 23S rRNA gene sequences,
were downloaded. Based on the most conserved regions in the
16S and 23S rRNA genes, primers wl-5793 (5'-TGT ACA CAC CGC
CCG TC-3') and wl-5794 (5'-GGT ACT TAG ATG TTT CAG TTC-3') were
designed. The primers were used to amplify ITS regions from
all 32
Klebsiella strains used in this study. PCR products with
estimated sizes of 550, 750, and 900 bp (including 152-bp 16S
rRNA and 209-bp 23S rRNA gene sequences) were detected from
all
K. pneumoniae subsp.
pneumoniae, K. pneumoniae subsp.
ozaenae, K. oxytoca, K. terrigena, K. planticola, and
K. ornithinolytica strains tested, and PCR products with estimated sizes of 750
and 900 bp were detected from
K. pneumoniae subsp.
rhinoscleromatis strains (Fig.
1).
Sequence analysis.
PCR products were cloned into
E. coli, and 7 to 16 clones per
Klebsiella strain were sequenced in order to reveal all possible
amplicons. A total of 336 sequences were obtained, and the ITS
regions were analyzed using tRNA-ScanE software (
http://lowelab.ucsc.edu/tRNAscan-SE/).
Three distinct ITS types were identified: ITS
none (without tRNA
genes), ITS
glu [with the tRNA
Glu (UUC) gene], and ITS
ile+ala [with the tRNA
Ile (GAU) and tRNA
Ala (UGC) genes] (Table
1).
In agreement with the PCR results, the three ITS types were
found in all
Klebsiella species and subspecies except for
K. pneumoniae subsp.
rhinoscleromatis, which has only ITS
glu and
ITS
ile+ala. Each type of tRNA gene [tRNA
Glu (UUC), tRNA
Ile (GAU),
and tRNA
Ala (UGC) genes] shares 99% DNA identity within the
genus.
Length polymorphisms were detected in all three ITS types; ITSile+ala was the most variable and ITSnone the least variable (Table 1). For ITSnone, 198 bp was the primary size in K. pneumoniae subsp. pneumoniae and K. pneumoniae subsp. ozaenae, and 194 bp was detected in a few cases due to the deletion of four bases (TGAA) at nucleotides (nt) 178 to 181; 206 bp was detected in K. oxytoca; and 232 or 233 bp was found in K. terrigena, K. planticola, and K. ornithinolytica. For ITSglu, 343 bp was predominantly found in K. pneumoniae subsp. pneumoniae, K. pneumoniae subsp. ozaenae, and K. pneumoniae subsp. rhinoscleromatis, and sizes as much as 9 bp different (337, 339, 351, and 352 bp) were also detected. The size of ITSglu was 351 and/or 352 bp in K. oxytoca, 376 and 388 bp in K. terrigena, and 379 bp in both K. planticola and K. ornithinolytica. Interestingly, 43 base variations were found between 351- and 352-bp ITSglu in K. oxytoca, indicating different origins for the two sequences. For ITSile+ala, 427 bp was predominantly detected in K. pneumoniae subsp. pneumoniae and K. pneumoniae subsp. ozaenae, and sizes as much as 10 bp different (422, 424, 426, 429, 434, 435, 436, and 437 bp) were also detected in some cases. In addition, ITSile+ala sequences of 498 or 495 bp are also present in K. pneumoniae subsp. pneumoniae strains NCTC5056, G1748, and G1751 and in K. pneumoniae subsp. ozaenae strain CCM5792 due to the insertion of 70 bp at nt 153. ITSile+ala sequences of 498 bp in K. pneumoniae subsp. rhinoscleromatis, 508 to 512 bp in K. oxytoca, and 535 to 542 bp in K. terrigena, K. planticola, and K. ornithinolytica were also detected.
Intraspecies conservation of ITS regions.
Apart from insertions or deletions, ITS sequences are highly conserved within the species/subspecies, with identity levels ranging from 0.961 to 1.000 for ITSnone, 0.967 to 1.000 for ITSglu, and 0.968 to 1.000 for ITSile+ala (Table 1). Insertion and/or deletion of nucleotide blocks is the cause for lower identity levels (less than 0.910) in some cases, except for ITSglu in K. oxytoca, in which the low identity (0.870) between the ITSglu sequences of 351 and 352 bp was due to the 43-bp variations.
The alignment of 24 sequences representing all amplicons of the three ITS types from eight representative K. pneumoniae subsp. pneumoniae strains revealed four conserved regions located at the first 47 nt (CR1), between nt 332 and 363 (CR2), between nt 373 and 408 (CR3), and between nt 413 and 429 (CR4) (Fig. 2). The four conserved regions and the conserved boxA region also exist in other Klebsiella species (data not shown), indicating that they are conserved within the genus.
Interspecies variations of ITS regions.
The ITS sequences from reference strains
K. pneumoniae subsp.
pneumoniae ATCC 10031,
K. pneumoniae subsp.
ozaenae ATCC 11297,
K. pneumoniae subsp.
rhinoscleromatis ATCC 13884,
K. oxytoca ATCC 49473,
K. planticola CCM3568,
K. terrigena CCM4428, and
K. ornithinolytica ATCC 31898, representing each of the species
or subspecies, were examined for interspecies variations. Pairwise
alignment of ITS sequences revealed identity levels between
species ranging from 0.775 to 0.989 for ITS
none (Table
2), 0.798
to 0.997 for ITS
glu (Table
3), and 0.712 to 0.985 for ITS
ile+ala (Table
4). The identity levels among
K. pneumoniae subspecies
(0.817 to 0.997) and among
K. terrigena, K. planticola, and
K. ornithinolytica (0.891 to 0.994) are relatively higher, as
expected, since the members in each of these groups are closely
related (
9). In general, the identity levels of ITS sequences
among species or subspecies are lower than those of 16S rRNA
gene sequences (0.966 to 0.986) (
4).
Several regions with high levels of interspecies variation were
identified in each ITS type (Fig.
3A to C). Two variable regions,
VR1 (135 to 169 nt) and VR2 (195 to 214 nt), located between
the
boxA region and the 23S rRNA gene, were found in ITS
none (Fig.
3A). Five variable regions, VR1 (297 to 330 nt) and VR2
(356 to 375 nt) between the
boxA region and the 23S rRNA gene,
VR3 (45 to 55 nt) between the 16S rRNA gene and the tRNA gene,
and VR4 (186 to 200 nt) and VR5 (212 to 239 nt) between the
tRNA gene and the
boxA region, were found in ITS
glu. Six variable
regions, VR1 (453 to 483 nt) and VR2 (513 to 528 nt) between
the
boxA region and the 23S rRNA gene, VR3 (50 to 71 nt) between
the 16S rRNA gene and the tRNA gene, and VR4 (154 to 229 nt),
VR5 (232 to 258 nt), and VR6 (342 to 359 nt) between the tRNA
gene and the
boxA region, were found in ITS
ile+ala. Notably,
all three ITS types share the same VR1 and VR2 sequences.
Phylogenetic analysis.
Three phylogenetic trees were constructed based on the ITS
none,
ITS
glu, and ITS
ile+ala sequences of
Klebsiella, respectively
(Fig.
4A to C). In all cases,
K. pneumoniae subsp.
pneumoniae, K. pneumoniae subsp.
ozaenae, and
K. pneumoniae subsp.
rhinoscleromatis form one branch, while
K. terrigena, K. planticola, and
K. ornithinolytica form another branch, as in the tree constructed on the basis
of 16S rRNA genes (Fig.
4D). The ITS
none-based tree reveals
not only topology but also bootstrap values similar to those
of the 16S rRNA gene tree, except for the absence of ITS
none in
K. pneumoniae subsp.
rhinoscleromatis (Fig.
4A). However,
the positions of
K. pneumoniae subsp.
ozaenae differ in the
ITS
glu and 16S rRNA gene trees. In the ITS
glu tree,
K. pneumoniae subsp.
ozaenae is close to
K. pneumoniae subsp.
rhinoscleromatis,
while in the 16S rRNA gene tree, it is close to
K. pneumoniae subsp.
pneumoniae. Also,
K. oxytoca clusters with the
K. pneumoniae group based on the 352-bp sequence but with the
K. terrigena group based on the 351-bp ITS
glu sequence (Fig.
4B). The latter
grouping is similar to that of the trees constructed based on
the 16S rRNA gene, ITS
none, and ITS
ile+ala, further indicating
that the two ITS
glu sequences originated from different ancestors
and that the 351-bp sequence is more conserved in
Klebsiella.
The ITS
ile+ala tree (Fig.
4C) fits well with the 16S rRNA gene
tree; therefore, the ITS
ile+ala sequences may be a useful tool
for phylogenetic delineation of genetic relationships in
Klebsiella.

DISCUSSION
In this study, we conducted an analysis of
Klebsiella ITS regions
and identified three types of ITS sequences: ITS
none, ITS
glu,
and ITS
ile+ala. ITS
glu and ITS
ile+ala are commonly found in
gram-negative bacteria (
14,
38), but ITS
none is rarely found.
We further searched all available genome sequences of
Enterobacteriaceae,
covering
Escherichia coli, Citrobacter koseri, Salmonella spp.,
Shigella spp.,
Enterobacter sakazakii, Serratia spp.,
Yersinia spp.,
Erwinia carotovora subsp.
atroseptica, and
Edwardsiella spp., and ITS
none was found in none of the genomes. Therefore,
Klebsiella appears to be the only exception in the family. The
maintenance of ITS
none in
Klebsiella (found in all
Klebsiella spp. except for
K. pneumoniae subsp.
rhinoscleromatis) is puzzling,
because the presence of any sequence without functional genes
is evolutionarily disadvantageous. ITS
none was also found in
a few gram-positive (
Staphylococcus aureus, Listeria monocytogenes,
and
Bacillus cereus) and gram-negative (
Vibrio parahaemolyticus)
bacteria (
5).
The copy number of rrn operons was not studied. However, the detection of multiple (two to five) ITS sequences indicates the presence of multiple copies of the ITS regions in Klebsiella. As revealed by the partial genome sequence of Klebsiella pneumoniae subsp. pneumoniae (http://genome.wustl.edu/genome.cgi?GENOME=Klebsiella%20), there are eight rrn operons located at equivalent loci, including three ITSile+ala sequences of 426 bp, 435 bp, and 499 bp, four ITSglu sequences of 343 bp, and one ITSnone sequence of 198 bp, consistent with our findings.
Due to the difficulties in obtaining strains of K. terrigena, K. planticola, and K. ornithinolytica, which are rarely isolated from the environment, only one or two strains from each of these species were examined in this study. Therefore, it is necessary to examine more strains of these species in future studies upon availability. However, based on the high intraspecies conservation observed in the ITS regions of K. pneumoniae subsp. pneumoniae, K. pneumoniae subsp. ozaenae, and K. oxytoca, it is expected that the ITS types and sequences are also conserved in the other three species.
Recently, due to their close relationships to Klebsiella species, Enterobacter aerogenes and Calymmatobacterium granulomatis were also included in the genus Klebsiella and named Klebsiella mobilis and Klebsiella granulomatis, respectively (7, 9). Therefore, the ITS regions of K. mobilis and K. granulomatis remain to be investigated.
Sequence and length polymorphisms of ITS regions have been increasingly used as tools for the identification of bacterial species and/or subspecies. Our separate study showed that K. pneumoniae subsp. pneumoniae and K. oxytoca, which are the most frequently isolated pathogenic Klebsiella species, can be discriminated confidently by a microarray using species-specific capture probes based on the variable regions of ITS sequences (unpublished data).
In conclusion, this study reveals that Klebsiella ITS sequences are highly conserved within the species or subspecies, while sufficient variations are present to allow differentiation between most of the species.

ACKNOWLEDGMENTS
This study was funded by the National High Technology Research
and Development Program of China (863 Program) (2006BAK02A14,
2006AA06Z409, and 2006AA020703).
We thank Jinying Chen for supplying the clinical isolates.

FOOTNOTES
* 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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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.
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