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Journal of Clinical Microbiology, June 1998, p. 1761-1764, Vol. 36, No. 6
0095-1137/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
16S rRNA Sequence Diversity in Mycobacterium
celatum Strains Caused by Presence of Two Different Copies of
16S rRNA Gene
U.
Reischl,1
K.
Feldmann,2
L.
Naumann,1
B. J. M.
Gaugler,2
B.
Ninet,3
B.
Hirschel,3 and
S.
Emler3,*
Institute for Medical Microbiology and
Hygiene, University of Regensburg, D-93053
Regensburg,1
Institute for Laboratory
Diagnosis, Zentralkrankenhaus Gauting, D-82131
Gauting,2 Germany, and
Laboratory of
Bacteriology, Division of Infectious Diseases, Hopital Cantonal
Universitaire, 1211 Geneva, Switzerland3
Received 29 August 1997/Returned for modification 6 October
1997/Accepted 13 February 1998
 |
ABSTRACT |
Direct sequencing of the 16S rRNA gene (16S rDNA) of
Mycobacterium celatum isolates showed ambiguities,
suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the
gene, which differed by insertion of a thymine at position 214 and by
additional mismatches. Restriction fragment length polymorphism
analysis confirmed the presence of two copies of 16S rDNA within the
bacterial chromosome.
 |
TEXT |
Mycobacterium celatum has
been isolated from samples of immunocompetent patients with pulmonary
disease (5) and from patients infected with human
immunodeficiency virus in whom it had caused disseminated disease
(20). While its resistance to antituberculosis treatment
requires rapid and accurate diagnosis, identification of M. celatum by conventional techniques often takes several weeks because of the slow growth of this organism (11).
Furthermore, rapid identification techniques, such as commercially
available DNA probes, may yield false-positive results for
Mycobacterium tuberculosis when they are applied to M. celatum (4, 11). Direct sequencing of the bacterial 16S
rRNA gene (16S rDNA) has proven to be a stable and specific marker for
mycobacterial identification (15, 16, 24); while the number
of copies of 16S rRNA genes may vary among bacterial species, their
sequences are assumed to be identical, with only minor differences
(14, 21). Fast-growing members of the genus
Mycobacterium generally have two identical copies of the 16S
rRNA gene (9), while slow growers are thought to have only
one (13) and, therefore, yield unambiguous sequence patterns. However, two different 16S rRNA genes were recently detected
in a slowly growing mycobacterium belonging to the Mycobacterium terrae complex (19). Here, we report the observation of
16S rDNA heterogeneity in three isolates of the clinically important M. celatum.
Mycobacterial isolates.
Three clinical laboratories each
provided one clinical isolate of M. celatum (1732, T322, and
MI1581). The isolates were grown on Loewenstein-Jensen medium and
examined for growth rate, microscopic colony morphology, and
pigmentation. Biochemical tests of all three clinical isolates yielded
identical results, which were consistent with those published by Butler
et al. (5).
Amplification and sequencing of genomic DNA.
A single colony
of each isolate was harvested and chromosomal DNA was extracted as
previously described (22). One microgram of bacterial DNA
was subjected to PCR with each of two primer pairs, i.e., biotinylated
M285 in combination with M264 (15) and primer R247
(GTAGTCCACGCCGTAAACGG) in combination with M261 (15), thus yielding the complete 16S rDNA in two fragments. Nonradioactive sequencing of all three isolates was performed with
forward primer M285 and reverse primer M259 (15) by using a
commercially available cycle sequencing kit (PRISM Ready Reaction Dye
Deoxy Terminator cycle sequencing kit; Applied Biosystems GmbH,
Weiterstadt, Germany). Electrophoresis of sequenced DNA and data
collection were performed with an automated sequencer (ABI 373A;
Applied Biosystems). The results revealed identical patterns, showing
heterogeneity consecutive to position 214 within helix 10 (first line
of Fig. 1); in position 214, all isolates showed a partial insertion of an additional T (TTTTT instead of TTTT),
thus leading to a duplication of the peaks seen on the electropherograms, consecutive to the point of insertion (Fig. 1).
Clear peak patterns were obtained for the stretch between the
sequencing primer and the insertion. These results were confirmed by
manual sequencing (data not shown).

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FIG. 1.
Graphic plot of the direct sequencing (lane 1) of
PCR-amplified 16S rDNA and cloned 16S rDNA (clones 1 and 4) of the
clinical isolate MI1581, obtained by automated sequencing. The stretch
of consecutive T's indicates the start of ambiguities in the pattern
obtained by direct sequencing with reverse primer M259.
|
|
RFLP.
Single colonies of each isolate were grown for as many
as 3 weeks in 5 ml of Middlebrook 7H9 broth supplemented with 0.05% Tween 80. The cultures were centrifuged, resuspended in 0.85% NaCl,
and inactivated by heat (30 min at 80°C). Thereafter, bacterial DNA
was extracted with cetytrimethylammonium bromide as described elsewhere (26). After digestion with 10 U of
PvuII (Boehringer Mannheim GmbH, Mannheim, Germany),
fragments were electrophoresed (1% agarose gel), transferred by
Southern blotting onto a nylon membrane, and hybridized to a
PCR-generated, genus-specific, digoxigenin-labelled probe (positions 9 to 341) (23). In the absence of a known PvuII restriction site within the 16S rDNA of M. celatum,
restriction fragment length polymorphism (RFLP) patterns of all three
isolates yielded two bands of equal sizes (Fig.
2).

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FIG. 2.
RFLP analysis. Southern blot of genomic DNAs of all
three clinical isolates of M. celatum, i.e., 1732 (lane 1),
T322 (lane 2), and MI1581 (lane 3), which were digested with
PvuII and hybridized with a 16S rDNA-specific probe. The
rapidly growing Mycobacterium hassiacum (lane 4) is shown as
a reference. Digoxigenin-labelled DNA molecular weight marker III
(Boehringer Mannheim GmbH) was applied (lane MW).
|
|
Cloning of 16S rDNA amplification products.
The complete 16S
rDNA from M. celatum was amplified from single colonies of
isolate MI1581 with primers M285 and M261. Amplicons were directly
cloned into a pCR 2.1 vector (Invitrogen Corp., San Diego, Calif.) and
transformed into competent cells (TOP10F'; Invitrogen Corp.). Plasmid
DNA extracted from 20 transformed colonies yielded seven interpretable
sequences of both hypervariable regions (>500 bp). In contrast to
direct sequencing, two unambiguous but slightly different types of
sequences were obtained; types A and B showed four and five consecutive
thymine residues, respectively, at positions 210 to 214 (Fig. 1 and
3). Both types could be further differentiated within positions 78 to 85. When the sequences of both
types of clones were compared with published sequences for M. celatum, type A was identical to M. celatum type 3 (MC3RNA16S [GenBank accession no. Z46664]) and type B resembled
M. celatum type 1 (MCRGDSA [GenBank accession no.
L08169]), differing only at positions 77 to 79 (additional CCT)
and 110 (A/G) (Fig. 3).
Advances in technology have made direct sequencing of 16S rDNA a
powerful tool for the identification of bacteria in medical
microbiology. 16S rDNA sequence analysis has become a standard
in
bacterial identification and in systematic bacterial taxonomy
(
1,
16). In mycobacteriology, this approach has been particularly
valuable in clinical diagnosis, since slow growth hampers diagnosis
by
conventional tests (
2,
10). Furthermore, 16S rDNA sequencing
has contributed to the description of many new species of this
family,
among them
M. celatum (
3,
5,
15).
16S rDNA analysis for mycobacterial identification depends on the
assumption that the sequences obtained from reference strains
represent
functional rRNA molecules typical of their taxa (
12,
27).
Although the level of intraspecific sequence variability
is assumed to
be low, some species are represented in international
databases by an
unexpectedly high number of deviating sequences
(e.g., 11 different 16S
rDNA sequences for
Mycobacterium paratuberculosis).
Some
authors have traced these deviations back to errors in laboratory
procedures, e.g., to sequencing techniques (
7) or to
subspecies
variations (
14,
21). However, recent findings
indicate the
presence of heterogeneity between different copies of 16S
rDNA
in
Escherichia coli (
6) and in
Thermospora bispora (
25),
as well as in a slowly
growing mycobacterium resembling
M. terrae (
19).
In
M. celatum, we suspected heterogeneity when identical
sequence patterns were obtained in different laboratories from clinical
strains from different patients; all patterns were characterized
by the
same ambiguities starting at position 214, regardless of
the strand
sequenced. However, the phenotypical features of all
strains were
consistent with
M. celatum type 1. Cloning of 16S
rDNA
finally resolved the ambiguities, yielding two types of unambiguous
sequences. Interestingly, the two types were almost identical
to the
reference sequences for
M. celatum type 1 (
5) and
M. celatum type 3 (
3), respectively. We take it
for granted that
analysis of single colonies from pure isolates ruled
out contamination.
Thus, our results indicate the presence of two
different 16S rRNA
genes within the genome of
M. celatum.
Little is known about heterogeneity in bacterial 16S rDNA. When
present, distinct types of 16S rDNA seemed to be equally expressed
(
19,
25), suggesting their functionality. With regard to the
origin of divergent 16S rDNAs, lateral gene transfer has been
discussed
(
18) but has not yet revealed unsuspected relationships
to
other species (
19,
25). However, in the present study both
sequences obtained by cloning were identical with either one of
the
GenBank reference sequences for subtypes 1 and 3 of
M. celatum,
which may not be distinguished by conventional techniques
(
3,
5).
With regard to unambiguous identification of mycobacteria, sequence
diversity in 16S rRNA genes may raise a problem. In agreement
with
Clayton et al. (
7), we would recommend that to define
a new
bacterial or mycobacterial taxon, one should investigate
multiple
isolates. Sequence analysis of cloned genes may complement
the
characterization of ambiguous positions, and possible heterogeneity
should be indicated in the published reference sequence by using
ambiguity codes such as IUPAC (Nomenclature Committee of Biochemistry)
(
8). Thus, the quality of sequence data in public databases
such as GenBank, EMBL, or the Ribosomal Database Project
(
17)
will improve and lead to higher accuracy in the
identification
of clinically important bacteria, including
mycobacteria, via
16S rDNA sequence analysis.
 |
ACKNOWLEDGMENTS |
We thank Mohamed Rifai and Norbert Lehn for their active support
and gratefully acknowledge the excellent technical assistance of Birgit
Haber, Isabelle Jan, and E. Schmidt.
The work of S. Emler was supported by the Fondation Lancardis du Centre
Valaisan de Pneumologie.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Laboratory of
Bacteriology, Division of Infectious Diseases, University Hospital
Geneva, CH-1211 Geneva 14, Switzerland. Phone: 41-22-37 23311 Bip 857 960. Fax: 41-22-37 27304. E-mail: Stefan.Emler{at}hcuge.ch.
 |
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Journal of Clinical Microbiology, June 1998, p. 1761-1764, Vol. 36, No. 6
0095-1137/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
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