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Applied and Environmental Microbiology, April 2001, p. 1793-1799, Vol. 67, No. 4
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.4.1793-1799.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Characterization of Listeria
monocytogenes Strains Involved in Invasive and Noninvasive
Listeriosis Outbreaks by PCR-Based Fingerprinting
Techniques
Giovanna
Franciosa,
Stefania
Tartaro,
Christina
Wedell-Neergaard, and
Paolo
Aureli*
Food Microbiology Laboratory, Food
Department, Istituto Superiore di Sanità, 00161 Rome, Italy
Received 5 June 2000/Accepted 22 January 2001
 |
ABSTRACT |
A total of 32 Listeria monocytogenes strains (16 from a
recent outbreak of invasive listeriosis and 16 from two outbreaks of
noninvasive listeriosis, all three occurring in Italy) were characterized by PCR-ribotyping, arbitrarily primed PCR (AP-PCR), and
the recently developed infrequent-restriction-site PCR (IRS-PCR). The
discriminatory ability of the techniques, first evaluated on 29 unrelated L. monocytogenes food isolates using Simpson's index of diversity, was 0.714 for PCR-ribotyping, 0.690 for AP-PCR, and
0.919 for IRS-PCR. IRS-PCR was also more capable of distinguishing among strains from the invasive listeriosis outbreak: three
different clusters were identified by IRS-PCR compared to two clusters
identified by both PCR-ribotyping and AP-PCR. Within each of the two
outbreaks of noninvasive listeriosis, the patterns were practically
identical, as demonstrated by all three techniques. Only IRS-PCR
succeeded in clearly discriminating the strains related to noninvasive
listeriosis from all of the other strains included in this study,
including those from the outbreak of invasive listeriosis. This finding may suggest the presence of unique differences in their DNA sequences.
 |
INTRODUCTION |
Listeria monocytogenes
has been recognized as a foodborne pathogen causing listeriosis in
humans since the 1980s, when a number of listeriosis outbreaks were
found to be associated with the consumption of contaminated foodstuffs.
Until recently, food-borne listeriosis was commonly regarded as an
invasive disease that affected only susceptible population groups
(e.g., immunocompromised persons, newborn children, and pregnant
women); it was considered to be associated with bacteremia only in
certain target organs and was only rarely associated with
gastrointestinal symptoms (24). However, recent reports of
a new noninvasive form of listeriosis that causes febrile
gastroenteritis clearly indicate that persons with no predisposing
conditions may be affected. This finding increases the public health
significance of L. monocytogenes (2, 3, 12, 19,
22), in that the emergence of this new form of food-borne
listeriosis could affect the epidemiology of the disease both in terms
of a higher attack rate and in terms of a wider range of potential
vehicles. However, the factors that influence the infectious dose and
the occurrence and course of infection still need to be clarified. It
is possible that the clonal variants of the pathogen each interact with
the host in a different way (6, 26). Of the
high-resolution molecular typing methods for assessing genetic
heterogeneity, fingerprinting techniques based on PCR have proven to be
among the most effective (27). They are generally based on
enzymatic amplification through PCR of DNA segments flanking either
undetermined sequences (e.g., randomly amplified polymorphic DNA
[RAPD] and arbitrarily primed PCR [AP-PCR] [15, 16])
or defined and conserved sequences (e.g., rRNA genes [PCR-ribotyping]
[25] and the repetitive-element families [ERIC- and
REP-PCR] [14, 23]).
A new PCR-based fingerprinting technique, known as
infrequent-restriction-site PCR (IRS-PCR), based on the selective
amplification of DNA restriction fragments, has recently been
developed and used to type several bacterial species (17,
21, 30). We applied this technique to related and
unrelated L. monocytogenes isolates and compared the
results to those obtained by PCR-ribotyping and AP-PCR. The
related strains were those isolated during the investigations of
an outbreak of invasive listeriosis and two outbreaks of noninvasive
listeriosis that recently occurred in Italy. The outbreak of invasive
listeriosis occurred in 1998: six hospitalized patients, three of whom
were heart transplanted, while the others, affected with Woldenstrom's
syndrome, hepatic cirrhosis, and chronic hepatitis, respectively, had
developed mild to severe (meningoencephalitis) symptoms of listeriosis
while in the same hospital (P. Aureli and G. Franciosa, unpublished data). The two outbreaks of noninvasive listeriosis occurred in 1994 and 1997 (2, 22); both involved a large number of
immunocompetent persons, and L. monocytogenes was detected
from the clinical specimens and from the environmental samples
collected where the suspected food sources had been prepared. However,
whereas in the 1994 outbreak the implicated food remained uncertain
(22), in the 1997 outbreak it was clearly identified as a
cold salad of corn and tuna fish (2).
The main objective of the present study was to verify the causal
relationships among the L. monocytogenes strains isolated from each outbreak and to compare the epidemic clones to isolates recovered from different types of foods.
 |
MATERIALS AND METHODS |
Bacterial isolates and culture conditions.
A total of 61 L. monocytogenes isolates were used in this study (Table
1). A total of 29 of them were unrelated
strains and, of these, 25 were from different types of food recovered
over a period of 2 years (i.e., 1997 and 1998) and were randomly
selected from the culture collection at the Food Microbiology
Laboratory of the Istituto Superiore di Sanità. L. monocytogenes ScottA (a clinical isolate of serotype 4b
[7]), kindly provided by M. P. Doyle, University of
Georgia, Griffin, was included in the experiments as a reference
strain. Strains 26 through 28 were clinical isolates of serotype 4b
obtained, respectively, from two elderly people (strains 26 and 27) and
a newborn (strain 28). These strains were sent to our laboratory by
some local health units of southern and northern Italy.
Of the 61 outbreak isolates, 32 (strains 30 to 61) were taken from
sources associated with three separate listeriosis outbreaks
(Table
1).
Strains 30 to 45 were from the outbreak of invasive
listeriosis (here
referred to as outbreak 1) (Aureli and Franciosa,
unpublished).
L. monocytogenes had been isolated from the body
or tissue
fluids of all six hospital patients involved, from some
of the foods
collected and stored for the hospital's routine quality
control
analyses (both cooked foods served to the patients and
frozen foods),
and from two environmental swabs from the hospital's
kitchen. Strains
46 through 52 (outbreak 2) and 53 through 61
(outbreak 3) included some
human, food, and environmental isolates
recovered during the
investigation of the 1994 and 1997 outbreaks
of noninvasive
listeriosis (
2,
22). All of the strains had
been
identified by conventional procedures (
5) at the time
of
isolation; they were further confirmed as
L. monocytogenes by PCR detection of some virulence genes (i.e.,
hly, plcA,
plcB,
and their transcriptional activator
prfA), as
previously described
(
10).
All cultures of the listeria strains were checked for purity on Oxford
agar plates (Oxoid, Basingstoke, United Kingdom) prior
to the
experiments. Single colonies were inoculated into tryptone
soy
broth (TSB; Oxoid) and incubated at 37°C for 24 h. Then, 1
ml of these broth cultures was used for DNA
extraction.
Serotyping.
All of the strains were serotyped on the basis
of somatic (O) and flagellar (H) antigens by a commercial kit (Listeria
O Antisera; Denka Seiken, Tokyo, Japan) according to the
manufacturer's instructions.
Preparation of template DNA.
Either purified DNA or DNA from
listeria cell lysates was used directly as the template in all PCR
amplification assays except for the IRS-PCR assay, which requires the
pretreatment of DNA, performed as described below.
Genomic DNA was extracted and purified as reported elsewhere
(
8). The DNA from each strain was dissolved in 150 µl of
1×
TE buffer (10 mM Tris, 1 mM EDTA; pH 8.0). Yields were
estimated
by using a UV spectrophotometer (GeneQuant II; Pharmacia
Biotech,
Cambridge, England), and DNA samples were stored at

20°C
until
use.
Listeria cell lysates were obtained by centrifuging 1 ml of 24-h TSB
cultures; the pellets were washed twice with 1× TE buffer,
suspended
in 1 ml of sterile distilled water, and subjected to
ultrasound
treatment (model T460; Trans-Sonic, Singen, Germany)
for 10 min to
facilitate lysis. Lysates were freshly prepared
for each
experiment.
To obtain the appropriate template for the IRS-PCR experiments, we
adopted the procedure of Riffard et al. (
21), with some
modifications. Bacterial DNA (either pure [2 µg] or from the crude
lysates [18 µl], without further purification) was first cleaved
with 40 U of
XbaI and 40 U of
PstI (Boehringer,
Mannheim, Germany)
in a total reaction volume of 25 µl overnight at
37°C. The resulting
restriction fragments were stored at

20°C
until subsequent ligation
to double-stranded restriction
halfsite-specific adapters (AX
and PS) (
17,
21).
Specifically, the adapters were the partially
complementary
oligonucleotides AX1 (5'-CTA GTA CTG GCA GAC TCT-3')
and AX2
(5'-GCCAGT A-3') (for
XbaI) and PS1 (5'-GAC
TCG ACT CGC
ATG CA-3') and PS2 (5'-TGC GAG T-3') (for
PstI) (Biogen, Rome,
Italy). Equal molar amounts of AX1
(previously phosphorylated
at the 5' end by T4 Polynucleotide Kinase
3'-Phosphatase Free
[Boehringer], as recommended by the manufacturer)
and AX2 and
of PS1 and PS2 were mixed in 1× PCR buffer (Perkin-Elmer
Cetus,
Branchburg, N.J.): annealing was performed with a thermal cycler
(Model PTC-150 Minicycler; M. J. Research, Inc., Watertown, Mass.)
programmed to decrease the temperature from 80 to 4°C over 1 h.
The restriction fragments were ligated to the adapters in accordance
with the procedures of Riffard et al. (
21). Finally, the
ligation
products were redigested with 10 U of
XbaI and 10 U
of
PstI at
37°C for 30
min.
XbaI-
PstI restriction fragments tagged with
specific adapters were kept at

20°C until their use as templates in
the IRS-PCR
experiments.
PCR conditions.
All reaction mixtures contained, in a total
volume of 50 µl, 1× PCR buffer II (10 mM Tris-HCl, 50 mM KCl [pH
8.3]; Perkin-Elmer Cetus), 200 µM concentrations of each
deoxynucleoside triphosphate (Pharmacia), and 1.25 U of Taq
polymerase (Perkin-Elmer Cetus). The final concentrations of
MgCl2 (Perkin-Elmer Cetus) were adjusted to 1.5 mM in the
IRS-PCR experiments and to 3 mM in the PCR-ribotyping and AP-PCR experiments.
The PCR-ribotyping and AP-PCR experiments were performed with both
purified DNA (2 ng) and crude lysates (2.5 µl); when crude
lysates
were used, PCR mixtures were heated in a thermal cycler
at 99°C for
10 min prior to the addition of the polymerase for
a better release of
the DNA. The IRS-PCR experiments were performed
using as templates for
amplification 5 µl of the ligation products
obtained after
restriction either of purified DNA or of the genetic
material released
from the lysed
bacteria.
We used different oligonucleotide primers (Biogen) and amplification
parameters for each technique, as
follows.
(i) PCR-ribotyping was carried out according to the method of Sontakke
and Farber (
25). The primers for the amplification
of the
DNA spacer regions between the 16S and 5S rRNA genes were
P
(5'-TTG TAC ACA CCG CCC GTC A-3') and M (5'-GCTTAA CTT
CCG TGT
TCG GTA TGG G-3'). Amplification was achieved after
initial denaturation
of the template at 94°C for 2 min, followed by
35 cycles at 94°C
for 1 min, 35°C for 1 min, and 72°C for 2.5 min, with a ramp time
of 2 min between 35 and 72°C; a final extension
phase was performed
at 72°C for 5
min.
(ii) For AP-PCR, the primer M13 (5'-GTT GTA AAA CGA CGG CCA
GT-3'), derived from the core sequence of the bacteriophage M13
genome, was used at a final concentration of 0.5 µM. This primer
was
selected from among 10 different 20-mer oligonucleotides,
previously
tested with different serotypes of
L. monocytogenes,
for its
higher discriminatory power. The use of primers selected
from the
bacteriophage M13 sequence has been recommended for detecting
DNA
polymorphisms in virtually all species (
4). The
temperature
profile consisted of two cycles at 94°C for 5 min, 40°C
for 5
min, and 72°C for 5 min, followed by 40 high-stringency cycles
at 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min. Both the
primer sequence and the temperature profile were adapted from
the
method of Vila et al. (
28).
(iii) For IRS-PCR, primers PS1 and PX-G (5'-AGA GTC TGC CAG TAC
TAG AG-3') (
17) for the selective amplification of
the
XbaI-
PstI
restriction fragments were used at
a final concentration of 1
µM. The cycling conditions were the same
as those described by
Mazurek et al. (
17). After initial
denaturation at 94°C for
5 min, the PCR mixtures were subjected to 30 cycles at 94°C for
30 s, 60°C for 30 s, and 72°C for 90 s; a final extension was
performed at 72°C for 5
min.
The amplification experiments were performed in duplicate with a
thermal cycler (model PT100; M. J. Research) to assess the
reproducibility of the
patterns.
Analysis of the amplification products.
The PCR products (35 µl) were separated by electrophoresis on a 1.5 or 2% agarose gel
containing ethidium bromide (0.5 µg/ml) at 60 V for 4 h in 1×
TAE (Tris-acetate-EDTA) buffer. Gel images were digitized through a
UV-gel image acquisition camera (Gel Doc 1000; Bio-Rad Laboratories,
Hercules, Calif.). Intergel comparison was performed with the GelCompar
3.1 system (Applied Maths, Kortrijk, Belgium) (9).
Following normalization and background subtraction with mathematical
algorithms, three separate lists were created for the reconstructed
patterns of PCR-ribotyping, AP-PCR, and IRS-PCR. Finally, the
similarities between profiles within each list were calculated by
applying the Pearson product-moment correlation coefficient
(r), and clustering was performed by the unweighted pair-group method using arithmetic averages (UPGMA). An intralinkage homology level of
80% between patterns was assumed as the cutoff for
defining a close genetic relationship between strains and was used to
define the clusters.
 |
RESULTS AND DISCUSSION |
Unrelated isolates.
Based on the results of serotyping, the 25 unrelated L. monocytogenes food strains were divided into
eight different serovars, distributed as follows: 1/2a (n = 9), 4b (n = 6), 1/2b (n = 4), 3a
(n = 2), 1/2c (n = 1), 3c (n = 1), 4ab (n = 1), and 4d (n = 1)
(Table 1). Hence, serovars 1/2a, 1/2b, and 4b, which commonly cause the
clinical disease, were the most frequently detected. In no case was the
prevalence of a serovar associated with a specific food. The clinical
isolates were confirmed as serotype 4b. The number of bands varied
according to the specific PCR-based fingerprinting technique:
PCR-ribotyping showed from 4 to 11 bands, AP-PCR showed from 5 to 13 bands, and the amplification of the XbaI-PstI
restriction fragments by IRS-PCR showed from 6 to 11 bands. All bands
were evenly distributed along the tracks and shorter than 2,036 bp (Fig. 1). PCR-ribotyping, AP-PCR, and
IRS-PCR revealed percentages of similarity greater than 83, 87, and
90%, respectively, when comparing the analysis using purified DNA to
that using crude cell lysates. Since these differences did not affect
the final clustering of the genetic profiles, we used the patterns
obtained with cell lysates to construct the UPGMA dendrograms.
Computer analysis showed that PCR-ribotyping and AP-PCR produced,
respectively, 7 and 6 clusters of strains and that neither technique
was capable of distinguishing among serotypes (Fig. 2a and
b), whereas IRS-PCR produced 13 clusters and was generally able to distinguish among serotypes.
Specifically, the degree of differentiation was greatest among the most
common serovars (i.e., 1/2a, 1/2b, and 4b), whereas the single
representatives of the rarer serovars was not distinguished (i.e., 1/2c
and 3a clustered with a 1/2a strain, 4d clustered with a 1/2b strain,
and 4ab clustered with a 4b strain) (Fig. 2c). These results are
consistent with the divisions of L. monocytogenes strains
obtained with other techniques, specifically, restriction fragment
length polymorphism analysis (29), multilocus enzyme electrophoresis (MEE) (11), ribotyping (11),
pulsed-field gel electrophoresis (PFGE) (20), and the
recently developed amplified fragment length polymorphism (AFLP)
technique (1). AFLP is conceptually similar to IRS-PCR, in
that both methods are based on the selective amplification by PCR of
double-digested genomic DNA. However, AFLP has a number of drawbacks,
all of which can be overcome with IRS-PCR; specifically, in AFLP, the
two adapters are of equal length, neither is phosphorylated (hence,
they are not prevented from acting as primers), one of the primers is
radioactively or fluorescently labeled, denaturing polyacrylamide gel
electrophoresis is required to resolve the large number of products
generated, and sophisticated detection systems must be employed to
detect the fingerprints. All replications with IRS-PCR showed identical profiles, demonstrating this technique's high level of
reproducibility.

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FIG. 1.
Representative fingerprints of outbreak-related L. monocytogenes strains produced by IRS-PCR (lanes 2 to 7), AP-PCR
(lanes 9 to 13), and PCR-ribotyping (lanes 15 to 19). Lanes 2, 9, and
15, strain 27; lanes 3, 10, and 16, strain 33; lanes 4, 11, and 17, strain 40; lanes 5, 12, and 18, strain 49; lane 6, strain 43; lanes 7, 13, and 19, strain 54; lanes 1, 8, 14, and 20, 1-kb DNA ladder
(Gibco-BRL).
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FIG. 2.
Dendrograms representing genetic relationships between
unrelated L. monocytogenes isolates based on profiles
obtained by PCR-ribotyping (a), AP-PCR (b), and IRS-PCR (c).
|
|
Interestingly, both PCR-ribotyping and IRS-PCR separated all the
unrelated clinical isolates of serotype 4b but
L. monocytogenes ScottA from the food isolates (Fig.
2a and c). At an
80% clone
cutoff value for the Pearson coefficient, the highest
discriminatory
ability, as determined by Simpson's index of diversity
(
13),
was found for IRS-PCR (0.919 compared to 0.714 for
PCR-ribotyping
and 0.690 for AP-PCR). We used the core sequence of
bacteriophage
M13 as the random primer for the AP-PCR experiments in
order to
assess this primer's suitability in discriminating among
L. monocytogenes isolates. However, low-resolution bands
with a high background
were mostly obtained, with a consequent low
degree of
discrimination.
Isolates from the outbreak of invasive listeriosis (outbreak
1).
One clinical L. monocytogenes isolate and all of
the isolates recovered from the frozen foods (Table 1) were identified
as serotype 1/2a, whereas the remaining isolates, including those from
the environment, were serotype 1/2b. The dendrograms of the profiles
obtained with PCR-ribotyping and AP-PCR also consisted of two clusters.
However, whereas the grouping obtained with PCR-ribotyping was
identical to that of serotyping, when using AP-PCR, the clinical isolate of serotype 1/2a clustered with the 1/2b isolates. In contrast
to the other techniques, IRS-PCR revealed three different clusters.
Specifically, five clinical isolates and all of the isolates from the
cooked foods and the environment, all serotype 1/2b, were in the same
cluster (89% intralinkage homology level), suggesting that this
outbreak was likely due to cross-contamination. A second cluster
consisted of all of the isolates from frozen foods, all serotype 1/2a,
which were strictly interrelated (87% homology level). The third
cluster consisted of the one clinical isolate of serotype 1/2a, which
showed a homology level of <70% with the second cluster and could
therefore be discriminated. These results can be considered as
plausible, since the frozen foods were boiled before being served and
thus probably did not account for any cases of listeriosis. The
clinical isolate of serotype 1/2a may have originated from a different
unidentified source of infection. Figure 1 shows representative
IRS-PCR, AP-PCR, and PCR-ribotyping profiles of the outbreak-related
L. monocytogenes strains.
Isolates from the outbreaks of noninvasive listeriosis (outbreaks 2 and 3).
The clinical, food, and environmental isolates from
outbreaks 2 and 3 were confirmed as belonging to serotypes 1/2b and 4b, respectively (Table 1). Highly homologous PCR-based fingerprints were
obtained for all of the isolates associated with outbreak 2, except for
isolate 52 (isolated from a mixer), which had a homology level of
<20% according to IRS-PCR and of <50% according to both
PCR-ribotyping and AP-PCR. These findings are consistent with the
previous subtyping of the same strains by MEE, PFGE, and RAPD, and they
substantiate the lack of causal relationship for the isolate from the
mixer (8, 22).
All of the strains from outbreak 3 showed nearly identical profiles
with all PCR-based typing techniques, resulting in homology
levels
among isolates of >90, 97, and 93% when IRS-PCR, AP-PCR,
and
PCR-ribotyping, respectively, were used. Previous analysis
of the same
strains, using PFGE and RAPD, also showed indistinguishable
patterns
(
2).
These results strongly support the hypothesis of extensive
cross-contamination as the primary cause of infection in both outbreaks
(
2,
22); indeed, some environmental isolates showed the
same
profiles as those of the food and clinical
isolates.
Comparison between related and unrelated strains.
The
comparison between the IRS-PCR patterns of the related and unrelated
isolates revealed the following: (i) the strains from outbreak 1 (invasive listeriosis) were divided into three clusters, all of which
included some unrelated food isolates of similar serotypes (i.e., 1/2a
and 1/2b); (ii) all but one of the related strains of outbreak 2 (noninvasive listeriosis) clustered apart from all of the other
isolates tested in this study, whereas the isolate from the mixer,
which was not apparently implicated in the outbreak, clustered with a
strain of serotype 3a; and (iii) the strains from outbreak 3 (noninvasive listeriosis) clustered apart from all other strains
tested, although the homology level was approximately 75% with respect
to some strains of serotype 1/2b, including those involved in outbreak
1 (Fig. 3). The strains from outbreak 3 were also distinguished from L. monocytogenes ScottA and the
other clinical isolates of serotype 4b, the relative genetic similarity
level between them being <50% (Fig. 3).

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FIG. 3.
Dendrogram representing the genetic relationships
between total L. monocytogenes isolates based on IRS-PCR
fingerprinting.
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|
The results of IRS-PCR indicate that the strains implicated in the two
outbreaks of noninvasive listeriosis can be separated
from all of the
other isolates considered in this study. For outbreak
2, this could be
partly due to the fact that the strains had been
isolated at least 3 years earlier than all of the other strains.
Alternatively, it has been
hypothesized that the different pathways
of the disease (invasive and
noninvasive) might be related to
differences in the pathogenicity of
the causative
L. monocytogenes strains, which is determined
by specific virulence-associated
genes (
19); consequently,
differences in these genes' sequences
and/or in the sequences of the
genes that control their phenotypic
expression might account for the
unique patterns. On the other
hand, strains involved in the outbreak of
invasive listeriosis
generated IRS-PCR profiles comparable to those
from some food
isolates randomly selected from our culture collection.
This may
suggest that strains potentially capable of causing invasive
listeriosis
are more widespread than those responsible for noninvasive
listeriosis,
thus explaining why noninvasive disease has been reported
only
rarely. Another currently accepted hypothesis is that the
occurrence
of noninvasive listeriosis may be underestimated because
L. monocytogenes is not among the pathogens routinely
investigated in outbreaks
of gastrointestinal illness (
2,
3,
22). These conclusions
cannot be drawn from the results obtained
with PCR-ribotyping
and AP-PCR, probably because of the lower
discriminative power
of these
techniques.
To verify the findings of this study, further analyses are currently
being conducted with additional
L. monocytogenes strains
from different sources and using other sensitive molecular
techniques.
 |
ACKNOWLEDGMENTS |
This work was supported by a grant from the National Research
Program of the Ministry of Health.
We thank Peter Ben Embarek of the Fisheries Department, Food and
Agriculture Organization of the United Nations (FAO), Rome, Italy, for
revision of the manuscript and Mark Kanjeff, Laboratorio Epidemiologia
e Biostatistica, ISS, for English editing.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Laboratorio
Alimenti, Istituto Superiore della Sanità, Viale Regina Elena
299, I-00161 Rome, Italy. Phone: 39-6-49902254. Fax: 39-6-49387101. E-mail: p.aureli{at}iss.it.
 |
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Applied and Environmental Microbiology, April 2001, p. 1793-1799, Vol. 67, No. 4
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.4.1793-1799.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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