Expanding the diagnostic use of PCR in leptospirosis: improved method for DNA extraction from blood cultures.
ABSTRACT Leptospirosis is a neglected zoonosis of ubiquitous distribution. Symptoms are often non-specific and may range from flu-like symptoms to multi-organ failure. Diagnosis can only be made by specific diagnostic tests like serology and PCR. In non-endemic countries, leptospirosis is often not suspected before antibiotic treatment has been initiated and consequently, relevant samples for diagnostic PCR are difficult to obtain. Blood cultures are obtained from most hospitalized patients before antibiotic therapy and incubated for at least five days, thus providing an important source of blood for PCR diagnosis. However, blood cultures contain inhibitors of PCR that are not readily removed by most DNA-extraction methods, primarily sodium polyanetholesulfonate (SPS).
In this study, two improved DNA extraction methods for use with blood cultures are presented and found to be superior in recovering DNA of Leptospira interrogans when compared with three previously described methods. The improved methods were easy and robust in use with all tested brands of blood culture media. Applied to 96 blood cultures obtained from 36 patients suspected of leptospirosis, all seven patients with positive convalescence serology were found positive by PCR if at least one anaerobic and one aerobic blood culture, sampled before antibiotic therapy were tested.
This study suggests that a specific and early diagnosis can be obtained in most cases of severe leptospirosis for up to five days after initiation of antimicrobial therapy, if PCR is applied to blood cultures already sampled as a routine procedure in most septic patients.
- SourceAvailable from: Jørgen Skov Jensen[Show abstract] [Hide abstract]
ABSTRACT: In the acute phase of leptospirosis, the diagnosis can be established with high sensitivity by testing blood and urine samples with polymerase chain reaction (PCR). However, only few real-time PCR assays have been validated for diagnostic use. The diagnostic accuracy of a novel TaqMan® PCR (LipL32 real-time PCR) targeting the lipl32 gene (or hap-1) and a previously described TaqMan® PCR (16S real-time PCR) targeting the rrs gene coding for 16S rRNA was evaluated when applied to both urine and blood specimens from humans suspected of leptospirosis. Applied to at least two blood cultures LipL32 real-time PCR had a sensitivity of 86%, and a specificity of 100%; and 16S real-time PCR had a sensitivity of 100%, and a specificity of 97%. Applied to urine samples, patients that were positive by the reference methods were also positive by both real-time PCR assays (n=4). For LipL32 real-time PCR the specificity was 100%, while for 16S real-time PCR it was only 91.5% due to unexpected cross-reactions with other bacteria. The analytical sensitivity was close to the theoretical limit-of-detection for both assays detecting all described human pathogenic species. We report a specific real-time PCR assay for detection of Leptospira, i.e., LipL32 real-time PCR that has been validated for diagnostic application in both urine and blood specimens from humans. We further show that a previously described 16S real-time PCR no longer can be recommended for diagnostic use due to a low specificity.Journal of microbiological methods 06/2012; 91(1):184-90. · 2.43 Impact Factor
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ABSTRACT: The use of broad range PCR and DNA sequencing of bacterial 16S ribosomal RNA genes for routine diagnostics of bacterial infections was evaluated. Here, the results from more than 2600 analyses during a 6-year period (2003-2009) are presented. Almost half of the samples were from joints and bones, and the second most frequent origin of samples was from the central nervous system. Overall, 26% of all samples were positive for bacterial DNA and bacterial identification was obtained in 80% of the PCR-positive samples by subsequent DNA sequencing. Ambiguous species identification was noticed among non-haemolytic streptococci, especially within the mitis group. The data show that ribosomal PCR with subsequent DNA sequencing of the PCR product is a most valuable supplement to culture for identifying bacterial agents of both acute and prolonged infections. However, some bacteria, including non-haemolytic streptococci, may not be precisely identified.Apmis 07/2013; · 2.07 Impact Factor
Expanding the Diagnostic Use of PCR in Leptospirosis:
Improved Method for DNA Extraction from Blood
Steen Villumsen, Rebecca Pedersen¤, Karen Angeliki Krogfelt, Jørgen Skov Jensen*
Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
Background: Leptospirosis is a neglected zoonosis of ubiquitous distribution. Symptoms are often non-specific and may
range from flu-like symptoms to multi-organ failure. Diagnosis can only be made by specific diagnostic tests like serology
and PCR. In non-endemic countries, leptospirosis is often not suspected before antibiotic treatment has been initiated and
consequently, relevant samples for diagnostic PCR are difficult to obtain. Blood cultures are obtained from most
hospitalized patients before antibiotic therapy and incubated for at least five days, thus providing an important source of
blood for PCR diagnosis. However, blood cultures contain inhibitors of PCR that are not readily removed by most DNA-
extraction methods, primarily sodium polyanetholesulfonate (SPS).
Methodology/Principal Findings: In this study, two improved DNA extraction methods for use with blood cultures are
presented and found to be superior in recovering DNA of Leptospira interrogans when compared with three previously
described methods. The improved methods were easy and robust in use with all tested brands of blood culture media.
Applied to 96 blood cultures obtained from 36 patients suspected of leptospirosis, all seven patients with positive
convalescence serology were found positive by PCR if at least one anaerobic and one aerobic blood culture, sampled before
antibiotic therapy were tested.
Conclusions/Significance: This study suggests that a specific and early diagnosis can be obtained in most cases of severe
leptospirosis for up to five days after initiation of antimicrobial therapy, if PCR is applied to blood cultures already sampled
as a routine procedure in most septic patients.
Citation: Villumsen S, Pedersen R, Krogfelt KA, Jensen JS (2010) Expanding the Diagnostic Use of PCR in Leptospirosis: Improved Method for DNA Extraction from
Blood Cultures. PLoS ONE 5(8): e12095. doi:10.1371/journal.pone.0012095
Editor: Stefan Bereswill, Charite ´-Universita ¨tsmedizin Berlin, Germany
Received June 28, 2010; Accepted July 14, 2010; Published August 11, 2010
Copyright: ? 2010 Villumsen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was financed by Statens Serum Institut, Copenhagen, Denmark, only. No external funders supported this work. The funders had no role in
study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: firstname.lastname@example.org
¤ Current address: Department of Microbial Ecology and Animal Health, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
Leptospira species is the causative agent of the leptospirosis, one
of the world’s most wide-spread zoonosis . Signs and symptoms
of the disease are often non-specific and range from flu-like
symptoms to multi-organ failure . Carrier animals excrete the
bacteria in large numbers with the urine and transmission to
humans occurs mainly through contact with water or crops
contaminated with infected urine . The disease is endemic in
developing countries mainly in the tropics where outbreaks occur
frequently after heavy rainfalls . Travellers may be exposed
during activities in fresh water, and leptospirosis has recently been
shown to be a relatively common cause of fever in Swedish
travellers . However, only few cases of leptospirosis are
diagnosed every year in the developed countries. These cases are
likely to represent an underestimate, since the diagnosis can only
be established by leptospira specific tests. The gold-standard in the
diagnosis of Leptospira spp. is detection of specific antibodies by
the microscopic agglutination test (MAT) . In most cases, a
diagnostic serum sample can not be obtained before the 7thday of
disease and the diagnosis is thereby delayed for the same period. In
the early phase of the disease, a rapid diagnosis can be obtained by
PCR of Leptospira spp. This method has a sensitivity of 28–96% in
severe leptospirosis when applied to whole blood samples [4,5].
However, to ensure a high sensitivity, samples have to be obtained
before or shortly after the start of antibiotic therapy, since
antimicrobials quickly remove Leptospira spp. from the blood. In a
non-endemic area, leptospirosis is rarely a first line diagnosis, and
as symptoms can be severe, antibiotic treatment is often initiated
before leptospirosis is suspected. It is, therefore, often impossible to
obtain a relevant sample for diagnostic PCR.
In a hospital setting, blood cultures (BCs) are sampled from
most septic patients before antimicrobial therapy is initiated and
incubated for at least five days. BCs are closed container systems
and consequently not prone to DNA-contamination but they
contain inhibitors of the PCR that requires special procedures to
remove . In previous studies where PCR has been applied to
BCs, only microorganisms that actually multiply in the BCs have
PLoS ONE | www.plosone.org1August 2010 | Volume 5 | Issue 8 | e12095
been targeted. Even though, the sensitivity of the assays is highly
dependent on the DNA-recovery, only little has been done to
optimize these procedures. In whole blood samples, a high
recovery is especially important, since the density of bacteria is
very limited. Further, only a small fraction equivalent to 5–10 ml of
the original sample is included in the final PCR assay.
The aim of this study was to evaluate five DNA extraction
methods for their effectiveness in recovering Leptospira DNA and in
removing inhibitors from spiked BCs. Moreover, we aimed to
evaluate if BCs sampled before antimicrobial therapy could be
used in the diagnosis of leptospirosis.
Materials and Methods
DNA extraction methods
The following five DNA extraction methods were used in the
Method 1 (M1).
DNA was extracted from 200 ml of the tested
specimens using the DNeasyH Blood & Tissue Kit (Qiagen,
Hilden, Germany) according to the manufacturer’s instructions
using the protocol for animal blood or cells. The final elution of
DNA was done in 200 ml buffer AE.
Method 2 (M2).
DNA was extracted from 200 ml of the tested
specimens using the MolYsis Plus Kit (Molzym GmbH & Co. KG,
Bremen, Germany) according to the manufacturer’s instructions
for direct bacterial DNA isolation from blood culture. The final
elution of DNA was done in 100 ml buffer EB.
Method 3 (M3).
DNA was extracted from 100 ml of the tested
specimens using the method described by Fredricks and Relman
. Briefly, cell lysis was obtained by a guanidine hydrochloride
based buffer. SPS (sodium polyanetholesulfonate) was removed by
adding benzyl alcohol to the solution and subsequently separated
from the aqueous phase containing the DNA by centrifugation.
DNA was precipitated from the supernatant by sodium acetate in
isopropanol. The pellet was ‘‘washed’’ in 70% ethanol and again
resuspended in 100 ml Tris-EDTA buffer.
Method 4 (M4).
Benzyl alcohol based removal of SPS and
other inhibitors in M3 was combined with the column based DNA
extraction of M1 in a new protocol, M4. A 100 ml aliquot of the
specimen was mixed with 100 ml lysis buffer (5 M UltraPureTM
guanidine hydrochloride (Invitrogen, CA) in 100mM UltraPureTM
Tris-HCl (pH 8.0; Invitrogen, Paisley, UK) and 10 ml proteinase
K (20 mg/ml; Qiagen) and incubated for 10 minutes at room
temperature. A total of 400 ml ultrapure water (Invitrogen) was
added followed by 800 ml .99% benzyl alcohol (ReagentPlusH,
Sigma-Aldrich, Brøndby, Denmark) and mixed. In order to
separate the phases, the sample was then centrifuged at 20.0006g
for 5 minutes at room temperature and 200 ml of supernatant (the
aqueous phase) was transferred to a new tube as described in
method 1, except that no proteinase K was added and that the
sample was not incubated during the lysis step. Only 100 ml of
buffer AE was added in the final elution step. This method was
developed to be used with anaerobic and paediatric blood culture
Method 5 (M5).
This method was equal to M4 except that
600 ml of ultrapure water was added before the phase separation.
This method was developed for use with all blood culture media.
The study consists of three experiments outlined in figure 1.
Experiment 1; evaluation of M1–M5 applied to one
One sample of BACTECTManaerobic Plus (BD
diagnostics, NJ) collected from an anonymous patient for
diagnostic purposes where no bacterial growth was detected
after at least 5 days of incubation at 37uC was spiked with Leptospira
interrogans (senso stricto) serovar Icterohaemorrhagiae strain M695
leptospirosis, the Netherlands). The bacterium was grown in
DifcoTMLeptospira medium - EMJH (Becton-Dickinson, Le Pont
de Claix, France) until late log phase with a final concentration of
1.46106Leptospira/ml. Bacterial cells were counted by dark field
microscopy using a Helber counting chamber (Hawksley, Lansing,
UK) as described by the manufacturer. The quantified culture was
then frozen at 280uC in smaller aliquots. Just before use, one
aliquot was thawed and added to blood culture material to yield a
final concentration of 10,000 Leptospira/ml. The concentration of
bacteria in the spiked samples was chosen to be at a level that
would allow quantification of the recovery in methods with high
and low recovery. The spiked sample was simultaneously extracted
10 times by each of the evaluated methods, M1–M5. The recovery
of Leptospira DNA was assessed in triplicates by the quantitative
PCR (qPCR) assay, described below. A total of 30 qPCR assays
was made for each evaluated method. All DNA extractions were
Experiment 2; evaluation of M5 applied to six different
blood cultures media.
In pre-study tests of M4, problems of
carry-over of inhibitors to the final eluate were observed when M4
was applied to BACTECTMaerobic Plus and BacT/ALERTH SA
(data not shown). The problem was identified as a very small water
phase in the phase separation step leading to carry-over of the
benzyl-alcohol phase on to the subsequent DNA extraction. The
changes made in M5 completely solved all problems of carry-over
of inhibitors and for that reason M5 is used in this experiment.
BACTECTManaerobic Plus, BACTECTMPaed Plus, BAC-
TECTMaerobic Plus (BD), BacT/ALERTH SA, BacT/ALERTH
SN and BacT/ALERTH PF (BioMerieux Inc., NC) collected for
diagnostic purposes as described under experiment 1 were
obtained from two Danish departments of clinical microbiology
(Hillerød Hospital, Hillerød, Denmark and Statens Serum Institut,
Copenhagen Denmark). For each of the six BC media tested,
material from five different anonymous patients was obtained and
spiked with Leptospira as described under experiment 1. DNA was
extracted once by M5 from each of the 30 spiked samples. All
DNA extractions were performed simultaneously. The recovery of
Leptospira DNA was assessed as triplicates by qPCR, as described
Experiment 3; clinical evaluation of M4 and M5.
material: Statens Serum Institut (SSI) is the only laboratory
performing routine diagnostic testing for Leptospira in Denmark. In
the period from January 2005 to June 2008, all BCs submitted for
culture of Leptospira for diagnostic purposes were inoculated in
DifcoTMLeptospira medium - EMJH in order to isolate Leptospira,
and the remainder of the BCs was stored at 220uC. When
diagnosticfollow-up had been
identifications were removed from the blood cultures and the
samples linked to the results of corresponding MAT and culture by
a unique, anonymous code and included in the ‘‘Leptospira: PCR
diagnostics’’ material collection (Danish Data Protection Agency:
journal number 2010-41-4862).
Some of the BCs had been incubated for at least 5 days at 37uC
at the local clinical microbiology laboratory before they were sent
to SSI for isolation of Leptospira spp. In all of these cases, contact
with SSI and the local clinical microbiology laboratory had been
established for diagnostic reasons, and samples were only
submitted if sampled before initiation of antimicrobial therapy.
Ninety-six blood cultures (BACTECTMaerobic Plus n=20;
BACTECTManaerobic Plus n=21; BACTECTMPaed Plus
Expanded Use of Leptospira PCR
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n=2; BacT/ALERTH SA n=23, BacT/ALERTH SN n=21;
BacT/ALERTH FA n=8; BacT/ALERTH FN n=1) were
obtained from 36 patients (4 (11%) females and 32 (89%) males;
median age 38 years; range 2 years to 78 years). Twenty-nine of
these patients had a serum sample tested for antibodies against
Leptospira spp. at some point during the acute phase of the disease.
Ten patients had a repeated test for antibodies taken during
Reference method: The test for antibodies against Leptospira spp.
in a convalescence serum sample by a microscopic agglutination
test (MAT) is a recognised reference standard in the diagnosis of
leptospirosis . Where requested by the clinicians, serum samples
were tested for antibodies against Leptospira spp. by a ISO 17025
certified microscopic agglutination test (MAT) conducted as
previously described by experienced laboratory technicians .
The MAT included Leptospira spp. of the following 13 serovars:
Patoc, Icterohaemorrhagiae (3 strains), Sejroe (2 strains), Saxkoeb-
ing, Javanica, Canicola, Ballum, Bratislava, Grippotyphosa,
Pomona, Bataviae, Hardjo and Hurstbridge. The following
dilutions of sera (in titer): 30, 100, 300, 1,000, 3,000, 10,000,
30,000 and 100,000 were tested by MAT. When only a single
serum sample was available for MAT, the test was considered
positive if the highest observed titer was above 1,000 and possibly
positive if the highest titer was with-in the range of 100–300.
When two serum samples were available and these were obtained
up to 4 weeks apart in the acute phase of the disease, then the test
was considered as positive when a seroconversion from no reaction
to a titer of at least 100 or a rise in the highest titer of two titer-
Figure 1. Flowchart for experiment 1–3. Figure shows flow over three independent experiments performed in the evaluation of five methods for
DNA extraction from blood cultures media. BD-AE: BACTECTMaerobic Plus, BD-AN: BACTECTManaerobic Plus, BD-Ped: BACTECTMPaed Plus, BacT-SA:
BacT/ALERTH SA, BacT-SN: BacT/ALERTH SN,BacT-PF: BacT/ALERTH PF, BacT-FA: BacT/ALERTH FA, BacT-FN: BacT/ALERTH FN. M1: Qiagen, DNeasyH
Blood & Tissue Kit; M2: Molzym, MolYsis Plus Kit; M3: Protocol described by Fredricks and Relman; M4: Improved method for anaerobic and paediatric
blood culture media; M5: Improved method adapted for all blood culture media.
Expanded Use of Leptospira PCR
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steps, was observed. If no change or a change of only one titer-step
were observed, the results were interpreted according to the results
of the last sample as described above. Finally, the test was classified
as false positive, if a decrease in titer of two titer steps or more were
observed during this period, a finding sometimes observed with
this test. All serological tests and culture were conducted before the
results of the PCR assays were known.
Procedure for DNA extraction and qPCR: DNA extraction
was performed by M4 for anaerobic and paediatric BCs while M5
was applied to the aerobic BCs. Recovery of Leptospira DNA was
assessed as duplicates by qPCR as described below. M4 and M5
were evaluated for their ability to remove inhibitors of the qPCR
by comparing the Ct value of the no-template controls (NTC) with
the Ct value of samples where no amplification of the target DNA
Exemption for review by the ethical committee system and for
obtaining informed consent was obtained from the Committee on
Biomedical Research Ethics for Capital Region (protocol number
H-1-2010-FSP-20) in accordance with Danish law on quality
Quantitative PCR assay
The Leptospira sp. DNA recovery of each extraction was assessed
by a quantitative PCR (qPCR) assay with previously described
primers and probe . An in-house master mix was used  and
included an internal amplification control (IAC) designed
according to principles previously described . All assays were
performed on an Applied Biosystems 7500 quantitative PCR
System platform using a previously described protocol . Strict
precautions to avoid PCR product carry-over was observed
according to principles previously described . A standard
curve was constructed from 10-fold dilutions of purified genomic
DNA of L. interrogans serovar Icterohaemorrhagiae strain M695
ranging in concentrations from approximately 100,000 leptospira
DNA-copies to 1 leptospira DNA-copy/assay by principles
previously described . The limit of quantification (LOQ) of
the assay was 100 Leptospira sp. DNA copies/assay and the limit of
detection was ,10 Leptospira sp. DNA copies/assay. Ultrapure
water (Invitrogen) was used as NTC. Seven to eight NTC were
included on each of the three qPCR plates used in the experiment.
The qPCR targets Leptospira spp. specific sequences of the 16S
rRNA gene present in two copies in the genome [1,8]. The IAC
included in the assay made it possible to detect even partial
inhibition in assays, where no amplification of the target DNA
The effect on the DNA-recovery by five different extraction
methods (n=50) and the six different blood culture systems
(n=30) was estimated by the copy-number and was assessed by
multiple t-tests on log-transformed data (Logn+1) under Bonferroni
multiple-comparison-test (LSMEANS analysis associated with
PROC GLM, SAS 9.1; SAS Institute, US). The effect of blood
culture media on the Ct value of the IAC was compared by a two-
sample t-test of the mean for each PCR plate.
figure 2 and table 1. M2–M5 removed inhibitors of the PCR to an
extent that allowed amplification of Leptospira DNA in all of the
corresponding qPCR assays. When M1 was applied to the samples,
no amplification of Leptospira DNA was possible and the IAC was
only amplified in two of the 30 corresponding qPCR-assays.
The results of experiment 1 are shown in
Figure 2. Leptospira sp. DNA recovery and inhibition of PCR.
Estimated total copy-number of Leptospira interrogans DNA recovered
from a spiked sample of BACTECTManaerobic Plus containing
approximately 50.000 Leptospira/5 ml by five DNA extraction methods.
The mean copy-numbers are given above each column. Error bars
indicate the 95% confidence interval. M1: Qiagen, DNeasyH Blood &
Tissue Kit; M2: Molzym, MolYsis Plus Kit; M3: Protocol described by
Fredricks and Relman; M4: Improved protocol for anaerobic and
paediatric blood culture media; M5: Improved protocol adapted for
all blood culture media.
Table 1. Effectiveness of DNA extraction method, M1–M5 in recovering Leptospira DNA from BACTECTManaerobic Plus.
Leptospira DNA recovered in percent
of M4 (95% confidence interval) P-value
M1 10020% (0 to 0.02%)P,0.001
M2 1030300.22% (0.16% to 0.29%)P,0.001
M310300 11% (9% to 14%)P,0.001
M5 1030058% (44% to 74%)P,0.031
M1: Qiagen, DNeasyH Blood & Tissue Kit; M2: Molzym, MolYsis Plus Kit; M3: Protocol described by Fredricks and Relman; M4: Improved method for anaerobic and
paediatric blood culture media; M5: Improved method adapted for all blood culture media.
Expanded Use of Leptospira PCR
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The highest effectiveness in recovering Leptospira DNA was
obtained by M4, while M5 resulted in a slightly lower recovery,
58% (95% CI, 44% to 74%; p,0.031) of M4. Due to the
increased dilution of the sample in M5 compared to M4, a
recovery of 76% was expected. Both methods were equally simple
to use and the results were highly reproducible.
The three established methods (M1–M3) all had a significantly
lower effectiveness in recovering Leptospira DNA than both M4 and
M5. For M3, this was reduced to 11% (9%–14%; p,0.001) of M4
and for M2 only 0.22% (95% CI, 0.16% to 0.29%; p,0.001) of
Results of experiment 2 are shown in figure 3.
There was no sign of inhibition of the qPCR in any of the tested
specimens, when M5 was applied to all of the tested blood culture
media. There was no significant difference (n=30; p=0.54) in the
Leptospira DNA-recovery obtained between the six different blood
culture media tested.
Seven of the 36 patients were diagnosed with
leptospirosis by serological findings of either a single serum MAT
titer $1,000 (n=6) or by seroconversion to a MAT titer of 100 in
several serovars in an early convalescence serum sample (n=1). In
one of the seven patients, EMJH-subculture of one of the BCs
(BACTECTMaerobic Plus) was found positive for Leptospira
borgpetersenii senso stricto. From the remaining 29 patients, a
serum sample was available from 21.In five of the 21 patients, a
repeated serum sample taken and tested by MAT during
convalescence and in one of the 21 patients the primary sample
was taken 12 days after the blood cultures. Of the 21 patients, two
had a MAT titer in the acute phase of the disease of 100 and 300
respectively, but on repeated testing during convalescence these
were normalized. These patients were classified as false positive by
All of the seven patients diagnosed with leptospirosis by serology
were positive by qPCR. One additional patient was positive by
qPCR, but negative by MAT. He had only one serum sample
taken at the same time as the blood cultures, and thus, it is likely
that antibodies were not present at the time of sampling. All the
remaining patients were negative by qPCR.
In 7 of the 8 positive patients the DNA-recovery was below
LOQ i.e. they contained less than 100 DNA copies pr. asssay. A
total of 17 BCs were positive by qPCR. The approximate median
recovery in all positive samples was 11 Leptospira DNA-copies pr.
assay (range 1 to 262). In four patients, all of the 2–5 analysed BCs
were positive, while in four patients, where the DNA-recovery was
close to LOD, only half of the 2 or 4 tested BCs were positive. In
one of these last four patients, only one of the duplicate qPCR
assays was positive in one BC.
The Ct value for the IAC was recorded for all 158 qPCR assays
performed on the 79 blood cultures (nBC) where no amplification
of leptospira DNA occurred in any of the two corresponding PCR
assays. The 79 BCs included BACTECTMaerobic Plus, n=17;
BACTECTManaerobic Plus, n=16; BACTECTMPaed Plus,
n=2; BacT/ALERTH SA, n=19, BacT/ALERTH SN, n=19;
BacT/ALERTH FA, n=5; BacT/ALERTH FN, n=1). The
results were compared to the Ct value recorded from the NTC
and the results shown in table 2. A total of 3 plates were used for
testing all clinical samples by qPCR.
In this study we present two improved DNA extraction methods
designed for extraction of DNA from blood culture media, M4 and
M5. The amount of Leptospira sp. DNA recovered by these
methods were 9 and 5 times higher, respectively than what was
obtained by M3, the best performing of the three previously
described methods. This difference can largely be explained by the
use of a column based DNA extraction in M4 and M5 in contrast
to the DNA precipitation method used in M3. The sensitivity of
the diagnostic set-up was remarkable when M4 and M5 were
validated on samples from patients suspected of leptospirosis. At
least one BC, from all of the seven patients that were tested
positive by convalescence serology was also positive by qPCR in at
least one of the duplicate qPCR assay wells. In addition, one
patient was positive by qPCR but never had convalescence
serology performed. These findings indicate that a very high
sensitivity close to 100% can be obtained by this diagnostic set-up.
The results are comparable to what have been found in a recent
study where qPCR was compared to culture of Leptospira spp. ,
but remarkably higher than the 28–50% sensitivity that has
previously been reported when PCR has been applied to whole
blood samples in severe leptospirosis and compared with MAT
[4,11]. Four factors are likely to be important for this difference. In
Figure 3. DNA recovery from different blood culture media.
Estimated total copy-number of Leptospira interrogans DNA recovered
from spiked samples of six different blood culture media containing
approximately 50.000 Leptospira/5ml. All DNA extractions were per-
formed with M5, the improved protocol adapted for all blood culture
media. The mean copy-numbers are given above each column. Error
bars indicate the 95% confidence interval. BD-AE: BACTECTMaerobic
Plus, BD-AN: BACTECTManaerobic Plus, BD-Ped: BACTECTMPaed Plus,
BacT-SA: BacT/ALERTH SA, BacT-SN: BacT/ALERTH SN and BacT-PF: BacT/
Table 2. Comparison of the mean Ct value of the internal
amplification control in no-template controls and blood
cultures tested negative for Leptospira sp. DNA.
qPCR run No-template controlNegative blood culture P-value
n CtSDn Ct SD
1733.8 0.4 52 33.5 0.3p.0.05
37 34.10.37234.0 0.2p.0.05
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PLoS ONE | www.plosone.org5 August 2010 | Volume 5 | Issue 8 | e12095
this study, at least two blood samples from each of the qPCR
positive patients were tested. Only in 4 of the 8 positive patients,
all BCs were positive by qPCR and this indicates that it is
important to test at least two samples. Further, in one patient only
one of duplicate qPCR assay wells was positive close to LOD.
Even though such a result in a clinical situation needs further
confirmation, the diagnosis might have been missed if the qPCR
assay had not been tested in duplicate. Previous studies do not
report having tested more than one sample from each patient nor
do they report having performed more than one PCR assay for
each sample [4,11]. Furthermore, in this study BCs were tested
and not serum or whole blood samples and this might affect the
number of Leptospira spp. present in the samples. Five of the eight
PCR positive patients were positive in more than one BC. The
recovery of Leptospira DNA from the aerobic and the anaerobic BC
were comparable in four of these patients but in one patient, the
recovery of Leptospira DNA in BacT/ALERTH SA and BacT/
ALERTH FA was .10 times higher than what was obtained from
BacT/ALERTH SN, sampled at the same time. This suggests that
some multiplication of the bacteria had occurred. The use of BCs
and time of incubation might, therefore, at least in some cases play
a role in the sensitivity of the assay, but we did not record the exact
incubation period. Lastly, DNA precipitation technique has been
used in previous studies for DNA-extraction and as we have shown
in experiment 1, this is likely to result in a lower recovery of DNA
compared with the column based method used in M4 and M5.
The low DNA-copy-number present in the clinical samples stresses
the importance of optimal microbial DNA recovery. It is therefore
likely that neither M2 nor M1 can be used for diagnostic PCR in
Fredricks and Relman were the first to effectively solve the
problems of removing all inhibitors of the PCR from BCs. They
indentified the anti-coagulant sodium polyanetholesulfonate (SPS)
present in a anaerobic media of BacT/ALERTH as a potent
inhibitor of PCR not readily removed by most extraction methods
 and came up with a benzyl alcohol based extraction method,
M3 to solve this problem . However, M3 is, in our experience,
not very robust in a clinical setting, especially when applied to
aerobic BCs and for that reason the method has previously been
rejected . M4 and M5 have been developed on the basis of
M3. By incorporating Proteinase K treatment in the lysis step,
increasing the speed of centrifugation to 20.0006g in the phase
separation step and for M5 by further adding extra water in the
phase separation step all problems of carry-over of inhibitors to the
final DNA preparation were completely solved. Throughout all
the experiments, M4 and M5 were very robust and easy to use and
as they are based on column-based DNA extraction, both methods
are amenable to automation.
The IAC is a very sensitive way to detect inhibitors of the PCR,
but in none of the experiments were there any signs of inhibition of
the qPCR assay when M4 and M5 were used. A more exact
estimate of this was given in experiment 3, by comparing for each
qPCR plate the Ct value of the IAC of the NTC with the Ct value
of the IAC in the BC samples where no amplification of Leptospira
spp. DNA occurred. These 79 BCs included 5 BCs containing
charcoal. No significant difference was observed in any of the
assays and, thus, no sign of inhibition of the qPCR assays (table 2).
Furthermore, no significant difference between in the recovery of
Leptospira sp. DNA was observed when M5 in experiment 2 was
applied to 6 different blood culture media from a total of 30
To our knowledge, only one study by Gebert et al. has
previously addressed the issue of recovering low amounts of
bacterial DNA from blood cultures . In that study, a near full
recovery of Staphylococcus aureus DNA was obtained by M2, but
when the method was applied to Escherichia coli the recovery was
somewhat lower. In general, Gram-negative bacteria like E. coli
and especially Leptospira spp. have a more fragile cell wall than
Gram-positive bacteria. In M2, human cells are lysed and the
DNA removed in the initial steps. Preliminary results suggest that
the low recovery obtained by M2 in our study partly can be
explained by a huge loss of bacterial DNA during these
If used with the described or slightly modified protocols, it is
likely that BCs can be used in the diagnosis of other fastidious
microorganisms like Coxiella burnetii  and dengue virus  in
the future. It is also likely that the protocols will find use in severe
infections like meningitis, where antibiotic treatment sometimes
foregoes sampling of BCs and there by prevents the causative
agent from growing in the media. Preliminary results suggest that
M4 and M5 can be applied to Neisseria meningitidis and Streptococcus
pneumoniae with a similarly high DNA recovery (data not shown).
The diagnosis of leptospirosis in non-endemic countries will
often rely on convalescence serology since relevant samples for
diagnostic PCR are difficult to obtain. In this study, two improved,
easy and robust DNA extraction methods are presented. Both
methods effectively removed all inhibitors of the PCR and they
were found superior to three previously described methods in
recovering Leptospira sp. DNA from blood cultures. This study,
further, suggests that most cases of severe leptospirosis can be
diagnosed by specific PCR if the described DNA extraction
methods are applied to blood cultures routinely obtained from
most septic patients and incubated for at least five days.
Consequently, in the future, most cases of severe leptospirosis
can be diagnosed by PCR in the early phase of the disease.
Laboratory technician Birthe Dohn is thanked for assisting during the
laboratory experiments. Per Moestrup Jensen is thanked for critic statistical
review. Klaus Leth Mortensen is thanked for critical review of the
Conceived and designed the experiments: SV KAK JSJ. Performed the
experiments: SV RP. Analyzed the data: SV RP JSJ. Contributed
reagents/materials/analysis tools: SV KAK JSJ. Wrote the paper: SV
RP KAK JSJ.
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