A Novel Real-Time PCR Assay For Specific Detection of Brucella Melitensis
A Novel Real-Time PCR Assay For Specific Detection of Brucella Melitensis
A Novel Real-Time PCR Assay For Specific Detection of Brucella Melitensis
Abstract
Background: Brucellosis is a zoonosis that occurs worldwide. The disease has been completely eradicated in
livestock in Sweden in 1994, and all cases of confirmed human brucellosis are imported into Sweden from other
countries. However, due to an increase in the number of refugees and asylum seekers from the middle-east to
Sweden, there is a need to improve the current diagnostic methodology for Brucella melitensis. Whilst culture of
Brucella species can be used as a diagnostic tool, real-time PCR approaches provide a much faster result. The aim of
this study was to set up a species-specific real-time PCR for the detection of all biovars of Brucella melitensis, which
could be used routinely in diagnostic laboratories.
Methods: A Brucella melitensis real-time PCR assay was designed using all available genomes in the public database
of Brucella (N = 96) including all complete genomes of Brucella melitensis (N = 17). The assay was validated with a
collection of 37 Brucella species reference strains, 120 Brucella melitensis human clinical isolates, and 45 clinically
relevant non-Brucella melitensis strains.
Results: In this study we developed a single real-time PCR for the specific detection of all biovars of Brucella melitensis.
Conclusions: This new real-time PCR method shows a high specificity (100%) and a high sensitivity (1.25 GE/μl) and
has been implemented in the laboratories of four governmental authorities across Sweden.
Keywords: Brucella melitensis, Brucellosis, Real-Time PCR
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Kaden et al. BMC Infectious Diseases (2017) 17:230 Page 2 of 6
(BSL-3) is mandatory when handling Brucella organisms. This as necessary due to the lack of necessary genome
Laboratory-acquired infections are rarely diagnosed or data in the publicly available databases at the start of this
reported, however they do occur [9, 10]. project [14]. The panel to validate the inclusivity and ex-
The application of DNA-based methods for Brucella clusivity of the real-time PCR assay contained all known
diagnosis is challenging, since all Brucella species have a biovars of Brucella, as well as 45 other non-Brucella
very high degree of genetic homology (up till 99.9%), as DNA from American Type Culture Collection (ATCC),
shown by whole genome sequencing of B. abortus, B. Culture Collection University of Gothenburg (CCUG)
melitensis, and B. suis [11–14]. However, several groups and National Collection of Type Cultures (NCTC) with
have recently developed PCR-based assays for the dis- clinical relevance. A number of environmental samples,
crimination among species and biovars of Brucella. as well as the closely related species Ochrobactrum
Three Brucella species B. abortus, B. melitensis, and B. anthropi, were also tested in this study (Tables 1 and 2).
suis have been sub-typed into biovars [15, 16]. All spe-
cies within the genus Brucella show an average similarity Bacterial strains and growth conditions
of 99% across the entire genome and a range between A collection of 31 Brucella sp. reference strains (Table 1)
93% and 99.9% based on analysis and nonparametric in- and 120 B. melitensis human clinical isolates were iso-
ference (ANI) analysis. Data from all public available lated in the BSL-3 laboratory at the FOHM, by cultiva-
complete genome sequences of all type strains and refer- tion on 5% sheep blood agar plates in a 5%–10% CO2
ence strains were included in the design of primers and atmosphere at 37 °C for 48 h. All non-Brucella strains
probes for the real-time PCR assay of this study. One were routinely cultivated on 5% sheep blood agar over
multiplex PCR (AMOS) developed by Bricker and Halling night at 37 °C.
in 1994, is applicable to differentiate between B. abortus The B. melitensis human clinical isolates were col-
biovars 1, 2 and 4, B. melitensis, and B. ovis, B. suis biovar 1 lected between 1994 and 2016 from Swedish patients,
by specific PCR products based on unique chromosomal who had returned from Brucella-endemic countries, in a
loci of the mobile genetic element IS711 in their genome biorepository of the FOHM and used as stipulated in the
[17]. This PCR was later improved by another laboratory by regulations for diagnostic development and quality as-
adding specific primers for the identification of B. abortus sessment. The FOHM performs all Brucella diagnostics
biovars 5, 6, 9 and genotype 3b of biovar 3 [18]. In 2009, on human samples in Sweden, and the B. melitensis iso-
Huber et al. developed a random amplified polymorphic lates used in this study have previously been confirmed
DNA PCR assay to differentiate all recognized Brucella by cultivation, a general real-time PCR amplifying DNA
species, including the marine mammals-infecting species B. of all Brucella strains, as well as by Matrix Assisted
ceti and B. pinnipedialis [19]. However, all published Laser Desorption/Ionization Time of Flight Mass Spec-
methods are developed to distinguish species and biovars trometry (MALDI-TOF MS) [22, 23]. Ethical review of
mainly by gel-based bar patterns and the majority of de- research involving humans is not applicable for diagnos-
scribed methods were tested with a few strains. tic development and quality assessment.
Kim et al. [20] developed a new real-time PCR for dis-
tinguishing B. abortus from other Brucella species, DNA extraction
which is based on a single nucleotide polymorphism. Bacterial DNA was extracted using the commercially
However, there was a need for a reliable real-time PCR available EZ1® DNA Tissue Kit from (Qiagen, Stockholm,
for the detection of B. melitensis at the species level [21]. Sweden) according to the protocol from the manufacturer
The method has to be validated for clinical purposes and stored at 4 °C until use. A volume of 5 μl of seal her-
with a large number of human isolates to fulfill the val- pes virus cell culture was used in each sample of the total
idation requirements of the certified laboratory of the volume of 200 μl in the extraction step as a process con-
public health institute. A Brucella genus specific real- trol. Each sample was eluted in 50 μl elution buffer.
time PCR assay is currently in use at the Public Health
Agency in Sweden (FOHM). However, B. melitensis is Bioinformatic analyses, primer & probe design and
the most prevalent species, and we need to be able to real-time PCR
differentiate to the species level, due to the epidemio- In order to identify a B. melitensis-specific target(s), all
logical significance of B. melitensis [21]. available genomes in the public database of Brucella
(N = 96) including all complete genomes of B. melitensis
Methods (N = 17) were used in the design of primers and probes.
With the aim of developing a real-time PCR assay for A 2 basepair deletion which is highly specific for B. meli-
the detection of all known species and biovars of B. tensis was found in the acetyl-CoA acetyltransferase
melitensis, the genomes of B. ceti, B. inopinata, B. neoto- gene. Primers were designed flanking this deletion and a
mae and B. suis biovar 4 were sequenced and analyzed. short 12-mer MGB probe was placed over the area with
Kaden et al. BMC Infectious Diseases (2017) 17:230 Page 3 of 6
Table 1 Reference strains tested to assess the sensitivity of The real-time PCR assays were carried out in 25 μL
Brucella melitensis specific real-time PCR assay reaction mixtures containing 5 μL template DNA, in
Species Biotype Strain PerfeCta Multiplex qPCR SuperMix (Applied Biosys-
B. melitensis 1 16 M tems®) diluted in UltraPure™ DNase/RNase-Free Distilled
1 ATCC 23456 Water (Invitrogen™), 0.9 μM of each primer, and 0.2 μM
probe. Amplification and detection were performed
1 NCTC 10094
using two different PCR machines, an ABI-7500/96-well
2 NCTC10508
plates real-time FAST PCR platform, and a StepOne
3 NCTC 10509 Plus real-time PCR system (Applied Biosystems®).
2065 Thermocycling parameters were as follows: inactivation
B. abortus 1 ATCC 23448 95 °C for 3 min, followed by 45 cycles 95 °C for 3 s, and
1 544 annealing at 60 °C for 30 s. The baseline and threshold
were set using the auto-baseline and threshold feature in
1 NCTC 00624
StepOneplus Software v2.2.2 (Applied Biosystems®). Sam-
2 NCTC10501
ples were considered positive if target amplification was
3 NCTC10502 detected within 40 cycles.
4 NCTC10503
5 NCTC10504 Determination of the real-time PCR limit of detection
6 NCTC10505 The limit of detection (LOD) was defined by using the
7 NCTC10506 Brucella ATCC 23456 strain with 106, 105, 104, 103, 102,
9 NCTC10507 50, 25, 12.5, 6.25, 3.125, 1.56, 0.78, 0.39 genome equiva-
lents per reaction. LOD samples were analysed in six
B. suis 1 ATCC 23444
replicates for each concentration and with five runs on 5
1 NCTC 10316
days (Fig. 1).
1 NCTC 12042–01
2 NCTC 10510
Internal amplification control (IAC)
3 NCTC 10511 As internal amplification control (IAC), Phocine Herpes-
4 NC 10385–02 virus 1 (PhHV-1) aliquots with a known DNA concen-
5 NCTC 11996 tration and a target quantification cycle (Cq) of 32 was
1720 used [24].
1030
B. canis ATCC 23365 Results and discussion
Real-time PCR is a rapid and reliable method for the
SVA13
analysis of Brucella in clinical samples. However, the
NCTC 10854
high genomic similarity between different Brucella spe-
3.4.2008/122 cies makes the design of a species-specific real-time PCR
E20140122–106 assay difficult. An alternative attempt to use a probe
B. ovis ATCC 25840 (FAM-CCGCCGAGATACAAA) with Tm 68–70 °C (Pri-
NCTC 10512 mer Express v 3.0) resulted in a signal for all Brucella
species, but also a signal for non-melitensis species. To
B. ceti NCTC 12891
increase the discriminatory effect, a shorter probe
B. inopinata CAPM 6436
(FAM-CCGAGATACAAA-MGB) with Tm 57 °C was
B. microti CAPM 6434 used. By using this shorter probe we could eliminate all
B. neotomae ATCC 23459 the non-specific amplification derived from other Bru-
B. pinnipedialis NCTC 12890 cella species than B. melitensis.
The method was validated according to Broeders et
al. 2014 [25] and according to the validation standards
the deletion. The forward nucleotide sequence 5′-GC of the Swedish National Veterinary Institute (SVA), the
TCGACACAAAGGGCCA-3′ (Biomers, Germany) and Public Health Agency of Sweden (FOHM), the Swedish
the reverse nucleotide sequence 5′-CAAGCGTGGTCT National Food Agency (NFA) and the Swedish Defense
GGCGA-3′ (Biomers, Germany) were used with the FAM- Research Agency (FOI). The validation comprised ap-
labelled hydrolysis probe -CCGAGATACAAA-MGB (Ap- plicability, practicability, specificity, linearity, and
plied Biosystems®). sensitivity.
Kaden et al. BMC Infectious Diseases (2017) 17:230 Page 4 of 6
Table 2 None Brucella strains used in the study for exclusivity Table 2 None Brucella strains used in the study for exclusivity
test test (Continued)
Species Strain Taylorella equigenitalis CCUG 16464
Actinobacillus pleuropneumoniae CCUG 12837 Yersinia enterocolitica CCUG 8239
Actinomyces pyogenes CCUG 13230 Yersinia pestis 570-04
Alcaligenes denitrificans CCUG 407 Yersinia pseudotuberculosis CCUG 5855
Bacillus antracis NCTC1328
Bacillus cereus CCUG 7414 Applicability
Bacillus subtilis ATCC 6633 No false positive or false negative result is acceptable in
Bacteroides fragilis ATCC 25285 clinical BSL3 pathogen diagnostics. To guarantee a cor-
Bordetella bronchiseptica CCUG 219 rect identification of BSL3- pathogens, we strongly rec-
ommend isolation of the bacteria on selective Brucella
Burkholderia mallei NCTC120
agar plates. This enables evaluation of the phenotypic
Burkholderia pseudomallei NCTC8707
properties of the strains, such as colony morphology,
Clostridium perfringens CCUG 1795 and enriches the molecular target of the PCR, as well as
Enterococcus fecalis ATCC 29212 reduces the concentration of potential PCR inhibitors.
Erysipelotrix rhusiopatiae CCUG 221 Even after the enrichment an internal PCR process con-
Escherichia coli ATCC 35218 trol is recommended as described above. All strains in
our validation were cultured under the same conditions
Escherichia coli (EHEC) EDL333
as bacterial strains were isolated in the clinical diagnos-
Escherichia coli (VTEC) 2954-06
tics workflow. The real-time PCR method was therefore
Fusobacterium necrophorum CCUG 9994 recognized as applicable in combination with the isola-
Haemophilus influenzae ATCC 49247 tion of bacteria from clinical specimens.
Haemophilus somnus CCUG 28029
Klebsiella oxytoca CCUG 15717 Specificity
The assay was tested with 120 human clinical B. meliten-
Klebsiella pneumoniae CCUG 225
sis isolates, 31 other non B. melitensis Brucella strains,
Listeria monocytogenes CCUG 15527
45 non B. melitensis strains, and 6 B. melitensis refer-
Nocardia asteroides CCUG 10073 ence strains. There was no amplification from any other
Ochrabactrum anthropi ATCC 49188 Brucella species other than B. melitensis. The specificity
Pasteurella multocida CCUG 229 of this method was 100% because all 126 B. melitensis
Pasteurella pneumotropica CCUG 12398 samples were tested positive while all 76 non-B. meliten-
sis samples gave no amplification in the real-time PCR.
Proteus mirabilis CCUG 26767
Pseudomonas aeruginosa CCUG 17619
Practicability
Rhodococcus equi CCUG 892 The assay was used for the identification of Brucella
Salmonella Dublin CCUG 35631 samples from the first External Quality Assurance Exer-
Salmonella Thyphimurium CCUG 31969 cises (EQAEs) on highly infectious agents (BSL-3) from
Salmonella Zanzibar CCUG 41921 the EU financed project “Efficient response to highly
dangerous and emerging pathogens” (EMERGE). The re-
Staphylococcus aureus CCUG 4151
sults obtained with this assay conformed to the results
Staphylococcus intermedius CCUG 49053
of other laboratories.
Streptobacillus moniliformis CCUG 33440
Streptococcus agalactiae CCUG 39325 Sensitivity
Streptococcus dysgalactiae CCUG 27436 The limit of detection was 6.25 genome equivalents of B.
Streptococcus equi CCUG 27367 melitensis (ATCC 23456) per reaction of template DNA
(1.25 GE/μl). At a DNA concentration of 3.125 genome
Streptococcus pyogenes CCUG 12701
equivalents per reaction, 80% of the reactions were still
Streptococcus uberis CCUG 27444
positive (Fig. 1).
Streptococcus zooepidemicus CCUG 23256
Linearity
The linear dynamic range of this PCR assay was deter-
mined by testing serially diluted DNA of B. melitensis
Kaden et al. BMC Infectious Diseases (2017) 17:230 Page 5 of 6
Fig. 1 Limit of detection was determined by assaying six replicates of ten and two fold serially diluted DNA of strain Brucella melitensis ATCC
23456 in five separate experiments. The number of positives per total number of replicates tested is shown in the figure
strain ATCC 23456. The regression coefficient calculated We thank Finnish Food Safety Authority Evira for sending us their two
from the regression line in the standard curve was Brucella canis isolates 3.4.2008/122 and E2014122-106.
Author details 20. Kim J-Y, Kang S-I, Lee JJ, Lee K, Sung S-R, Erdenebaataar J, Vanaabaatar B,
1
Department of Medical Sciences, Clinical Microbiology, Uppsala University, Jung SC, Park YH, Yoo H-S, et al. Differential diagnosis of Brucella abortus by
Uppsala, Sweden. 2National Veterinary Institute, Uppsala, Sweden. 3Swedish real-time PCR based on a single-nucleotide polymorphisms. J Vet Med Sci.
Forum for Biopreparedness Diagnostics, Stockholm, Umeå and Uppsala, 2016;78(4):557–62.
Sweden. 4Department of Microbiology, The Public Health Agency of Sweden, 21. Andriopoulos P, Tsironi M. Molecular Diagnosis of Brucellosis: A Brief Report.
Stockholm, Sweden. Adv Mol Diagn. 2016;1(2):108-10.
22. Drevinek M, Dresler J, Klimentova J, Pisa L, Hubalek M. Evaluation of sample
Received: 16 November 2016 Accepted: 16 March 2017 preparation methods for MALDI-TOF MS identification of highly dangerous
bacteria. Lett Appl Microbiol. 2012;55(1):40–6.
23. Lista F, Reubsaet FA, De Santis R, Parchen RR, de Jong AL, Kieboom J, van der
Laaken AL, Voskamp-Visser IA, Fillo S, Jansen HJ, et al. Reliable identification at
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