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Applied and Environmental Microbiology, October 2005, p. 5759-5764, Vol. 71, No. 10
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.10.5759-5764.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Department of Applied Microbiology, Lund Institute of Technology, Lund University, SE-221 00 Lund, Sweden,1 Canadian Research Institute for Food Safety, Guelph University, Guelph, Ontario N1G2W1, Canada,2 Quintessence Research AB, SE-746 93 Bålsta, Sweden,3 Danish Institute for Food and Veterinary Research, DK-1790 Copenhagen, Denmark4
Received 18 January 2005/ Accepted 29 April 2005
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Due to the aforementioned problems with Campylobacter detection, PCR and real-time PCR have been increasingly used for detection (12, 17, 21, 25). While this technology has tremendous potential for sensitive and simple identification, further studies addressing the quantification aspect of this technology are required before it can be widely accepted. There are limitations to the application of PCR technology. First of all, detection from food samples such as poultry or poultry rinses may be limited due to the presence of PCR inhibitors (12). Secondly, nucleic acid-based detection methods do not differentiate between nucleic acids originating from dead or viable/VNC cells, introducing a risk for false-positive results (21). This has resulted in a great demand for sample treatment methods that can overcome PCR inhibition and are capable of differentiating between viable and dead cells (17).
Recently, a novel sample treatment method called flotation, which is based on traditional buoyant density centrifugation, was developed (26). Using Yersinia enterocolitica as a model system, it was shown that this method can separate the target organism from environmental sample matrices and background flora (BGF) based on differences in buoyant densities. Further studies showed that this method could be successfully employed to reduce the risk of false-negative results due to detection of DNA originating from dead cells (27). The aim of the present study was to develop a flotation real-time PCR method which can be used to rapidly detect and quantify viable and VNC cells of C. coli, C. jejuni, and C. lari without false-positive results due to detection of DNA originating from dead cells. Also, to ensure correct detection of naturally contaminated samples, the buoyant density behavior of different Campylobacter spp. strains was investigated at different time points during growth. Finally, this method was tested on spiked and naturally contaminated samples.
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Buoyant density measurements.
Throughout the study three different colloidal density gradient media, all formulated from RediGrad (Amersham Biosciences AB, Uppsala, Sweden) were used: BactXtractor-L (BX-L), with a density of 1.058 g/ml, pH of 7.5, and osmolality of 322 mOsm/kg; BactXtractor-M (BX-M), with a density of 1.132 g/ml, pH of 7.5, and osmolality of 300 mOsm/kg; and BactXtractor-H (BX-H), with a density of 1.309 g/ml, pH of 7.5, and osmolality of 340 mOsm/kg (BactXtractor is a registered trademark of QRAB, Bålsta, Sweden). For all three media the pH was adjusted with 1 M HCl and the osmolality was adjusted using a Roebling osmometer (Labex Instruments AB, Helsingborg, Sweden) by the addition of ultrapure (99.99%) NaCl. The final densities of BX-L and BX-H were reached after dilution and concentration of RediGrad. After the pH and the osmolality had been set, BX-M had a density of 1.132 g/ml and needed no further adjustment. Densities were measured using a DMA46 density meter (Instrument AB Lambda, Stockholm, Sweden).
Buoyant densities of microorganisms and food particles were determined as described by Pertoft (19). Briefly, 6 ml of BX-M was mixed with 2 ml sample, 2 ml physiological saline, and 50 µl of a density marker bead (DMB) solution (Amersham Biosciences AB) in a plastic 15-ml conical tube. Centrifugation was performed at 10,000 x gav for 30 min at room temperature, using an angle rotor. A plot describing the density of different locations in the self-generating gradient was made by measuring the distance from the bottom of the tube to the different layers of DMB and plotting the known densities of the different DMB (in g/ml) versus distance (in cm).
Flotation conditions.
For flotation prior to quantitative PCR, a one-step flotation setup was used, based on a method described by Wolffs et al. (26) and redesigned for Campylobacter (see Fig. 2). In brief, three layers with different densities were carefully layered below each other. The bottom layer consisted of a high-density solution mixed with the sample to a density of approximately 1.200 g/ml. The middle and top layers had densities of 1.109 and 1.065 g/ml, respectively. The resulting discontinuous gradients were centrifuged for 15 min at 4,500 x gmax in a swing-out rotor, and afterwards 1-ml samples were taken, using sterile 2-ml syringes, for further analysis. The samples were added to 2-ml Eppendorf tubes, diluted with physiological saline to 2 ml (to obtain a density of the solution that allowed pelleting of cells), and centrifuged at 13,000 x gmax in a benchtop Eppendorf centrifuge for 5 min. Afterwards, 1.5 ml of the supernatant was removed and the cells were resuspended in the remaining 0.5 ml to obtain a 2x concentrated sample.
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FIG. 2. Overview of the flotation setup. This setup is used to recover viable and VNC cells with buoyant densities of 1.065 and 1.109 g/ml. The Campylobacter recovery location is at the upper interface. The buoyant densities of the different colloidal solutions used in the two setups are shown. *, the density of the lowest layer may vary slightly because it consists of sample mixed with colloidal silica solution. Since the density of the sample may vary, this can impact the final buoyant density of this layer.
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Campylobacter DNA was purified using an Invitrogen EasyDNA kit (Invitrogen, Groningen, The Netherlands). Tenfold dilutions of Campylobacter between 0.01 and 1.36 x 107 genomic DNA copies were used to obtain standard curves. The number of genomic copies was determined according to previous studies, in one of which Josefsen et al. calculated that 1 C. jejuni genome weighs 1.7 fg (5,15). Standard curves with cells were created using 10-fold dilutions of cell cultures. Cells were lysed by incubation at 95°C for 5 min. All measurements were run at least in independent duplicate runs. After amplification, Cp results were plotted against the log of the initial number of genomes. From this graph, the linear range was determined. After determination of the linear range of amplification, linear regression was used to calculate the slope of the Cp-versus-log initial DNA or cell concentration plot using the points in the linear range. From this slope the amplification efficiency (AE) was calculated using the following equation: AE = (10-1/slope) 1 (6).
Quantification of viable cells and mixtures of VNC and dead cells.
For the spiked and naturally contaminated samples, chicken samples were spiked or analyzed directly by two different methods: direct plating using Preston agar and real-time PCR. To obtain quantitative real-time PCR measurements, a standard curve created for whole cells was used. For the second experiment, i.e., the VNC/dead cell experiment, cells of C. jejuni ATCC 33291, C. jejuni ATCC 29428, and C. jejuni CCUG 10937 were kept in Bolton broth for a period of 21 days at three different storage temperatures, i.e., 4°C, 20°C, or 42°C, under a microaerobic atmosphere and then stained with CTC (5-cyano-2,3-ditolyl tetrazolium chloride) and DAPI (4'-6-diamino-2-phenylindole, dihydrochloride) as described by Cappelier et al. (2). Briefly, 0.5 ml brain heart infusion medium (Oxoid) was mixed with 0.1 ml of a 0.05 g/liter solution of pyruvic acid (Sigma) and 0.5 ml cell suspension. CTC was added to a final concentration of 5 mM and incubated for 4 h at 37°C. Cells were then harvested by filtration on black isopore polycarbonate membrane filters (0.2-µm pore size and 25-mm diameter; Millipore, Watford, England) and covered with 5 mg/liter DAPI (Sigma) solution for 5 min for counterstaining. Counts were obtained randomly by counting 2 times 20 fields per filter and, for each sample, two filters were counted.
The number of metabolically active cells (VNC) was divided by the total number of cells as determined by DAPI staining in order to acquire a relative amount of VNC cells in the mixture. To ensure the absence of culturable cells, plate counts were performed. After this, 1 ml of each mixture was subjected to flotation. After flotation, 1-ml samples were withdrawn from the Campylobacter recovery location and, as a control, from the top of the lower layer and the top of the upper layer. Afterwards the cells were added to 2-ml Eppendorf tubes, diluted with physiological saline to 2 ml (to obtain a density of the solution that allowed pelleting of cells), and centrifuged at 13,000 x gmax in a benchtop Eppendorf centrifuge for 5 min. Afterwards, 1.75 ml of the supernatant was removed and the cells were resuspended in the remaining 0.25 ml, after which they were heated for 5 min at 95°C to obtain cell lysis. These final samples were analyzed by quantitative PCR. Standard curves for absolute quantification were made with overnight cultures of known CFU/ml diluted in physiological saline. This implied that data acquired from both layers, even when originating from dead and VNC cells, were expressed in terms of CFU/ml.
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FIG. 1. Changes in buoyant densities of three C. jejuni strains during a period of 14 days. (A) C. jejuni CCUG 10937; (B) C. jejuni ATCC 33291; (C) C. jejuni ATCC 29428. , cell counts observed over time (y axis). The vertical lines represent the buoyant density window (z axis). *, faint bands due to low cell densities. The horizontal dotted lines indicate the limits between the two upper flotation solutions. To concentrate the target at the Campylobacter recovery location, the density has to fall between these two marked densities.
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Quantification of viable and VNC Campylobacter cells.
In order to have a highly specific quantitative PCR assay compatible for use with the LightCycler real-time PCR machines, a set of hybridization probes was developed for an already published primer pair. The linear range of amplification for the developed method was between 1.39 and 1.39 x 107 genomic DNA copies per PCR (Fig. 3). The amplification efficiency was calculated from the slope over the linear range of amplification and was 0.87 (R2 = 0.9985). To test the developed method on chicken samples, two experiments were set up. In the first experiment the detection of artificially and naturally contaminated samples with different populations and amounts of viable and dead cells was tested (Table 1). The first group of samples consisted of artificially spiked chicken skin rinses. The samples were tested both with plate counts and with real-time PCR after flotation. Results showed that cell concentrations from 2.6 x 107 CFU/ml to as low as 2.6 x 103 CFU/ml or 10 CFU/PCR mixture could be quantified after performing flotation and quantitative PCR. The cell counts obtained by plate counts and flotation followed by real-time PCR were of the same order of magnitude but in most cases were lower for the flotation. A second group of samples consisted of uninoculated samples that were purchased at local supermarkets and tested for the presence of Campylobacter. After analysis by selective plate counts and flotation combined with quantitative PCR, Campylobacter spp. were detected in only 3 out of 30 samples. Of those samples, two samples had cell counts that fell within the linear range of amplification and could be correctly amplified, whereas one sample had a lower cell number (<2.6 x 103 CFU/ml). Concentrations below the linear range of amplification can still be identified as positive (as was confirmed by melting curve analysis). These results are considered to be semiquantitative, and in this case cell numbers were estimated by extrapolation of the standard curve.
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FIG. 3. Standard curve for hybridization probe Campylobacter real-time PCR assay. Data are the results from duplicate analyses.
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TABLE 1. Quantification of Campylobacter spp. in artificially and naturally contaminated chicken samples
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TABLE 2. Quantification of VNC C. jejuni after flotation, by real-time PCRe
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Because of the relatively large density window chosen for the flotation setup, it was not possible to avoid concentration of some BGF and chicken particles at the Campylobacter recovery location. Still, no PCR inhibition was observed, which can be explained by the use of the alternative DNA polymerase Tth. Previous studies have already shown that when using this enzyme in real-time PCR, a lower sensitivity towards PCR inhibitors was observed (11, 13).
To optimize possibilities for quantification, fluorescent hybridization probes were designed with an existing primer pair. The specificity of the assay was not extensively tested again, as it is based on specific primers, previously validated against 150 related and nonrelated species (12). The use of fluorescent probes was selected due to an increased sensitivity compared to the use of SYBR Green and to allow possible combination with simultaneous detection of an internal control. With a linear range of amplification stretching from 1.36 genomic copies to 1.36 x 107, this assay was shown to be as sensitive or up to 1 log unit more sensitive than previously published real-time probe-based PCR assays, based on the same (5, 18) and other (4, 8) primer sets.
Finally, applying flotation and the developed real-time PCR assay to different types of samples showed that cell concentrations as low as 860 CFU/ml or 3.4 CFU/PCR mixture could be positively identified without culture enrichment. Also, it confirmed that flotation and real-time PCR combined methods can be applied to a wide range of cell concentrations. Currently, flotation is run without concentration, i.e., 1 ml of sample is subjected to flotation and 1 ml is recovered afterwards. For future applications where lower cell concentrations are expected, it is possible that larger sample volumes can be used in flotation and in determining target concentrations. Although the results between plate counts and flotation followed by real-time PCR were on the same order of magnitude, the samples subjected to flotation showed lower concentrations (on average, 75% of the plate counts). Previous flotation studies have shown that this is due to inefficient sampling from the target recovery location. However, the recovered fractions in this study are higher than previously reported for Y. enterocolitica (26).
Results on dead and VNC cells showed that false-positive results due to detection of DNA originating from dead cells were minimized, since no signals were recovered from the Campylobacter recovery location containing 99% dead cells (Table 2). This is in agreement with previous flotation studies, which have shown that due to the low flotation speed of DNA it does not reach the target recovery location (26, 27). Furthermore, results indicated that VNC cells are detected together in the same density window with viable cells after flotation and real-time PCR. This was the original aim of the procedure, since previous studies indicated that VNC cells are still infectious (22). In the present study it was impossible to obtain fractions of VNC cells large enough to allow visual buoyant density determinations. Nonetheless, it seems possible that, keeping in mind results by Tholozan et al. concerning uptake of water by VNC cells (24) and the observed lowering in buoyant density in most strains after 14 days (Fig. 1), a lower buoyant density could indicate a transition into the VNC state. This suggests that it might be possible to separate VNC and viable cells in the future.
In conclusion, we have developed a new flotation technique for isolation of C. coli, C. jejuni, and C. lari in chicken rinse to be used prior to quantitative PCR, and the combined methods could detect Campylobacter spp. as low as 8.6 x 102 CFU/ml without culture enrichment. The method reduced PCR inhibition by BGF and chicken rinse samples and was able to minimize the risk of false-positive results due to detection of DNA from dead cells. Also, results indicated that VNC cells were recovered with viable cells and, therefore, false-negative results were avoided. Finally, the results emphasized the importance of studies concerning changes in buoyant density in different growth phases, especially when buoyant density is used for separation of target cells in sample treatment.
This work was financially supported by the Commission of the European Communities within the program "Quality of Life and Management of Living Resources," QLK1-1999-00226, the Nordic Innovation Centre, and the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 2001-4068.
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