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Applied and Environmental Microbiology, February 2003, p. 1082-1088, Vol. 69, No. 2
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.2.1082-1088.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Department of Food Science, College of Life Science and Agriculture, North Carolina State University, and Southeast Dairy Foods Research Center, Raleigh, North Carolina 27695-7624
Received 20 March 2002/ Accepted 1 November 2002
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An important rate-limiting step for the PCR lies in the fact that amplification products are detected most commonly by postamplification agarose gel electrophoresis and/or DNA hybridization. In an effort to reduce the time necessary for detection and confirmation, a number of investigators have described methods to simplify or even eliminate the need to perform postamplification assays. For example, molybdate (7) and some intercalating agents (9) have been used to measure the degree of DNA amplification, but these protocols are limited because they do not consider amplicon sequence specificity. Other investigators have focused their efforts on adapting the fluorescence resonance energy transfer (FRET) phenomenon to the detection of specific PCR amplicons, including AmpliSensor (5), molecular beacons (16, 25), Amplifluor (17), Scorpions primers (26), and adjacent hybridization probes (29). Of particular note in recent years is the TaqMan assay (Applied Biosystems, Foster City, Calif.), which has been applied to the detection of food-borne pathogens, including Listeria monocytogenes (1, 6, 8, 19) and Escherichia coli O157:H7 (20, 21, 22, 28).
Although many variations of the FRET concept have been reported, in most of them a single oligonucleotide labeled on both the 5' (reporter) and 3' (quencher) ends is used for selective generation of fluorescence. In an effort to reduce the development and assay costs associated with FRET-based PCR assays, we (14) described the use of an inexpensive asymmetric probe set which consists of a long 5' fluorescein-labeled (reporter) oligonucleotide and a short 3' 4-[4'-dimethylaminophenylazo]benzoic acid-labeled (quencher) oligonucleotide (Fig. 1). These probes are able to form an asymmetrical double-stranded conformation at room temperature such that the 5' fluorescein-labeled probe is quenched by the nearby quencher oligonucleotide. During the normal annealing-primer extension step of the PCR, the reporter probe molecules are available to hybridize with the target amplicons, and the fluorescein label is digested by the 5' nuclease activity of Taq DNA polymerase (10). After the DNA amplification is complete, the residual reporter probe reanneals to the short quencher oligonucleotide at room temperature. The increase in fluorescence at the end of the assay indicates that specific amplicons are produced. Although this assay is not a real-time assay in the sense that the detection of PCR products occurs simultaneously as the PCR is progressing, it is, however, an endpoint detection assay in that specific PCR products can be detected by fluorescence immediately following termination of the PCR. As such, this protocol takes advantage of the lower cost of single labeling (approximately $225 for 250 nmol of the single-label probe versus $400 for the same amount of the dual-label probe) and provides a promising alternative for rapid and efficient endpoint detection of PCR amplicons in a single reaction tube.
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FIG. 1. Detection of PCR products by using 5' nuclease activity and an asymmetric fluorogenic probe set. P, probe; F, fluorescein label; Q, quencher.
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Isolation of L. monocytogenes nucleic acids from NFDM.
Twenty-four-milliliter samples of reconstituted nonfat dry milk (NFDM) were each inoculated with 1 ml of a serially diluted overnight culture of L. monocytogenes to obtain a final concentration of 1 x 102 to 1 x 105 CFU/25 ml. The samples were pretreated by adding 1.5 ml of 25% (wt/vol) sodium citrate with 10 min of shaking at room temperature, as previously reported (15). After this, cells were collected by centrifugation at 10,000 x g for 10 min at 4°C and extracted for DNA or RNA isolation.
For isolation of DNA, the pellet was resuspended in 0.1 ml of 1% sodium dodecyl sulfate and solubilized by adding 0.4 ml of 60% (wt/vol) guanidinium thiocyanate. The DNA was extracted by adding 0.5 ml of phenol-chloroform-isoamyl alcohol (25:24:1) and was precipitated by using isopropanol. The air-dried DNA pellet was resuspended in 25 µl of distilled water; 10 µl of a reconstituted DNA suspension was used in each PCR amplification.
For RNA extraction, the cell pellet was resuspended in 0.1 ml of 1% sodium dodecyl sulfate-0.5% diethyl pyrocarbonate and solubilized by adding 0.4 ml of 60% (wt/vol) guanidinium thiocyanate and 40 µl of 3 M sodium acetate (pH 4.8). The RNA was extracted by adding 0.4 ml of water-saturated phenol and 0.2 ml of chloroform. To enhance the efficiency of recovery of RNA after isopropanol precipitation, 10 µg of yeast tRNA (Sigma, St. Louis, Mo.) was added as a coprecipitant. The air-dried RNA pellet was resuspended in 30 µl of distilled water; 5 µl of reconstituted RNA was used in each reverse transcription (RT) reaction. Because of the special design of the RT-PCR primer set (13), RNase-free DNase treatment of RNA extracts was not necessary prior to RT.
Oligonucleotide primers and probes.
The sequences of amplification primers and detection probes and the sizes of amplicons are shown in Fig. 2. The oligonucleotides were designed based on DNA sequence data from GenBank and information previously published by Bassler et al. (1) and Bubert et al. (3). To reduce false-positive signals in RT-PCR due to the presence of residual genomic DNA, the reverse primer used for RT-PCR targeting of the hly mRNA was modified by incorporating three consecutive mismatched bases near its 3' terminus, as previously reported (13). The oligonucleotide primers and fluorescein-labeled probes were synthesized by Integrated DNA Technologies, Inc. (Coralville, Iowa).
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FIG. 2. Oligonucleotide primer and probe sets used for amplification of hly and iap gene-specific fragments by PCR and RT-PCR. The hly-specific primer-probe set was designed on the basis of data obtained from GenBank (accession numbers U25443, U25446, U25449, and U25452) and previously published information (1). The iap-specific primer set was also designed on the basis of data obtained from GenBank (accession numbers X52268, M80348, M80349, M80350, M80351, M80352, and M80353) and previous reports (3).
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For amplification of target gene fragments, 40 µl of a PCR solution was mixed with 10 µl of a genomic DNA extract or RT mixture for further amplification. The 50-µl PCR mixture, which contained 1x PCR buffer, 3 mM MgCl2, 0.2 mM dATP, 0.2 mM dCTP, 0.2 mM dGTP, 0.4 mM dUTP (PCR) or 0.3 mM dUTP plus 0.05 mM dTTP (RT-PCR), 10 pmol of each forward and reverse primer, 5 pmol of each reporter and quencher probe, 1 U of Taq DNA polymerase, 1 U of anti-Taq antibody (Invitrogen, Carlsbad, Calif.), and 0.2 U of uracil-N-glycosylase, was used for amplification. To digest possible carryover contaminating DNA by uracil-N-glycosylase and to denature the target template, 1 cycle of 45°C for 5 min and 94°C for 5 min was used. After this, the DNA was amplified by using 40 cycles of 94°C for 30 s, 60°C (in some experiments, an annealing temperature of 58°C was also tested) for 30 s, and 72°C for 45 s. The PCR was carried out with a GeneAmp PCR system 9600 (Applied Biosystems). Each PCR tube was removed from the thermal cycler after completion of amplification and was equilibrated to room temperature. Forty microliters of each PCR solution was transferred into a 96-well microtiter plate, and the fluorescence was measured (excitation wavelength, 485 nm; emission wavelength, 530 nm) with a CytoFluor II fluorescence plate reader (PerSeptive Biosystems, Framingham, Mass.). Amplification was confirmed by agarose (1%) gel electrophoresis and ethidium bromide (EtBr) staining.
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500 CFU/reaction mixture.
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FIG. 3. Amplification of hly (A and B) and iap (C and D) genes from pure cultures of L. monocytogenes. (A and C) PCR profiles for hly gene amplification and iap gene amplification, respectively, as measured with a fluorescence plate reader. The values are means ± standard deviations for three replicate samples. (B and D) Agarose (1%) gel electrophoresis and EtBr staining of PCR products for hly gene amplification (273 bp) and iap gene amplification (330 bp), respectively. Lane M, 100-bp DNA ladder; lanes 1 to 4, PCR products amplified from suspensions corresponding to 5 x 104, 5 x 103, 5 x 102, and 0 CFU of L. monocytogenes per reaction mixture, respectively.
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TABLE 1. Primer specificity for amplification of gene fragments from L. monocytogenes compared to other species of the genus Listeria
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FIG. 4. Detection of L. monocytogenes hly (A and B) and iap (C and D) genes (genomic DNA) from food samples. (A and C) Fluorescence from hly-specific amplification and iap-specific amplification, respectively. The values are means ± standard deviations for three replicate samples. (B and D) Agarose (1%) gel electrophoresis and EtBr staining of PCR amplicons for hly gene amplification (273 bp) and iap gene amplification (330 bp), respectively. Lane M, 100-bp DNA ladder; lanes 1 to 4, PCR products amplified from DNA extracts corresponding to 105, 104, 103, and 0 CFU of L. monocytogenes/25-ml NFDM sample, respectively.
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FIG. 5. Detection of L. monocytogenes hly gene product (mRNA) from food samples. (A) Fluorescence from hly-specific amplification of RNA extracts obtained from seeded 25-ml NFDM samples amplified by RT-PCR (open bars) and PCR (shaded bars). The values are means ± standard deviations for three replicate samples. (B) Agarose (1%) gel electrophoresis and EtBr staining of amplicons (273 bp). Lane M contained a 100-bp DNA ladder. The amplicons of RT-PCR (lanes 1 to 5) and PCR (lanes 6 to 10) were obtained by amplification performed with RNA extracts corresponding to 105, 104, 103, 102, and 0 CFU of L. monocytogenes/25-ml NFDM sample, respectively.
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There are still important issues that must be addressed if rapid fluorogenically based detection of food-borne pathogens is to become a routine reality. Critical methodological issues include, but are not limited to, the following: (i) the need to utilize large realistic sample sizes (
25 ml or
25 g) to obtain bacterial nucleic acid, compared to requisite PCR amplification volumes (10 to 50 µl); (ii) the presence of low levels of contaminating pathogens; (iii) the need to assure that nonviable cells are not detected; and (iv) the need to confirm PCR amplification products with more lengthy DNA hybridization assays (2, 27). While in many studies the workers have reported development of PCR and RT-PCR protocols for pure cultures, few researchers have addressed the critical issue of food sample preparation prior to detection. As with the commercial PCR detection kits for food-borne pathogens (23, 24), in almost all other studies the workers also report the need for cultural enrichment prior to nucleic acid extraction and detection in order to achieve detection limits approaching 1 CFU/25-g food sample (4, 12, 18, 20). In the case of fluorogenic PCR detection of food-borne pathogens, the usual approach is either to extract the nucleic acids from a 1-ml portion of an enrichment culture (4, 6) or to precede the extraction with a paramagnetic capture step (18). For instance, Nogva et al. (18) reported fluorogenic PCR detection limits of 60 to 6,000 CFU of L. monocytogenes when the amplifications were preceded by a paramagnetic concentration step done on 1.4 ml of artificially inoculated skim or whole milk. Our approach is unique in that we begin with 25-ml samples and concentrate the bacteria by centrifugation, which is followed by nucleic acid extraction and amplification. Using this type of approach, we obtained detection limits of 103 to 104 CFU of L. monocytogenes per 25-ml sample of our model food commodity without prior cultural enrichment. By targeting mRNA rather than DNA and incorporating the fluorogenic endpoint detection strategy, our approach addresses several of the issues cited above. We recognize that the reconstituted NFDM matrix is compositionally simple and that additional work in matrix processing to concentrate pathogens and to remove inhibitors is critical (15). A next logical step would be to address such matrix issues by adapting this type of technology to the detection of L. monocytogenes in at-risk products (cheeses, processed meats) or environmental samples.
Recent studies have demonstrated a better correlation between the presence and amplification of bacterial mRNA and cell viability (12, 19). When mRNA is used as a target template, RNA extraction is considered necessary to avoid coamplification of genomic DNA. Furthermore, a DNase treatment prior to RT is usually employed to further avoid false-positive signals that might occur due to the contamination of RNA extracts with small amounts of genomic DNA. However, when samples contain low copy numbers of target RNA, the optional DNA removal and subsequent purification steps can cause further loss of RNA, resulting in a decrease in RT-PCR detection limits and overall test sensitivity (11). To address this issue, we (13) described an RT-PCR method designed to reduce false-positive results due to coamplification of contaminating genomic DNA using a Bacillus cereus model. Briefly, when a DNA oligonucleotide primer containing three consecutive mismatched bases near its 3' terminus was constructed and RT was performed at a low temperature (40 or 45°C), the cDNA produced contained the mismatched sequence. When this was followed by PCR amplification at high annealing temperatures (
60°C), the amplification of contaminating genomic DNA was hindered relative to the amplification of the cDNA. In the present study, we were able to design RT-PCR primers targeting the hly gene mRNA of L. monocytogenes using the same general format. This effectively eliminated the need to perform DNase treatment in order to avoid false-positive signals from residual genomic DNA, further simplifying the assay design and most likely improving the detection limit.
For rapid detection of specific amplicons, FRET-based PCR with internal amplicon-specific probes remains an excellent choice. Unlike protocols in which molybdate (7), intercalating agents (9), and fluorescein-labeled amplification primers (17) are used, in which detection is not based on sequence specificity, FRET-based PCR offers exquisite specificity and allows discrimination of nonspecific amplicons from specific amplicons. While the TaqMan assay and molecular beacon approaches are the most popular protocols, they use a dual-label oligonucleotide rather than two singly labeled complementary oligonucleotides for the selective generation of fluorescence. This theoretically simplifies FRET-based assays but also adds expense. The design described here takes advantage of the fact that the cost of single labeling is about one-half the cost of dual labeling ($225 versus $400 for 250-nmol portions of the two probes, respectively), which results in reduced cost in assay development and also maintains the simplicity provided by dual-label probes. For example, a minor change in the sequence or length of the probe during assay optimization would normally necessitate the purchase of a new dual-label probe. In the case of our asymmetric probe design, the use of two separate modules (i.e., a signal module [fluorescein-labeled primer] and a switch module [quencher-labeled short oligonucleotide]) means that only a new signal module would be needed under the same circumstances. Furthermore, the assay can be completed with any PCR thermocycler and fluorescence reader that are routinely available, which means that it is not necessary to purchase expensive real-time amplification equipment. This concept makes our design a good choice for assay development and optimization for a research laboratory on a limited budget.
In this study we demonstrated that 103 to 104 CFU of L. monocytogenes DNA or mRNA in 25 ml of NFDM could be amplified and detected by an asymmetric FRET-based amplification protocol with endpoint detection in about 2.5 h. The ease of use, high specificity, and relatively low cost of this method make it a promising alternative to other fluorescent PCR protocols. However, before any of the methods can be practically used in routine assays of low numbers of pathogens in foods, issues such as pathogen concentration, nucleic acid recovery, and inhibitor removal must be dealt with. Indeed, technical breakthroughs in these issues will be critical to the success of future nucleic acid amplification methods. Currently, research and modification of preamplification processing, amplification optimization, and protocol integration are under way in our laboratory and other laboratories.
The use of trade names in this paper does not imply endorsement by the North Carolina Agricultural Research Service or criticism of similar products not mentioned.
Paper no. FSR 02-14 of the Journal Series of the Department of Food Science, North Carolina State University, Raleigh. ![]()
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3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA 88:7276-7280.
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