Development of a sensitive and specific qPCR assay in conjunction with propidium monoazide for enhanced detection of live Salmonellaspp. in food
© Li and Chen; licensee BioMed Central Ltd. 2013
Received: 24 May 2013
Accepted: 23 November 2013
Published: 1 December 2013
Although a variety of methodologies are available for detection of Salmonella, sensitive, specific, and efficient methods are urgently needed for differentiation of live Salmonella cells from dead cells in food and environmental samples. Propidium monoazide (PMA) can preferentially penetrate the compromised membranes of dead cells and inhibit their DNA amplification, however, such inhibition has been reported to be incomplete by some studies. In the present study, we report an efficient qPCR assay targeting a conserved region of the invA gene of Salmonella in conjunction with PMA treatment for detection of DNA from live Salmonella cells in food samples.
We investigated the relationship between amplicon length and inhibitory effect of PMA treatment to prevent DNA amplification from dead cells while allowing for DNA amplification from live cells, and found that the two factors are well correlated with each other. An amplicon that is 130 bp in length was determined to be optimal for PMA treatment and was selected for further PMA-qPCR assay development. A PMA-qPCR assay was established by utilizing this amplicon and adopting a modified PMA-treatment procedure. The PMA-qPCR assay provided excellent inhibition of DNA amplification from dead cells (a 17-C T -value, or 128,000-fold reduction) while only a slight DNA amplification difference (0.5 C T value) was noted between the PMA-treated and untreated live cells. This assay has been validated through stringent inclusivity and exclusivity studies using a large number of (n = 167) Salmonella, including all strains of SARA and SARB collections, and non-Salmonella strains (n = 36). This PMA-qPCR assay is capable of detecting live Salmonella cells in live/dead cell mixtures, or 30 CFU/g live Salmonella cells from enriched spiked spinach samples as early as 4 h.
A 130-bp amplicon in invA gene was demonstrated to be optimal for PMA treatment for selective detection of live Salmonella cells by PCR. This PMA-qPCR assay provides a sensitive, specific, and efficient method for detecting live Salmonella cells in foods and environmental samples and may have an impact on the accurate microbiological monitoring of Salmonella in foods and environment samples.
KeywordsSalmonella qPCR Propidium monoazide Live cells invA gene
Salmonella is one of the most common foodborne pathogens, which causes diseases in humans, animals, and poultry worldwide [1, 2]. It has been estimated that in the United States alone, Salmonella infection causes 1.4 million foodborne illnesses per year, which accounts for approximately 30% of total outbreaks and outbreak-related cases [1–3]. Furthermore, Salmonella infection has not declined significantly in more than a decade, resulting in an estimated $365 million in direct medical cost annually . Salmonella infections in humans have been linked to a wide variety of sources such as under-cooked meats [5–7] and fresh produce [8, 9]. Therefore, development of rapid, sensitive, and accurate methodologies for the detection of Salmonella in foods and environmental samples may have an impact on the public health burden caused by this foodborne pathogen.
Traditional methods for isolating and identifying Salmonella in food rely on nonselective and selective pre-enrichment, followed by isolation using selective and differential media. Isolated colonies are identified biochemically and by using serology . The major limitation of these methods is that they typically take 4–8 days to obtain results. In addition, the sensitivity of the culture method, which is currently considered the gold standard for detection of Salmonella, is lower compared with that of DNA-based methods. This limitation may result in an increased false-negative rate [10, 11]. To shorten detection time and reduce tedious work to perform traditional culture methods, immunoassays such as enzyme-linked immunosorbent assay (ELISA) have been used for detection of Salmonella[10, 12], but poor performance in sensitivity and specificity as compared with other methods has relegated these methods to be a less than an ideal option for the field work . Therefore, there is a need to develop rapid, sensitive and specific methodologies to detect this pathogen in foods. Recently, DNA-based molecular detection tools such as conventional and qPCR have been used for bacterial diagnostics [11, 13–15]. More recently, qPCR is gaining popularity for its sensitivity, specificity, and rapid turnaround time. However, the use of these methods is hampered by their inability to distinguish DNA signals originated from live or dead cells. Because detection of live cells is most relevant in molecular diagnostics , it is essential to have reliable methods for selective detection of DNA from live Salmonella cells. To differentiate live and dead cells, several strategies have been used in molecular detection; one of the most commonly used strategies is to detect the presence of RNA which is inherently unstable [9, 17, 18]. However, it is known that working with RNA is cumbersome due to the risk of contamination with RNases and, hence can be labor intensive. Recent development of a photoreactive binding dye, propidium monoazide (PMA) offers an alternative way to differentiate dead cells from live cells [17, 19, 20] and has been successfully used for selective detection of live Escherichia coli O157H:7 cells from food by our group . PMA is capable of penetrating membrane-compromised dead cells, but not intact live cells. Once the dye enters a cell, it can bind to DNA and covalently cross-link to the DNA upon light-exposure. Consequently, the amplification of such modified DNA is inhibited. However, in some cases, such inhibition of amplification of DNA of dead cells was found incomplete by several research groups [22–25].
Considering these factors, the present study embraced two objectives: first, we developed and evaluated a qPCR assay that not only improves sensitivity and specificity for detection of Salmonella but also is compatible in PMA-mediated inhibition of DNA amplification from dead cells; second, we developed a PMA-qPCR assay by combining the qPCR assay with PMA-treatment for selective detection of DNA from live cells from dead cells. Furthermore, we applied this assay for the selective detection of DNA from live Salmonella cells in spiked spinach and beef.
Effect of amplicon length on inhibition of amplification of DNA from dead cells
Effect of amplicon length on PMA-mediated inhibition of DNA amplification from dead cells in qPCR targeting invA gene a
Sequence of primers or probe
Amplicon length (bp)
C T value with PMA
C T value w/o PMA
C T value differenceb
Sensitivity of the qPCR assay
Exclusivity and inclusivity of the qPCR assay
Bacterial strains used in this study a
Group/genus and species
Strain name and serotype
Salmonella (n = 24)
Non-Salmonella strain (n = 36)
Differentiation of live cells from live/dead cell mixtures
Detection of live salmonella cells from spiked spinach and beef
We further tested the PMA-qPCR assay for detection of DNA from live Salmonella cells in the presence of a large number of dead cells from spiked spinach samples (Figure 3B). The samples inoculated with 3 × 101, 3 × 102, and 3 × 103 CFU/g of cells without (0-h) enrichment generated C T values of 25.94, 26.89, and 26.29 without PMA treatment but three samples after PMA treatment yielded C T values all >35, indicating that the positive readings were due to the presence of a large number of dead cells. With 4-h enrichment, the sample with 3 × 102 CFU/g of cells was positive for Salmonella with C T values of 29.85 or 26.89 with or without PMA treatment (Figure 3B II). Similar trends were found in the samples inoculated with 3 × 103 (Figure 3B I), 3 × 101 (Figure 3B III). A downward trend in C T values was seen as a function of time. These results indicated the incapability of PCR alone to differentiate DNA from live and dead cells and the necessity for PMA treatment before DNA extraction.
Similar results were obtained with spiked beef samples. The beef samples inoculated with 30 CFU/g of cells were detected Salmonella after 4-h enrichment with C T values of 32.81. (Additional file 2: Table S2). Together, these results confirmed that this PMA-qPCR assay selectively detected 30 CFU/g live Salmonella cells from spiked spinach samples after 4-h enrichment (Figure 3B).
In spite of the fact that there are numerous DNA-based molecular methods available for detection of Salmonella, there is still room for improvement in qPCR assays to detect live Salmonella cells from foods and environment samples. To our knowledge, this is a first new qPCR assay for selectively detect live Salmonella cells that has been validated with such a comprehensive coverage of the Salmonella group, including strains of SARA (n = 72) and SARB (n = 72) collections and strains of recent outbreaks (n = 23). Furthermore, this assay is highly sensitive and specific for the detection of live Salmonella cells, and PMA-treatment is able to efficiently inhibit the DNA amplification from dead cells but has little effect on the DNA amplification from live cells.
PCR primer pairs used for targeting invA gene for detection of Salmonella
Primer sequence (5′---3′)
Type of PCR
Ferretti et al. (2001)
Chiu and Ou (1996)
Malorny and Hoorfar (2005)
Rahn et al. (1992) 
Mainar-Jaime et. al. ( 2013) 
Banihashemi et al. (2012) 
Arnold et al. (2004) 
Braun et al. (2011) 
Hoorfar et al. (2000) 
Liang et al. (2011) 
Chen et al. (2011) 
Our second objective was to remedy a drawback of PCR’s inability to distinguish signals originated from live or dead cells, by combining the qPCR with PMA treatment. Recently, PMA has been used for differentiation of live cells in qPCR [16, 19–21, 24, 32, 34, 37, 38] However, several studies revealed that the inhibition of amplification of DNA of dead cells was incomplete [22, 23, 37, 39]. In order to improve the efficacy of PMA treatment, we evaluated the effect of amplicon length on PMA-mediated inhibition of DNA amplification from dead cells by qPCR (Table 1). We found efficacy of PMA treatment appeared to be well correlated to the amplicon length, which is in good agreement with the previous finding . However, our results showed significant differences with their conclusion on efficiency of amplicon length, i.e. PMA-mediated suppression of DNA amplification from dead cells was incomplete with amplicons shorter than 190 bp . With amplicon D (130 bp), we were able to achieve a C T value difference of 13.1 between the treated and untreated dead cells (Table 1). Although amplicon E (260 bp) generated a bigger C T value difference (15.44), the C T value for DNA of untreated dead cells increased from 18.34 to 21.19, reflecting about a 3-C T -value decrease in sensitivity of the PMA-qPCR assay (Table 1). This finding is of importance because it can give guidance for selection of primer pairs for the development of qPMA-PCR assays. There are no good theoretical explanations for this “amplicon length effect” associated with PMA treatment. It may be related to the mechanism of the PMA-treatment. When dead cells are treated with PMA, the DNA is blocked by covalent bonds and thus it cannot be amplified in PCR . It could be understood that the larger an amplicon is, the longer the region that the polymerase needs to cover, the higher probability for the target DNA being blocked by a covalent bond (s). On the other hand, if the amplicon length is too long (over 200 bp), the sensitivity of the qPCR will be compromised, resulting in lower sensitivity of the assay. This finding has significance to future designs of qPCR assay in general.
Consumption of fresh produce including salads, lettuce, juice, melon, sprouts, and berries has been identified as important sources for Salmonella outbreaks . It is important to accurately monitor live cells in food samples, because only live bacteria can cause disease . We applied PMA-qPCR technology to selectively detect low numbers of live Salmonella cells in spiked spinach samples. This PMA-qPCR assay positively detected Salmonella in spinach spiked with 30 CFU/g at 4-h enrichment or from samples inoculated with 3 × 103 CFU/g without enrichment (Figure 3A). Additionally, with this PMA-qPCR assay, we were able to detect 30 CFU/g live cells with a 4-h enrichment in the presence of large number of dead Salmonella cells (3 × 107/g) (Figure 3B). This is an improvement in sensitivity compared with recent reports on detection of Salmonella. Live Salmonella cells were detected from spiked lettuce samples at the concentration of 101 CFU/g with 12-h enrichment . Another study reported that the detection limit of PMA-LAMP (loop-mediated isothermal amplification) was 6.1 × 103-104 CFU/g in spiked produce and PMA-PCR was up to 100-fold less sensitive compared with qPCR assay . It is noteworthy to mention that this PMA-qPCR assay reported here appears to be more sensitive. Two factors might explain this: first, it may be due to the qPCR assay we developed in this study, which offers higher sensitivity with detection limit as low as 3 CFU; whereas the two previous assays used longer amplicons (269 bp and 285 bp) in their qPCR assays [32, 34], which would make the qPCR assay less efficient compared with the assays with shorter amplicons; second, it might be due to the usage of our previously modified PMA-treatment procedure, which was shown to increase the PMA-qPCR efficiency . With this modified PMA-treatment procedure, not only could we achieve a relatively small C T value difference (0.5) between treated and untreated live cells (Figure 1A), but we were also able to obtain efficient inhibition (17-C T -value difference, 128,000-fold) of DNA amplification with dead cells (Figure 1B). These improvements made it possible for efficient and accurate differentiation of live Salmonella cells from dead cells by this PMA-qPCR assay . Furthermore, we have successfully applied this assay to detect live Salmonella cells from beef (Additional file 2: Table S2) and environmental water samples . It may be applied to other food matrices as well, fostering improvement of accurate monitoring Salmonella.
We have developed a PMA-qPCR assay for selective detection of live Salmonella cells from dead cells in food. This assay is sensitive and specific and has been validated with a large number of Salmonella strains. We were able to differentiate live Salmonella cells from live/dead cell mixtures. This PMA-qPCR has been applied for selective detection of live Salmonella cells in spiked spinach. It allows selective detection of 30 CFU/g Salmonella from spiked spinach with 4-h enrichment. Additionally, we evaluated the effect of amplicon length on PMA-mediated inhibition of DNA amplification of dead cells. The limitation of this PMA-qPCR assay is that PMA treatment slightly increases the cost and reduces the sensitivity of PCR assay.
Salmonella Enteritidis (SARB16) was used in designed experiments of optimization, sensitivity, and spinach spiking. Salmonella strains used for inclusive and exclusive evaluations included all strains from the Salmonella Reference A (SARA) (n = 72)  and Salmonella Reference B (SARB) (n = 72) , strains from recent Salmonella outbreaks and internal strain collections (n = 23) of the Division of Molecular Biology (DMB), Food and Drug Administration (FDA), (Additional file 1: Table S1; Table 2). Additionally, numerous non-Salmonella strains (n = 36) were shown in Table 3 for exclusivity testing, including E. coli O157:H7, non-O157 Shiga toxin-producing E. coli (STEC) strains, Shigella and other foodborne pathogen strains.
All bacteria were grown in Luria Bertani (LB) broth (Becton Dickinson and Company, Sparks, MD) at 37°C with shaking at 180 rpm, or as otherwise stated. Growth of Salmonella Enteritidis (SARB16) was monitored by determining the turbidity at 600 nm (OD600) using a DU530 spectrophotometer (Beckman, CA). To enumerate bacterial cells, cultures were diluted serially in 10-fold increments with LB medium and plated onto LB agar plates at 37°C overnight.
DNA was extracted from bacterial cultures using the Puregene cell and tissue kit (Gentra, Minneapolis, MN) according to the manufacturer’s instructions. Briefly, 1 ml of overnight grown culture was centrifuged, resuspended with 3 ml of cell lysate solution, and incubated at 80°C for 5 min. Fifteen microliters of RNase A solution was added, mixed, and incubated at 37°C for 60 min. One milliliter of protein precipitation solution was added, vortexed and centrifuged. The supernatant was combined with 3 ml of 2-propanol, mixed, and centrifuged. The pellets were washed with 70% ethanol, rehydrated with 500 l of DNA hydration solution, and incubated at 65°C for 1 h. The DNA concentrations were determined by measuring optical density (OD260) using a spectrophotometer (NanoDrop Technology, Wilmington, DE).
Primers and probes
The sequence of the invA gene used in this study was identified from the genomic sequence of GenBank accession number M90846. Primers and probe were designed using Primer Express© 3.0 software from Applied Biosystems Inc. (ABI, Foster City, CA). Five primer pairs that encode different lengths of amplicons were designed and are listed in Table 1.
qPCR assay conditions
Reaction mixtures consisted of 12.5 μl of 2 × Universal Master Mix (ABI), 200 nM of forward and reverse primers targeting invA gene in Salmonella and 100 nM of probe. Template DNA (5 μl of 20 pg/μl) and an appropriate volume of nuclease-free water (Qiagen Sciences, MD) were added to reach a final reaction volume of 25 μl. qPCR conditions were set as follows: activation of TaqMan at 95°C for 10 min; followed by 40 cycles of denaturation at 95°C for 10 s and annealing/extension at 60°C for 1 min.
qPCR with internal amplification control
To ensure the amplification was free of inhibitory factors from examined samples, an internal amplification control (IAC) was set. The primers and probe for IAC were designed [21, 44] based on the pUC19 DNA (Promega, Madison, MI), which was diluted to 50 fg/μl. The sequences of primers and probe used in the study were as follows: IAC-Forward, 5′-CAGGATTGACAGAGCGAGGTATG; IAC-Reverse, 5′-CGTAGTTAGGCCACCACTTCAAG; and IAC-probe, VIC-AGGCGGTGCTACAGAG- MGBNFQ. For each reaction, 0.5 μl of IAC forward and reverse primers (100 μM), 0.25 μl of IAC-probe (10 μM), and 1 μl of diluted pUC19 DNA (1.8 × 104 copies) were added to the regular qPCR reaction mixture components as described above to reach the final reaction volume of 25 μl. qPCR was performed using the same conditions as described above.
Sensitivity test and detection limit of the qPCR assay
A Salmonella Enteritidis (SARB16) culture was grown at 37°C to mid-exponential phase (OD600 = 0.5), and was divided into two aliquots. One aliquot was boiled for 10 min in a water bath to produce heat-killed cells; the other aliquot was used for live cells. The absence of live cells from the heat-killed cells was confirmed by plating the cells onto LB agar plates. The live and heat-killed aliquots were serially 10-fold diluted from 3 × 10° to 3 × 107 CFU/ml with LB medium. Both the live and heat-killed cells suspensions were equally divided to make four sets of cell suspensions. One set of the live cell suspensions was treated with PMA and the other set was left untreated. Subsequently, standard curves were generated side by side for PMA-treated cells and untreated cells in the qPCR assay (Figure 1A). Likewise, PMA-treated or untreated dead cell suspensions were also subjected to qPCR analysis for generation of standard curves (Figure 1B).
Inclusivity and exclusivity tests
A large number (n = 167) of Salmonella strains, including strain from FDA collections and recent outbreak isolates (Additional file 1: Table S1; Table 2), were used in inclusivity study. Salmonella strains from the SARA and SARB collections and other groups. E. coli O157:H7, non-O157 STEC strains, Shigella, and other pathogenic strains were used for exclusivity test (Table 2). DNA samples were prepared from the cultures of strains (Additional file 1: Table S1; Table 2) grown overnight at 37°C with a Wizard Plus Minipreps DNA Purification System Kit (Promega, Madison, WI). DNA concentration was adjusted to 20 pg/μl with water and 100 pg (5 μl) of DNA was used for the inclusivity and exclusivity studies in qPCR, and 5 μl of water was used as a no-template-control.
Preparation of mixtures of live and dead cells for PMA-qPCR
Salmonella Enteriditis SARB 16, grown at 37°C to mid-exponential phase (OD600 = 0.5), was divided into two aliquots. One aliquot was boiled for 10 min in a water bath for heat-killed cells; the other was not boiled to represent corresponding live for live cells. The absence of live cells from the heat-killed cells was confirmed by plating the cells onto LB agar plates. Both the live and the heat-killed aliquots were diluted (10 fold) to 3 × 101 to 3 × 107 CFU/ml with LB medium and equally divided to make four sets of cell suspensions. The first two sets were used for cell mixtures of live and dead cells; one set was for the PMA-treated cells and the other was for the untreated cells. The third and fourth sets of cells were for PMA-treated live cell dilutions and untreated live cell dilutions.
Combination of qPCR with PMA treatment
PMA treatment was performed as described earlier . Briefly, separate live cells, heat-killed cells, and live/dead cell mixtures were aliquoted 100 μl in three 1.5-ml microtubes. Two microliters of 10 mM PMA was added to each aliquot to a final concentration of 50 μM. The samples were first incubated at room temperature in the dark for 5 min, with gentle shaking. Then the samples were exposed to a 650-W halogen light source, followed by DNA preparation, and qPCR analysis.
Detection of live salmonella cells in spiked spinach and beef samples using PMA-qPCR
Fresh spinach and ground beef purchased from a local retail source, which were confirmed to be free of Salmonella by standard FDA BAM methods , was used for the spiking studies. The studies consisted of two parts. In part 1, three spinach samples (25 g) and three beef samples (25 g) were inoculated with 3 × 101, 3 × 102 and 3 × 103 CFU/g Salmonella strain SARB16. In part 2, three samples three beef samples (25 g) were each inoculated with 3 × 107/g dead cells and with 3 × 101, 3 × 102, and 3 × 103 CFU/g of live cells, respectively. Each spinach or beef sample was mixed with 225 ml of LB medium and homogenized for 2 min using a stomacher (Seward, England). Five milliliters of the enriched cultures was collected at 0, 4, 8, 12 and 24 h after incubation at 37°C with shaking at 180 rpm. The collected samples were centrifuged at 600 × g for 1 min to collect leaf or fat tissues. The supernatants were transferred to 2.0-ml microtubes and centrifuged at 3000 × g for 5 min to collect cells. The cell pellets were suspended in 1.5 ml of LB medium and treated with PMA before DNA extraction and qPCR analysis.
Polymerase chain reaction
- E. coli:
The authors are in debt to Christopher A. Elkins and Ben Tall for critically reviewing this manuscript and providing insightful comments and suggestions. We thank Huanli Liu for reading this manuscript and giving useful suggestions and Mark Mammel for help in getting the background information on bacterial collections in DMB. Additionally, we want to thank the three reviewers who critically reviewed the manuscript and provided useful suggestions for revising the manuscript.
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