PMA-qPCR Assay Research Articles

Development of a Long-Amplicon Propidium Monoazide-Quantitative PCR Assay for Detection of Viable Xanthomonas arboricola pv. pruni Cells in Peach Trees.

Bacterial spot is one of the most serious diseases of peach caused by the pathogen Xanthomonas arboricola pv. pruni (XAP), leading to early defoliation and unmarketable fruit. The pathogen can overwinter in peach twigs and form spring cankers, which are considered the primary inoculum source for early season leaf and fruitlet infection. The amount of overwintering bacterial inoculum plays a critical role for the bacterial spot development, but no reliable quantification method is available. Thus, we developed a long-amplicon propidium monoazide (PMA)-quantitative PCR (qPCR) assay for specific detection of viable XAP cells. The optimized PMA-qPCR assay used 20 μM of PMAxx for pure bacterial suspensions and 100 μM for peach twig tissues. The Qiagen Plant Pro Kit with an additional lysozyme digestion step was the DNA extraction protocol that yielded the best detection sensitivity with the bacteria-spiked peach twig extracts. The PMA-qPCR assay was tested with different mixtures of viable and heat-killed XAP cells in pure bacterial suspensions and bacteria-spiked peach twig tissues. The results showed that this assay enabled sensitive, specific, and accurate quantification of viable XAP cells as low as 103 CFU/ml with the presence of up to 107 CFU/ml of dead XAP cells, while suppressing the amplification of DNA from dead cells. For mixtures of viable and dead cells, the PMA-qPCR results were linearly correlated with the predicted concentrations of viable XAP (R2 > 0.98). Thus, the PMA-qPCR assay will be a suitable tool for quantifying overwintering XAP population on peach trees.

Improving the Efficiency of Viability-qPCR with Lactic Acid Enhancer for the Selective Detection of Live Pathogens in Foods.

Pathogenic Escherichia coli are the most prevalent foodborne bacteria, and their accurate detection in food samples is critical for ensuring food safety. Therefore, a quick technique named viability-qPCR (v-qPCR), which is based on the ability of a selective dye, such as propidium monoazide (PMA), to differentiate between alive and dead cells, has been developed. Despite diverse, successful applications, v-qPCR is impaired by some practical limitations, including the ability of PMA to penetrate the outer membrane of dead Gram-negative bacteria. The objective of this study is to evaluate the ability of lactic acid (LA) to improve PMA penetration and, thus, the efficiency of v-qPCR in detecting the live fraction of pathogens. The pre-treatment of E. coli ATCC 8739 cells with 10 mM LA greatly increased PMA penetration into dead cells compared to conventional PMA-qPCR assay, avoiding false positive results. The limit of detection when using LA-PMA qPCR is 1% viable cells in a mixture of dead and alive cells. The optimized LA-PMA qPCR method was reliably able to detect log 2 CFU/mL culturable E. coli in milk spiked with viable and non-viable bacteria. Lactic acid is cheap, has low toxicity, and can be used to improve the efficiency of the v-qPCR assay, which is economically interesting for larger-scale pathogen detection applications intended for food matrices.

Propidium Monoazide-Treated, Cell-Direct, Quantitative PCR for Detecting Viable Chloramphenicol-Resistant Escherichia coli and Corynebacterium glutamicum Cells.

With the rapid development and commercialization of industrial genetically modified microorganisms (GMMs), public concerns regarding their potential effects are on the rise. It is imperative to promptly monitor the unintended release of viable GMMs into wastewater, the air, and the surrounding ecosystems to prevent the risk of horizontal gene transfer to native microorganisms. In this study, we have developed a method that combines propidium monoazide (PMA) with a dual-plex quantitative PCR (qPCR) approach based on TaqMan probes. This method targets the chloramphenicol-resistant gene (CmR) along with the endogenous genes D-1-deoxyxylulose 5-phosphate synthase (dxs) and chromosomal replication initiator protein (dnaA). It allows for the direct quantitative detection of viable genetically modified Escherichia coli and Corynebacterium glutamicum cells, eliminating the requirement for DNA isolation. The dual-plex qPCR targeting CmR/dxs and CmR/dnaA demonstrated excellent performance across various templates, including DNA, cultured cells, and PMA-treated cells. Repeatability and precision, defined as RSDr% and bias%, respectively, were calculated and found to fall within the acceptable limits specified by the European Network of GMO Laboratories (ENGL). Through PMA-qPCR assays, we determined the detection limits for viable chloramphenicol-resistant E. coli and C. glutamicum strains to be 20 and 51 cells, respectively, at a 95% confidence level. Notably, this method demonstrated superior sensitivity compared to Enzyme-Linked Immunosorbent Assay (ELISA), which has a detection limit exceeding 1000 viable cells for both GM bacterial strains. This approach offers the potential to accurately and efficiently detect viable cells of GMMs, providing a time-saving and cost-effective solution.

Development of PMA-qPCR assay to accurately and reproducible quantify viable bacteria of Paenibacillus polymyxa.

Paenibacillus polymyxa is an important biocontrol bacterium. The combination of propidium monoazide (PMA) and quantitative polymerase chain reactionq (qPCR) has proven effective in quantifying live bacteria from various microorganisms. The objective was to create a PMA-qPCR assay to precisely and consistently measure the number of living bacteria of biocontrol P. polymyxa. The primers were designed for the spo0A gene of P. polymyxa HY96-2. The optimal conditions for treating the target strain with PMA were a PMA concentration of 15 μg/mL, an incubation time of 5 min, and an exposure time of 10 min. The PMA-qPCR method had a limit of quantification (LOQ) of 1.0×103 CFU/mL for measuring the amount of viable P. polymyxa bacteria. The PMA-qPCR method is more sensitive than the qPCR method in detecting viable bacteria in the mixtures of viable and dead bacteria. The accuracy and reproducibility of quantifying viable P. polymyxa bacteria using the PMA-qPCR method were higher compared to the plate count method.

Rapid Monitoring of Viable Genetically Modified Escherichia coli Using a Cell-Direct Quantitative PCR Method Combined with Propidium Monoazide Treatment.

The commercialization of industrial genetically modified microorganisms (GMMs) has highlighted their impact on public health and the environment. Rapid and effective monitoring methods detecting live GMMs are essential to enhance current safety management protocols. This study aims to develop a novel cell-direct quantitative polymerase chain reaction (qPCR) method targeting two antibiotic-resistant genes, KmR and nptII, conferring resistance against kanamycin and neomycin, along with propidium monoazide, to precisely detect viable Escherichia coli. The E. coli single-copy taxon-specific gene of D-1-deoxyxylulose 5-phosphate synthase (dxs) was used as the internal control. The qPCR assays demonstrated good performance, with dual-plex primer/probe combinations exhibiting specificity, absence of matrix effects, linear dynamic ranges with acceptable amplification efficiencies, and repeatability for DNA, cells, and PMA-treated cells targeting KmR/dxs and nptII/dxs. Following the PMA-qPCR assays, the viable cell counts for KmR-resistant and nptII-resistant E. coli strains exhibited a bias% of 24.09% and 0.49%, respectively, which were within the acceptable limit of ±25%, as specified by the European Network of GMO Laboratories. This method successfully established detection limits of 69 and 67 viable genetically modified E. coli cells targeting KmR and nptII, respectively. This provides a feasible monitoring approach as an alternative to DNA processing techniques to detect viable GMMs.

Evaluation of a Viable-Cell Detection Assay for Xanthomonas fragariae with Latent Class Analysis

Most molecular diagnostic assays are designed to detect the simple presence of a protein or nucleic acid without regard to whether that protein or nucleic acid originated from a viable and presumably pathogenic organism at the time of isolation. We recently developed a viable-cell detection assay (propidium monoazide [PMA]-qPCR) for specific detection of viable (living) cells of Xanthomonas fragariae, the pathogen causing angular leaf spot of strawberry, and herein describe a unique set of statistical analyses for validation of this assay. For any detection assay or test, calculation of its sensitivity and specificity is essential for determining its diagnostic capabilities, particularly when evaluating competing assays or tests. This is often achieved by running competing tests concurrently on a set of samples with known pathogen density or disease status and cross-tabulating results. However, the PMA-qPCR assay is unique among PCR-based diagnostics because it is designed specifically to detect DNA from living cells only, whereas most traditional PCR assays are designed to detect DNA from the target organism regardless of its state of viability. Thus, one cannot directly compare the results from a cell-viability assay with those from a general assay to gauge the performance of either assay because the assays target two different but overlapping populations (i.e., the viable-cell population and the viable- plus nonviable-cell population). To address this challenge, two standard statistical approaches to diagnostic test evaluation were used jointly to estimate the test performance of the PMA-qPCR assay relative to two common assays for detection of X. fragariae. In both analyses, the PMA-qPCR outperformed the qPCR for detection of viable cells under a range of conditions. Viability testing is extremely useful in certification and disease management applications, and with the information on test performance generated here, the test can be put to practical use to design sampling strategies to account for the errors in testing. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.

An Improved Method for Quantification of Viable Fusarium Cells in Infected Soil Products by Propidium Monoazide Coupled with Real-Time PCR.

Fusarium is a soil-borne pathogen that causes root rot disease in cucumber. To date, quantitative real-time PCR (qPCR) is a common tool to detect the content of Fusarium in soil. However, qPCR cannot distinguish between viable and nonviable cells. The aim of this study was to develop a detection technique to pretreat tissue fluid with propidium monoazide (PMA) followed by extract DNA, and then to quantify viable Fusarium cells in contaminated soil. In this work, the specific primer pair F8-1/F8-2 was designed based on the translation elongation factor (EF) gene and a PMA-qPCR assay was established to amplify and quantify soils of viable Fusarium cells. The PMA pretreatment test was optimized, which indicated that the optimal PMA concentration and light exposure time were 50 mmol L−1 and 15 min, respectively. The lowest limit of viable cells in suspension detected and soil by PMA-qPCR were 82 spore mL−1 and 91.24 spore g−1, respectively. For naturally contaminated soil, viable Fusarium cells were detected in eight of the 18 samples, and the Fusarium amount ranged from 104 to 106 spore g−1. In conclusion, the PMA-qPCR method has the characteristics of high sensitivity, efficiency, and time saving, which could support nursery plants to avoid Fusarium infection and agro-industry losses.

A Long-Amplicon Viability-qPCR Test for Quantifying Living Pathogens that Cause Bacterial Spot in Tomato Seed.

Bacterial spot is one of the most serious diseases of tomato. It is caused by four species of Xanthomonas: X. euvesicatoria, X. gardneri, X. perforans, and X. vesicatoria. Contaminated or infected seed can be a major source of inoculum for this disease. The use of certified pathogen-free seed is one of the primary management practices to reduce the inoculum load in commercial production. Current seed testing protocols rely mainly on plating the seed extract and conventional PCR; however, the plating method cannot detect viable but nonculturable cells, and the conventional PCR assay has limited capability to differentiate DNA extracted from viable or dead bacterial cells. To improve the sensitivity and specificity of the tomato seed testing method for bacterial spot pathogens, a long-amplicon quantitative PCR (qPCR) assay coupled with propidium monoazide (PMA-qPCR) was developed to quantify selectively the four pathogenic Xanthomonas species in tomato seed. The optimized PMA-qPCR procedure was evaluated on pure bacterial suspensions, bacteria-spiked seed extracts, and seed extracts of inoculated and naturally infected seed. A crude DNA extraction protocol also was developed, and PMA-qPCR with crude bacterial DNA extracts resulted in accurate quantification of 104 to 108 CFU/ml of viable bacteria when mixed with dead cells at concentrations as high as 107 CFU/ml in the seed extracts. With DNA purified from concentrated seed extracts, the PMA-qPCR assay was able to detect DNA of the target pathogens in seed samples spiked with ≥75 CFU/ml (about 0.5 CFU/seed) of the viable pathogens. Latent class analysis of the inoculated and naturally infected seed samples showed that the PMA-qPCR assay had greater sensitivity than plating the seed extracts on the semiselective modified Tween Medium B and CKTM media for all four target species. Being much faster and more sensitive than dilution plating, the PMA-qPCR assay has potential to be used as a standalone tool or in combination with the plating method to improve tomato seed testing and advance the production of clean seed.

A viability assay combining palladium compound treatment with quantitative PCR to detect viable Mycobacterium avium subsp. paratuberculosis cells

Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogenic bacterium causing the paratuberculosis, chronic and infectious disease common particularly in wild and domestic ruminants. Currently, culture techniques to detect viable MAP are still used most commonly, although these require a long incubation period. Consequently, a faster molecular method for assessing MAP cell viability based on cell membrane integrity was introduced consisting of sample treatment with the intercalation dye propidium monoazide (PMA) followed by quantitative PCR (qPCR). However, the PMA-qPCR assay is complicated by demanding procedures involving work in a darkroom and on ice. In this study, we therefore optimized a viability assay combining sample treatment with palladium (Pd) compounds as an alternative viability marker to PMA, which does not require such laborious procedures, with subsequent qPCR. The optimized Pd-qPCR conditions consisting of 90 min exposure to 30 µM bis(benzonitrile)dichloropalladium(II) or 30 µM palladium(II)acetate at 5 °C and using ultrapure water as a resuspension medium resulted in differences in quantification cycle (Cq) values between treated live and dead MAP cells of 8.5 and 7.9, respectively, corresponding to approximately 2.5 log units. In addition, Pd-qPCR proved to be superior to PMA-qPCR in distinguishing between live and dead MAP cells. The Pd-qPCR viability assay thus has the potential to replace time-consuming culture methods and demanding PMA-qPCR in the detection and quantification of viable MAP cells with possible application in food, feed, clinical and environmental samples.

Modified PMA-qPCR Method for Rapid Quantification of Viable Lactobacillus spp. in Fermented Dairy Products

Quantification of viable lactic acid bacteria is an important quality index of fermented dairy products, but the current detection method, which is plate counting, is time-consuming. This study describes a modified PMA-qPCR assay that allows the detection and enumeration of total viable Lactobacillus spp. in commercial fermented milk products. Here, a new pair of genus-specific primers and minor groove binder probes was designed based on the 16S rRNA gene sequences of 24 reference strains, 13 of which were from different Lactobacillus species commonly used in commercial fermented dairy products. Subsequently, compared with the heat killing method, the 20-cycle homogenization method was chosen for initial PMA-qPCR optimization. Standard curves were prepared, and the efficiency obtained was 97% (R2 = 0.992), demonstrating that this PMA-qPCR method was feasible and effective. Additionally, the viable Lactobacillus spp. detection range was 103–109 CFU/mL, which meets the detection requirements in fermented dairy products. Furthermore, total number of viable Lactobacillus spp. in six different commercial fermented dairy products was estimated by three individual methods (plate count in MRS agar, qPCR, and PMA-qPCR). Comparison of results obtained by PMA-qPCR and plate counts was similar, and both decreased accordingly, showing a good correlation with the decline of strain vitality, 30 days after the expiration date. The PMA-qPCR procedure established in this paper allows the quantification of viable Lactobacillus spp. in approximately 3 h, greatly improving detection efficiency, and has broad application prospects in the testing of fermented dairy products.

An Optimized Method to Assess Viable Escherichia coli O157:H7 in Agricultural Soil Using Combined Propidium Monoazide Staining and Quantitative PCR.

Agricultural soil contaminated by manure is becoming an important source for the transmission of foodborne pathogens. There is an urgent need for a rapid and accurate method for viable pathogen detection in agricultural soil samples. Propidium monoazide (PMA) is a DNA-binding dye that can inhibit the amplification of DNA from dead cells through subsequent quantitative polymerase chain reaction (qPCR), thus allowing for viable cells detection and quantification. The objective of this study was to detect viable Escherichia coli O157:H7 in the agricultural soils by PMA-qPCR. In this study, cell extraction and gradient density centrifugation were incorporated before PMA-qPCR to reduce the interference of soil particle including turbidity and a high ratio of dead cells. The optimized treatment conditions were determined as follows, the maximum removal of DNA from dead cells was achieved by 1.067 g/mL Percoll of centrifugation and 50 μM PMA treatment. Under these conditions, the turbidity of paddy soil suspensions decreased from 3500 to 28.4 nephelometric turbidity units (NTU), and the ratio of viable cells to dead cells increased from 0.001 to 1.025%. For typical agricultural soils collected in China, as low as 102colony-forming units (CFU)/g of viable cells could be accurately detected in the presence of a large number of dead cells (107 CFU/g) by the optimized PMA-qPCR. Significantly, with comparable accuracy, the optimized PMA-qPCR assay was more sensitive, accessible and rapid than conventional culture methods. In addition, the viable but non-culturable (VBNC) state of E. coli O157:H7 cells in paddy soils, which often escaped the detection by conventional culture methods, could be quantitatively characterized by the optimized PMA-qPCR method. Potentially, the optimized PMA-qPCR can be further applied for viable pathogens detection and give insight into the prevalence of VBNC E. coli O157:H7 in agricultural soil.

Application of propidium monoazide coupled with quantitative PCR to evaluate cell viability of Bifidobacterium animalis subsp. lactis in a non-dairy probiotic beverage

PurposeIn this study, a PMA-qPCR assay was developed for the enumeration of Bifidobacterium animalis subsp. lactis BB-12 viable cells in a non-dairy probiotic beverage.MethodsProbiotic viability was monitored in three formulations of probiotic passion fruit juice microencapsulated by spray drying, during 30 days of storage at 4 °C. Viable cells were quantified using qPCR and PMA-qPCR assays targeting tuf gene and by plate counting method.ResultsThe limit of detection for all samples was 103 genome copies, corresponding to 21.3 pg of DNA. Higher CFU values were obtained for B. lactis BB-12 enumeration by qPCR, when compared to those obtained by PMA-qPCR and plate count, for all probiotic juice microcapsules. Similar quantification values were obtained by PMA-qPCR and plate counting for all samples and remained above 8 log CFU/g during the storage period.ConclusionThese results demonstrated that the PMA-qPCR technique is a promising approach for B. lactis BB-12 viable cell enumeration in complex matrices such as passion fruit juice microcapsules. This PMA-qPCR assay allowed the achievement of reliable results faster than with the traditional plate counting method.

Azospirillum brasilense viable cells enumeration using propidium monoazide-quantitative PCR.

Azospirillum brasilense is a plant growth promoting bacteria used as an inoculant in diverse crops. Accurate analytical methods are required to enumerate viable cells in inoculant formulations or in planta. We developed a quantitative polymerase chain reaction (qPCR) assay associated to propidium monoazide (PMA) to evaluate the cell viability of A. brasilense in inoculant and in maize roots. A. brasilense was grown in culture medium and was exposed to 50℃. Maize roots were grown in vitro and harvested 7days after inoculation. Quantification was performed by qPCR, PMA-qPCR, and plate counting. Standard curves efficiency values ranged from 85 to 99%. The limit of detection was 104CFU per gram of fresh root. Enumeration obtained in maize roots by qPCR where higher than enumeration by PMA-qPCR and by plate counting. PMA-qPCR assay was efficient in quantifying inoculant viable cells and provides reliable results in a quickly and accurately way compared to culture-dependent methods.

Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk Microbiota.

The temporal instability of raw milk microbiota drastically affects the reliability of microbiome studies. However, little is known about the microbial integrity in preserved samples. Raw cow milk samples were preserved with azidiol or bronopol and stored at 4 °C, or with dimethyl sulfoxide (DMSO) or a mixture of azidiol and DMSO and stored at −20 °C for up to 30 days. Aliquots of 5-, 10-, and 30-day post-storage were treated with propidium monoazide (PMA), then analyzed by sequencing the 16S rRNA gene V3-V4 and V6-V8 regions. The V6-V8 gave a higher richness and lower diversity than the V3-V4 region. After 5-day storage at 4 °C, the microbiota of unpreserved samples was characterized by a drastic decrease in diversity, and a significant shift in community structure. The treatment with azidiol and DMSO conferred the best community stabilization in preserved raw milk. Interestingly, the azidiol treatment performed as well for up to 10 days, thus appearing as a suitable alternative. However, neither azidiol nor bronopol could minimize fungal proliferation as revealed by PMA-qPCR assays. This study demonstrates the preservative ability of a mixture of azidiol and DMSO and provides deeper insights into the microbial changes occurring during the cold storage of preserved raw milk.

A novel method for rapid and sensitive detection of viable Escherichia coli cells using UV-induced PMA-coupled quantitative PCR.

We report a specific and sensitive method to improve the coupling of propidium monoazide (PMA) with DNA derived from killed cells of Escherichia coli using UV light of 365nm. UV light of three different intensities mainly 2.4 × 103, 4.8 × 103, and 7.2 × 103μJ/cm2 was applied to E. coli cells each for 1, 3, and 5min. PMA was found to be successfully cross-linked with the DNA from killed cells of E. coli at 4.8 × 103μJ/cm2 in 3min leading to the complete inhibition of PCR amplification of DNA derived from PMA-treated heat-killed cells. In spiked phosphate-buffered saline and potable water samples, the difference of the Cq values between PMA-treated viable cells and PMA-untreated viable cells ranged from -0.17 to 0.2, demonstrating that UV-induced PMA activation had a negligible effect on viable cells. In contrast, the difference of the Cq values between PMA-treated heat-killed cells and PMA-untreated heat-killed cells ranged from 8.9 to 9.99, indicating the ability of PMA to inhibit PCR amplification of DNA derived from killed cells to an equivalent as low as 100CFU. In conclusion, this UV-coupled PMA-qPCR assay provided a rapid and sensitive methodology to selectively detect viable E. coli cells in spiked water samples within 4h.

Quantitative detection of viable Escherichia coli O157:H7 using a photoreactive DNA-binding dye propidium monoazide in irrigation water

Escherichia coli O157:H7 is a kind of waterborne pathogen and recognized as a common pathogenic microorganism in irrigation water. In this study, a quantitative PCR (qPCR) assay with propidium monoazide (PMA) treatment called PMA-qPCR assay was developed to detect the presence of E. coli O157:H7 in natural irrigation water that was more specific, more sensitive, and was unaffected by dead cells compared with traditional and conventional methods. Specific gene, fliC from E. coli O157:H7 was selected to design the unique primer and probe for the assay while propidium monoazide (PMA) was used to effectively prevent the interference of DNA from dead cells. Evaluation of the effect of PMA treatment exhibited permeation of the dead cell membranes that was observed under confocal laser scanning microscope (CLSM). The PMA-qPCR assay efficiently detected viable cells even in the presence of 104 CFU/mL dead cells. Under optimized conditions the limit of detection for viable cells was 102 CFU/mL or 10 CFU/mL in pure culture and spiked irrigation water in a 3 h assay. The PMA-qPCR assay did not show significant difference in the absence of the dead bacteria indicating specificity and selectivity for viable E. coli O157:H7. The PMA-qPCR assay developed in this study has potential for precise and sensitive detection of viable E. coli O157:H7 in irrigation water.

Rapid and quantitative detection of viable emetic Bacillus cereus by PMA-qPCR assay in milk

Emetic Bacillus cereus is one of the causative agents of foodborne diseases which can cause vomiting-type food poisoning after ingestion of contaminated food. To minimize B. cereus food poisoning, propidium monoazide (PMA) combined with quantitative polymerase chain reaction (qPCR) called PMA-qPCR was applied for detecting viable emetic B. cereus in milk. The cereulide synthetase gene of emetic B. cereus (cesB) was chosen for the primer, and PMA treatment was optimized at 3 μg/mL to inhibit the PCR amplification of DNA from dead cells. Under optimized assay parameters, the limit of detection (LOD) using this method were 102 CFU/mL in both pure culture and in spiked milk matrix. The cycle threshold (Ct) values obtained for this assay was not significantly affected by the presence of non-target bacteria such as E. coli O157:H7 which indicated the high selectivity of the assay for emetic B. cereus. The PMA-qPCR assay used in this study has the potential for sensitive detection of viable emetic B. cereus in milk.

Molecular monitoring of disinfection efficacy of E. coli O157:H7 in bottled purified drinking water by quantitative PCR with a novel dye

A new method was developed using a novel dye thiazole orange monoazide (TOMA) combined with quantitative real-time PCR (qPCR) to detect viable Escherichia coli O157:H7 cells. Different from the commonly used PMA-qPCR assay that is based on membrane integrity, this TOMA-qPCR method is based on the concept of metabolic activity. TOMA consists of three components: a nucleic acid-intercalating moiety, a crosslinkable moiety and a linker. TOMA concentration at 50 μg/ml, 20 min incubation time, and 30 min light exposure time were suggested to use for detecting viable cells. When the inoculum concentration was 103 CFU/100 ml, TOMA-qPCR assay could completely exclude the effect of dead cells treated with heat, chlorine, or UV. Moreover, TOMA-qPCR could also be used to detect viable but nonculturable state (VBNC) cells. The result shows that TOMA-qPCR would be an alternative choice for the detection of viable cells. Practical applications To specifically detect only viable cells is of great importance in most detection of microbial diagnostics, especially for detection of foodborne pathogens such as E. coli O157:H7, which could cause health risk at low concentrations. The existing detection methods have some defects in detecting only viable cells. In this article, a novel dye was developed and combined with qPCR, to monitor sanitizing efficacy of different disinfection methods on E. coli O157:H7 at low concentrations. When detecting viable E. coli in bottled water, the established TOMA-qPCR assay completely exclude the effect of dead cells when the inoculated concentration is 103 CFU/100 ml. This method is also suitable for the detection of VBNC samples. Therefore, this method can be used to detect pathogenic bacteria with low contamination under extreme conditions such as low temperature, oligotrophic, strong radiation, and so on.

Heavy Metal Ion Stress on Halobacterium salinarum R1 Planktonic Cells and Biofilms

Halobacterium salinarum R1 is an extremely halophilic archaeon, able to attach to the surface and to form characteristic biofilm structures under physiological conditions. However, the effect of environmental stress factors like heavy metals on biofilms was still unknown. Here, we report on the first insights into H. salinarum biofilm formation when exposed to copper, nickel and zinc and describe the effects of metal ions on the architecture of mature biofilms. We also studied the effects on gene expression in planktonic cells. Investigation of planktonic growth and cell adhesion in the presence of sub-lethal metal concentrations yielded an up to 60% reduced adhesion in case of copper and a significantly enhanced adhesion in case of zinc, whereas nickel treatment had no effect on adhesion. A PMA-qPCR assay was developed to quantify live/dead cells in planktonic cultures and mature biofilms, enabling the investigation of cell vitality after metal exposure. An increased resistance was observed in biofilms with up to 80% in case of copper- and up to 50% in case of zinc exposure compared to planktonic cells. However, nickel-treated biofilms showed no significant increase of cell survival. Microscopic investigation of the architecture of mature biofilms exposed to lethal metal concentrations demonstrated an increased detachment and the formation of large microcolonies after copper treatment, whereas the number of adherent cells increased strongly in nickel-exposed biofilms. In contrast, zinc exposed-biofilms showed no differences compared to the control. Analysis of the expression of genes encoding putative metal transporters by qRT-PCR revealed specific changes upon treatment of the cells with heavy metals. Our results demonstrate diverse effects of heavy metal ions on H. salinarum and imply a metal-specific protective response of cells in biofilms.

Detection of viable Escherichia coli in environmental water using combined propidium monoazide staining and quantitative PCR

The objectives of this study were to specifically detect viable Escherichia coli in environmental waters by targeting the ycjM gene in a propidium monoazide (PMA)-qPCR assay. PMA is a viability dye that can inhibit the amplification of DNA from dead cells, thus allowing for the detection and quantification of only viable cells. The ycjM primers were used to target E. coli that directly originated from the feces of warm blooded animals, and avoid false positive detection caused by “naturalized” E. coli that can exist in the environment. In this study, tap water and environmental waters were inoculated with E. coli isolated from animal feces. Following cell collection, samples were treated with PMA, followed by DNA isolation and qPCR detection. For pure cultures, 5 μM PMA with a 10-min light exposure was efficient at inhibiting the amplification of DNA from 105 CFU/mL dead E. coli cells, with a detection limit of 102 CFU/100 mL viable cells. For tap and environmental waters collected in the winter, a 10 μM PMA was required and as low as 103 CFU/100 mL viable cells could be detected in the presence of 105 CFU/100 mL dead cells. For water samples collected during the summer, 102 CFU/10 mL viable cells could be detected in the presence of 104 CFU/10 mL dead cells, after a 20 μM PMA treatment. No significant differences were found among the PMA-qPCR assay and two other standard culture-based methods for detection of viable E. coli in environmental water. In conclusion, with proper pretreatment of environmental water samples, this PMA-qPCR assay that targets the ycjM gene could quantify viable E. coli cells that directly come from the feces of warm-blooded animals, and therefore effectively and accurately indicate the quality of environmental water.