A comparison of methods for the detection of Escherichia coli O157:H7 from artificially-contaminated dairy products using PCR

Evaluation of DNA extraction methods for the detection of Shiga toxin producing Escherichia coli in food by polymerase chain reaction

Reported food-borne outbreaks of Shiga toxin producing Escherichia coli (STEC) have involved a very diverse range of foods. Contemporary analytical methods for the detection of STEC in foods typically include PCR screening of enrichment media. However, PCR inhibitors present in food enrichments can produce false negative results when screening for DNA sequences associated with the pathogen. To avoid false negative results in enrichment screening, it is advantageous to have DNA extraction methods that are effective at removing PCR inhibitors from a wide range of foods. The standard Canadian STEC method MFLP-52 uses Bio-Rad Instagene Matrix for DNA extraction. In this study, three DNA extraction protocols using commercial kits (Instagene Matrix with Beckman Coulter Ampure XP Beads; Qiagen Gentra Puregene Yeast/Bact. Kit; Qiagen DNeasy Blood & Tissue) were assessed as alternative DNA extraction methods for the detection of the Shiga toxin gene by PCR in enrichments from sixteen different foods inoculated with STEC O157. The inoculated foods were bean sprouts, blackberries, blue cheese, cilantro, cocoa powder, coleslaw, cream of mushroom dried soup mix, cream of vegetable dried soup mix, flaxseed, guacamole, peanut butter, soft cheese, soy butter, spinach, walnut, and wheat flour. Two of the protocols, Instagene Matrix with Ampure XP Beads, and Gentra Puregene Yeast/Bact, produced no false-negative or false positive results in the analysis of triplicate enrichment samples from sixteen inoculated foods.

DNA-based qualitative and quantitative identification of bovine whey powder in goat dairy products

As one of the main ingredients in some milk powders, whey powder is sometimes added to pure goat milk products, which causes health risks, economic fraud, and unfair competition of food industries. This study is the first to explore qualitative and quantitative methods to identify adulteration of bovine whey powder in goat dairy products based on DNA. We extracted DNA from whey powder using a modified DNA extraction method; this exhibited good quality and integrity, with purity of 1.53 to 1.75 and concentration of 122 to 179 ng/μL. Conventional PCR and real-time PCR were compared for qualitative detection of bovine whey powder; real-time PCR demonstrated sensitivity of 0.01 ng/μL, which was higher than the 0.05 ng/μL detected by the conventional PCR method. Furthermore, real-time PCR was conducted for DNA quantitative detection, with good linearity (R² = 0.9858) obtained for bovine whey powder contents from 0.1% to 30%. Relative error decreased with increase of the mixing proportion of whey powder; the coefficient of variation above 0.1% of the mixing ratio was close to or less than 5%; and the relative standard deviation of repeatability results was less than 5%. Considering the economic costs of testing, conventional PCR could be performed first, and samples with obvious intentional adulteration detected can be further accurately quantified by real-time PCR. Overall, this research provides a realistic and effective method for qualitative and quantitative identification of bovine whey powder in goat dairy products, thus laying a good foundation for verification of goat dairy product label claims and industrial control.

Development of PCR assays for detection of Escherichia coli O157:H7 in meat products

A multiplex polymerase chain reaction (PCR) procedure based on fliC(h7) and rfbE genes was developed for the detection of Escherichia coli O157:H7 in raw pork meat and ready-to-eat (RTE) meat products. Two different DNA extraction procedures were evaluated for application on meat products. MasterPure™ DNA Purification kit in combination with immunomagnetic separation was found to be the best method in a meat system. The optimized PCR included an enrichment step in brilliant green bile 2% broth at 37 °C. This method was applied to artificially inoculated meat and RTE meat products with different concentrations of E. coli O157:H7. The results indicate that the PCR assay developed could sensitively and specifically detect E. coli O157:H7 in raw pork meat and RTE meat products in approximately 10h, including a 6h enrichment step. Thus, this method could be proposed for screening E. coli O157:H7 in raw pork and RTE meat products.

Efeito protetor das frações proteicas do soro de leite em camundongos Balb/C infectados por Escherichia coli O157: H7

Avaliou-se o efeito protetor das frações proteicas do soro do leite sobre as vilosidades intestinais de camundongos Balb/C, fêmeas, infectadas por Escherichia coli O157:H7. Foram utilizados 48 animais, distribuídos aleatoriamente em oito grupos de seis fêmeas cada um. Os animais dos grupos 1 e 2 (controles) receberam dieta AIN93G padrão; os dos grupos 3 e 4, AIN93G + alfalactalbumina; os dos grupos 5 e 6, AIN93G + betalactoglobulina e os dos grupos 7 e 8, AIN93G + concentrado proteico total e água ad libitum por sete dias. No dia zero, os animais dos grupos 2, 4, 6 e 8 foram inoculados, por meio de cânula de gavagem, com 0,5mL de E. coli O157:H7, na concentração de 7 x 10(10)UFC/mL. Os animais foram acompanhados clinicamente e sacrificados, no oitavo dia experimental. Verificou-se, por meio de exames histológicos e da morfometria, que as frações betalactoglobulina e alfalactalbumina exerceram efeito protetor sobre as vilosidades intestinais do jejuno distal e do íleo (P<0,05), respectivamente. O concentrado proteico total não demonstrou efeito protetor sobre as vilosidades intestinais.

Extraction of RNA from cheese without prior separation of microbial cells

In situ gene expression studies are promising approaches for improving our understanding of the cheese microbial flora. This requires efficient RNA extraction methods, but studies of cheeses are scarce. The objective of the present study was to determine whether RNA samples compatible with quantitative mRNA transcript analyses can be obtained without separating the cells from the cheese matrix. In the method that we describe, the cellular processes are stopped at the very beginning of the procedure. When cheeses were produced with Lactococcus lactis LD61 as the only starter microorganism, the integrity of the purified RNA was good, even for 2-week-old cheeses that had been incubated at 30 degrees C. In addition, the RNA samples did not contain any traces of RNases, and the amount of genomic DNA was negligible. A good level of reproducibility could also be achieved. When real-time reverse transcription-PCR analyses were normalized to the total RNA concentration, the amounts of 16S and 23S rRNA transcripts were constant during the 2-week incubation period, whereas the amount of tuf mRNA transcripts decreased substantially. RNA samples obtained using the method described in this study were compared to samples obtained using the method described by Ulvé et al. (J. Appl. Microbiol., in press), which is based on separation of the cells from the cheese matrix. For most of the 29 genes investigated, the transcript abundance was the same for both types of samples. Differences were observed mainly for genes whose expression has previously been shown to be modified by heat, acid, or osmotic stresses, such as busAA and glnQ.

Quantitative detection of Corynebacterium casei in cheese by real-time PCR

The flora on the surface of smear-ripened cheeses is composed of numerous species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. Due to the absence of selective media, it is very difficult to quantify cheese surface bacteria, and, consequently, the ecology of the cheese surface microflora has not been extensively investigated. We developed a SYBR green I real-time PCR method to quantify Corynebacterium casei, a major species of smear-ripened cheeses, using primers designed to target the 16S rRNA gene. It was possible to recover C. casei genomic DNA from the cheese matrix with nearly the same yield that C. casei genomic DNA is recovered from cells recovered by centrifugation from liquid cultures. Quantification was linear over a range from 10(5) to 10(10) CFU per g of cheese. The specificity of the assay was demonstrated with DNA from species related to C. casei and from other bacteria and yeasts belonging to the cheese flora. Nine commercial cheeses were analyzed by real-time PCR, and six of them were found to contain more than 10(5) CFU equivalents of C. casei per g. In two of them, the proportion of C. casei in the total bacterial flora was nearly 40%. The presence of C. casei in these samples was further confirmed by single-strand conformation polymorphism analysis and by a combined approach consisting of plate counting and 16S rRNA gene sequencing. We concluded that SYBR green I real-time PCR may be used as a reliable species-specific method for quantification of bacteria from the surface of cheeses.

Upstream sample processing facilitates PCR detection of Listeria monocytogenes in mayonnaise-based ready-to-eat (RTE) salads

Sample pretreatment to reduce volume and concentrate cells of the target organism(s) prior to molecular detection offers a useful supplement or alternative to cultural enrichment. The purpose of this study was to develop an upstream processing method to facilitate the detection of Listeria monocytogenes in ready-to-eat (RTE) salads by PCR. Potato salad, a model RTE commodity, was seeded with L. monocytogenes and processed by two alternative upstream sample processing methods (designated one-step and two-step centrifugation), followed by DNA extraction, PCR amplification, and Southern hybridization. The two-step method resulted in 1,000-fold improvements in the PCR detection limit, from 10(6) Cfu/g (no sample processing) to 10(3) Cfu/g. The two-step method was applied for upstream sample processing of four representative deli salad items artificially inoculated with L. monocytogenes at levels ranging from 10(1)-10(6) Cfu/g. Following DNA extraction, PCR amplification, and Southern hybridization, detection was achieved at input levels of 10(5) Cfu/g for chicken salad, 10(4) Cfu/g for macaroni salad, and 10(3) Cfu/g for potato and seafood salads. The two-step method reported here facilitates the production of a final sample concentrate of reduced volume and improved purity which was compatible with PCR amplification. This approach offers further progress in our efforts to reduce or eliminate cultural enrichment in an effort to speed time to results when applying molecular methods to the detection of pathogens in foods.

Detection of viable Salmonella using microelectrode-based capacitance measurement coupled with immunomagnetic separation

In this study, we demonstrated the use of a general medium--brain heart infusion (BHI) broth that is not specifically formulated for impedance measurement, to achieve detectable impedance signals by using an interdigitated microelectrode (IME) with capacitance measurement at low frequencies. Anti-Salmonella antibody coated immunomagnetic beads were used to separate S. typhimurium from samples to provide the selectivity to this method. From analysis based on the equivalent circuit of the IME system, we found that the impedance change in BHI broth resulting from the growth of Salmonella was indeed the change in the double layer capacitance and could be monitored at 10 Hz using the IME. The results indicated that medium modification to improve impedance signal is not necessary with this IME system. However, effective immunological separation for the target organism is required for the selectivity when non-selective media are used. This finding provides a more flexible option of medium in impedance methods, which may provide opportunities to test those species of bacteria that have no suitable conductance growth medium. The detection time, t(d), was obtained from the impedance growth curve (impedance against bacterial growth time) at 10 Hz at the point where the impedance started to change. A linear relationship between the detection time and the logarithmic value of the initial cell number (N) was found in the Salmonella cell number ranging from 10(1) to 10(6) cfu/ml. The regression equation was t(d) = -1.22Log N + 8.90, with R2 = 0.95. The detection times for the initial cell number of 10(1) CFU/ml and 10(6) CFU/ml are 8 h and 1.5 h, respectively. This method is more sensitive than impedance methods using conventional electrodes.

Semiquantitative determination of Alicyclobacillus acidoterrestris in orange juice by reverse-transcriptase polymerase chain reaction and capillary electrophoresis--laser induced fluorescence using microchip technology

The semiquantitative detection of Alicyclobacillus acidoterrrestris in orange juice by reverse-transcriptase polymerase chain reaction (RT-PCR) with a linear dynamic range of 2 x 10(5)-2 colony forming units (CFU)/mL in terms of cell count is described. Separation, detection, and quantification of the RT-PCR products were accomplished using the Agilent 2100 bioanalyzer in conjunction with the DNA 1000 LabChip kit. After 0 and 12 h of enrichment, it was possible to generate a linear standard curve between the amount of cells and amplicon concentration of RT-PCR and PCR products. Using this method, cell diminution was verified in samples of orange juice treated with a natural inhibitor (Sapindus saponaria), determining the persistence of viable cells. Semiquantitative RT-PCR using the Agilent 2100 bioanalyzer is a potentially useful approach for rapid in vitro determination of A. acidoterrestris and monitoring of inhibitor susceptibility for the orange juice-producing industry.

Effect of food matrix and cell growth on PCR-based detection of Escherichia coli O157:H7 in ground beef

The purpose of this work was (i) to investigate the feasibility of a previously reported upstream processing method for PCR template preparation to facilitate the detection of Escherichia coli O157:H7 from ground beef and (ii) to assess the impact of cell growth (no growth in the matrix versus growth in the matrix) on molecular detection limits. Two food matrices (autoclaved and raw ground beef) were evaluated in all studies. For no-growth experiments, 10-g meat samples were inoculated with 10(2) to 10(7) CFU/g E. coli O157:H7 and then homogenized. The homogenates were processed to remove large particulates and inhibitors using a two-phase upstream processing method consisting of two sequential centrifugation steps, the second of which used titanous hydroxide to facilitate bacterial immobilization. After upstream processing, sample concentrates were extracted for DNA isolation and amplified by PCR. For growth experiments, 10-g meat samples were inoculated at 1 CFU of E. coli O157:H7 per gram, allowed to grow to 10(2) to 10(7) CFU/g, and then processed for PCR assay. Cell recoveries after upstream processing ranged from 15.9 to 77.6% and were not facilitated by the use of titanous hydroxide, as compared with a saline control (P > 0.05). Bacterial cell recovery and PCR detection limits were similar when comparing autoclaved ground beef and raw ground beef, but cell recoveries were highly variable for raw ground beef samples in which E. coli O157:H7 cells were allowed to grow before processing for detection. Overall, PCR detection limits approximated 10(3) CFU/g of ground beef for all treatments. These results indicate that use of model food systems may not always provide an accurate replication of real-world conditions when evaluating PCR detection limits.

Detection of tet(M) gene from raw milk by rapid DNA extraction followed by a two-step PCR with nested primers

The likelihood that milk and milk products may act as a vehicle for antibiotic-resistant bacterial genes has become a concern to the food industry and a public health issue, and the demand for rapid tests has increased. The purity of DNA extracted from food samples is a key issue in the sensitivity and usefulness of biological analyses, such as PCR for pathogens and nonpathogens. A rapid, phenol-chloroform free method based on a modification of a sodium iodide DNA extraction, followed by a two-step PCR was developed for direct detection of the tet(M) gene in milk samples within a single working day. This study compares the proposed method with a traditional phenol solvent extraction method and with a commercial kit (QIAamp DNA blood mini kit, Qiagen). The three DNA extraction methods were used to ensure access to the tet(M) gene from 1 ml of raw milk, inoculated with a strain of Enterococcus faecalis, which carries the tet(M) gene. The proposed method, followed by a two-step PCR with nested primers specific for the tet(M) gene, was able to reach a detection limit below 10 CFU/ml in less than 4 h, including the two amplification cycles, thus outperforming in sensitivity and rapidity both the traditional and the commercial method.

A review of conventional detection and enumeration methods for pathogenic bacteria in food

With continued development of novel molecular-based technologies for rapid, high-throughput detection of foodborne pathogenic bacteria, the future of conventional microbiological methods such as viable cell enumeration, selective isolation of bacteria on commercial media, and immunoassays seems tenuous. In fact, a number of unique approaches and variations on existing techniques are currently on the market or are being implemented that offer ease of use, reliability, and low cost compared with molecular tools. Approaches that enhance recovery of sublethally injured bacteria, differentiation among species using fluorogenics or chromogenics, dry plate culturing, differentiation among bacteria of interest using biochemical profiling, enumeration using impedence technology, techniques to confirm the presence of target pathogens using immunological methods, and bioluminescence applications for hygiene monitoring are summarized here and discussed in relation to their specific advantages or disadvantages when implemented in a food microbiology setting.Key words: food pathogen, detection, enumeration methods, food safety.

Real-time nucleic acid-based detection methods for pathogenic bacteria in food

Quality assurance in the food industry in recent years has involved the acceptance and implementation of a variety of nucleic acid-based methods for rapid and sensitive detection of food-associated pathogenic bacteria. Techniques such as polymerase chain reaction have greatly expedited the process of pathogen detection and have in some cases replaced traditional methods for bacterial enumeration in food. Conventional PCR, albeit sensitive and specific under optimized conditions, obligates the user to employ agarose gel electrophoresis as the means for endpoint analysis following sample processing. For the last few years, a variety of real-time PCR chemistries and detection instruments have appeared on the market, and many of these lend themselves to applications in food microbiology. These approaches afford a user the ability to amplify DNA or RNA, as well as detect and confirm target sequence identity in a closed-tube format with the use of a variety of fluorophores, labeled probes, or both, without the need to run gels. Such real-time chemistries also offer greater sensitivity than traditional gel visualization and can be semiquantitative and multiplexed depending on the specific experimental objectives. This review emphasizes the current systems available for real-time PCR-based pathogen detection, the basic mechanisms and requirements for each, and the prospects for development over the next few years in the food industry.

Nucleic acid purification using microfabricated silicon structures

A microfluidic device has been designed, fabricated and tested for its ability to purify bacteriophage lambda DNA and bacterial chromosomal DNA, a necessary prerequisite for its incorporation into a biosensor. This device consists of a microfabricated channel in which silica-coated pillars were etched to increase the surface area within the channel by 300-600%, when the etch depth is varied from 20 to 50 microm. DNA was selectively bound to these pillars in the presence of the chaotropic salt guanidinium isothiocyanate, followed by washing with ethanol and elution with low-ionic strength buffer. Positive pressure was used to move solutions through the device, removing the need for centrifugation steps. The binding capacity for DNA in the device was approximately 82 ng/cm2 and on average, 10% of the bound DNA could be purified and recovered in the first 50 microl of elution buffer. Additionally, the device removed approximately 87% of the protein from a cell lysate. Nucleic acids recovered from the device were efficiently amplified by the polymerase chain reaction suggesting the utility of these components in an integrated, DNA amplification-based biosensor. The miniaturized format of this purification device, along with its excellent purification characteristics make it an ideal component for nucleic acid-based biosensors, especially those in which nucleic acid amplification is a critical step.

Methods for rapid separation and concentration of bacteria in food that bypass time-consuming cultural enrichment

The rapid detection of pathogenic organisms that cause foodborne illnesses is needed to insure food safety. Conventional methods for the detection of pathogens in foods are time-consuming and labor-intensive. New advanced rapid methods (i.e., polymerase chain reaction, DNA probes) are more sensitive and selective than conventional techniques, but many of these tests are inhibited by food components, rendering them dependent on slow cultural enrichment. The need for alternative methods that will rapidly separate and concentrate bacteria directly from food samples, thereby reducing the time required for these new rapid detection techniques, is evident. Separation and concentration methods extract target bacteria from interfering food components and/or concentrate bacteria to detectable levels. This review describes several methods used to separate and/or concentrate bacteria in food samples. Several methods discussed here, including centrifugation and immunomagnetic separation, have been successfully used, individually and in combination, to rapidly separate and/or concentrate bacteria from food samples in less time than is required for cultural enrichment.

Detection of viable Shiga toxin-producing Escherichia coli by quantitative competitive polymerase chain reaction

With the use of Escherichia coli O157:H7 as a model, a procedure for the quantitative detection of viable Shiga toxin-producing E. coli (STEC) in broth and cooked ground beef enrichments with multiple-time point quantitative competitive polymerase chain reaction (QC-PCR) was developed. The A subunit (a 401-bp fragment) of the stx2 gene was chosen as a target sequence. Immunomagnetic separation (IMS) was used to isolate and concentrate cells from ground beef enrichments. Cell viability was confirmed on the basis of the quantitative increase in the signal of target bands from QC-PCR across multiple time points. The application of IMS increased detection limits relative to those for QC-PCR without IMS. E. coli O157:H7 inoculated at 0.20 CFU/g of cooked ground beef (25 g of ground beef plus 225 ml of Bacto modified EC medium plus novobiocin) was detected and confirmed to be viable in <15 h. A DNA-based molecular approach can be used to determine cell viability.

Influence of growth in a food medium on the detection of Escherichia coli O157:H7 by polymerase chain reaction

The effects of storage time and growth in broth culture and in a food medium on the efficiency of Escherichia coli O157: H7 DNA extraction and on the sensitivity of polymerase chain reaction (PCR) detection of E. coli O157:H7 were investigated. Detection limits were evaluated with dilution series PCR targeting the slt-II gene. The relationship between cell density and DNA yield was generally log-linear for pure cultures of E coli O157:H7. When the bacteria were suspended in skim milk at a density of 10(6) CFU/ml. held at 4 degrees C, and sampled at 24-h intervals, cell density, total DNA yield, and PCR detection limits remained stable throughout the 96-h storage period. However, when E coli O157:H7 was grown in skim milk to a final cell density of 10(6) CFU/ml, PCR amplification efficiency was drastically reduced, although overall DNA yields from these samples were consistent with those for the samples in which E. coli O157:H7 growth was static over 96 h of storage at 4 degrees C. This result is most likely due to poor DNA purity, which was consistently observed when DNA was extracted from food matrices in which the pathogen was grown rather than stored. The results of this investigation underscore the likelihood that multiple components may drastically affect DNA extraction and PCR amplification efficiency in the detection of pathogens in the food matrix. It is clear that before nucleic acid amplification technologies are widely applied to food systems, it would be prudent to test their efficacy in multiple food matrices and under conditions in which the bacterial population is both static and actively growing.

Optimization of reverse transcriptase PCR to detect viable Shiga-toxin-producing Escherichia coli

The ability of reverse transcriptase PCR (RT-PCR) to detect viable Shiga-toxin-producing Escherichia coli (STEC) was investigated. Four primer sets, each targeting a specific region in the slt-II operon, were evaluated for their stringency and specificity for slt-II mRNA. STEC were evaluated for toxin expression under various conditions, including cell growth phase, growth medium, incubation temperature, and aeration. Following primer optimization, STEC were inoculated into Trypticase soy broth and cooked ground beef enrichments. Cells were harvested and RNA or DNA was extracted at 4, 8, 12, and 24 h. RT-PCR or PCR was conducted, and the products were visualized by gel electrophoresis and by Southern blots. mRNA targets were detected in 12-h cooked ground meat enrichments with an initial inoculum of 1 CFU/g. These results indicate that RT-PCR of E. coli slt-II mRNA is useful for detection of viable STEC in ground beef.

Development of a quantitative competitive PCR assay for detection and quantification of Escherichia coli O157:H7 cells

A quantitative competitive PCR (QC-PCR) assay was developed to detect and quantify Escherichia coli O157:H7 cells. From 10(3) to 10(8) CFU of E. coli O157:H7 cells/ml was quantified in broth or skim milk, and cell densities predicted by QC-PCR were highly related to viable cell counts (r(2) = 0.99 and 0.93, respectively). QC-PCR has potential for quantitative detection of pathogenic bacteria in foods.

Development of a multiplex polymerase chain reaction assay for detection and differentiation of Staphylococcus aureus in dairy products

A multiplex polymerase chain reaction (PCR) assay was developed for the detection and differentiation of enterotoxigenic Staphylococcus aureus in dairy products. A solvent extraction procedure was successfully modified for extraction of S. aureus DNA from 10 ml of artificially contaminated skim milk or 20 g cheddar cheese. Primers targeting the enterotoxin C gene (entC) and thermostable nuclease gene (nuc) were used in the multiplex PCR. PCR products were confirmed using restriction fragment length polymorphism analysis. DNA was consistently quantified and amplified by uniplex PCR from 10 CFU/ml of S. aureus in skim milk or 10 CFU/20 g cheddar cheese. The sensitivity of the multiplex PCR was 100 CFU/ml of skim milk or 100 CFU/20 g cheddar cheese. The developed methodology allows presumptive identification and differentiation of enterotoxigenic S. aureus in less than 6 h.