Polymerase chain reaction in food microbiology

Isothermal target and probe amplification assay for the real-time rapid detection of Staphylococcus aureus

Staphylococcus aureus, the species most commonly associated with staphylococcal food poisoning, is one of the most prevalent causes of foodborne disease in Korea and other parts of the world, with much damage inflicted to the health of individuals and economic losses estimated at $120 million. To reduce food poisoning outbreaks by implementing prevention methods, rapid detection of S. aureus in foods is essential. Various types of detection methods for S. aureus are available. Although each method has advantages and disadvantages, high levels of sensitivity and specificity are key aspects of a robust detection method. Here, we describe a novel real-time isothermal target and probe amplification (iTPA) method that allows the rapid and simultaneous amplification of target DNA (the S. aureus nuc gene) and a fluorescence resonance energy transfer-based signal probe under isothermal conditions at 61 °C or detection of S. aureus in real time. The assay was able to specifically detect all 91 S. aureus strains tested without nonspecific detection of 51 non-S. aureus strains. The real-time iTPA assay detected S. aureus at an initial level of 10(1) CFU in overnight cultures of preenriched food samples (kiwi dressing, soybean milk, and custard cream). The advantage of this detection system is that it does not require a thermal cycler, reducing the cost of the real-time PCR and its footprint. Combined with a miniaturized fluorescence detector, this system can be developed into a simplified quantitative hand-held real-time device, which is often required. The iTPA assay was highly reliable and therefore may be used as a rapid and sensitive means of identifying S. aureus in foods.

Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control

Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

Evaluation of target sequences for the polymerase chain reaction-based detection of Salmonella in artificially contaminated beef

Salmonella is a major cause of foodborne diseases worldwide, which has fueled the demand for the development and evaluation of sensitive, specific, and rapid detection methodologies, such as polymerase chain reaction (PCR). In this study, six primer pairs for the detection of Salmonella were evaluated by PCR with isolates of Salmonella spp. (115) and other bacteria (104). The primers designed for the sifB gene provided the best performance regarding specificity and sensitivity (100%). These primers were selected and used to develop a PCR assay for Salmonella detection during the enrichment steps of the conventional detection method in spiked beef samples. The enrichment steps were: buffered peptone water (BPW), Rappaport-Vassiliadis soya broth (RVS) and at the Müller-Kauffmann tetrathionate novobiocin broth (MKTTn), after 18 h (BPW) and 24 h (RVS and MKTTn) of incubation. The initial concentrations of the Salmonella inocula were 10¹, 10², and 10³ colony-forming units/25 g. The protocol was able to detect Salmonella at all concentrations in the enrichment steps, but not in the nonenriched samples. These results indicated that the proposed protocol was suitable to detect Salmonella in beef during the intermediate stages of the conventional isolation protocol, substantially reducing the time required to obtain the final results.

Polymerase chain reaction-based detection of total and specific Vibrio species

The polymerase chain reaction (PCR) technique is widely used for efficient detection of food-borne pathogens because of speed and specificity. However, PCR methods have focused mostly on species-specific detection. In the present work, we describe a PCR-based method for the simultaneous detection of all Vibrio species because lots of them are notorious food-borne human pathogens. We then combined this total detection method with specific detection of Vibrio cholerae pathogen. Using a degenerate primer set based on the sequence of the potassium uptake gene, trkA, we were able to successfully detect all Vibrio species. Specific detection of V. cholerae was also possible using primer sets based on putative flagellin sequence. Importantly, simultaneous total and species-specific Vibrio detection was possible using all two primer sets in a multiplexed PCR strategy. Thus, the PCR method we have developed is applicable to both simultaneous and two-step detection of total and specific Vibrio species.

Molecular study of Salmonella enteritidis in poultry samples by PCR, plasmid curing, antibiotic resistance and protein pattern analysis

In this study two control isolates of Salmonella enteritidis, RTCC1623 and RTCC1624, were obtained from the institute ofRazi (Karaj-Iran) and 14 strains were isolated from poultry samples in Kermanshah province of Iran, according to a standard protocol. These isolates were confirmed by PCR amplification of SefA gene fragments. Results showed that, 6 isolates of 14 isolates of Salmonella which their biochemical tests were positive contain 511 bp amplified fragments of the SefA gene. In other purpose, to correlating the presence of plasmids with antibiotic resistance and protein pattern, plasmid DNA was isolated before and after plasmid curing by using the alkaline lysis method. Strains of S. enteritidis contain seven different plasmid profiles (P1-P7) which were characterized by antibiotic resistance and protein pattern. Our observed showed, there was a high molecular weight plasmid with Rf 0.17 in all strains and the frequency of other plasmids was low. The plasmid with Rf about 0.2 is responsible for resistance to Cephalothin and the isolates that lost it were susceptible to this antibiotic. All strains, 100%, were resistant to ampicillin before and after curing of strains. According to present findings, PCR is a rapid and sensitive method for typing of S. enteritidis and plasmid profiling; antibiotic resistance and protein pattern are suitable methods for subtyping of S. enteritidis isolates. No direct correlation was found between plasmid contents, antibiotic resistance patterns and protein profiles of local S. enteritidis isolates.

Evaluation of three different molecular markers for the detection of Staphylococcus aureus by polymerase chain reaction

The aim of this study was to target three genes of Staphylococcus aureus-fmhA (coding for a factor of unknown function), catalase and femA (coding for a factor essential for methicillin resistance) to establish and validate a PCR assay for the detection of this pathogen. Two pairs of primers were designed for fmhA and one pair each for catalase and femA genes. The PCR assays were standardized and found to give specific amplicons under similar reaction parameters. Target specificity of the primers was confirmed by DNA sequencing of the amplicons. While the initial inclusivity and exclusivity test reactions were in agreement in case of three of the primer pairs, one pair based on fmhA gene produced a non-specific product with a template DNA used in exclusivity test reactions. Forty-five strains of S. aureus were subjected to these PCR assays for their evaluation. Three among the four pairs of primers, one against each gene detected all the 45 strains precisely whereas one of the PCR assays using primers targeting the fmhA gene did not generate the specific amplicon with several of the strains. Seven unidentified strains of Gram-positive cocci subjected to these PCR assays produced negative results for each culture. Six of the strains were identified as Staphylococcus haemolyticus and one strain as Staphylococcus arlettae by 16S ribosomal gene analyses. All the three assay systems showed a detection limit of 100 cells per 20mul reaction assay. For validation of these assay systems, 80 coded samples of 11% skimmed milk spiked with different pathogens were received from NICED (National Institute of Cholera and Enteric Diseases), Kolkata and subjected to these PCR assays. All the three assays could detect S. aureus correctly in two of the samples. Amongst 150 raw milk samples, 36 (24%) were found positive for S. aureus. We conclude that fmhA, catalase and femA genes are conserved in S. aureus and, therefore, could be used as specific targets for its detection and identification by PCR. The protocols developed herein could be used for rapid and specific detection of this pathogen in food, clinical and environmental samples, especially milk.

PCR-based procedures for detection and quantification of Staphylococcus aureus and their application in food

AIMS

To evaluate the specificity of nuc targeted primers for PCR detection of Staphylococcus aureus in different food matrices and to establish a RTQ-PCR procedure suitable for the routine detection and quantification of this pathogen in food.

METHODS AND RESULTS

Specificity of nuc targeted primers (Pri1-Pri2 and the newly designed RTQ-PCR primers) was tested on a total of 157 strains of genetically confirmed identity, including reference and food isolates. PCR detection on artificially inoculated beef samples by DNA extraction using a DNeasy Tissue Kit (Qiagen GmhH, Hilden, Germany) showed a sensitivity value around 10(3) CFU g(-1). The two RTQ-PCR systems, incorporating SYBR-Green I and TaqMan, respectively, applied in the present work improved the sensitivity of conventional PCR by lowering the detection level to 10 and 100 cells, respectively. Out of 164 naturally contaminated foods tested for the presence of Staph. aureus, 74 were positive by conventional PCR and 69 by the traditional culture method with a high degree of result agreement between both methodologies (93.3%).

CONCLUSIONS

PCR approaches, using nuc targeted primers, have proved specific and combined with growth techniques may improve detection of Staph. aureus in different types of food.

SIGNIFICANCE AND IMPACT OF THE STUDY

The SYBR-Green I real-time PCR approach established allows the sensitive, automated and quantitative detection of Staph. aureus for routine analysis at a reasonable cost.

Identification and typing of food-borne Staphylococcus aureus by PCR-based techniques

The possibility of using PCR for rapid identification of food-borne Staphylococcus aureus isolates was evaluated as an alternative to the API-Staph system. A total of 158 strains, 15 S. aureus, 12 other staphylococcal species, and 131 isolates recovered from 164 food samples were studied. They were phenotypically characterized by API-Staph profiles and tested for PCR amplification with specific primers directed to thermonuclease (nuc) and enterotoxin (sea to see) genes. Disagreement between the PCR results and API-Staph identification was further assessed by the analysis of randomly amplified polymorphic DNA (RAPD) profiles obtained with three universal primers (M13, T3, and T7) and 16S rDNA sequencing. Forty out of 131 isolates (31%) tested positive for PCR enterotoxin. Of these, 14 (11%) were positive for sea, 22 (17%) for sec, one (0.8%) for sed, and three (2.2%) for sea and sec. No amplification corresponding to seb nor see was obtained. Cluster analysis based on RAPD profiles revealed that most of the sec positive food isolates grouped together in three clusters. Cluster analysis combining the three RAPD fingerprints (M 13, T3, and T7), PCR-enterotoxin genotype and API-Staph profiles, grouped the nuc PCR positive isolates together with S. aureus reference strains and the nuc PCR negative isolates with reference strains of other staphylococcal species. The only nuc PCR positive food isolate that remained unclustered was a sed positive strain identified by 16S rDNA sequence as S. simulans. The high concordance between S. aureus and nuc PCR positive strains (99%) corroborates the specificity of the primers used and the suitability of nuc PCR for rapid identification of S. aureus in routine food analysis.

Polymerase chain reaction detection of foodborne Salmonella spp. in animal feeds

Foodborne salmonellosis continues to be a public health issue of considerable concern. Animal feed has been a major link in pre-harvest food animal production. Although monitoring systems and control measures are available to limit Salmonella spp. contamination on animal feeds detection methodology is relatively time consuming in the context of time inputs for feed processing and mixing. Current cultural methods of Salmonella spp. detection in feeds require several days for confirmation. This amount of time represents significant problems if control measures are to be effectively implemented in a fashion that keeps feed processing costs low. Molecular methods offer improved sensitivity and potential reduction in assay time. In particular, several commercial polymerase chain reaction (PCR) assays, and combined PCR-hybridization assays have been suggested as possible means to implement more rapid detection of Salmonella spp. extracted from animal feeds. It has now become possible to rapidly detect and confirm the presence of foodborne Salmonella spp. in feed matrices by commercial amplification detection systems. The primary challenges remaining are to develop more reliable recovery and extraction procedures for routine processing of samples from a wide variety of feed matrices and apply molecular techniques for assessing physiological status of Salmonella spp. contaminants in animal feeds.

Simultaneous detection of Carnobacterium and Leuconostoc in meat products by multiplex PCR

AIMS

To develop a multiplex PCR approach for simultaneous detection of Leuconostoc and Carnobacterium and its validation in meat products.

METHODS AND RESULTS

Two multiplex PCR assays were developed using newly designed 16S rDNA-directed primers adapted to the current taxonomic situation of genera Leuconostoc and Carnobacterium that allow: (i) simultaneous detection of both genera, and members of the nonmotile species of genus Carnobacterium and (ii) identification in a single assay of the nonmotile species C. divergens, C. maltaromicum and C. gallinarum. Sensitivity values of 10(3) and 10(4) CFU g(-1) were determined for multiplex PCR detection of Carnobacterium and Leuconostoc, respectively, following artificially inoculated meat trials. In addition, both multiplex PCR assays were validated in 14 naturally contaminated samples covering nine types of meat products. Results obtained by colony identification were confirmed by PCR detection.

CONCLUSIONS

The methods described in this study provide a rapid and reliable tool for PCR detection of Carnobacterium and Leuconostoc, in meat products, and for colony identification.

SIGNIFICANCE AND IMPACT OF THE STUDY

This multiplex PCR approach will help in the analysis of the spoilage microbiota of refrigerated vacuum-packaged meat product in order to determine the appropriate preservation method.

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.

PCR detection of Listeria monocytogenes: a study of multiple factors affecting sensitivity

AIMS

To test, under comparable conditions, several parameters affecting sensitivity of PCR detection in order to establish a PCR procedure suitable for the routine detection of Listeria monocytogenes in food.

METHODS AND RESULTS

Beef samples artificially inoculated were used to determine sensitivity of PCR detection under different parameters. As few as 1 CFU g(-1) were detected by DNA extraction using a DNeasy Tissue Kit (Qiagen GmhH, Hilden, Germany) of 1 ml aliquot and PCR amplification with primers directed to the hlyA gene. This PCR protocol was applied in 60 naturally contaminated foods, comparing two enrichment procedures with the traditional culture method. The highest number of positives was recorded by PCR following a 24-h pre-enrichment step at 30 degrees C and a 24-h enrichment step at 37 degrees C. Afterwards, it was applied in 217 naturally contaminated foods and 56 of them tested positive for L. monocytogenes in which only 17 tested positive using the culture method.

CONCLUSIONS

The PCR procedure described has proved to be a rapid and sensitive method suitable for the routine analysis of different types of food.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method proposed for the detection of L. monocytogenes, has been validated in naturally contaminated food and is suitable to implement in the food industry.

Salmonella contamination of pigs and pork in an integrated pig production system

This paper describes the monitoring of Salmonella in a closed pig production system in Belgium over a 2-year period. A sampling scheme including animal feeds and carcasses was designed to cover the entire chain of production from farrow to finishing pigs. Salmonella was detected by a method based on the use of semisolid Rappaport-Vassiliadis as a selective medium. The serotypes of the isolated strains were determined, and the antibiotic resistance of these strains to six antibiotics was also investigated. Feeds were found to be more contaminated than expected (10.2%, 34 of 332 samples). The percentage of positive fecal samples for pregnant sows (8.1%, 11 of 135 samples) was significantly higher than that for young and lactating sows (2.9%, 11 of 378 samples) (P<0.05). The percentage of positive samples for colon contents collected at the slaughterhouse (47.3%, 88 of 186 samples) was significantly higher than that for feces collected during the fattening stage (5.6%, 18 of 320 samples) (P<0.001). For carcass swab samples, the observed prevalence was 11.2% (17 of 152 samples). On farms, Salmonella recovery levels were higher for overshoe samples than for fecal samples, except for pregnant sows. Salmonella Typhimurium was the most frequently isolated serotype (32.2%, 55 of 171 samples), while Salmonella Brandenburg was predominant in the colon contents collected at the abattoir (21.4%, 18 of 84 samples). Feeds harbored a wide diversity of serotypes of minor epidemiological significance. Of 55 isolated strains of Salmonella Typhimurium, 11 (20%) were resistant to tetracycline, ampicillin, choramphenicol, streptomycin, trimethoprim, and nalidixic acid (R Type TeAmCSNa), while 12 (21.8%) were resistant to all of these antibiotics except nalidixic acid (R Type TeAmCS). The majority of Salmonella Typhimurium strains that exhibited resistance to more than four antimicrobial agents were characterized as Salmonella Typhimurium DT104 or as being closely related to Salmonella Typhimurium DT104 (7 of 12 isolates). In conclusion, our system of surveillance is effective in identifying most points of contamination in the production chain and will be useful in ongoing efforts to develop a Salmonella-free production system.

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.

Evaluation of selective and non-selective enrichment PCR procedures for Salmonella detection

AIMS

To compare PCR combined with enrichment media with the standard microbiological techniques (SMT) and to determine the most sensitive method for the detection of Salmonella and the identification of Salm. typhimurium (ST), Salm. enteritidis (SE), Salm. gallinarum (SG) and Salm. pullorum (SP).

METHODS AND RESULTS

We analysed 87 samples from poultry using PCR and SMT, PCR being performed from non-selective (NS) and Rappaport-Vassiliadis (RV) media. PCR-NS was less sensitive than PCR-RV and SMT for the detection and identification of Salmonella. PCR-RV detected more positive samples of Salmonella sp. than SMT but both these methods showed similar sensitivity regarding the identification of Salmonella serovars.

CONCLUSIONS

PCR-RV was more sensitive and decreased the time necessary to detect and identify Salmonella.

SIGNIFICANCE AND IMPACT OF THE STUDY

PCR-RV is a powerful tool for the rapid and accurate detection and identification of Salmonella and can be implemented in diagnostic and food analysis laboratories.

The use of NASBA for the detection of microbial pathogens in food and environmental samples

The isothermal amplification method nucleic acid sequence-based amplification (NASBA), which amplifies RNA, has been reported as useful for the detection of microbial pathogens in food and environmental samples. Methods have been published for Campylobacter spp., Listeria monocytogenes and Salmonella enterica ser. Enteritidis in various foods and for Cryptosporidium parvum in water. Both 16S rRNA and various mRNAs have been used as target molecules for detection; the latter may have advantages in allowing specific detection of viable cells. Most of the methods to detect pathogens in foods have employed enrichment in nutrient medium prior to NASBA, as this can ensure sensitivity of detection and encourage the detection of only viable target cells. Although a relatively recent method, NASBA has the potential for adoption as a diagnostic tool for environmental pathogens.

Development of a semi-nested PCR for the improved detection of Mycoplasma bovis from bovine milk and mucosal samples

A new forward primer, Mb-F, was designed to improve the sensitivity and reproducibility of the Mycoplasma bovis-specific PCR developed by Ghadersohi et al. [Vet. Microbiol. 56 (1997) 87] for testing clinical samples. A semi-nested (SN) PCR configuration was developed and this provided enhanced sensitivity and reproducibility. The detection limit of the SN PCR was in the range of 10-100cfu/ml and the correct amplicon was amplified from 9.15pg/microliter of total extracted DNA (mixture of M. bovis and bovine cellular DNA). A dot blot assay was also developed and compared with the SN PCR on a number of randomly selected milk and mucosal samples. The dot blot had the same level of detection as the SN PCR. The specificity of the SN configuration was confirmed by Southern blot analysis and automated sequencing of the PCR product. The results from the tests on the samples from cattle, together with those from sheep, provided evidence that M. bovis is host-specific and that most cattle are colonised. The assay was shown to be specific, sensitive and reproducible and could be used successfully to detect M. bovis directly from clinical material without pre-enrichment.

Detection and identification of salmonellas from poultry-related samples by PCR

A polymerase chain reaction (PCR) assay was developed for the generic detection of Salmonella sp. and the identification of S. Enteritidis (SE), S. Gallinarum (SG), S. Pullorum (SP) and S. Typhimurium (ST) in material collected in the field from poultry. The specificity and sensitivity of the assay combined with Rappaport-Vassiliadis selective enrichment broth (PCR-RV) were determined, and field samples were analyzed to verify the validity of the method application. Specificity of the assay was tested using 29 SE, 11 SG, 10 ST and 10 SP strains, along with 75 strains of 28 other Salmonella serovars and 21 strains of other bacterial genera. The assay was 100% specific for Salmonella detection and ST identification. The primer pair for SE, SG and SP also detected S. Berta. PCR detection limits for Salmonella at the genus level were 2 ST, 8 SE, 1.1x10(3) SG and 1.8x10(5) SP cells. At the serovar level, detection limits were 7 ST, 1.2x10(3) SE, 4.4x10(7) SG and 1.8x10(6) SP cells. At the genus level, PCR-RV detected approximately 128% more positive field samples than the standard microbiological techniques and results were ready in 48h instead of 7 days. PCR-RV method is diagnostic of Salmonella at the genus level and ST at the serovar level, although other tests are needed to identify SE, SG and SP to serovar level.

Detection of Campylobacter jejuni and Campylobacter coli in foods by enrichment culture and polymerase chain reaction enzyme-linked immunosorbent assay

A polymerase chain reaction (PCR) assay based on a solution hybridization format with colorimetric end-point detection (PCR ELISA) was investigated for the specific detection of Campylobacter jejuni and Campylobacter coli in food samples following enrichment culture. One hundred fifteen samples of raw meat and offal (poultry, porcine, ovine, and bovine), raw shellfish, and artificially contaminated milk were enriched in blood-free Campylobacter Enrichment Broth for 48 h. Enrichment cultures were subcultured to Campylobacter blood-free selective agar plates, and presumptive isolates were identified by phenotypic methods. DNA was extracted from 1-ml aliquots of the enrichment cultures using a rapid extraction method, and the DNA was used as the template in a PCR ELISA. A comparison of the PCR ELISA with the enrichment culture and subculture to selective agar method showed that the results of 112 of the 115 samples tested were in agreement by both methods. Seventy-one of the various food samples were positive in the PCR ELISA, and 70 samples were positive by culture. The PCR ELISA had a sensitivity of 99% and a specificity of 96%, with a positive predictive value of 97% and a negative predictive value of 98%. The PCR ELISA is a rapid, sensitive, and specific method for the detection of C. jejuni and C. coli in foods following enrichment culture and significantly reduces the time required for their detection.

On the specificity of PCR detection of Listeria monocytogenes in food: a comparison of published primers

A total of nine pairs of primers, seven previously published and two newly developed, have been assayed for PCR detection of Listeria monocytogenes in food. They have been tested for specificity on a total of 72 strains including reference and food isolates belonging to L. monocytogenes and other species in the genus. First of all, a polyphasic approach has been carried out in order to establish a reference strain collection. They were biochemically and genetically characterized by API-Lis and randomly amplified polymorphic DNA PCR (RAPD-PCR), respectively. Random amplification of DNA was performed with M13, T7 and T3 universal primers and a data bank was created to compile the RAPD patterns of all the analyzed strains. The UPGMA cluster analysis of RAPD profiles with primer M13 showed eight clusters at 72.3% similarity. Clusters 2 and 7 corresponded to L. monocytogenes. Clusters 1 and 6 grouped L. ivanovii strains. Clusters 3, 4, 5 and 8 corresponded to L. grayi, L. innocua, L. welshimeri and L. seeligeri, respectively. Pattern analysis revealed the existence of miss-identified reference strains which was confirmed by 16S rDNA sequence analysis. RAPD-PCR is a rapid genetic test which helped to confirm strain identity. On the basis of PCR specificity results, primers LM1-LM2 were the best combination for the detection of L. monocytogenes since they only amplified the specific fragment in strains that had been genetically and biochemically assessed as belonging to the species. Specificity of other assayed primers is discussed.

Evaluation of two commercial methods for the detection of Listeria sp. and Listeria monocytogenes in a chicken nugget processing plant

This study measures the detection performances of two rapid test systems (Listeria Rapid Test Clearview and Bax system) for the screening of Listeria sp. and Listeria monocytogenes, respectively. A total of 413 samples from different sources (product from (i) different stages of processing, (ii) different environments, and (iii) different food handlers), collected from a chicken nugget processing plant, were analysed by both rapid methods and a cultural method consisting of pre-enrichment, enrichment, and isolation onto selective agars (PALCAM, LPM, and HCLA). Overall, results showed an excellent correlation between data obtained using Clearview and the cultural method, with Clearview presenting an efficiency of 99%. Bax showed a lower correlation using the cultural method, with an efficiency of 71.1%. The type of sample did not affect the efficiency of Clearview, which varied from 98.1% for product samples to 100% for environmental and food handler samples, while for Bax it had a marked influence. Efficiency of Bax varied from as high as 100% for food handlers to 37.9% for product samples.

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.

Screening for clostridium botulinum type A, B, and E in cooked chilled foods containing vegetables and raw material using polymerase chain reaction and molecular probes

A molecular method was used for the detection of Clostridium botulinum spores of type A, B, and E in commercial cooked and pasteurized vegetable purées and in the raw materials (vegetables and other ingredients). The method allowed the detection of less than 8 spores/g of product for C. botulinum type A, less than 1 spore/g for proteolytic type B, less than 21 spores/g for nonproteolytic type B, and less than 0.1 spore/g for type E. Thirty-seven samples of raw vegetables and ingredients were tested for the presence of C. botulinum type A, B, and E; 88 and 90 samples of vegetable purées were tested, respectively, for the presence of C. botulinum type A and B and for the presence of C. botulinum type E. All samples were negative, suggesting that the prevalence of C. botulinum in these vegetable purées and the raw ingredients is probably low.

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

Rapid nucleic acid-based methods to detect human pathogens in foods are dependent on the reliability of the DNA or RNA extraction method used. Skim milk, non-fat dry milk, Cheddar and Brie cheese, and reconstituted whey powder were seeded with serially diluted (10(0)-10(7) cfu 10 ml(-1)) Escherichia coli O157:H7 and subjected to DNA extraction (i) directly from the food product using a solvent-based procedure and (ii) using a guanidinium isothiocyanate (GITC) procedure after previous bacterial concentration. Both the efficiency of DNA extraction and the overall PCR detection limits were evaluated. In almost all instances, the total DNA yield using the solvent method was greater than that obtained for the concentration method. However, the purity of the DNA obtained after bacterial concentration was significantly better than that obtained after organic extraction alone. PCR detection limits after each DNA recovery method varied with the specific food, ranging from 10(1) to 10(4) cfu ml(-1) for all products except whey powder. DNA yields and subsequent PCR detection limits for reconstituted whey powder were extremely poor, and neither procedural changes nor the addition of PCR enhancement agents were able to improve recovery and/or detection. It is concluded that the efficiency of DNA extraction is an extremely important and frequently overlooked variable impacting the overall detection limits of PCR-based detection strategies.

Molecular beacon polymerase chain reaction detection of Escherichia coli O157:H7 in milk

A fluorescently labeled oligonucleotide probe (molecular beacon) was applied to detect Escherichia coli O157:H7 in artificially contaminated skim milk during polymerase chain reaction (PCR) amplification of extracted DNA. The probe was designed to hybridize with a region of the slt-II gene coding for the A subunit and to fluoresce when the hairpin-stem conformation was linearized upon hybridization to the target sequence. The molecular beacon was incorporated into PCR reactions containing DNA extracted from artificially contaminated skim milk. The degree of fluorescence was monitored in PCR reactions containing 10(3), 10(5), and 10(7) CFU of E. coli O157:H7 per ml and was found to correlate with the amount of template in each reaction. Fluorescence significantly increased above background levels by cycle 8, 14, or 14 in reactions containing DNA from the 10(7)-, 10(5)-, or 10(3)-CFU/ml template, respectively (P < 0.05). Molecular beacon PCR demonstrated positive results more rapidly than traditional agarose gel electrophoresis analysis of PCR products. Use of molecular beacons allows real-time monitoring of PCR reactions, and the closed-tube format allows simultaneous detection and confirmation of target amplicons without the need for agarose gel electrophoresis and/or Southern blotting. This is the first report of a stem-and-loop molecular beacon being applied for direct detection of a pathogen in food.

PCR assay for detection of the E. coli O157:H7 eae-gene and effect of the sample preparation method on PCR detection of heat-killed E. coli O157:H7 in ground beef

A PCR assay targeting the 3' end of the eae-gene of E. coli O157:H7 has been developed. It was shown to be specific for the E. coli O157:H7 eae-gene. Sensitivity of the PCR assay was 1 pg DNA or 10(3) cfu per PCR reaction. Subsequently, a study was conducted to examine the effect of the food matrix and the sample preparation method on PCR detection of non-viable cells using heat-killed E. coli O157:H7 in ground beef as a model system. Inoculated ground beef samples were subjected to either selective enrichment or immediately prepared for PCR analysis. Four sample preparation methods were applied: centrifugation, buoyant density centrifugation (BDC), immunomagnetic separation (IMS), and chelex extraction. Production of false-positive results due to amplification of the DNA of dead cells occurred if the number of heat-killed cells exceeded 10(8) cfu/g. For inocula <10(8) cfu/g, PCR results for heat- killed E. coli O157:H7 cells depended upon the sample preparation method. It was shown that the inclusion of two washings steps of the bacterial pellet before DNA extraction was the critical factor for elimination of false-positive results due to heat-killed cells in the centrifugation and BDC procedure. IMS did not produce false-positive results due to heat-killed cells (two washing steps were included in the IMS procedure). With the chelex-extraction method, false-positive results due to heat-killed cells were obtained. An effect of the ground beef food matrix on the presence of amplifiable DNA was noted.

The development of a combined surface adhesion and polymerase chain reaction technique in the rapid detection of Listeria monocytogenes in meat and poultry

A procedure combining enrichment surface adhesion and polymerase chain detection (SA-PCR) was developed and applied in the detection of Listeria monocytogenes in meat products. Minced beef samples were inoculated with L. monocytogenes (log(10)3 cfu g(-1)) and incubated for 10 h at 30 degrees C in buffered peptone water. L. monocytogenes was recovered from the culture by attachment to a polycarbonate membrane immersed for 15 min in the enriched meat culture. The membrane and attached bacteria were removed from the culture and the membrane dissolved in phenol:chloroform. The DNA was extracted from the bacteria and a PCR assay was carried out using primers directed against the listerolysin O gene of L. monocytogenes. The combined (SA-PCR) technique had a detection limit of log10 4.0 cfu ml(-1) in enriched meat cultures. The rapid technique was applied to a small number of retail samples (n = 100) and was found to compare favourably to the standard cultural method. A total of 12 samples were confirmed positive for L. monocytogenes using the standard cultural method and the SA-PCR assay. No false positives or negatives were recorded by either method.

Conventional and molecular methods for understanding probiotic bacteria functionality in gastrointestinal tracts

The recent successes of probiotic application to limit colonization of foodborne pathogens in the gastrointestinal tracts of food animals ensures continued commercialization and widespread use of such cultures. Given that the the fermentation response and ecological balance of the probiotic consortium appears to be essential for the effectiveness of the cultures, it is essential to develop a methodology to accurately identify and quantitate these organisms during commercial production as well as successful in vivo colonization after administration. However, if further optimization of the effectiveness of defined cultures is to be achieved, methods to assess expression of key metabolic processes occurring during establishment of the probiotic culture as well as its subsequent ability to limit foodborne pathogen colonization are needed. Conventional methods to study individual probiotic gastrointestinal organisms include selective plating to identify specific nutritional groups, but the requirement of strict anaerobiosis for the obligate anaerobic members of these cultures can confound sample handling and preparation. Immunological methods can circumvent some of these problems but are somewhat limited for assessing functionality. The main advantage of using molecular tools is that the genetic diversity of the microflora, as well as their gene activity data are obtainable, both at the community level and at the single species level. Methods are currently available that permit studying individual members of microbial consortia, fluxes in community diversity, spatial distribution of consortia members, and the expression of specific microbial genes within communities. These methods involve the utilization of both DNA- and RNA-targeted probes, gene amplification protocols, and mRNA analysis. The study of mechanisms and functionality can only enhance the potential of probiotic cultures for limiting foodborne pathogen colonization.

Rapid molecular detection of microbial pathogens: breakthroughs and challenges

Microbiological contamination of foods and drinking water is a global problem, and a significant amount of expense is being incurred as a result of such contamination. The microorganisms associated with almost half of all disease outbreaks still go unidentified, primarily as a result of inadequate monitoring and surveillance. Though significant improvements have been made in refining molecular methods for detecting infectious agents, a majority of these methods are being employed only on clinical samples where pathogen densities are much higher than those found in environmental and food samples. Comparative evaluations of the various protocols in terms of cost, sensitivity, specificity, speed, and reproducibility need to be undertaken so that the true applicability of these methods can determined. In the future, molecular methods, especially gene amplifications and in situ hybridizations, will find increasing applications in the differentiation of viable and non-viable organisms, in predicting antimicrobial resistance, and in the identification and characterization of unculturable microorganisms. Though molecular detection methods will not totally replace conventional methods, they will significantly enhance our ability to detect microbial pathogens rapidly.

Rapid PCR with nested primers for direct detection of Campylobacter jejuni in chicken washes

Rapid detection of Campylobacter jejuni by PCR directly from foods, without prior growth steps, would be beneficial for the poultry industry. We have previously reported a PCR assay that allows detection of this bacterium after 48 h growth on Campy cefex agar. We have now developed a more rapid nested PCR assay that specifically detects C. jejuni in chicken washes that have not undergone any lengthy growth steps prior to PCR. For the nested reaction, an external set of primers, C-1 and C-4, are used for 24 cycles. At this time, 1 microl of the PCR product is removed and added to a second reaction. The second PCR assay is run with C-1 and an internal primer, C-2, for 24 cycles. A single band on a 4% NuSieve agarose gel at 122 bp was apparent with C. jejuni cells at a sensitivity of 10(2) cfu ml-1. With this method chicken carcasses can be washed and C. jejuni identified all within 1 day. We detected C. jejuni in approximately 80% of four groups of chickens using this method. The identifications have been confirmed by standard microbiological techniques.

MPN-PCR-quantification method for staphylococcal enterotoxin c1 gene from fresh cheese

PCR detection methods have been extensively used in diagnostic microbiology. However, a lack of a simple and reliable method for quantification of the PCR products has partly hindered the use of PCR in routine food laboratories. The quantification of PCR products can be done by combining the principles of MPN statistics and PCR technique. We have developed a simple and sensitive MPN-PCR assay for detection and enumeration of enterotoxin C producing Staphylococcus aureus NCTC 10655 from fresh cheese. By amplifying single copy chromosomal enterotoxin C gene fragment, we could detect as little as 20 cfu/g. By Moran's test, most of the DNA dilution series appeared to fulfill the basic mathematical assumptions of ordinary MPN methods. The analysis with MPN-PCR took one day to perform compared with three days analysis time with plate counting. This MPN-PCR method can be readily applied with different primer systems without extensive development work.

Strategies to accelerate the applicability of gene amplification protocols for pathogen detection in meat and meat products

Traditionally, microbiological testing of meat products has involved isolating microorganisms and performing specific biochemical, and in some cases serological, tests to confirm the presence or absence of suspected food-borne pathogens. Given the public attention meat products have received as sources of food-borne disease, there has been considerable interest in the application of rapid detection techniques that require hours rather than days for completion. Theoretically, rapid detection methods could reduce the time from the initial sampling to confirmation so that conclusive results would be available by the time to process the meat product. Both direct gene probe hybridization as well as gene amplification methods show promise as rapid detection techniques. At present, direct gene probe hybridization are being commercially utilized to confirm the presence of a suspected pathogen. A number of gene amplification protocols for detecting food-borne bacterial pathogens have been published. However, many of these studies have utilized spiked samples rather than naturally contaminated samples and many of them have involved extended template extraction/purification methodologies. There is still only a very limited amount of information on the efficacies of the various protocols in detecting bacterial pathogens, especially toxigenic Escherichia coli, Salmonella spp., Campylobacter spp., and Listeria spp., in naturally contaminated food samples. In order to develop gene amplification protocols that have relevance to the meat industry, there must be a concerted effort to utilize naturally contaminated samples in the development and evaluation of protocols, as well as to initiate multilaboratory round robin evaluations of select protocols. Availability of multilaboratory tested methodologies would provide a means to design pathogen detection strategies at the quality control level rather than an end product confirmatory response to an already documented outbreak.