Detection of Salmonella spp. in oysters by PCR

Evaluation of Microbial Contamination in Cold Dishes and Prevalence of Foodborne Pathogens in Jilin Province

ABSTRACT

This study evaluated the microbial contamination status of cold dishes consumed by residents of Jilin Province and investigated to determine the incidence of four pathogenic bacteria in cold dishes. A total of 300 samples of cold dishes, including meat, vegetable, and mixed products, were collected from three purchasing places: supermarkets, farmers' markets, and mobile vendors. Viable bacteria were isolated using conventional culture methods. After separation, a quick and easy PCR was used to detect Listeria monocytogenes, Staphylococcus aureus, enterotoxigenic Escherichia coli, and Salmonella. The results showed that the total number of microbial colonies in the vegetable samples exceeded the standard rate of 8% and the total number of microbial colonies in the meat and mixed samples did not exceed the standard. The total microbial colony count exceeded the standard in all three procurement sites, with the highest exceedance of 7.4% in the mobile vendor sites. The detection rates of enterotoxigenic E. coli, S. aureus, L. monocytogenes, and Salmonella, among the four pathogenic bacteria detected in all samples, were 4.3, 3.3, 3.0, and 1.0%, respectively. This study can be used to qualitatively assess the microbiological quality associated with cold dishes. It provides data to support the detection of possible food safety problems.

HIGHLIGHTS

An ultra-fast, one-step RNA amplification method for the detection of Salmonella in seafood

Salmonella is one of the most common pathogens associated with food-borne illness resulting from seafood consumption. Herein, an accelerated strand exchange amplification (ASEA) requiring only a pair of primers and one polymerase was first reported for ultra-fast, one-step RNA amplification detection of Salmonella in seafood. The ASEA method could detect Salmonella typhimurium DNA in dilutions as low as 10 copies per reaction and displayed good specificity for Salmonella under the interference of a variety of food-borne pathogens. In particular, ASEA could detect RNA in one step without additional reverse transcription. The detection limit for Salmonella in artificially contaminated oyster was 1 CFU mL^-1 following 12 h of enrichment. Moreover, excellent performance of this assay was observed with 99.02% consistency relative to real-time PCR through actual sample detection. Combined with the rapid nucleic acid extraction method, the entire detection process could be completed within 20 min. Therefore, this assay opens up new prospects for the detection of food-borne pathogens in seafood with its rapidity, which would be very beneficial for food safety supervision and pathogen detection of high-throughput samples.

Evaluation of E. coli in sediment for assessing irrigation water quality using machine learning

Fresh produce irrigated with contaminated water poses a substantial risk to human health. This study evaluated the impact of incorporating sediment information on improving the performance of machine learning models to quantify E. coli level in irrigation water. Field samples were collected from irrigation canals in the Southwest U.S., for which meteorological, chemical, and physical water quality variables as well as three additional flow and sediment properties: the concentration of E. coli in sediment, sediment median size, and bed shear stress. Water quality was classified based on E. coli concentration exceeding two standard levels: 1 E. coli and 126 E. coli colony forming units (CFU) per 100 ml of irrigation water. Two series of features, including (FIS) and excluding (FES) sediment features, were selected using multi-variant filter feature selection. The correlation analysis revealed the inclusion of sediment features improves the correlation with the target standards for E. coli compared to the models excluding these features. Support vector machine, logistic regression, and ridge classifier were tested in this study. The support vector machine model performed the best for both targeted standards. Besides, incorporating sediment features improved all models' performance. Therefore, the concentration of E. coli in sediment and bed shear stress are major factors influencing E. coli concentration in irrigation water.

Detection of Salmonella Typhimurium in Romaine Lettuce Using a Surface Plasmon Resonance Biosensor

Leafy vegetables have been associated with high-profile outbreaks causing severe illnesses. Timely and accurate identification of potential contamination is essential to ensure food safety. A surface plasmon resonance (SPR) assay has been developed for the detection of Salmonella Typhimurium in leafy vegetables. The assay utilizes a pair of well characterized monoclonal antibodies specific to the flagellin of S. Typhimurium. Samples of romaine lettuce contaminated with S. Typhimurium at different levels (between 0.9 and 5.9 log cfu/g) were pre-enriched in buffered peptone water. Three SPR assay formats, direct assay, sequential two-step sandwich assay, and pre-incubation one-step sandwich assay were evaluated. All three assay formats detect well even at a low level of contamination (0.9 log cfu/g). The SPR assay showed a high specificity for the detection of S. Typhimurium in the presence of other commensal bacteria in the romaine lettuce samples. The results also suggested that further purification of flagellin from the sample preparation using immunomagnetic separation did not improve the detection sensitivity of the SPR assay. The functional protocol developed in this study can be readily used for the detection of S. Typhimurium in leafy vegetables with high sensitivity and specificity.

Zoonotic potential of Salmonella enterica carried by pet tortoises

The prevalence of Salmonella in chelonians is not known in the UK and it is not clear whether such Salmonella strains would be pathogenic for human beings. Some strains, such as members of the Arizonae subgroup, may be unable to cause anything more than very mild disease. To determine the carriage of Salmonella in pet tortoises, cloacal swabs were taken for culture. Salmonella enterica Group D was isolated from 5 of the 89 samples. All five were from the same household of seven tortoises. Salmonella isolates were shown by PCR to carry the invA and spiC genes associated with pathogenicity islands 1 and 2. Each isolate carried both genes indicating they had the genetic basis for disease and enterocyte invasion in human beings. The study indicates a low rate of asymptomatic carriage among the general population of pet tortoises. However, it does suggest that those Salmonella strains colonising the tortoise can carry Salmonellapathogenicity island (SPI)-1 and SPI-2 conferring the potential to cause disease in human beings and other animals.

Detection of Salmonella enterica in Meat in Less than 5 Hours by a Low-Cost and Noncomplex Sample Preparation Method

Salmonella is recognized as one of the most important foodborne bacteria and has wide health and socioeconomic impacts worldwide. Fresh pork meat is one of the main sources of Salmonella, and efficient and fast methods for detection are therefore necessary. Current methods for Salmonella detection in fresh meat usually include >16 h of culture enrichment, in a few cases <12 h, thus requiring at least two working shifts. Here, we report a rapid (<5 h) and high-throughput method for screening of Salmonella in samples from fresh pork meat, consisting of a 3-h enrichment in standard buffered peptone water and a real-time PCR-compatible sample preparation method based on filtration, centrifugation, and enzymatic digestion, followed by fast-cycling real-time PCR detection. The method was validated in an unpaired comparative study against the Nordic Committee on Food Analysis (NMKL) reference culture method 187. Pork meat samples (n = 140) were either artificially contaminated with Salmonella at 0, 1 to 10, or 10 to 100 CFU/25 g of meat or naturally contaminated. Cohen's kappa for the degree of agreement between the rapid method and the reference was 0.64, and the relative accuracy, sensitivity, and specificity for the rapid method were 81.4, 95.1, and 97.9%, respectively. The 50% limit of detections (LOD50s) were 8.8 CFU/25 g for the rapid method and 7.7 CFU/25 g for the reference method. Implementation of this method will enable faster release of Salmonella low-risk meat, providing savings for meat producers, and it will help contribute to improved food safety.IMPORTANCE While the cost of analysis and hands-on time of the presented rapid method were comparable to those of reference culture methods, the fast product release by this method can provide the meat industry with a competitive advantage. Not only will the abattoirs save costs for work hours and cold storage, but consumers and retailers will also benefit from fresher meat with a longer shelf life. Furthermore, the presented sample preparation might be adjusted for application in the detection of other pathogenic bacteria in different sample types.

Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar Sloterdijk (ATCC 15791)

Salmonella enterica spp. are pathogenic bacteria commonly associated with food-borne outbreaks in human and animals. Salmonella enterica spp. are characterized into more than 2,500 different serotypes, which makes epidemiological surveillance and outbreak control more difficult. In this report, we announce the first complete genome and methylome sequences from two Salmonella type strains associated with food-borne outbreaks, Salmonella enterica subsp. enterica serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica serovar Sloterdijk (ATCC 15791).

Epidemiology of <i>Salmonella</i> and <i>Salmonellosis</i>

The prevalence of enteritis and its accompanying diarrheal and other health challenges linked to infections with Salmonella has continuously plagued sub Saharan Africa. In Nigeria, typhoid fever is among the major widespread diseases affecting both young and old as a result of many interrelated factors such as inadequate sanitaion, indiscriminate use of antibiotics and fecal contamination of water sources. Morbidity associated with illness due to Salmonella continues to increase with untold fatal consequences, often resulting in death. An accurate figure of cases is difficult to arrive at because only large outbreaks are mostly investigated whereas sporadic cases are under-reported. A vast majority of rural dwellers in Africa often resort to self-medication or seek no treatment at all, hence serving as carries of this disease. Non typhoidal cases of salmonellosis account for about 1.3 billion cases with 3 million deaths annually. Given the magnitude of the economic losses incurred by African nations in the battle against salmonella and salmonellosis, this article takes a critical look at the genus Salmonella, its morphology, isolation, physiological and biochemical characteristics, typing methods, methods of detection, virulence factor, epidemiology and methods of spread within the environment.

Molecular methods for microbiological quality control of meat and meat products: a review

Achieving food safety is a global health goal and the food-borne diseases take a major check on global health. Therefore, detection of microbial pathogens in food is the solution to the prevention and recognition of problems related to health and safety. Conventional and standard bacterial detection methods such as culture and colony counting methods and immunology-based methods may take up to several hours or even a few days to yield a result. Obviously, this is inadequate, and recently many researchers are focusing towards the progress of rapid diagnostic methods. The advent of molecular techniques has led to the development of a diverse array of assay for quality control of meat and meat products. Rapid analysis using DNA hybridization and amplification techniques offer more sensitivity and specificity to get results than culture based methods as well as dramatic reduction in the time to get results. Many methods have also achieved the high level automation, facilitating their application as routine sample screening assays. This review is intended to provide an overview of the molecular methods for microbiological quality control of meat and meat products.

Enumeration of salmonellae in table eggs, pasteurized egg products, and egg-containing dishes by using quantitative real-time PCR

Salmonellae are a major cause of food-borne outbreaks in Europe, with eggs and egg products being identified as major sources. Due to the low levels of salmonellae in eggs and egg products, direct quantification is difficult. In the present study, enrichment quantitative real-time PCR (qPCR) was employed for enumeration of salmonellae in different matrices: table eggs, pasteurized egg products, and egg-containing dishes. Salmonella enterica serovar Enteritidis and S. enterica serovar Tennessee were used to artificially contaminate these matrices. The results showed a linear regression between the numbers of salmonellae and the quantification cycle (Cq) values for all matrices used, with the exception of pasteurized egg white. Standard curves were constructed by using both stationary-phase cells and heat-stressed cells, with similar results. Finally, this method was used to evaluate the fate of salmonellae in two egg-containing dishes, long egg and tiramisu, at abused refrigeration temperatures, and results indicated the growth of bacteria over a 1-week period. In conclusion, enrichment qPCR was shown to be reliable for enumeration of salmonellae in different egg products.

Prevalence and characterization of Salmonella serovars isolated from oysters served raw in restaurants

To determine if Salmonella-contaminated oysters are reaching consumer tables, a survey of raw oysters served in eight Tucson restaurants was performed from October 2007 to September 2008. Salmonella spp. were isolated during 7 of the 8 months surveyed and were present in 1.2% of 2,281 oysters tested. This observed prevalence is lower than that seen in a previous study in which U.S. market oysters were purchased from producers at bays where oysters are harvested. To test whether the process of refrigerating oysters in restaurants for several days reduces Salmonella levels, oysters were artificially infected with Salmonella and kept at 4°C for up to 13 days. Direct plate counts of oyster homogenate showed that Salmonella levels within oysters did not decrease during refrigeration. Six different serovars of Salmonella enterica were found in the restaurant oysters, indicating multiple incidences of Salmonella contamination of U.S. oyster stocks. Of the 28 contaminated oysters, 12 (43%) contained a strain of S. enterica serovar Newport that matched by pulsed-field gel electrophoresis a serovar Newport strain seen predominantly in the study of bay oysters performed in 2002. The repeated occurrence of this strain in oyster surveys is concerning, since the strain was resistant to seven antimicrobials tested and thus presents a possible health risk to consumers of raw oysters.

Differentiation of Salmonella typhimurium from Salmonella enteritidis and other Salmonella serotypes using random amplified polymorphic DNA analysis

Salmonella enterica ssp. enterica serovar Typhimurium and Salmonella enterica ssp. enterica serovar Enteritidis are the major dominating serotypes of Salmonella in poultry and poultry products. Infection by Salmonella Typhimurium is an important cause of morbidity and mortality in poultry. Rapid differentiation of Salmonella Typhimurium from other Salmonella serotypes including Salmonella Enteritidis can be very crutial for public health and for epidemiologists and for the poultry industry. Ten arbitrarily designed short primers (8 to 10 bases) were used in the random amplified polymorphic DNA analysis of Salmonella Typhimurium. One of the primers, primer 3 (5'-CGT GCA CGC-3'), resulted in the amplification of a band pattern that was unique to Salmonella Typhimurium. In total, 24 strains of serotype Salmonella Typhimurium were used during the study. Eighteen of them are clinical isolates, 2 of them chicken isolates (A6, A20), 2 of them from the Pasteur Institute, 1 from Refik Saydam National Culture Collection, and 1 is a type culture strain from National Culture Type Collection. Serotype Salmonella Typhimurium strains, which were collected from several different hospitals, institutes, and culture collections, have all displayed the same amplification band by primer 3. Twenty-three strains of 16 different serotypes of salmoneallae including 11 Salmonella Enteritidis strains gave only a 300-bp amplification band or no bands, whereas an additional 700-bp amplification band was observed only in samples of Salmonella Typhimurium serotype. It is concluded that random amplified polymorphic DNA analysis with primer 3 is of potential use as a serotype-specific marker for Salmonella Typhimurium.

Primers specific for the fimbrial major subunit gene stdA can be used to detect Salmonella enterica serovars

The feasibility of using two primers internal to the stdA gene (which encodes the fimbrial major subunit of the std fimbrial gene cluster in Salmonella enterica serovar Typhi) to detect Salmonella by PCR was explored. The 518-bp stdA specific sequence was conserved among 268 strains from 45 serovars of S. enterica. One Salmonella bongori CCUG 30042 strain and 34 non-Salmonella strains did not possess this sequence. A sensitivity test revealed that the stdA-specific primer set detected 3.4 x 10(-1) pg of genomic DNA and 3.0 x 10(5) CFU/ml with serial dilutions of Salmonella Typhimurium cells. In vitro testing for specificity using pig carcass sponge samples contaminated with Salmonella Typhimurium also was performed. An initial Salmonella Typhimurium inoculum of 4.4 x 10(1) CFU/ml in pig carcass exudates reached the stdA primer detection level after preenrichment in buffered peptone water at 37 degrees C for 18 h in the presence of indigenous non-Salmonella flora at 4.0 X 10(7) CFU/ml, but the detection level decreased to 4.4 x 10(0) CFU/ml after selective enrichment in Rappaport-Vassiliadis R10 broth for 18 h at 42 degrees C. The PCR method with primers specific for stdA is a quick and sensitive tool for detecting S. enterica, which is an important cause of foodborne disease.

Label-free flow-enhanced specific detection of Bacillus anthracis using a piezoelectric microcantilever sensor

Differentiation between species of similar biological structure is of critical importance in biosensing applications. Here, we report specific detection of Bacillus anthracis (BA) spores from that of close relatives, such as B. thuringiensis (BT), B. cereus (BC), and B. subtilis (BS) by varying the flow speed of the sampling liquid over the surface of a piezoelectric microcantilever sensor (PEMS). Spore binding to the anti-BA spore IgG coated PEMS surface is determined by monitoring the resonance frequency change in the sensor's impedance vs. frequency spectrum. Flow increases the resonance frequency shift at lower flow rates until the impingement force from the flow overcomes the binding strength of the antigen and decreases the resonance frequency shift at higher flow rates. We showed that the change from increasing to decreasing resonance frequency shift occurred at a lower fluid flow speed for BT, BC, and BS spores than for BA spores. This trend reduces the cross reactivity ratio of BC, BS, and BT to the anti-BA spore IgG immobilized PEMS from around 0.4 at low flow velocities to less than 0.05 at 3.8 mm s(-1). This cross reactivity ratio of 0.05 was essentially negligible considering the experimental uncertainty. The use of the same flow that is used for detection to further distinguish the specific binding (BA to anti-BA spore antibody) from nonspecific binding (BT, BC, and BS to anti-BA spore antibody) is unique and has great potential in the detection of general biological species.

Development of a PCR protocol for the detection of Aeromonas salmonicida in fish by amplification of the fstA (ferric siderophore receptor) gene

The aims of the study were to evaluate a new PCR protocol designed to detect Aeromonas salmonicida in fish tissues and to develop a non-destructive method for the diagnosis of furunculosis. A set of primers (Fer3, Fer4), flanking a fragment of the fstA gene (coding for the ferric-siderophore receptor) was designed, showing to be sensitive and specific. When compared to PCR methods previously reported, the new protocol recognized all the 69 A. salmonicida strains evaluated, with no cross-reactions with the other bacterial species analysed. Sensitivity assays were performed in fish tissues seeded with serial dilutions of pure cultures of A. salmonicida and mixed cultures of this bacterium with Vibrio anguillarum and Aeromonas hydrophila. Detection limits obtained were of 60 and 450 bacterial cells 100 mg(-1) of tissue, respectively. Mucus and blood were evaluated in order to develop a non-destructive tool to detect the pathogen. The detection limits in seeded mucus and blood samples were 2.5 x 10(2) and 1 x 10(5) bacterial cells mL(-1), respectively. When the method was used to detect A. salmonicida in asymptomatic wild salmon, four samples of mucus and six of blood were positive, corresponding to 6 out of the 31 fish examined, whereas only one of the samples resulted positive by culture methods. It is concluded that the PCR protocol evaluated is fast, specific and sensitive to detect A. salmonicida in infected and asymptomatic fish, and will be helpful for the control of the disease through the prompt detection of carriers within fish populations.

Detection and characterization of Salmonella associated with tropical seafood

The prevalence of Salmonella in seafood samples collected from the southwest coast of India was studied by conventional culture and by a DNA based molecular technique, polymerase chain reaction (PCR). While conventional culture techniques detected Salmonella in only 20 out of the 100 samples analyzed, direct enrichment lysate PCR detected 52 as positive for Salmonella. A set of three different PCR primers viz., hns, invA and invE were used. It was observed that hns primer detected Salmonella in a significantly higher number of samples. Fourteen out of nineteen isolates belonged to serovar S. enterica Weltevreden. S. Weltevreden isolates were genotyped yielding 4 different patterns both by RAPD and ERIC-PCR but when combined, the overall results discriminated the isolates of S. Weltevreden into 6 different types. This suggests that genetically diverse Salmonella Weltevreden are prevalent in seafood.

In situ detection of Bacillus anthracis spores using fully submersible, self-exciting, self-sensing PMN-PT/Sn piezoelectric microcantilevers

In this study, we have demonstrated in situ, all-electrical detection of Bacillus anthracis (BA) spores using lead magnesium niobate-lead titanate/tin (PMN-PT/Sn) piezoelectric microcantilever sensors (PEMS) fabricated from PMN-PT freestanding films and electrically insulated with methyltrimethoxysilane (MTMS) coatings on the tin surface. Antibody specific to BA spore surface antigen was immobilized on the platinum electrode of the PMN-PT layer. In phosphate-buffered saline (PBS) solution, the PMN-PT/Sn PEMS exhibited quality (Q) values ranging from 50 to 75. The detection was carried out in a closed-loop flow cell with a liquid volume of 0.8 ml and a flow rate of 1 ml min(-1). It was shown that one sensor, "PEMS-A" (500 microm long, 800 microm wide, with a 22 microm thick PMN-PT layer, a 20 microm thick tin layer and a 1 +/- 0.5 x 10(-12) g Hz(-1) mass detection sensitivity) exhibited resonance frequency shifts of 2100 +/- 200, 1100 +/- 100 and 700 +/- 100 Hz at concentrations of 20,000, 2000, and 200 spores ml(-1) or 16,000, 1600, and 160 total spores, respectively. Additionally, "PEMS-B" (350 microm long, 800 microm wide, with an 8 microm thick PMN-PT layer, a 6 microm thick tin layer and a 2 +/- 1 x 10(-13) g Hz(-1) mass detection sensitivity) exhibited resonance frequency shifts of 2400 +/- 200, 1500 +/- 200, 500 +/- 150 and 200 +/- 100 Hz at concentrations of 20,000, 2000, 100, and 45 spores ml(-1) or 16,000, 1600, 80, and 36 total spores, respectively.

Comparison of methods of extracting Salmonella enterica serovar Enteritidis DNA from environmental substrates and quantification of organisms by using a general internal procedural control

This paper compares five commercially available DNA extraction methods with respect to DNA extraction efficiency of Salmonella enterica serovar Enteritidis from soil, manure, and compost and uses an Escherichia coli strain harboring a plasmid expressing green fluorescent protein as a general internal procedural control. Inclusion of this general internal procedural control permitted more accurate quantification of extraction and amplification of S. enterica serovar Enteritidis in these samples and reduced the possibility of false negatives. With this protocol it was found that the optimal extraction method differed for soil (Mobio soil DNA extraction kit), manure (Bio101 soil DNA extraction kit), and compost (Mobio fecal DNA extraction kit). With each method, as little as 1.2 x 10(3) to 1.8 x 10(3) CFU of added serovar Enteritidis per 100 mg of substrate could be detected by direct DNA extraction and subsequent S. enterica-specific TaqMan PCR. After bacterial enrichment, as little as 1 CFU/100 mg of original substrate was detected. Finally, the study presents a more accurate molecular analysis for quantification of serovar Enteritidis initially present in soil or manure using DNA extraction and TaqMan PCR.

Use of oligonucleotide array for identification of six foodborne pathogens and Pseudomonas aeruginosa grown on selective media

Identification of presumptive foodborne pathogens grown on selective media may take one to several days and requires a different battery of biochemical tests for each microorganism. A molecular identification method was developed in which universal primers were used to amplify the 16S to 23S rDNA intergenic spacer of target microorganisms, and PCR products were hybridized to a panel of species-specific oligonucleotides that were immobilized on a nylon membrane. The seven target microorganisms were Bacillus cereus, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella, Staphylococcus aureus, and Vibrio parahaemolyticus. After testing a large collection of target bacteria (29 to 51 strains) and nontarget bacteria (> 500 strains), the performances (sensitivity and specificity) of the oligonucleotide array were as follows: B. cereus (100 and 77%), E. coli (100 and 100%), L. monocytogenes (100 and 90%), P. aeruginosa (100 and 100%), Salmonella (100 and 100%), S. aureus (100 and 100%), and V. parahaemolyticus (100 and 94.2%). Other species in the B. cereus group cross-hybridized to the probes used for identification of B. cereus, and positive results should be confirmed by additional morphological observation of colonies. Listeria innocua cross-reacted with probes used to identify L. monocytogenes, but a simple hemolysis test was used to differentiate the two species. Some strains of Vibrio harveyi and Vibrio mimicus cross-hybridized with probes used for identification of V. parahaemolyticus and caused false-positive reactions. The advantage of the array is that a common protocol was used to identify the seven target microorganisms and multiple different microorganisms could be simultaneously identified on a single array.

Detection of Salmonella in environmental water and sediment by a nested-multiplex polymerase chain reaction assay

From 1995 to 2002, 53 serovars of Salmonella were isolated in the Seine estuary (France). The 3 serovars most frequently found were S. enterica serovar Typhimurium, S. enterica serovar Infantis and S. enterica serovar Virchow. A nested multiplex PCR (nm-PCR) assay was developed to detect the presence of Salmonella in estuarine water and sediment samples. The target gene used was the phase 1 flagellin fliC chromosomal gene, present in all Salmonella serovars. A set of 4 primers was first used to amplify an 890-bp sequence of the fliC gene, and then a second set of 3 primers was used for the nested PCR. The nmPCR method has been successfully tested for 28 serovars, 13 of which are of epidemiological significance. The detection limit of the assay, without any pre-enrichment step, was estimated at 1 CFU in deionized water, and at 4-5 CFU in the reaction mixture when tested on estuarine water seeded with a Salmonella strain. When the nmPCR was used together with the classical culture method in environmental samples, it gave additional positive results for 11.3% of the sediment samples and 20% of the water samples despite a high background of other bacteria. Overall, the results demonstrated that this molecular approach informed us about the contamination by Salmonella of estuarine water and sediment samples. Positive amplifications suggested the presence of Salmonella DNA and could thus provide information about a recent (culturable) or past (non-culturable, released DNA) contamination of environmental samples by this pathogenic bacteria.

Genotypes and Antibiotic Resistance ofSalmonellaNewport Isolates from U.S. Market Oysters

The consumption of raw oysters contributes to food-borne diseases such as salmonellosis. Prevalence studies in our laboratory have shown that Salmonella spp. were present in 7.4% of U.S. market oysters, with the majority (78/101) of isolates being of the Salmonella enterica Newport serovar. E-tests were performed to assess the susceptibility of the S. Newport oyster isolates to antibiotics used for treatment of Salmonella infections. The oyster isolates were susceptible to Gentamicin, Trimethoprim/Sulphamethoxazole, and Ciprofloxacin, while for the most part they were resistant to Ampicillin and Tetracycline. Consistent with the uniform antibiotic susceptibility profile of these isolates, only three pulsed-field gel electrophoresis (PFGE) profiles were identified among the isolates. Of these three profiles, one was present in 63 of the 78 isolates, indicating not only the presence of S. Newport in oysters, but the predominance of a single PFGE type.

Eight-hour PCR-based procedure for the detection ofSalmonellain raw oysters

The aim of this study was to evaluate the ability of a nested PCR system to detect Salmonella senftenberg in raw oysters. The specific primers of the PCR were derived from the invA gene sequence, essential for Salmonella invasiveness into epithelial cells. First, for the extraction of DNA, four methods (guanidine isothiocyanate, E.Z.N.A. Mollusc Kit, Chelex-100, and lysis with detergents) were compared. A nested PCR method combined with 3.5 h pre-enrichment in buffered peptone water (BPW) and DNA extraction by the resin Chelex-100 is proposed for the detection of S. senftenberg in oyster samples. The detection limit of the method is less than 0.1 CFU/ml (<1 CFU/g of oyster). This procedure is shown to be an excellent tool for the sensitive detection of S. senftenberg from naturally contaminated oysters, with results being obtained within 8 h.

Prevalence of Salmonella spp. in oysters in the United States

Food-borne diseases such as salmonellosis can be attributed, in part, to the consumption of raw oysters. To determine the prevalence of Salmonella spp. in oysters, oysters harvested from 36 U.S. bays (12 each from the West, East, and Gulf coasts in the summer of 2002, and 12 bays, four per coast, in the winter of 2002-2003) were tested. Salmonella was isolated from oysters from each coast of the United States, and 7.4% of all oysters tested contained Salmonella. Isolation tended to be bay specific, with some bays having a high prevalence of Salmonella, while other bays had none. Differences in the percentage of oysters from which Salmonella was isolated were observed between the summer and winter months, with winter numbers much lower probably due to a variety of weather-related events. The vast majority (78/101) of Salmonella isolates from oysters were Salmonella enterica serovar Newport, a major human pathogen, confirming the human health hazard of raw oyster consumption. Contrary to previous findings, no relationship was found between the isolation of fecal coliforms and Salmonella from oysters, indicating a necessity for specific monitoring for Salmonella and other pathogens rather than the current reliance on fecal coliform testing.

Rapid detection of food-borne pathogens by using molecular techniques

Traditional methods of identification of food-borne pathogens, which cause disease in humans, are time-consuming and laborious, so there is a need for the development of innovative methods for the rapid identification of food-borne pathogens. Recent advances in molecular cloning and recombinant DNA techniques have revolutionized the detection of pathogens in foods. In this study the development of a PCR-based technique for the rapid identification of the food-borne pathogens Salmonella and Escherichia coli was undertaken. Suitable primers were designed based on specific gene fimA of Salmonella and gene afa of pathogenic E. coli for amplification. Agarose gel electrophoresis and subsequent staining with ethidium bromide were used for the identification of PCR products. The size of the amplified product was 120 bp as shown by comparison with marker DNA. These studies have established that fimA and afa primers were specific for detecting Salmonella and pathogenic E. coli, respectively, in the environmental samples. Thus a rapid, sensitive and reliable technique for the detection of Salmonella and pathogenic E. coli was developed.

Comparison of real-time PCR methods for detection of Salmonella enterica and Escherichia coli O157:H7, and introduction of a general internal amplification control

The objectives of this study were to compare different real-time PCR-based methods for detection of either Salmonella spp. or E. coli O157:H7 with respect to sensitivity, precision and accuracy. In addition, a general internal amplification control (IAC) is presented, allowing prevention of false negative results. The IAC allows insight in amplification efficiency and enables a more accurate quantification with the evaluated real-time PCR methods. Implementation of the IAC with the different PCR methods did not affect the precision of the methods, but the sensitivity was reduced 10-fold. Introduction of an IAC with the Salmonella enterica specific detection method showed a shift in Ct-value (increase of target Ct-value with 0.45+/-0.17 cycles), while with the method to detect E. coli O157:H7 no influence of IAC co-amplification was observed. The quantification threshold of the methods in which the IAC was included was determined at 1 pg of target DNA (equal to 200 CFU) per reaction. Qualitative detection was feasible down to 10 fg of target DNA per reaction using both methods in which the IAC was incorporated. The adjusted methods have the potential to provide fast and sensitive detection of Salmonella spp. or E. coli O157:H7, enabling accurate quantification and preventing false negative results by using the general IAC.

AnDiaTec Salmonella sp. PCR-ELISA for analysis of food samples

A commercially available PCR kit (AnDiaTec Salmonella sp. PCR-ELISA) was developed and evaluated for the detection of Salmonella sp. in food samples. The test is based on PCR amplification and hybridization of the amplified DNA to a microtiter plate followed by the detection of PCR product in the manner of an enzyme-linked immunosorbent assay test. The sensitivity and specificity were evaluated first with Salmonella pure cultures and artificially contaminated food samples, including food types for which an inhibition of the PCR reaction was expected. Both experiments proved a very good sensitivity, specificity, and reliability of the test with a very broad range of food types. In a second evaluation study, more than 1,100 food samples of different types were tested in parallel with the PCR method and with the International Standardization Organization 6579 bacteriological reference method. The results of this evaluation study and the results from other experiments on dilutions of artificially contaminated food samples led to the establishment of a positive-negative cutoff value (optical density at 450 nm of more than 0.9) with respect to the conventional bacteriological method. Using this positive-negative cutoff, 98% agreement to the bacteriological method was obtained.

Detection of Salmonella spp. in tropical seafood by polymerase chain reaction

The incidence of Salmonella spp. in tropical seafood was studied using standard microbiological techniques and polymerase chain reaction (PCR). Six of 20 finfish (30%), 4 of 20 clams (20%) and 1 of 20 shrimp (5%) were positive by culture techniques and by PCR. In a comparative study of different selective enrichment broths and selective plating media, more than one enrichment broth and selective agar were found to be necessary for efficient detection of Salmonella from seafood. Selenite cystine broth (SCB) was found to be more efficient compared to tetrathionate broth (TTB) while both bismuth sulfite agar (BSA) and hektoen enteric agar (HEA) were equally effective as selective plating media for fish. In the case of clams, HEA was found to be more effective. The presence of Salmonella spp. could be detected by PCR amplification of DNA extracted directly from the enrichment broths. In two cases, enrichment broths that were positive by PCR did not yield Salmonella by conventional methods.

Detection of pathogenic bacteria in shellfish using multiplex PCR followed by CovaLink NH microwell plate sandwich hybridization

Outbreak of diseases associated with consumption of raw shellfish especially oysters is a major concern to the seafood industry and public health agencies. A multiplex PCR amplification of targeted gene segments followed by DNA-DNA sandwich hybridization was optimized to detect the etiologic agents. First, a multiplex PCR amplification of hns, spvB, vvh, ctx and tl was developed enabling simultaneous detection of total Salmonella enterica serotype Typhimurium, Vibrio vulnificus, Vibrio cholerae and Vibrio parahaemolyticus from both pure cultures and seeded oysters. Amplicons were then subjected to a colorimetric CovaLink NH microwell plate sandwich hybridization using phosphorylated and biotinlylated oligonucleotide probes, the nucleotide sequences of which were located internal to the amplified DNA. The results from the hybridization with the multiplexed PCR amplified DNA exhibited a high signal/noise ratio ranging between 14.1 and 43.2 measured at 405 nm wavelength. The sensitivity of detection for each pathogen was 10(2) cells/g of oyster tissue homogenate. The results from this study showed that the combination of the multiplex PCR with a colorimetric microwell plate sandwich hybridization assay permits a specific, sensitive, and reproducible system for the detection of the microbial pathogens in shellfish, thereby improving the microbiological safety of shellfish to consumers.

Application of the PCR technique for a rapid, specific and sensitive detection of Salmonella spp. in foods

We report here the use of a PCR based assay modified by us for the detection of Salmonella spp. in foods, based on amplification of a 236 bp Salmonella specific hin/H2 region [Way et al. (1993) Applied and Environmental Microbiology 59, 1473-1479], using Ampli Taq Gold polymerase. Using this assay we were able to detect all the Salmonella serovars tested. The limit of detection was 1 fg of purified target DNA or N x 10(0) (1-3 cells) cfu ml(-1) of pure bacterial culture. This assay could detect N x 10(0) cfu Salmonella cells g(-1) of the food sample unambiguously in presence of endogenous microflora following 6 h enrichment, thus requires a duration of approximately 10 h for the full processing from DNA template preparation, PCR and visualization of DNA product on agarose gel. The main advantage of this PCR detection method is its sensitivity, and specificity. We also tried to adopt DNA template isolation method simply by boiling the bacterial cells thereby reducing the possibility of contamination, cutting the processing time and cost considerably. This can be an added advantage for the use of this system in simple lab setups.

Biotechnical use of polymerase chain reaction for microbiological analysis of biological samples

Since its introduction in the mid-80s, polymerase chain reaction (PCR) technology has been recognised as a rapid, sensitive and specific molecular diagnostic tool for the analysis of micro-organisms in clinical, environmental and food samples. Although this technique can be extremely effective with pure solutions of nucleic acids, it's sensitivity may be reduced dramatically when applied directly to biological samples. This review describes PCR technology as a microbial detection method, PCR inhibitors in biological samples and various sample preparation techniques that can be used to facilitate PCR detection, by either separating the micro-organisms from PCR inhibitors and/or by concentrating the micro-organisms to detectable concentrations. Parts of this review are updated and based on a doctoral thesis by Lantz [1] and on a review discussing methods to overcome PCR inhibition in foods [2].

Detection of low numbers of Salmonella in environmental water, sewage and food samples by a nested polymerase chain reaction assay

A polymerase chain reaction (PCR) assay with two nested pairs of primers selected from conserved sequences within a 2.3 kb randomly cloned DNA fragment from the Salmonella typhimurium chromosome was developed. The nested PCR assay correctly identified 128 of a total of 129 Salmonella strains belonging to subspecies I, II, IIIb and IV. One strain of Salm. arizona (ssp. IIIa) tested negative. No PCR products were obtained from any of the 31 non-Salmonella strains examined. The sensitivity of the assay was 2 cfu, as determined by analysis of proteinase K-treated boiled lysates of Salm. typhimurium. The performance of the assay was evaluated for environmental water, sewage and food samples spiked with Salm. typhimurium. Water and sewage samples were filtered and filters were enriched overnight in a non-selective medium. Prior to PCR, the broth cultures were subjected to a rapid and simple preparation procedure consisting of centrifugation, proteinase K treatment and boiling. This assay enabled detection of 10 cfu 100 ml(-1) water with background levels of up to 8700 heterotrophic organisms ml(-1) and 10000 cfu of coliform organisms 100 ml(-1) water. Spiked food samples were analysed with and without overnight enrichment in a non-selective medium using the same assay as above. Nested PCR performed on enriched broths enabled detection of <10 cfu g(-1) food. Variable results were obtained for food samples examined without prior enrichment and most results were negative. This rapid and simple assay provides a sensitive and specific means of screening drinking water or environmental water samples, as well as food samples, for the presence of Salmonella spp.