The Pathogen-annotated Tracking Resource Network (PATRN) system: a web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease.

Investigation of foodborne diseases requires the capture and analysis of time-sensitive information on microbial pathogens that is derived from multiple analytical methods and sources. The web-based Pathogen-annotated Tracking Resource Network (PATRN) system (www.patrn.net) was developed to address the data aggregation, analysis, and communication needs important to the global food safety community for the investigation of foodborne disease. PATRN incorporates a standard vocabulary for describing isolate metadata and provides a representational schema for a prototypic data exchange standard using a novel data loading wizard for aggregation of assay and attribution information. PATRN currently houses expert-curated, high-quality "foundational datasets" consisting of published experimental results from conventional assays and next generation analysis platforms for isolates of Escherichia coli, Listeria monocytogenes, and Salmonella, Shigella, Vibrio and Cronobacter species. A suite of computational tools for data mining, clustering, and graphical representation is available. Within PATRN, the public curated data repository is complemented by a secure private workspace for user-driven analyses, and for sharing data among collaborators. To demonstrate the data curation, loading wizard features, and analytical capabilities of PATRN, three use-case scenarios are presented. Use-case scenario one is a comparison of the distribution and prevalence of plasmid-encoded virulence factor genes among 249 Cronobacter strains with similar attributes to that of nine Cronobacter isolates from recent cases obtained between March and October, 2010-2011. To highlight PATRN's data management and trend finding tools, analysis of datasets, stored in PATRN as part of an ongoing surveillance project to identify the predominant molecular serogroups among Cronobacter sakazakii isolates observed in the USA is shown. Use-case scenario two demonstrates the secure workspace available for private users to upload and analyze sensitive data, and for collating cross-platform datasets to identify and validate congruent datapoints. SNP datasets from WGS assemblies and pan-genome microarrays are analyzed in a combinatorial fashion to determine relatedness of 33 Salmonella enterica strains to six strains collected as part of an outbreak investigation. Use-case scenario three utilizes published surveillance results that describe the incidence and sources of O157:H7 E. coli isolates associated with a produce pre-harvest surveillance study that occurred during 2002-2006. In summary, PATRN is a web-based integrated platform containing tools for the management, analysis and visualization of data about foodborne pathogens.

Enhancement of virulence of two environmental strains of Vibrio vulnificus after passage through mice.

The virulence of two environmental strains of Vibrio vulnificus to iron-loaded adult mice was enhanced by passage through mice. Estimates of 50% lethal dose values (LD50) determined by end point titration were reduced 100- and 1000-fold for the two strains. Passage through mice also selected for the opaque colony type phase variation of V. vulnificus, reported by others to be more virulent to mice than a translucent colony type.

Determination of tri-n-butyltin in oysters by reaction-gas chromatography of hydride derivatives.

A reaction-gas chromatography method for determining tri-n-butyltin (TBT) as the hydride derivative has been adapted to allow determination of TBT in oysters. The extraction method has been modified to prevent fouling of the hydride formation reactor and the gas chromatography has been made faster by employing a different column and temperature program. The detection limit is 3-6 ng/g in oyster tissue. Apparent recoveries of TBT from oyster tissue at 25 and 125 ng/g levels are 107 and 97%, respectively.

Survival of Anisakis simplex in microwave-processed arrowtooth flounder (Atheresthes stomias).

The purpose of this study was to define the relationship between survival and temperature of nematodes of the species Anisakis simplex in microwave-processed arrowtooth flounder (Atheresthes stomias). Ten fillets (each 126 to 467 g, 0.5 to 1.75 cm thick), with an average of five larvae of Anisakis simplex per fillet, were processed to target temperatures on high (100%) power using a commercial 700-W microwave oven. Fillets were neither covered nor rotated and had a temperature probe inserted to two-thirds depth into the thickest portion. After the fillet was digested using a 1% pepsin solution, the viability of nematodes was determined by viewing them under a dissecting microscope. Survival rates were 31% at 140 degrees F (60 degrees C), 11% at 150 degrees F (65 degrees C), 2% at 160 degrees F (71 degrees C), 3% at 165 degrees F (74 degrees C), and 0% at 170 degrees F (77 degrees C). Microwave processing of standardized fillet "sandwiches," 14 cm long, 4.5 cm wide, and approximately 1.75 cm high, each of which was preinoculated with 10 live nematodes, resulted in no survival at either 160 degrees F or 170 degrees F. Using ultraviolet light to detect both viable and nonviable nematodes in fillet sandwiches as an alternative method to pepsin digestion resulted in survival rates of 1% at 140 degrees F (60 degrees C), 3% at 145 degrees F (63 degrees C), and 0% at 150 degrees F (65 degrees C). Smaller fillet sandwiches, which most likely had fewer cold spots during microwave processing, required 150 degrees F (65 degrees C), whereas larger whole fillets required 170 degrees F (77 degrees C) to kill larvae of Anisakis simplex. The parasites were most likely inactivated by a thermal mechanism of microwave treatment. Damage to the nematodes was often evident from ruptured cuticles that were no longer resistant to digestive enzymes. The high hydrostatic pressure and low chloride content of the pseudocoelomic fluid probably contributed greatly to the damage incurred by the larvae.

Template preparation for PCR and RFLP of amplification products for the detection and identification of Cyclospora sp. and Eimeria spp. Oocysts directly from raspberries.

Raspberries were epidemiologically associated with cyclosporiasis outbreaks during 1996 and 1997. The 18S rRNA genes of Cyclospora cayetanensis and several species of a closely related genus, Eimeria, were sequenced and primers for a nested PCR developed in a previous study. The ability to distinguish amplified products of Cyclospora sp. from those of Eimeria spp. is important for testing food and environmental samples. Therefore, an RFLP analysis of amplified products was used to differentiate Cyclospora cayetanensis from Eimeria spp. PCR inhibitors and the low levels of Cyclospora oocysts present in raspberries make template preparation for PCR challenging. Several approaches for PCR template preparation from raspberry samples were evaluated. Template preparation methods using various washing and concentration steps, oocyst disruption protocols, resin matrix treatment, DNA precipitation, and/or the addition of nonfat dried milk solution to a PCR using modified primers were evaluated first with oocysts of Eimeria tenella then refined with oocysts of C. cayetanensis. Approximately 10 E. tenella oocysts per PCR or approximately 19 C. cayetanensis oocysts per PCR were detected with the optimized template preparation method. The addition of 20 microliters of raspberry wash sediment extract and nonfat dried milk solution did not inhibit the amplification of DNA from as few as 10 E. tenella and 25 C. cayetanensis oocysts in a 100-microliter PCR. The nucleotide sequences of C. cayetanensis and the Eimeria spp. are 94 to 96% similar in the amplified region, but the amplification products from the two genera were distinguished using an RFLP analysis with the restriction enzyme MnlI.

An oligonucleotide-ligation assay for the differentiation between Cyclospora and Eimeria spp. polymerase chain reaction amplification products.

An oligonucleotide-ligation assay (OLA) was developed and compared to a restriction fragment length polymorphism (RFLP) test for distinguishing between 294-bp polymerase chain reaction (PCR) amplification products of the 18S rRNA gene from Cyclospora and Eimeria spp. The PCR/OLA correctly distinguished between three Cyclospora, three E. tenella, and one E. mitis strains and the ratio of positive to negative spectrophotometric absorbance (A490) values for each strain ranged from 4.086 to 15.280 (median 9.5). PCR/OLA provides a rapid, reliable, spectrophotometric alternative to PCR/RFLP.

Detection of sodium channel toxins: directed cytotoxicity assays of purified ciguatoxins, brevetoxins, saxitoxins, and seafood extracts.

Neuroblastoma cells in culture were used to detect sodium channel-specific marine toxins based on an end-point determination of mitochondrial dehydrogenase activity. The assay responds in a dose-dependent manner to ciguatoxins, brevetoxins, and saxitoxins, and delineates the toxic activity as either sodium channel enhancing or sodium channel blocking. The assay responds rapidly to sodium channel activating toxins, allowing dose dependent detection in 4 to 6 h. Brevetoxins can be detected at 250 pg, and purified ciguatoxins are detected in the low picogram and subpicogram levels. The results obtained from cell bioassay of ciguatoxic finfish extracts correlates with those obtained from mouse bioassays. Sodium channel blocking toxins can also be detected with an approximate sensitivity of 20 pg in 24 to 48 h. This cell-based technique is simple, sensitive, demonstrates potential as an alternative to animal testing for sodium channel activating and blocking toxins, and can be automated.

Incidence of increased numbers of Clostridium perfringens in the intestinal tract of rats fed xylitol.

Sprague-Dawley rats were fed diets containing up to 20% xylitol for 49 days. When the rats were fed a xylitol regimen intended to produce adaptation to xylitol, approximately half of the animals adapted to xylitol and remained free from diarrhea during the feeding regimen. The other half did not adapt to xylitol and developed severe and persistent diarrhea accompanied by large volumes of intestinal gas. These non-adapted rats had significantly higher levels of intestinal tract Clostridium perfringens (10(6)--10(11) organisms per gram intestinal contents) than did control rats fed a xylitol-free cornstarch diet (0-10(4) organisms per gram). Rats adapted to dietary xylitol did not have detectable levels of C. perfringens in the gastrointestinal tract.

Effects of dietary xylitol on redox state and gluconeogenesis in the rat liver.

Rats fed a 20% xylitol diet were compared to rats fed for 6 weeks a diet of either 20% glucose, cornstarch or sucrose (plus 45% cornstarch), or the AIN-76TM diet (basal diet). There were no differences between the rats (diarrhea-free) fed xylitol and those fed the other carbohydrate sources in the lactate/pyruvate ratio in freeze clamped livers. Gluconeogenesis was measured from 10 mM of various precursors in isolated hepatocytes. Rats fed xylitol had: a) a lower rate of glucose production from lactate compared to rats fed the sucrose, glucose or basal diet; b) a lower rate of gluconeogenesis from xylitol than in rats fed either the basal or glucose diets, and c) equal capacity to produce glucose from pyruvate, glycerol, dihydroxyacetone or alanine as rats fed the other diets. Ethanol added to isolated hepatocyte incubations did not have a greater inhibitory effect on gluconeogenesis in xylitol-fed animals than in those fed the other carbohydrates. Results of this study indicate that dietary xylitol has little effect on the hepatic cytosolic redox state or on the ability of the rat liver to produce glucose in the presence of ethanol, but may have an effect on the rate of glucose production from some precursors.

Incidence of urea-hydrolyzing Vibrio parahaemolyticus in Willapa Bay, Washington.

A high incidence (71.5%) of Vibrio parahaemolyticus was found in samples of water, oysters, and sediment from a Washington State estuary which produces a significant amount of commercial product. Strains of V. parahaemolyticus capable of hydrolyzing urea comprised 58.4% of all V. parahaemolyticus isolates tested. Values for fecal coliforms were within certification criteria for commercial harvest and were not correlated with levels of V. parahaemolyticus.

Listeria species in a California coast estuarine environment.

Listeria species and L. monocytogenes were found in 81 and 62%, respectively, of fresh or low-salinity waters (37 samples) in tributaries draining into Humboldt-Arcata Bay, Calif., during a winter (January-February) sampling period. The incidence of Listeria species and L. monocytogenes in sediment (46 samples) from the same sites where water was sampled was 30.4 and 17.4%, respectively. One of three bay water samples contained Listeria species (including L. monocytogenes), while of 35 samples of oysters examined, only 1 was found positive for Listeria species (L. innocua). A given species or L. monocytogenes serogroup appeared to predominate in fresh water when domesticated animals (cows, horses) were nearby, whereas greater variety with no species predominance was observed in areas with no direct animal influence.

Incidence of Vibrio cholerae from estuaries of the United States West Coast.

The incidence of Vibrio cholerae in shellfish, sediment, and waters of California, Oregon, and Washington was determined during the summer of 1984. Samples from 24 distinct estuaries were analyzed qualitatively. V. cholerae non-O1 was found in 23 estuaries and in 44.6% of the 529 samples examined. V. cholerae O1 Inaba was isolated from water samples in Morro Bay, Calif. Vibrio mimicus was found in 2.3% of the samples. Cholera enterotoxin was not found in cell-free filtrates of the 100 isolates tested in the Y-1 mouse adrenal cell assay, but heat-labile cytotoxic activity was observed with 3% of the isolates.

Virulent strains of Vibrio vulnificus isolated from estuaries of the United States West Coast.

Vibrio vulnificus was isolated from United States West Coast estuaries at a low frequency (5.9%) from 529 samples of water, shellfish, and sediment. Four strains tested with iron-treated mice had 50% lethal dose values ranging from 7.6 to 360 CFU, compared with a 50% lethal dose of 4.9 CFU for a clinical isolate that caused the death of a septicemic patient. The presence of this pathogen may be a hazard to users of marine beaches and consumers of raw shellfish on the West Coast, especially to persons most susceptible to V. vulnificus septicemia. Species-specific antiflagellar serum and a gene probe for cytotoxin-hemolysin production were useful for screening these environmental isolates.

Headspace gas chromatographic method for determination of ethanol in canned salmon: collaborative study.

Six laboratories collaboratively studied a headspace gas chromatographic method for determination of ethanol in the aqueous phase of canned salmon. Ethanol is determined by a headspace sampling technique with tert-butanol as the internal standard, using a gas chromatograph equipped with a Super Q column and a flame ionization detector. With outliers excluded, the mean recoveries from samples spiked with 25.1 and 78.4 ppm ethanol were 112 and 110%, respectively. For the 4 sample pairs quantitated, repeatability coefficients of variation ranged from 1.42 to 4.25% and reproducibility coefficients of variation from 2.55 to 8.09%, with 3 of the 4 reported values less than 5%. The method has been adopted official first action.

Determination of sulfite in food by flow injection analysis.

A method is described for the determination of sulfite levels in food products by flow injection analysis (FIA). The method is based on the decolorization of malachite green by SO2, which is isolated from the flowing sample stream by means of a gas diffusion cell. The FIA method has a detection limit in food sample extracts of 0.1 ppm SO2 (3 times peak height of blank), which corresponds to 1-10 ppm SO2 in a food product, depending on the extraction procedure used. At the 5 ppm SO2 level in a food extract, the precision of replicate injections is +/- 1-2%. The method was tested on a variety of both sulfite-treated and untreated food products and the results compared favorably with those obtained by the Monier-Williams, colorimetric (pararosaniline), and enzymatic (sulfite oxidase) methods. The average differences from the FIA results were 19, 11, and 12%, respectively, for those samples (n = 12) above 50 ppm SO2. At lower levels the results were somewhat more erratic due to inaccuracies of the various methods at low concentrations.

Selective determination of histamine by flow injection analysis.

A flow injection analysis (FIA) method for the determination of histamine is described. Control of reaction timing allows exploitation of a transient, chemical-kinetic increase in selectivity that occurs when o-phthalaldehyde reacts with histamine. The molar fluorescence ratio (selectivity) of histamine/histidine reaches a maximum value of 800 in 32 s, precluding the need for separation of histamine from histidine, spermidine, and other potential interferences in biological samples. On-line dilution prevents matrix effects and affords a linear response up to approximately 4.45 mM histamine, or 500 mg of histamine free base/100 g. Under these conditions the detection limit (3 times peak-to-peak baseline noise) is 5.5 pg (corresponding to 0.60 mg of histamine free base/100 g of sample) and throughput is 60 injections per hour. The high sensitivity and high selectivity of the method allow the rapid determination of histamine in fish with minimal sample conditioning and will find application in the determination of endogenous histamine as well, such as in blood plasma and brain tissue.

Survival of Vibrio vulnificus in shellstock and shucked oysters (Crassostrea gigas and Crassostrea virginica) and effects of isolation medium on recovery.

When two species of shellstock oysters were artificially contaminated with Vibrio vulnificus, the bacterium survived when the oysters were stored at 10 degrees C and below. Large numbers of endogenous V. vulnificus cells were found after 7 days at both 0.5 and 10 degrees C in uninoculated control oysters (Crassostrea virginica). Oysters allowed to take up V. vulnificus from seawater retained the bacterium for 14 days at 2 degrees C. The presence of V. vulnificus in the drip exuded from the shellstock presented a possibility of contamination of other shellstock in storage. V. vulnificus injected into shucked Pacific (Crassostrea gigas) and Eastern (C. virginica) oysters survived at 4 degrees C for at least 6 days. An 18-h most-probable-number enrichment step in alkaline peptone water gave higher recovery levels of V. vulnificus than did direct plating to selective agars. The survival of this pathogen in both shellstock and shucked oysters suggests a potential for human illness, even though the product is refrigerated.

Tetrazolium-based cell bioassay for neurotoxins active on voltage-sensitive sodium channels: semiautomated assay for saxitoxins, brevetoxins, and ciguatoxins.

In the present study we have developed an assay for the detection of sodium channel-specific marine toxins based upon mitochondrial dehydrogenase activity in the presence of veratridine and ouabain. This cell bioassay allows detection of either sodium channel enhancers, such as the brevetoxins and the ciguatoxins, or sodium channel blocking agents, such as the saxitoxins. The assay responds in a dose dependent manner and differentiates the toxic activity as either sodium channel blocking or enhancing. In addition, the assay is highly sensitive, with present detection limits of 2 ng/ml for either saxitoxins or brevetoxins (PbTx-1 and PbTx-3). Assay response to a ciguatoxic extract and to brevetoxins is rapid, allowing dose dependent detection within 4 to 6 h. The method is simple, utilizes readily available reagents, uses substantially less sample than required for mouse bioassay, and is well within the scope of even modest tissue culture facilities. This cell-based protocol has the potential to serve as an alternate and complementary method to the standard mouse bioassay.

Determination of free (pH 2.2) sulfite in wines by flow injection analysis: collaborative study.

A method for the determination of free sulfite in wine by flow injection analysis (FIA) is described. The method involves liberation of sulfur dioxide from the wine at pH 2.2, with detection by decolorization of a malachite green solution. The method was collaboratively studied, and the results indicated an average reproducibility of 12% for white wine samples (average level 12.1 ppm SO2) and 26% for red wine samples (average level 3.1 ppm). When the FIA method was compared to an aeration/oxidation method, the results indicated a high degree of correlation between the 2 methods. The FIA method has been adopted by AOAC official first action.

Urea hydrolysis can predict the potential pathogenicity of Vibrio parahaemolyticus strains isolated in the Pacific Northwest.

The ability of some strains of Vibrio parahaemolyticus to hydrolyze urea (uh+) can be used as a marker to predict which strains isolated from molluscan shellfish harvested in the Pacific Northwest are potentially pathogenic. The thermostable direct hemolysin-producing (TDH+) characteristic is a marker that is correlated with potential pathogenicity, and all of the TDH+ strains that we have isolated have been found to be uh+. Most of the uh+ strains belong to somatic antigen groups O3, O4 and O5. TDH+ strains are usually members of groups O4 and O5. The strains most often associated with human illness are members of the uh+, O4 group. The test for urease production is a simple screening test that can be helpful in predicting which strains are potentially pathogenic.