Polymerase chain reaction screening for Salmonella and enterohemorrhagic Escherichia coli on beef products in processing establishments.

Pathogenic Escherichia coli strains on raw or insufficiently cooked foods are of public health concern as serious disease may result from their ingestion. Therefore, many commercial producers of beef products screen for E. coli O157:H7 before shipment. While Salmonella is not considered an adulterant on raw beef products, it is used as an indication of process control. To detect these microorganisms, rapid screening methods are often used to provide results within 8-24 hours after sampling. During 2005-2008, about 971,389 samples from several commercial beef production plants were tested using a rapid screening method based on the polymerase chain reaction to determine if they were presumptively positive for bacterial cells carrying Salmonella or Shiga toxin-producing E. coli-specific genes. Of the product lots sampled (trim, ground beef, and variety meats), 15% were positive for the stx(1) and/or stx(2) (Shiga toxin genes), 9.1% for the eae gene (the attaching and effacing gene [eae] encoding intimin), 3.0% for an rfb gene region (encoding the O157-specific O side chain polysaccharide), and 1.67% for Salmonella by the polymerase chain reaction assay. In general, lots of ground beef showed the lowest frequency of contamination, and variety meats (by-products of carcass evisceration), the highest. Overall, 4.6%, 4.6%, and 0.8% samples were screen-positive for enteropathogenic E. coli, enterohemorrhagic E. coli, and E. coli O157, respectively. Of the E. coli O157-positive samples, 14% were also Salmonella positive. The frequency of screen-positive samples increases during the summer months, probably because of the prevalence of climatic conditions more conducive to microbial growth. The presence of fecal organisms in beef products suggests a failure of sanitary controls during processing and the more prevalent relatives of E. coli O157, Shiga toxin-producing Escherichia coli, enteropathogenic E. coli, and enterohemorrhagic E. coli, serve as more sensitive indicators of contamination than O157 strains alone.

Discovery and analysis of 4H-pyridopyrimidines, a class of selective bacterial protein synthesis inhibitors.

Bacterial protein synthesis is the target for numerous natural and synthetic antibacterial agents. We have developed a poly(U) mRNA-directed aminoacylation/translation protein synthesis system composed of phenyl-tRNA synthetases, ribosomes, and ribosomal factors from Escherichia coli. This system, utilizing purified components, has been used for high-throughput screening of a small-molecule chemical library. We have identified a series of compounds that inhibit protein synthesis with 50% inhibitory concentrations (IC(50)s) ranging from 3 to 14 µM. This series of compounds all contained the same central scaffold composed of tetrahydropyrido[4,3-d]pyrimidin-4-ol (e.g., 4H-pyridopyrimidine). All analogs contained an ortho pyridine ring attached to the central scaffold in the 2 position and either a five- or a six-member ring tethered to the 6-methylene nitrogen atom of the central scaffold. These compounds inhibited the growth of E. coli, Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis, with MICs ranging from 0.25 to 32 µg/ml. Macromolecular synthesis (MMS) assays with E. coli and S. aureus confirmed that antibacterial activity resulted from specific inhibition of protein synthesis. Assays were developed for the steps performed by each component of the system in order to ascertain the target of the compounds, and the ribosome was found to be the site of inhibition.

Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia.

The use of a DNA-based identification system (DNA barcoding) founded on the mitochondrial gene cytochrome c oxidase subunit I (COI) was investigated for updating the U.S. Food and Drug Administration Regulatory Fish Encyclopedia (RFE; http://www.cfsan.fda.gov/-frf/rfe0.html). The RFE is a compilation of data used to identify fish species. It was compiled to help regulators identify species substitution that could result in potential adverse health consequences or could be a source of economic fraud. For each of many aquatic species commonly sold in the United States, the RFE includes high-resolution photographs of whole fish and their marketed product forms and species-specific biochemical patterns for authenticated fish species. These patterns currently include data from isoelectric focusing studies. In this article, we describe the generation of DNA barcodes for 172 individual authenticated fish representing 72 species from 27 families contained in the RFE. These barcode sequences can be used as an additional identification resource. In a blind study, 60 unknown fish muscle samples were barcoded, and the results were compared with the RFE barcode reference library. All 60 samples were correctly identified to species based on the barcoding data. Our study indicates that DNA barcoding can be a powerful tool for species identification and has broad potential applications.

A time-resolved investigation of ribosomal subunit association.

The notion that the ribosome is dynamic has been supported by various biochemical techniques, as well as by differences observed in high-resolution structures of ribosomal complexes frozen in various functional states. Yet, the mechanisms and extent of rRNA dynamics are still largely unknown. We have used a novel, fast chemical-modification technique to provide time-resolved details of 16 S rRNA structural changes that occur as bridges are formed between the ribosomal subunits as they associate. Association of different 16 S rRNA regions was found to be a sequential, multi-step process involving conformational rearrangements within the 30 S subunit. Our results suggest that key regions of 16 S rRNA, necessary for decoding and tRNA A-site binding, are structurally altered in a time-dependent manner by association with the 50 S ribosomal subunits.

The translation initiation functions of IF2: targets for thiostrepton inhibition.

Bacterial translation initiation factor IF2 was localized on the ribosome by rRNA cleavage using free Cu(II):1,10-orthophenanthroline. The results indicated proximity of IF2 to helix 89, to the sarcin-ricin loop and to helices 43 and 44, which constitute the "L11/thiostrepton" stem-loops of 23S rRNA. These findings prompted an investigation of the L11 contribution to IF2 activity and a re-examination of the controversial issue of the effect on IF2 functions of thiostrepton, a peptide antibiotic known primarily as a powerful inhibitor of translocation. Ribosomes lacking L11 were found to have wild-type capacity to bind IF2 but a strongly reduced ability to elicit its GTPase activity. We found that thiostrepton caused a faster recycling of this factor on and off the 70S ribosomes and 50S subunits, which in turn resulted in an increased rate of the multiple turnover IF2-dependent GTPase. Although thiostrepton did not inhibit the P-site binding of fMet-tRNA, the A-site binding of the EF-Tu-GTP-Phe-tRNA or the activity of the ribosomal peptidyl transferase center (as measured by the formation of fMet-puromycin), it severely inhibited IF2-dependent initiation dipeptide formation. This inhibition can probably be traced back to a thiostrepton-induced distortion of the ribosomal-binding site of IF2, which leads to a non-productive interaction between the ribosome and the aminoacyl-tRNA substrates of the peptidyl transferase reaction. Overall, our data indicate that the translation initiation function of IF2 is as sensitive as the translocation function of EF-G to thiostrepton inhibition.

Testing for Salmonella in raw meat and poultry products collected at federally inspected establishments in the United States, 1998 through 2000.

The Food Safety and Inspection Service (FSIS) issued Pathogen Reduction; Hazard Analysis and Critical Control Point (HACCP) Systems; Final Rule (the PR/HACCP rule) on 25 July 1996. To verify that industry PR/HACCP systems are effective in controlling the contamination of raw meat and poultry products with human disease-causing bacteria, this rule sets product-specific Salmonella performance standards that must be met by slaughter establishments and establishments producing raw ground products. These performance standards are based on the prevalence of Salmonella as determined from the FSIS's nationwide microbial baseline studies and are expressed in terms of the maximum number of Salmonella-positive samples that are allowed in a given sample set. From 26 January 1998 through 31 December 2000, federal inspectors collected 98,204 samples and 1,502 completed sample sets for Salmonella analysis from large, small, and very small establishments that produced at least one of seven raw meat and poultry products: broilers, market hogs, cows and bulls, steers and heifers, ground beef, ground chicken, and ground turkey. Salmonella prevalence in most of the product categories was lower after the implementation of PR/HACCP than in pre-PR/HACCP baseline studies and surveys conducted by the FSIS. The results of 3 years of testing at establishments of all sizes combined show that >80% of the sample sets met the following Salmonella prevalence performance standards: 20.0% for broilers, 8.7% for market hogs, 2.7% for cows and bulls, 1.0% for steers and heifers, 7.5% for ground beef, 44.6% for ground chicken, and 49.9% for ground turkey. The decreased Salmonella prevalences may partly reflect industry improvements, such as improved process control, incorporation of antimicrobial interventions, and increased microbial-process control monitoring, in conjunction with PR/HACCP implementation.

Real-time evidence for EF-G-induced dynamics of helix 44 in 16S rRNA.

The penultimate stem-loop of 16S ribosomal RNA (rRNA), helix 44, plays a central role in ribosome function. Using time-resolved dimethyl sulfate (DMS) probing, we have analyzed time-dependent modifications that occur at specific bases in this helix near the decoding region, resulting from the binding of elongation factor G (EF-G) in various forms. When EF-G-GTP is bound to 70S ribosomes, bases A1492 and A1493 are immediately protected, while other bases in the region show either no change or enhanced modification. When apo-EF-G is bound to 70S ribosomes and GTP is added, substantial transient time-dependent enhancement occurs at bases A1492 and A1493, with somewhat less enhancement occurring at base A1483, all in the first 45 ms. When mRNA and deacylated tRNAs are bound to the 70S ribosome and EF-G-GTP is added, bases A1492 and A1493 again show substantial and continued enhancement, while bases A1408, A1413, and A1418 all show time-dependent protection. These results provide primary, real-time evidence that EF-G induces direct or indirect structural changes in this region as EF-G is bound and as GTP is hydrolyzed.

The formation of a potential spring in the ribosome.

Time-dependent chemical modification and cleavage results have provided intriguing insights into structural changes that occur in the distal loop of helix 11 in 16S ribosomal RNA (rRNA). Located distant from the decoding region, between proteins S17 and S20, the results of this study suggest that this region of rRNA may act as a buffer or a spring between these two proteins during protein biosynthesis. During the assembly process, protein S17 apparently produces the major structural deformations in this region, causing it to be folded in a spring-like structure. Base C264 in this region shows erratic behavior during assembly and also shows time-dependent enhancement when elongation factor G with GTP is added to 70S ribosomes. Evidence is presented to suggest that this region of rRNA may be used to allow relative motion to occur between proteins S17 and S20 during translocation.

Protein S20 binds two 16S rRNA sites as assembly is initiated.

Ribosomal protein S20 is a primary binding protein that bridges the 5' domain and the 3' minor domain of the 16S ribosomal RNA (rRNA) in the 30S ribosomal subunit. Using time-dependent dimethyl sulfate modification, we have determined that as it is bound to 16S rRNA, protein S20 causes rapid protection of bases A246, A274, A279, and A282 in the stem region of helix 11 in the 5' domain and moderately fast modifications of helix 44 bases A1433 and A1434 in the 3' minor domain. At a later time, enhancements occur with bases A181and A190 in helix 9, bases A325 and A327 in helix 13, and base C264 at the distal end of helix 11 in the 5' domain of 16S rRNA. The modifications that occur in the stem region of helix 11 are distant from the binding site of protein S20, as determined from the crystal structure. Simultaneous addition of protein S17 with S20 to the complex significantly alters the modifications caused by protein S20 in the stem region of helix 11 but does not alter the remaining modifications. Our results indicate that protein S20 is binding to at least two alternate 16S rRNA sites during the early assembly process.

The genesis of ribosome structure: how a protein generates RNA structure in real time.

Ribosomal subunit assembly is initiated by the binding of several primary binding proteins. Results from chemical modification studies show that 16S ribosomal RNA undergoes striking structural rearrangements when protein S17 is bound. For the first time, we are able to distinguish and order these structural rearrangements by using time-dependent chemical probing. Initially, protein S17 binds to a portion of helix 11, inducing a kink-turn in that helix that bends helix 7 toward the S17-helix 11 complex in a hairpin-like manner, allowing helix 7 to bind to protein S17. This structural change is rapidly stabilized by interactions at the distal and proximal ends of both RNA helices. Identifying the dynamic nature of interactions between RNA and proteins is not only essential in unraveling ribosome assembly, but also has more general application to all protein-RNA interactions.

The real-time path of translation factor IF3 onto and off the ribosome.

Translation initiation factor IF3 is an essential bacterial protein, consisting of two domains (IF3C and IF3N) separated by a linker, which interferes with ribosomal subunit association, promotes codon-anticodon interaction in the P site, and ensures translation initiation fidelity. Using time-resolved chemical probing, we followed the dynamic binding path of IF3 on the 30S subunit and its release upon 30S-50S association. During binding, IF3 first contacts the platform (near G700) of the 30S subunit with the C domain and then the P-decoding region (near A790) with its N domain. At equilibrium, attained within less than a second, both sites are protected, but before reaching binding equilibrium, IF3 causes additional transient perturbations of both the platform edge and the solvent side of the subunit. Upon 30S-50S association, IF3 dissociates concomitantly with the establishment of the 30S-50S bridges, following the reverse path of its binding with the IF3N-A790 interaction being lost before the IF3C-G700 interaction.

Interaction of thiostrepton and elongation factor-G with the ribosomal protein L11-binding domain.

Ribosomal protein L11 and the L11 binding region of ribosomal RNA constitute an important domain involved in active functions of the ribosome during translation. We studied the effects of L11 knock-out and truncation mutations on the structure of the rRNA in this region and on its interactions with a translation elongation factor and the antibiotic thiostrepton. The results indicated that the structure of the L11-binding rRNA becomes conformationally flexible when ribosomes lack the entire L11 protein, but not when the C-terminal domain is present on ribosomes. Probing wild type and mutant ribosomes in the presence of the antibiotic thiostrepton and elongation factor-G (EF-G) rigorously localized the binding cleft of thiostrepton and suggested a role for the rRNA in the L11-binding domain in modulating factor binding. Our results also provide evidence that the structure of the rRNA stabilized by the C-terminal domain of L11 is necessary to stabilize EF-G binding in the post-translocation state, and thiostrepton may modulate this structure in a manner that interferes with the ribosome-EF-G interaction. The implications for recent models of thiostrepton activity and factor interactions are discussed.

Polymerase Chain Reaction Identification of Enteroinvasive Escherichia coli Seeded into Raw Milk.

Molecular biological techniques for identifying pathogenic foodborne bacteria use small amounts of bacterial nucleic acids that must be purified and concentrated from complex food matrices. The polymerase chain reaction (PCR) amplifies specific segments of DNA and speeds the identification of bacterial strains. Methods for preparing DNA for PCR analysis were tested by seeding enteroinvasive Escherichia coli (EIEC) cells into raw milk. Test samples of milk were heated at 35°C and were treated with proteinase and detergent. As few as 102 cells of EIEC per ml of seeded milk were identified after amplification of a plasmid-borne gene required for invasion.

Survival of Shigella flexneri on Vegetables and Detection by Polymerase Chain Reaction.

Commercially prepared and packaged fresh vegetables were tested to determine the types and levels of indigenous microflora. Sixteen species of bacteria from 11 genera were identified and titers of up to 1 × 1010 cells per gram of vegetable were observed. To evaluate the survival of Shigella spp. on packaged vegetables, an avirulent insertion mutant of Shigella flexneri 5 (pHS 1059) was added to vegetables. This strain survived in phosphate-buffered saline at pH 7.3 at 5 to 10°C for more than 3 months. It also survived for several days at both ambient and refrigerator temperatures when inoculated onto various commercially prepared vegetables. A rapid method for detecting Shigella spp. on vegetables was developed by using the polymerase chain reaction (PCR) to amplify a 118-base-pair DNA fragment from the S. flexneri virulence-associated spa region. The PCR also generated the corresponding fragments from S. sonnei , S. boydii , and Shigella sp. This fragment was also observed when S. flexneri cells were used to artificially contaminate sterile and nonsterile vegetables, but no amplified fragment was observed when the normal microflora of the vegetables were eluted and tested by PCR.

Enumeration and Differentiation of Vibrio parahaemolyticus and Vibrio vuinificus by DNA-DNA Colony Hybridization Using the Hydrophobic Grid Membrane Filtration Technique for Isolation.

We have developed a means of differentiating and enumerating Vibrio parahaemolyticus and Vibrio vuinificus by DNA-DNA colony hybridization directly on HGMF filters. V. parahaemolyticus can be detected by a tdh-3-radiolabeled gene probe and V. vuinificus detected by a specific cytotoxin-hemolysin-radiolabeled probe with enumeration directly from autoradiograms. This procedure is more rapid than current techniques allowing enumeration and identification of these two species in samples as diverse as seawater, oyster ( Crassostrea gigas ), and shrimp (Pandalidae family) within 4 d. Our method is based on a rapid technique (18 h) for isolation and enumeration of V. parahaemolyticus from food using a membrane filtration technique with hydrophobic grid filters (HGMF). With the HGMF method, however, it is not possible to differentiate V. parahaemolyticus from V. vuinificus since on the HGMF-sucrose-based agar used, the two species are indistinguishable as both species are unable to ferment sucrose. Using a combination of the HGMF and selective gene probes, these two species can be differentiated.

Yersiniosis Associated with Tofu Consumption: Serological, Biochemical and Pathogenicity Studies of Yersinia enterocolitica Isolates.

From December 1981 to February 1982, 87 individuals (ages two months to 74 years) in the Seattle, WA, area developed the clinical symptoms of yersiniosis. Illness was related to consumption of commercial tofu (soybean curd) contaminated with Yersinia enterocolitica . The six Y. enterocolitica strains recovered from the hospitalized patients indicated that two antigenically distinct strains, 0:8 and 0:Tacoma, were involved. At the manufacturing site of the incriminated tofu, 112 Y. enterocolitica strains were recovered, of which two were serotype 0:8. The reactions of these strains were similar to those of clinical 0:8 strains in biochemical tests and in eight virulence factor tests. The LD50 for suckling mice was identical for all strains which killed mice. Although the causative organism(s) was not recovered from other samples of packaged tofu, our findings incriminated water used in the processing of tofu as the source of infection. The source of the second Y. enterocolitica strain (0:Tacoma) in this outbreak was not identified.

Pathogenicity of Yersinia enterocolitica Demonstrated in the Suckling Mouse.

An experimental suckling mouse intraperitoneal injection test was compared with four plasmid-associated tests (adult mouse peroral exposure, adult mouse intraperitoneal injection, auto-agglutination and plasmid detection by gel electrophoresis) to measure Yersinia enterocolitica pathogenicity. Of eight Vwa plasmid-harboring strains (O:3; O:4,32; O:5,27; O:8; O:9; O:13; O:21; and O:Tacoma) and one isogenic plasmidless strain (O:8), all Vwa plasmid-harboring strains gave identical results in all tests except the two adult mouse tests. In studies of 35 clinical strains of Y. enterocolitica recently isolated during two foodborne outbreaks, a comparison of the autoagglutination, gel electrophoresis for Vwa plasmid detection and suckling mouse tests showed that 29 strains (83%) gave identical results in all three tests. The other six strains produced different reactions in the plasmid detection and autoagglutination tests, indicating that neither test alone is sufficient to evaluate the virulence of Y. enterocolitica . To compare the sensitivity of these in vitro tests with a biological assay (the suckling mouse intraperitoneal injection test), a mixture of plasmid-harboring (P+) and plasmidless (P-) isogenic Y. enterocolitica cells was examined. The suckling mouse test was more sensitive and consistent in detecting the Vwa plasmid (as evidenced by mouse lethality). A bacterial population containing 0.1 % P + cells induced a lethal infection in the suckling mouse, whereas the other two tests required at least 10% P + cells for detection of the Vwa plasmid. The 50% lethal dose (LD50) in the suckling mouse was directly proportional to the number of Vwa-harboring cells in the culture.

Comparison of Template Preparation Methods from Foods for Amplification of Escherichia coli O157 Shiga-Like Toxins Type I and II DNA by Multiplex Polymerase Chain Reaction.

Escherichia coli O157:H7 has been responsible for several recent food-borne outbreaks in the United States. To protect the public health, it is essential that rapid and sensitive methods be developed for detection of this pathogen in foods. Methods were compared for preparation of template DNA for the polymerase chain reaction (PCR) from enrichments of food homogenates seeded with E. coli O157:H7. Samples were enriched for 6 h at 37°C in modified tryptic soy broth supplemented with vancomycin, cefsulodin, and cefixime. Aliquots of the enrichments (10 ml or 1 ml) were analyzed by either washing twice with physiological saline or incubating with antibodies to O157 coupled to immunomagnetic beads (Dynal®) followed by resuspending and boiling the samples. A portion of the preparation was used in a multiplex PCR to amplify a 274-bp fragment from the sltI gene and a 364-bp fragment from the sltII gene. PCR amplification of 1-ml portions of enrichment broth was successful at inoculation levels of about 10 cells per g of food. Increasing the test sample volume to 10 ml and/or using an immunomagnetic separation step improved the PCR detection sensitivity to about 1 cell per g; the entire analysis can be completed within 12 h.

Ribosomal localization of translation initiation factor IF2.

Bacterial translation initiation factor IF2 is a GTP-binding protein that catalyzes binding of initiator fMet-tRNA in the ribosomal P site. The topographical localization of IF2 on the ribosomal subunits, a prerequisite for understanding the mechanism of initiation complex formation, has remained elusive. Here, we present a model for the positioning of IF2 in the 70S initiation complex as determined by cleavage of rRNA by the chemical nucleases Cu(II):1,10-orthophenanthroline and Fe(II):EDTA tethered to cysteine residues introduced into IF2. Two specific amino acids in the GII domain of IF2 are in proximity to helices H3, H4, H17, and H18 of 16S rRNA. Furthermore, the junction of the C-1 and C-2 domains is in proximity to H89 and the thiostrepton region of 23S rRNA. The docking is further constrained by the requisite proximity of the C-2 domain with P-site-bound tRNA and by the conserved GI domain of the IF2 with the large subunit's factor-binding center. Comparison of our present findings with previous data further suggests that the IF2 orientation on the 30S subunit changes during the transition from the 30S to 70S initiation complex.