An eight-hour PCR-based technique for detection of <Emphasis Type="Italic">Salmonella</Emphasis> serovars in seafood

A rapid and sensitive 8-h PCR assay has been developed for detection of Salmonella serovars in seafood. A total of 110 fresh and raw seafood samples were analysed for the presence of Salmonella using different enrichment periods prior to PCR assay. Seafood samples included in this study were fish, shrimps, mussels, crabs, edible oysters, and clams, collected from local fish markets in Cochin (India). The assay was performed with a Salmonella-specific 284 bp invA gene amplicon. Specificity and sensitivity of the assay were ascertained with seafoods spiked with viable Salmonella cells to a level of 10⁶ to 2 CFU per 25 g. Detection efficiency of the assay increased with increasing enrichment period for seafood, and 33.6% of seafood samples were found positive for Salmonella by 8-h PCR assay. Detection limit for the 8-h PCR assay showed visible 284 bp amplicon from seafood homogenates spiked with 2 CFU per 25 g. Seafood samples spiked with different Salmonella serovars, namely Salmonella typhi, Salmonella typhimurium, Salmonella enteritidis, Salmonella mbandka, Salmonella bareilly, and Salmonella weltevreden, were detected, confirming this technique would be ideal for detection of the Salmonella serovars prevalent in seafood. This study also covered inhibition by the seafood matrix and the detection limit for dead Salmonella cells during the PCR assay. There was no visible inhibition of this Salmonella PCR assay by seafood matrices. The detection limit for dead Salmonella cells by 8-h PCR assay was 2 × 10³ CFU per 25 g seafood. The data indicated that dead cells of Salmonella in naturally contaminated seafood samples do not interfere with the assay resulting in false positives.     

Design of a core–shell type immuno-magnetic separation system and multiplex PCR for rapid detection of pathogens from food samples

We report an immuno-magnetic separation system developed by the immobilization of pathogen-specific antibodies on the core–shell magnetic beads. The magnetic beads were grafted with glycidylmethacrylate (GMA) using surface-initiated atom transfer radical polymerization (SI-ATRP). For immuno-magnetic separation (IMS) of target bacterial cells from others, antibodies for Escherichia coli and Salmonella enterica serovar Typhimurium cells were immobilized on the magnetic beads via glutaraldehyde coupling reaction. Our IMS system successfully separated Salmonella cells when the concentrations of target (i.e., Salmonella) and interfering (i.e., E. coli) cells were at the same level. Polymerase chain reaction (PCR) assays amplifying the rfb/rfbE region of the E. coli genome and a 647-bp fragment of the invA region of Salmonella were performed as the specific selection to accurately confirm the presence of E. coli and Salmonella, respectively. IMS and multiplex PCR methods can be used for specific and quantitative detection of pathogens from food samples. Thus, this study developed a reliable and direct system for rapid detection of Salmonella and E. coli in food samples. In addition, IMS method could be easily adapted to detect other pathogens by selecting the pertinent antibody.     

Molecular identification of Salmonella isolates from poultry and meat productsin Irbid City,Jordan

The sensitivity and accuracy of molecular diagnosis of Salmonella from meat and poultry products using polymerase chain reaction (PCR) was compared with conventional microbiological methods. A total of 212 samples representing the most frequently used fresh and frozen meat and poultry products (whole, cut, ground, and processed) were collected from different locations within the city of Irbid. DNA was extracted directly from each food sample and amplified using Salmonella-specific primers. Samples were also analysed using conventional microbiological methods for the presence of Salmonella spp. Results showed that Salmonella was detected in 185 samples out of 212 (87%) by PCR technique, while 172 (81%) samples were detected Salmonella positive by conventional microbiological methods. On the other hand, 27 (12.7%) samples were negative by PCR and 40 (18.8%) samples were negative by conventional microbiological methods. PCR assay proved to be an effective method for Salmonella detection in meat and poultry products with high specificity and sensitivity and more importantly a less time-consuming procedure. Using PCR, Salmonella spp. detection could be achieved within 24–36 h compared to 3–8 days for the conventional microbiological methods.     

Detection of Salmonella enterica serovar Typhimurium by selective amplification of fliC, fljB, iroB, invA, rfbJ, STM2755, STM4497 genes by polymerase chain reaction in a monoplex and multiplex format

The aim of the work was to specifically differentiate S. typhimurium from other closely related Salmonella serovars by monoplex or multiplex PCR and to detect it from water and food samples. Genes targeted were invA, iroB, STM4497, STM2755, fliC, fljB and rfbJ and evaluated on 58 Salmonella standard serovars/strains including 9 S. typhimurium strains, 7 suspected Salmonella isolates and 8 other organisms as negative controls. Both invA and iroB showed a uniform amplification with all serovars of S. enterica group. STM2755 and STM4497 gene based PCR’s specifically exhibited amplification in all the nine confirmed S. typhimurium strains. The rfbJ PCR produced amplification with confirmed S. typhimurium strains, in addition showed reaction with S. abony. Both STM4497, STM2755 PCR’s and rfbJ could identify two of the seven biochemically suspected Salmonella isolates that were later confirmed to be S. typhimurium on the basis of sequence data. PCR for fliC genes had amplification exhibited by a large number of serovars of the S. enterica group, including S. typhimurium strains but not to S. brunei, S. newporti, S. abony and S. weltevreden. fljB was detected in all strains of S. enterica and E. coli with the exception of S. typhi. fljB and fliC were amplified in 6/7 and 5/7 presumptive Salmonella isolates. The same PCR’s were converted into two multiplex formats for simultaneous identification of the Salmonella genus, S. enterica group and S. typhimurium as a species. The first multiplex set comprised on invA, iroB, STM4497, STM2755 and the IAC. The second multiplex set comprised of invA, iroB, fljB, fliC, rfbJ along with IAC. The detection limit for S. typhimurium in the two multiplex PCR sets was in the range of 350–400 cfu/PCR reaction and that of DNA around 2 pg. The multiplex PCR (format 1) was first evaluated on spiked water, chicken and mutton samples and the detection limit for S. typhimurium was in the range of 100 cfu/100 ml, <60 and <50 cfu/gm, respectively. Further evaluation of multiplex PCR (format 1) was undertaken on 50 natural samples of chicken, eggs, litter, soil etc. and the comparison done with conventional culture isolation and identification procedure. The multiplex PCR could identify the presence of Salmonellla in three samples and the same three samples also yielded Salmonella by the conventional method. Therefore, the presently described multiplex PCR can serve as an alternative to the tedious time-consuming procedure of Salmonella culture and identification in food safety laboratories.     

Development of duplex PCR for the detection of Salmonella and Vibrio in drinking water

We report here a rapid protocol for the detection of Vibrio and Salmonella in drinking water using a duplex PCR reaction. The developed protocol can detect as few as 500 cells in a single reaction, which has been achieved by optimizing the temperature steps and magnesium chloride concentration for the reactions. The described PCR protocol could detect Vibrio and Salmonella spiked in drinking water.     

A <Emphasis Type="Italic">gyrB</Emphasis>-targeted PCR for Rapid Identification of <Emphasis Type="Italic">Salmonella</Emphasis>

Salmonella causes the majority of infections in humans and homeothermic animals. This article describes a specific polymerase chain reaction (PCR) method developed for a rapid identification of Salmonella. A gyrB-targeted species-specific primer pair, S-P-for (5′-GGT GGT TTC CGT AAA AGT A-3′) and S-P-rev (5′-GAA TCG CCT GGT TCT TGC-3′), was successfully designed. PCR with all the Salmonella strains produced a 366- bp DNA fragment that was absent from all the non-Salmonella strains tested. The detection limit of the PCR was 0.01 ng with genomic DNA or 3.2 cells per assay. Good specificity was also demonstrated by fecal samples, from which only the gyrB gene of Salmonella was amplified. Using the culture-PCR method, 27 isolates on Salmonella-Shigella (SS) medium were rapidly identified as Salmonella, which was confirmed by the sequencing of the gyrB gene.     

A Rapid Method for the Pre‐Enrichment and Detection of Salmonella Typhimurium by Immunomagnetic Separation and Subsequent Fluorescence Microscopical Techniques

Detection of food‐borne pathogens is of great importance in order to minimize the risk of infection for customers. These analyses should be as fast as possible. Any detection method requires enrichment and quantitative analysis of the enriched microbes. Conventional enrichment methods, which take several days, need to be replaced by faster techniques such as immunomagnetic separation (IMS). This technique is based on the use of paramagnetic microspheres coated with antibodies as ligands that have specific affinity to the microbes that have to be detected. In the studies reported here, a rapid method for the detection of Salmonella enterica serovar Typhimurium (Salmonella Typhimurium), combining IMS and Direct Epifluorescence Filter Technique (DEFT), was developed. It was focused on releasing the target cells from the magnetic beads after IMS, because this is a premise for combining IMS, as an alternative pre‐enrichment, with DEFT. Otherwise, the high number of beads form a layer on the filter membrane that makes the following microscopic analysis for the detection of the contaminants impossible. The CELLection^TM Dynabeads^® used in this study, are coated with recombinant streptavidin (rSA) via a DNA linker. The rSA binds biotinylated antibodies that are able to capture target cells. The DNA linker provides the cleavable site, so that the beads can be removed from the captured cells after isolation. In this study a releasing procedure was developed. This procedure allows for an average 74 % ± 4 % of the bead‐bound Salmonella Typhimurium cells to be released from the beads after IMS, so that the detection of the separated cells by DEFT will be possible.     

Lactobacillusacidophilus S-layer protein-mediated inhibition of Salmonella-induced apoptosis in Caco-2 cells

Surface layer (S-layer) proteins are crystalline arrays of proteinaceous subunits present as the outermost component of the cell wall in several Lactobacillus species. The underlying mechanism for how S-layer proteins inhibit pathogen infections remains unclear. To gain insights into the mechanism of the antimicrobial activity of Lactobacillus S-layer proteins, we examined how Lactobacillus S-layer proteins impact Salmonella Typhimurium-induced apoptosis in vitro in Caco-2 human colon epithelial cells. When Caco-2 cells infected with Salmonella Typhimurium SL1344, we found that apoptosis was mediated by activation of caspase-3, but not caspase-1. When Salmonella Typhimurium SL1344 and S-layer proteins were coincubated simultaneously, Caco-2 cell apoptosis was markedly decreased and the cell damage was modified, as evaluated by flow cytometry and microscopy. Detailed analyses showed that the S-layer proteins inhibited the caspase-3 activity and activated the extracellular signal-regulated kinases 1 and 2 (ERK1/2) signaling pathway. Taken together, these findings suggest that Lactobacillus S-layer proteins protected against Salmonella-induced apoptosis through reduced caspase-3 activation. In addition, Salmonella-induced apoptotic cell damage was modified by S-layer proteins through the ERK1/2 signaling pathway. This mechanism may represent a novel approach for antagonizing Salmonella infection.     

The ability of nisin F to control Staphylococcus aureus infection in the peritoneal cavity, as studied in mice

Aims: To evaluate the outer membrane porin F gene (ompF) for the specific detection of Salmonella species by real‐time PCR assay. Methods and Results: Two hundred and eighteen isolates belonging to Salmonella enterica (subspecies I‐VI) and Salmonella bongori were examined using primers designed to detect the ompF gene. The DNA of the bacteria was extracted from pure culture. The target was present in all the 218 Salmonella isolates including all the subspecies of Salm. enterica and Salm. bongori. The ompF gene was absent in 180 non‐Salmonella strains tested. The limit of detection was determined to be three colony forming units per reaction in pure culture. In artificially contaminated food experiments with ten or less colony forming units per 25 g, the assay was successful in identifying the target in 100% of the samples after 22‐ to 24‐h incubation in enrichment broth. Conclusions: Based on this study, the ompF gene is 100% inclusive for Salmonella species and 100% exclusive for non‐Salmonella species for the strains tested. Significance and Impact of the Study: ompF gene was present in all the Salmonella strains tested and has the potential to be a good target for the rapid molecular identification of Salmonella.     

Amplification of rfbE and fliC Genes by Polymerase Chain Reaction for Identification and Detection of Salmonella Serovar Enteritidis,Dublin and Gallinarum-Pullorum

Polymerase chain reaction (PCR) primers for O9 antigen (rfbE) and phase 1 flagellin antigen (fliC) were designed for the rapid identification and detection of Salmonella serovar Enteritidis and Dublin. The rfbE primer pairs selectively amplified the rfbE region of group O9 Salmonella serovars. The fliC primer pairs amplified the DNAs of g,m and g,p-type flagellar antigen; Salmonella serovar Enteritidis, Dublin, and Essen. However, DNA from flagellar-negative Salmonella serovar Gallinarum-Pullorum was also amplified. The sensitivity of PCR primer pairs was 10 CFU/assay by boiled DNA preparation and 10² CFU/assay by proteinase K-treated DNA preparation.     

Rapid detection of Salmonella enterica serovars by multiplex PCR

A multiplex PCR based assay was developed for the identification of the genus Salmonella. Five sets of primers from different genomic sequences such as fimA, himA, hns, invA and hto genes were selected for the identification of serogroups of Salmonella enterica such as S. Typhi, S. ParatyphiA, S. Typhimurium, S. Enteritidis and S. Weltevreden. The selected primers amplified products with the sizes of 85, 123, 152, 275 and 496 bp, respectively, for the genus Salmonella. This assay was found to be highly sensitive, as it could detect 5 cells of Salmonella and 1,000 fg of genomic DNA. Amplification of DNA extracted from other genera viz. V. cholerae and E. coli yielded negative results. This assay provides specific and reliable results and allows for the cost–effective detection of Salmonella in one reaction tube in mixed bacterial communities.     

Zn finger-based direct detection system for PCR products of<Emphasis Type="Italic"> Salmonella</Emphasis> spp. and the Influenza A virus

We have detected PCR products from Salmonella spp. and Influenza A virus using Zn finger protein Zif268 and Sp1, respectively. Previously, we demonstrated a novel method of rapid and specific detection of PCR products from Legionella pneumophila genome using Zn finger protein Sp1. In principle, this methodology might be applied to the detection of most bacteria and viruses using various Zn finger proteins. Here, to demonstrate the wider applicability of our method, we detected PCR products from Salmonella spp. and the Influenza A virus. BLAST data indicated the Zif268 and Sp1 recognition sequence were located on the gyrB gene of Salmonella spp. and the nucleoprotein gene of Influenza A virus, respectively. The PCR products from the oligonucleotide corresponding to the gyrB gene of Salmonella spp. or the nucleoprotein gene of the Influenza A virus could be specifically detected by ELISA or fluorescence depolarization measurement using Zif268 or Sp1. These results indicate the wide applicability of our novel methodology. An erratum to this article can be found at     

Evaluation of culture, ELISA and PCR assays for the detection of Salmonella in seafood

Aims: The study evaluated the efficiency of culture, enzyme‐linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) assays for the detection of Salmonella in naturally contaminated seafood. Methods and Results: In this study, 215 seafood samples comprising fish, shrimp, crab, clam, mussel, oyster, squid, cuttlefish and octopus from fish market of Cochin (India), were compared by culture, ELISA and PCR methods. Bacteriological Analytical Manual (BAM), U.S. Food and Drug Administration (USFDA) method was followed for culture assay, and Salmonella Tek, a commercial sandwich ELISA kit, was used for ELISA assay. Salmonella‐specific PCR assay was developed for 284 bp Salmonella‐specific invA gene amplicon. PCR assay exhibited 31·6% seafood positive for Salmonella followed by ELISA (23·7%) and culture method (21·3%). There was fair to excellent agreement between culture, ELISA and PCR assays (kappa coefficient values ranging from 0·385 to 1·0) for different seafood samples. Conclusion: The investigation revealed the greater concordance between culture and ELISA methods for seafood. Among the three methods, PCR assay was most sensitive. Lower detection rate with culture and ELISA assays could be attributed to greater sensitivity of the PCR method in the detection of Salmonella in seafood. Significance and Impact of the Study: We propose the incorporation of dual tests based on different principle and procedure for the routine analysis of Salmonella in seafood.     

Comparison of Salmonella enterica Serovar Typhimurium LT2 and Non-LT2 Salmonella Genomic Sequences, and Genotyping of Salmonellae by Using PCR

Genes of Salmonella enterica serovar Typhimurium LT2 expected to be specifically present in Salmonella were selected using the Basic Local Alignment Search Tool (BLAST) program. The 152 selected genes were compared with 11 genomic sequences of Salmonella serovars, including Salmonella enterica subsp. I and IIIb and Salmonella bongori (V), and were clustered into 17 groups by their comparison patterns. A total of 38 primer pairs were constructed to represent each of the 17 groups, and PCR was performed with various Salmonella subspecies including Salmonella enterica subsp. I, II, IIIa, IIIb, IV, VI, and V to evaluate a comprehensive DNA-based scheme for identification of Salmonella subspecies and the major disease-causing Salmonella serovars. Analysis of PCR results showed that Salmonella enterica subsp. I was critically divided from other subspecies, and Salmonella strains belonging to S. enterica subsp. I were clustered based on their serovars. In addition, genotypic relationships within S. enterica subsp. I by PCR results were investigated. Also, Salmonella signature genes, Salmonella enterica serovar Typhimurium signature genes, and Salmonella enterica subsp. I signature genes were demonstrated based on their PCR results. The described PCR method suggests a rapid and convenient method for identification of Salmonella serovars that can be used by nonspecialized laboratories. Genome sequence comparison can be a useful tool in epidemiologic and taxonomic studies of Salmonella.     

Validation of ERIC PCR as a tool in epidemiologic research of Salmonella in slaughter pigs

The purpose of this study was to test a protocol for a standardized ERIC PCR for its capability of genotyping Salmonella, isolated from pigs and their environment, in an epidemiologic approach. To test repeatability, four different Salmonella isolates were subjected to PCR three times. Furthermore, it was tested if the profiles on gel differed when a higher annealing temperature was used. Four Salmonella isolates were subjected to four different annealing temperatures (36, 40, 48 and 55°C). Moreover it was tested if the differentiation of Salmonella isolates, based on the genotypes, differed when a higher annealing temperature was used. Eight Salmonella isolates were tested at normal (36°C) and high (55°C) annealing temperatures. The results showed that this standardized ERIC PCR protocol was an efficient tool for typing many Salmonella isolates within a short period of time. The profiles were repeatable within one PCR reaction, but some profiles differed when they were compared between reactions. A higher annealing temperature resulted in profiles that contained more or fewer bands. The differentiation between isolates, when comparing profiles, remained the same. It was concluded that the standardized ERIC PCR protocol is useful for genotyping Salmonella. Received 26 January 1998/ Accepted in revised form 3 August 1998     

Detection of E. coli O157:H7 by immunomagnetic separation coupled with fluorescence immunoassay

Conventional culture-based methods for detection of E. coli O157:H7 in foods and water sources are time-consuming, and results can be ambiguous, requiring further confirmation by biochemical testing and PCR. A rapid immunoassay prior to cultivation to identify presumptive positive sample would save considerable time and resources. Immunomagnetic separation (IMS) techniques are routinely used for isolation of E. coli O157:H7 from enriched food and water samples, typically in conjunction with cultural detection followed by biochemical and serological confirmation. In this study, we developed a new method that combines IMS with fluorescence immunoassay, termed immunomagnetic fluorescence assay (IMFA), for the detection of E. coli O157:H7. E. coli O157:H7 cells were first captured by anti-O157 antibody-coated magnetic beads and then recognized by a fluorescent detector antibody, forming an immunosandwich complex. This complex was subsequently dissociated for measurement of fluorescence intensity with Signalyte™-II spectrofluorometer. Experiments were conducted to evaluate both linearity and sensitivity of the assay. Capture efficiencies were greater than 98%, as determined by cultural plating and quantitative real-time PCR, when cell concentrations were <10⁵ cells/mL. Capture efficiency decreased at higher cell concentrations, due to the limitation of bead binding capacity. At lower cell concentrations (10–10⁴ cells/mL), the fluorescence intensity of dissociated Cy5 solution was highly correlated with E. coli 157:H7 cell concentrations. The detection limit was 10 CFU per mL of water. The assay can be completed in less than 3 h since enrichment is not required, as compared to existing techniques that typically require a 24 h incubation for pre-enrichment, followed by confirmatory tests.     

Direct Detection by PCR of Escherichia coli O157 and Enteropathogens in Patients with Bloody Diarrhea

Direct detection of Escherichia coli O157 and foodborne pathogens associated with bloody diarrhea were achieved using polymerase chain reaction (PCR) after the preparation of DNA from stool specimens using the microspin technique. PCR was compared with cultivation and toxin production tests with respect to the efficiency of detection of each pathogen; E. coli O157, Vibrio parahaemolyticus, Salmonella serovar Enteritidis and Campylobacter jejuni. Detection of some or all of the above pathogens in clinical stool specimens was achieved using PCR. The minimum number of cells required for the detection of the above pathogens by PCR was 10¹ CFUs/0.5 g of stool sample. PCR was completed within 6 hr. The above pathogens were also detected in cultivation and toxin production tests. Partial purification of the template DNA using the microspin technique was essential for the elimination of PCR inhibitors from the DNA samples. This PCR method is an accurate, easy-to-read screening method for the detection of Shiga-like toxin producing E. coli O157 and enteropathogens associated with bloody diarrhea in stool specimens.     

Antibiotic resistance and molecular characterization of poultry isolates of Salmonella by RAPD-PCR

The antibiotic resistance profile of 17 poultry isolates of Salmonella was studied against 24 different antibiotics. 69–88% of the Salmonella isolates displayed a high level of resistance, particularly against penicillin, rifampicin, erythromycin, clarithromycin, clindamycin, sulphamethoxazole and vancomycin. In contrast, a relatively low or moderate level of resistance was observed against furazolidone, spectinomycin, ciprofloxacin, chloramphenicol, cefepime, carbenicillin, nalidixic acid, streptomycin, oxacillin and cephalothin (11–59%). Moreover, resistance to multiple antibiotics (2–5) was also observed among the Salmonella strains, and none of the isolates was found susceptible to all the antibiotics used. Similarity coefficient among Salmonella strains by RAPD-PCR analysis varied from 0.60 to 0.86, and all the salmonellae could be classified into seven groups on the basis of dendrogram analysis. Generally, a very high level of concordance between RAPD-PCR profile and antibiotic profile was not observed, which indicates that genes for antibiotic resistance may not always be present on genomic DNA rather may be plasmid-borne.     

High-throughput Universal Probe Salmonella Serotyping (UPSS) by nanoPCR

Salmonella enterica subsp. enterica serovar identification is of great importance with respect to outbreak monitoring and case verification. Therefore rapid, sensitive and cost efficient detection of Salmonella spp. is indispensable within microbiology labs. To amalgamate single tube isolate identification with Salmonella typing, we developed the high-throughput Universal Probe Salmonella Serotyping (UPSS) technique based on nano liter PCR. In comparison to the classical approach, where O- and H-antisera are applied, the UPSS relies on specific gene content amplification of Salmonella spp. by a universal TaqMan assay for all markers and identification of the specific amplicon pattern. To enable high-throughput technology we employed a chip format containing 1024 wells loaded by an automated liquid-handling system which allowed us to perform TaqMan PCR reactions in volumes of 100 nL per well. Herein we present proof of principle of the UPSS method by the use of a test panel of 100 previously serotyped Salmonella isolates to successfully verify the usability, accuracy and feasibility of the newly developed UPSS approach. We found that the methodology of the UPSS technology is capable of unequivocally identifying 30 Salmonella serotypes on a single chip within 3 hours but can be highly parallelized by the use of multiple PCR machines. Therefore the UPSS method offers a robust and straightforward molecular alternative for Salmonella detection and typing that saves expensive chemistry and can be easily automated.