Probeliatrade mark PCR system for rapid detection of Salmonella in milk powder and ricotta cheese

How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles

A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay.

Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations

The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.

Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations

The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.

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

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

Rapid detection of Salmonella by polymerase chain reaction

Salmonella enterotoxin gene (stn) was sequenced from Salmonella enterica serotypes: Typhimurium, Typhi, Paratyphi A and B. The sequences from all the four serotypes showed complete homology with the already reported stn gene sequence of the serotype Typhimurium. As a tool for detection of this organism, four pairs of oligonucleotide primers were designed to amplify different fragments of this important pathological marker. The protocols were standardized with serotype Typhimurium in such a way so as to complete the PCR reaction in 75-90 min. These primers were found to generate specific amplicons with all the serotypes of Salmonella tested. The PCR protocols were found to be highly specific as no amplifications, specific or non-specific, were found when reactions were run using non-Salmonella DNA as template. The employment of a nested PCR markedly increased the sensitivity of the assay system in natural water samples. The protocol described herein is highly sensitive as it detects less than 10 cells of Salmonella in 250 microl of blood and approx. 1 cell in 1 ml of water without any enrichment. For the validation of this protocol, 72 coded samples of 11% skimmed milk spiked with different pathogens were received from NICED, Kolkata and analyzed for the presence of Salmonella. Our procedures detected correctly the presence of Salmonella in nine samples. 50 samples of raw milk were subjected to this PCR after enrichment for 8 h and 6 samples were found positive for Salmonella. The study indicates that Salmonella enterotoxin (stn) gene is highly conserved and the protocol devised in this study can be used as rapid and reliable method for detection of Salmonella spp. in water, milk and blood samples.

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.

An improved PCR primer pair based on 16S rDNA for the specific detection of Salmonella serovars in food samples

Salmonella serovars are some of the major bacterial pathogens that can cause sporadic cases and outbreaks of foodborne illness. Based on the sequence data in the V3 region of the 16S rRNA gene, two PCR primer pairs have been designed for the detection of all serovars of Salmonella. However, none of these primers were specific for Salmonella because complete sequence homology with certain non-Salmonella strains has been found within each of them. Thus, the specificities of these two primer pairs could not rely on only one of the two primers. In this study, we modified our previous 16SFI primer by extending one base at the 5' end and three bases at the 3' end. The modified primer, 16S-Sal, was designed with one or more mismatched bases near the 3' end of the primer annealing to the corresponding sequences of non-Salmonella strains. Such modification eliminates interference from Citrobacter freundii and Enterobacter cloacae as occurs with the 16SFI primer. When 16S-Sal and a degenerate primer, 16S-CCR, were used as a primer pair, detection specificity of Salmonella serovars was achieved. Because this primer pair was used for PCR detection of the salmonellae in food samples, such as whole milk and chicken meat, as low as 1 to 9 CFU/g (ml) of the food sample could be detected when a 8-h preculture step was performed prior to the PCR. For chicken meat, the endogenous microflora did not interfere with the PCR results.

Evaluation of real-time PCR vs automated ELISA and a conventional culture method using a semi-solid medium for detection of Salmonella

AIMS

Evaluation of iQ-Check PCR Salmonella for Salmonella detection in artificially and naturally contaminated food and environmental field samples.

METHODS AND RESULTS

Artificially contaminated samples (poultry meat and ground red meat) subjected to cold- and freeze-stress, and 120 naturally contaminated samples (swabs and meat) were tested for Salmonella using the diagnostic semi-solid Salmonella medium (DIASALM) method, the Vidas assay and the iQ-Check PCR assay after 24 h enrichment in buffered peptone water.

CONCLUSIONS

Both the iQ-Check PCR and the Vidas assay provide a rapid and user friendly screening method for detection of Salmonella. False negative samples were obtained for the inoculated samples using both the iQ-Check PCR assay and the Vidas method when Salmonella cells were severely stressed. In total 45 of 120 naturally contaminated field samples showed Salmonella positive using the DIASALM method. The agreement percentage with the DIASALM method was respectively 92% for the iQ-Check PCR and 95% for the Vidas method.

SIGNIFICANCE AND IMPACT OF THE STUDY

False-negative samples were obtained for the inoculated samples using both the iQ-Check PCR assay and the Vidas method when Salmonella cells were severely stressed, e.g. freezing at -18 degrees C for 7 days. Of the 120 naturally contaminated field samples 45 showed Salmonella positive using the DIASALM method. The agreement percentage with the DIASALM method was 92% for the iQ-Check PCR and 95% for the Vidas method respectively.

The prevalence and PCR detection of Salmonella contamination in raw poultry

Contaminated poultry meat has been identified as one of the principal foodborne sources of Salmonella. The development of rapid detection assays for Salmonella would enable official agencies and food industries to identify contaminated foodstuffs in a more timely manner. In addition, these diagnostic tools could allow more 'real time' decisions to be made regarding end product acceptability. In this study, a survey was carried out to determine the prevalence of Salmonella in raw broiler carcasses. A total of 198 neck skin samples were obtained from within 40 flocks at a commercial broiler slaughtering facility. The presence of Salmonella was assessed by traditional culture methods and by a Salmonella-specific polymerase chain reaction (PCR) test. Salmonella was recovered from 32 (16%) of all samples using traditional culture methods. In contrast, the PCR assay proved to be more sensitive and detected Salmonella DNA in 38 (19%) of the samples tested. The pathogen was detected in 45 (23%) of the 198 samples when culture and PCR results were combined. The sensitivity of the PCR test was also greater than culture when detecting Salmonella from within flocks (53% of flocks by PCR, 30% of flocks by culture). The combination of both tests revealed that 55% of the flocks were contaminated with Salmonella. The PCR assay proved to be a highly specific and sensitive method for detecting Salmonella and the incorporation of a routine PCR test in conjunction with standard culture could be effective in providing a more accurate profile of the prevalence of this pathogen in broiler carcasses.

Laboratory-scale preparation of soft cheese artificially contaminated with low levels of Escherichia coli O157, Listeria monocytogenes, and Salmonella enterica serovars Typhimurium, Enteritidis, and Dublin

The production of cheese with incurred low levels of pathogenic microorganisms stressed by the production process was the aim of the study. A standard protocol for the preparation of artificially contaminated soft cheese on a laboratory scale was developed. Milk for cheese preparation was artificially contaminated with pathogenic target microorganisms at low levels, between 1 and 10 CFU/ml. Two strains of Escherichia coli OI157:H7, two strains of Listeria monocytogenes, and three Salmonella spp. (Salmonella enterica serovars Typhimurium, Enteritidis, and Dublin) were investigated. The food pathogens in the cheese were exposed to the entire production process. All three microorganism species survived the cheese production process and were detected in the final product at concentrations between 1 and 50 CFU/g. The cheese produced contains target microorganisms that have been exposed to curd formation, drainage, setting, and ripening. This cheese can be used to validate microbiological methods or to examine the target microorganisms in a natural food environment at low concentrations. It represents an alternative to artificial contamination of cheese by adding target microorganisms to a final cheese product.