The Use of Multiplex Real-Time PCR for the Simultaneous Detection of Foodborne Bacterial Pathogens

Foodborne pathogens continue to be a major health concern worldwide. Culture-dependent methodologies are still considered the gold standard to perform pathogen detection and quantification. These methods present several drawbacks, such as being time-consuming and labor intensive. The implementation of real-time PCR has allowed to overcome these limitations, and even reduce the cost associated with the analyses, due to the possibility of simultaneously and accurately detecting several pathogens in one single assay, with results comparable to those obtained by classical approaches. In this chapter, a protocol for the simultaneous detection of two of the most important foodborne pathogens, Salmonella spp. and Listeria monocytogenes, is described.

Evaluation of the Novel mTA10 Selective Broth, MSB, for the Co-Enrichment and Detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in Ready-to-Eat Salad Samples

Multiplex assays implementing DNA-based methods have been demonstrated as suitable alternatives to culture-based microbiological methods; however, in most cases, they still require a suitable enrichment step. Finding suitable enrichment conditions for different bacteria may result in challenges. In the present study, a novel selective broth named MSB (mTA10 selective broth) was formulated for the simultaneous recovery of Salmonella spp., E. coli O157:H7 and L. monocytogenes. Attention was paid to ensure the optimal enrichment of L. monocytogenes as its enrichment is more challenging. To this end, cellobiose was added to increase the growth of L. monocytogenes, and sodium pyruvate was also added to improve the recovery of stressed bacteria. Four selective agents were added, namely nalidixic acid, sodium cholate, lithium chloride and potassium tellurite, to control the growth of interfering microorganisms. It was concluded that the novel broth was suitable for the simultaneous enrichment of the target pathogens, allowing them to reach concentrations higher than 7 log CFU/mL for each bacterium in pure culture. Furthermore, all heavily contaminated ready-to-eat salad samples reached concentrations higher than 5 log CFU/g. Finally, after 24 h of enrichment of spiked salad, it was possible to detect concentrations below 10 CFU/25 g.

Recent Developments in Lateral Flow Assays for Salmonella Detection in Food Products: A Review

Salmonellosis is a disease transmitted by contaminated food and is one of the leading causes of infections worldwide, making the early detection of Salmonella of crucial importance for public health. However, current detection methods are laborious and time-consuming, thus impacting the entire food supply chain and leading to production losses and economic sanctions. To mitigate these issues, a number of different biosensors have been developed, including lateral flow assays (LFAs), which have emerged as valuable tools in pathogen detection due to their portability, ease of use, time efficiency, and cost effectiveness. The performance of LFAs has been considerably enhanced by the development of new nanomaterials over the years. In this review, we address the principles and formats of the assay and discuss future prospects and challenges with an emphasis on LFAs developed for the detection of different Salmonella serovars in food.

The Use of Multiplex Real-Time PCR for the Simultaneous Detection of Foodborne Bacterial Pathogens

Foodborne pathogens continue to be a major health issue worldwide. Culture-dependent methodologies are still considered the gold-standard to perform pathogen detection and quantification. These methods present several drawbacks, such as being time-consuming and labor-intensive. The implementation of real-time PCR has allowed to overcome these limitations and even reduce costs associated with the analyses, due to the possibility of simultaneously and accurately detecting several pathogens in one single assay, with results comparable to those obtained by classical approaches. In this chapter a protocol for the simultaneous detection of two of the most important foodborne pathogens, Salmonella spp. and Listeria monocytogenes, is described.

Microbial Contamination of Organically and Conventionally Produced Fresh Vegetable Salads and Herbs from Retail Markets in Southwest Germany

A total of 189 samples of fresh products (leafy salads, ready-to-eat mixed salads, and fresh herbs) bought in retail in Southwest Germany were investigated for their microbiological quality and the presence of pathogenic bacteria, including Salmonella spp., Listeria monocytogenes, and presumptive Bacillus cereus. Total aerobic mesophilic plate counts (TAC) ranged from 5.5 to 9.6 log colony-forming units (CFUs) per gram. Enterobacteria and pseudomonads were the predominant microorganisms and were detected in all samples with counts between 5.0 and 9.2 log CFU/g. Strains of Escherichia coli were detected in 9 salad (7.9%) and 25 herb samples (33.3%). Significant differences in bacterial counts were found between conventionally and organically-grown products: in herbs the counts of moulds were significantly higher in organically-grown products, while E. coli was only detected in conventionally-grown products. In conventionally-grown salad samples, yeast counts were significantly higher. Salmonella Enteritidis was only detected in two conventionally- and in one organically-produced salad samples (2.6%). No coagulase-positive staphylococci were detected in fresh salads as well as in herbs. High levels of B. cereus sensu lato (≥3 log CFU/g) were detected in 19 vegetable salads (16.7%) and even in 55 samples of fresh herbs (73.3%). Listeria monocytogenes could not be detected in fresh herbs; however, three L. monocytogenes strains were isolated from two conventionally-produced salad samples and belonged to PCR serogroup IIa. Although our results indicate a high microbial load in fresh salads and herbs in Southwest Germany in 2015, the incidences of human pathogenic bacteria, that is, L. monocytogenes, Salmonella spp., and coagulase-positive staphylococci strains, were low.

A Novel Selective Medium for Simultaneous Enrichment of Shiga Toxin-Producing Escherichia coli and Salmonella in Ground Beef

Microbiological analysis of ground beef for contamination by both Salmonella and Shiga toxin-producing Escherichia coli (STEC) is performed by the U.S. Department of Agriculture, Food Safety Inspection Service (FSIS), as part of its Performance Standards Verification Testing program. FSIS has established a zero tolerance for STEC serotype O157:H7 and serogroups O26, O45, O103, O111, O121, and O145 because they are regarded as adulterants. The detection and isolation of these specific serogroups presents a technical challenge necessitating time-consuming and costly laboratory procedures that often exceed the technical capabilities of many small internal and reference laboratories. We describe here a method using a novel STEC and Salmonella selective (SSS) broth that allows for simultaneous selective enrichment of STEC and Salmonella sp., providing isolation and detection from the same broth. The method only involves direct plating from beef enrichments to detect suspect isolates that can be easily confirmed by using immunoassays or PCR, rendering the isolation simpler and less costly than the current described methods. In a side-by-side comparison with modified tryptic soy broth (mTSB), the use of SSS broth resulted in primarily isolating STEC and Salmonella sp., while substantially suppressing the growth of other gram-negative Enterobacteriacae by 90%. Significantly more (χ² < 3.84) samples containing E. coli O157:H7 and STEC O26, O111, O121, and O145 and a nondifferent (χ² > 3.84) number of samples containing STEC O103 and O45 were identified when enriching in SSS broth. Coenrichment using six different Salmonella serovars showed numerically greater but not significant (χ² < 3.84) positive samples by using SSS broth compared with mTSB for a majority of serotypes.

Optimal Conditions for the Asymmetric Polymerase Chain Reaction for Detecting Food Pathogenic Bacteria Using a Personal SPR Sensor

We have been developing quick and simple system for detecting food-poisoning bacteria using a combination of an asymmetric PCR and a portable surface plasmon resonance (SPR) sensor. The system would be suitable for point-of-care detection of food-poisoning bacteria in the field of food industry. In this study, we established a novel method for quantifying the amplified forward (F) and reverse (R) chains of Staphylococcus aureus separately by high-performance liquid chromatography (HPLC). The concentration of single-stranded DNA amplicon excessively amplified, which is crucial for the system, could be calculated as the difference between those of the F- and R-chains. For the R-chain, a correction based on the F-chain concentration in the sample was used to obtain a more accurate value, because the determination of the R-chain concentration was affected by that of the coexisting F-chain. The concentration values were also determined by fluorescence imaging for electrophoresis gels of amplicons with FITC- or Cy5-conjugated primers, and they were in good agreement with the values by the HPLC. The measured concentration of the single-strand F-chain correlated well with the value of the SPR response against the probe that was a complementary sequence of the F-chain, immobilized on the sensor chip of the SPR sensor.

A Single-Step Enrichment Medium for Nonchromogenic Isolation of Healthy and Cold-Injured Salmonella spp. from Fresh Vegetables

Culture-based detection of nontyphoidal Salmonella spp. in foods requires at least four working days; therefore, new detection methods that shorten the test time are needed. In this study, we developed a novel single-step Salmonella enrichment broth, SSE-1, and compared its detection capability with that of commercial single-step ONE broth-Salmonella (OBS) medium and a conventional two-step enrichment method using buffered peptone water and Rappaport-Vassiliadis soy broth (BPW-RVS). Minimally processed lettuce samples were artificially inoculated with low levels of healthy and cold-injured Salmonella Enteritidis (100 or 101 colony-forming unit/25 g), incubated in OBS, BPW-RVS, and SSE-1 broths, and streaked on xylose lysine deoxycholate (XLD) agar. Salmonella recoverability was significantly higher in BPW-RVS (79.2%) and SSE-1 (83.3%) compared to OBS (39.3%) (p < 0.05). Our data suggest that the SSE-1 single-step enrichment broth could completely replace two-step enrichment with reduced enrichment time from 48 to 24 h, performing better than commercial single-step enrichment medium in the conventional nonchromogenic Salmonella detection, thus saving time, labor, and cost.

Multiplex PCR for simultaneous identification of E. coli O157:H7, Salmonella spp. and L. monocytogenes in food

The rapid detection of pathogens in food is becoming increasingly critical for ensuring the safety of consumers, since the majority of food-borne illnesses and deaths are caused by pathogenic bacteria. Hence, rapid, sensitive, inexpensive and convenient approaches to detect food-borne pathogenic bacteria is essential in controlling food safety. In this study, a multiplex PCR assay for the rapid and simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes was established. The invA, stx and hlyA genes specifically amplified DNA fragments of 284, 404 and 510 bp from Salmonella spp., L. monocytogenes and E. coli O157:H7, respectively. The 16S rRNA gene was targeted as an internal control gene in the presence of bacterial DNA. The specificity and sensitivity of the multiplex PCR were performed by testing different strains. The multiplex PCR assay was able to specifically simultaneously detect ten colony-forming unit/mL of each pathogen in artificially inoculated samples after enrichment for 12 h. The whole process took less than 24 h to complete, indicating that the assay is suitable for reliable and rapid identification of these three food-borne pathogens, which could be suitable in microbial epidemiology investigation.

Dynabeads protein G antibody conjugates combined with modified brain heart infusion broth for the enrichment and separation of Bacillus cereus in artificially contaminated vegetables

A modified brain heart infusion (MBHI) broth and a protocol of immunomagnetic separation (IMS) using antibody-coated Dynabeads^® protein G were developed for the enrichment and separation of Bacillus cereus in artificially contaminated vegetable samples. The MBHI consisted of BHI and 0.34 g/L magnesium sulfate, 12.08 g/L sodium pyruvate, 1.82 g/L yeast extract, and polymyxin B. The amount of immunomagnetic beads (IMBs) and immunoreaction time were optimized. The capture efficiency was 58.32% with 0.4 mg IMBs when the immunoreaction time was 20 min. Capture of B. cereus by IMBs did not interfere with competing flora. Pre-enrichment IMS was validated with four B. cereus strains in artificially contaminated baby sprouts, bean sprouts, lettuce, and spinach at two levels (∼0.1 and ∼1 CFU/g). We were able to detect and isolate B. cereus in 40/40 samples of vegetables contaminated at 0.1 CFU/g with IMS after 6 h of enrichment in MBHI.

A multiplex PCR assay for simultaneous detection of Escherichia coli O157:H7, Bacillus cereus, Vibrio parahaemolyticus, Salmonella spp., Listeria monocytogenes, and Staphylococcus aureus in Korean ready-to-eat food

A multiplex polymerase chain reaction (PCR) assay was developed for simultaneous detection of Escherichia coli O157:H7, Bacillus cereus, Vibrio parahaemolyticus, Salmonella spp., Listeria monocytogenes, and Staphylococcus aureus in various Korean ready-to-eat foods. The six specific primer pairs for multiplex PCR were selected based on the O157 antigen (rfbE) gene of E. coli O157:H7, the DNA gyrase subunit B (gyrB) gene of B. cereus, the toxin regulatory protein (toxR) gene of V. parahaemolyticus, the invasion protein A (invA) gene of Salmonella spp., the hemolysin (hly) gene of L. monocytogenes, and the thermonuclease (nuc) gene of S. aureus. The 16S rRNA gene was targeted as an internal control gene in the presence of bacterial DNA. The specificity and sensitivity assays for multiplex primer pairs were investigated by testing different strains. When this multiplex PCR assay was applied to evaluate the validity of detecting six foodborne pathogens in artificially inoculated several ready-to-eat food samples, the assay was able to specifically simultaneously detect as few as 1 colony-forming unit/mL of each pathogen after enrichment for 12 h. Their presence in naturally contaminated samples also indicates that the developed multiplex PCR assay is an effective and informative supplement for practical use.

In-house validation of a multiplex real-time PCR method for simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes

A wide variety of qPCR methods currently exist for Salmonella spp., Escherichia coli O157 and Listeria monocytogenes detection. These methods target several genes and use different detection chemistries, either in simplex or in multiplex formats. However, the majority of these methods have not been carefully validated, and the number of validated methods that use multiplex qPCR is even lower. The aim of the present study was to develop and validate a multiplex qPCR method from previously validated simplex qPCR primers and probes. A modified broth medium was selected and primary and secondary enrichment times were further optimized. Efficiency of the newly combined qPCR system was comprised between 91% and 108%, for simplex and multiplex analyses. A total of 152 food and environmental, natural and spiked samples, were analyzed for the evaluation of the method obtaining values above 91% that were reached for all the quality parameters analyzed. A very low limit of detection (5 cfu/25 g after enrichment) for simultaneous identification of these 3 pathogens was obtained.

Multiplex quantitative foodborne pathogen detection using high resolution CE-SSCP coupled stuffer-free multiplex ligation-dependent probe amplification

Sensitive multiplex detection methods for foodborne pathogens are important in controlling food safety, and detection of genetic markers is accepted to be one of the best tools for sensitive detection. Although CE technology offers great potential in terms of sensitive multiplex detection, the necessary amplification is confined to markers sharing common primers such as the 16S rRNA gene. For precise and sensitive detection, pathogen-specific genes are optimal markers. Although multiplex ligation-dependent probe amplification (MLPA) is appropriate for amplification of specific markers, the requirement for stuffers, to ensure length-dependent separation on CE, is a major obstacle in detection of foodborne pathogens. In the present study, we developed stuffer-free MLPA using high-resolution CE-SSCP to sensitively detect ten foodborne pathogens. The probe set for MLPA prior to CE-SSCP analysis was designed for species-specific detection. After careful optimization of each MLPA step, to ensure that CE-SSCP analysis was informative, we found that all ten pathogens could be reliably identified; the limits of detection were 0.5-5 pg of genomic DNA, and more than 100-fold increase could be quantitatively determined. Thus, MLPA-CE-SSCP is a sensitive and reliable technique for pathogen detection.