Application of a multiplex PCR for the simultaneous detection of Escherichia coli O157:H7, Salmonella and Shigella in raw and ready-to-eat meat products

Rapid and Multiplexed Detection of Single Cells of Salmonella, Escherichia coli O157, and Shigella flexneri in Ground Beef by Flow Cytometry

Salmonella, Escherichia coli O157, and Shigella flexneri are typical foodborne pathogens in ground beef, which can cause severe infection even when present as a single cell. Flow cytometry (FCM) methods are widely applied in the rapid detection of pathogens in food products. In this study, we report an FCM-based method for detecting single cells of Salmonella, E. coli O157, and S. flexneri in 25 g ground beef samples. We fluorescently labeled specific antibodies that could effectively identify bacterial cells, prepared single-cell samples by serial dilution, and optimized the pre-enrichment time. The results showed that 7 h of pre-enrichment is appropriate for sensitive single-cell detection by FCM. Finally, we evaluated this method in artificially contaminated and retail beef samples. This study outlines a novel highly sensitive FCM-based method to detect Salmonella, E. coli O157, and S. flexneri in beef samples within 8 h that can be applied to the rapid and multiplexed detection of foodborne pathogens.

Rapid and multiplexed quantification of Salmonella, Escherichia coli O157:H7, and Shigella flexneri in ground beef using flow cytometry

Salmonella, Escherichia coli O157:H7 (E. coli O157:H7) and Shigella flexneri (S. flexneri) might contaminate similar types of meat products and cause deadly diseases in humans. In reality, ground beef samples may carry more than one pathogen and a rapid and accurate detection method for the simultaneous identification of multiple specific pathogenic strains in ground beef is crucial. In this study, a sample pretreatment protocol and a flow cytometry method were developed for rapid and multiplexed quantification of the three pathogens without cultural enrichment in ground beef. The whole process of sample pretreatment, staining, and instrument analysis can be accomplished within 1 h. The three bacteria upon sample pretreatment were demonstrated good recoveries (93.8%-101.2%). The quantitative detection range of the mothed was 10³ to 10⁸ cells/g for all three pathogens, and the detection limit for Salmonella, E. coli O157:H7 and S. flexneri in ground beef were 3.1 × 10³ cells/g, 2.1 × 10³ cells/g and 2.3 × 10³ cells/g, respectively. Therefore, the as-developed approach is a rapid and quantitative method for multiplexed detection of Salmonella, E. coli O157:H7, and S. flexneri in ground beef.

Characterization of chicken meat contaminated with Salmonella by fluorescence spectroscopy

Contaminated poultry products as eggs and meat are the primary vehicles of Salmonella infection. Conventional methods for microorganisms detections involve multiple steps, and despite its accuracy, these assays are time-consuming. Biosensing methods have shown great potential for the rapid detection of foodborne pathogens. Some of the biosensors are based on fluorescence. Various fluorophores such as collagen, elastin, NAD(P)H, and porphyrins can be used to evaluate possible chemical changes in meat. In this manuscript, the fluorescence properties of chicken meat contaminated with Salmonella enterica (ATCC 14028) cell suspensions (500; 5000; 50,000 and 500,000 cells/mL) were obtained and compared with non-contaminated control, for meat kept at 25 °C for 24 and 48 h. The effects of ambient light were also considered. Our results indicated that free NAD(P)H and coproporphyrin emission bands present in contaminated meat, increased over time, and can provide access to valuable information for the detection of Salmonella in chicken meat.

Rapid and Sensitive Pathogen Detection by DNA Amplification Using Janus Particle-Enabled Rotational Diffusometry

Rapid and sensitive detection of infectious bacteria is in all-time high demand to prevent the further spread of the infection and allow early medical intervention. In this study, we use rotational diffusometry (RD), a natural phenomenon characterized by Janus particles, to detect pathogens like Escherichia coli by performing amplification of specific genes. This biosensing method is used to measure the change in viscosity of the fluid in the presence and absence of DNA in the solution by capturing images of modified microbeads at 10 Hz by a CCD camera followed by cross-correlation algorithm analysis. Using rotational diffusometry, we have achieved E. coli detection with 50 pg/μL DNA with a measurement time of 30 s and a sample volume of 2 μL. This sensitivity was achieved with 30 thermal cycles for three different amplicons, viz., 84, 147, and 246 bp. Meanwhile, in the case of 10 and 20 thermal cycles, the detection sensitivity was achieved with 0.1 and 1 ng/μL DNA concentrations for a 246 bp amplicon. Compared with conventional PCR, this technique appears to improve the detection time, thereby reaching a turnaround time of less than 60 min. Other studies showed a successful identification of DNA amplification up to 10 thermal cycles with different sizes of amplicons. The effect of DNA concentration, amplicon size, and the number of thermal cycles on the detection of E. coli was examined in detail and represented in the form of three maps. These maps show the clear difference and the advantages of RD method in comparison with conventional PCR. This unconventional and rapid biosensing method can be used further for downstream application of nucleic acid amplification-based pathogen detection and early disease control.

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.

Centrifugal sedimentation immunoassays for multiplexed detection of enteric bacteria in ground water

Waterborne pathogens pose significant threat to the global population and early detection plays an important role both in making drinking water safe, as well as in diagnostics and treatment of water-borne diseases. We present an innovative centrifugal sedimentation immunoassay platform for detection of bacterial pathogens in water. Our approach is based on binding of pathogens to antibody-functionalized capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk. Beads at the distal end of the disk are imaged to quantify the fluorescence and determine the bacterial concentration. Our platform is fast (20 min), can detect as few as ∼10 bacteria with minimal sample preparation, and can detect multiple pathogens simultaneously. The platform was used to detect a panel of enteric bacteria (Escherichia coli, Salmonella typhimurium, Shigella, Listeria, and Campylobacter) spiked in tap and ground water samples.

Efficient and Specific Detection of Salmonella in Food Samples Using a stn-Based Loop-Mediated Isothermal Amplification Method

The Salmonella enterotoxin (stn) gene exhibits high homology among S. enterica serovars and S. bongori. A set of 6 specific primers targeting the stn gene were designed for detection of Salmonella spp. using the loop-mediated isothermal amplification (LAMP) method. The primers amplified target sequences in all 102 strains of 87 serovars of Salmonella tested and no products were detected in 57 non-Salmonella strains. The detection limit in pure cultures was 5 fg DNA/reaction when amplified at 65°C for 25 min. The LAMP assay could detect Salmonella in artificially contaminated food samples as low as 220 cells/g of food without a preenrichment step. However, the sensitivity was increased 100-fold (~2 cells/g) following 5 hr preenrichment at 35°C. The LAMP technique, with a preenrichment step for 5 and 16 hr, was shown to give 100% specificity with food samples compared to the reference culture method in which 67 out of 90 food samples gave positive results. Different food matrixes did not interfere with LAMP detection which employed a simple boiling method for DNA template preparation. The results indicate that the LAMP method, targeting the stn gene, has great potential for detection of Salmonella in food samples with both high specificity and high sensitivity.

A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species

Salmonella enterica and Shigella species are commonly associated with food and water borne infections leading to gastrointestinal diseases. The present work was undertaken to develop a sensitive and reliable PCR based detection system for simultaneous detection of Salmonella enterica and Shigella at species level. For this the conserved regions of specific genes namely ipaH1, ipaH, wbgZ, wzy and invA were targeted for detection of Shigella genus, S. flexneri, S. sonnei, S. boydii and Salmonella enterica respectively along with an internal amplification control (IAC). The results showed that twenty Salmonella and eleven Shigella spp., were accurately identified by the assay without showing non-specificity against closely related other Enterobacteriaceae organisms and also against other pathogens. Further evaluation of multiplex PCR was undertaken on 50 natural samples of chicken, eggs and poultry litter and results compared with conventional culture isolation and identification procedure. The multiplex PCR identified the presence of Salmonella and Shigella strains with a short pre-enrichment step of 5 h in peptone water and the same samples were processed by conventional procedures for comparison. Therefore, this reported multiplex PCR can serve as an alternative to the tedious time-consuming procedure of culture and identification in food safety laboratories.

Response surface methodology to design a selective co-enrichment broth of Escherichia coli, Salmonella spp. and Staphylococcus aureus for simultaneous detection by multiplex PCR

Escherichia coli, Salmonella spp. and Staphylococcus aureus are frequent co-visitors of contaminated foods to cause food-borne diseases. To achieve rapid detection of three organisms by multiplex PCR, a selective co-enrichment broth was considered to design using response surface methodology (RSM) in this work. NaCl, LiCl and KSCN as selective bacterial inhibitors were selected to optimize their concentrations for a matched composition of bacterial biomass with uniform amplification of three targets. Central composite design was employed to collect the data and fit the responses. Three quadratic polynomial models were derived by computer simulation. A statistical analysis was carried out to explore the effects of the variables on the composition of bacterial biomass and PCR amplification yields. In the end, a novel broth (ESS-3 broth) of NaCl 1.60%, LiCl 0.70%, KSCN 0.10% was formulated to allow co-enrichment of the target pathogens and suppress growth of some non-target pathogens. The simultaneous detection of E. coli, Salmonella spp. and S. aureus was developed on a rapid, convenient and sensitive method consisting of selective co-enrichment in ESS-3 broth, DNA extraction with the boiling method and robust test by multiplex PCR. Our work provided broader application of RSM for the simultaneous detection of other combinations of multiple pathogens.

Development of multiplex loop-mediated isothermal amplification-RFLP (mLAMP-RFLP) to detect Salmonella spp. and Shigella spp. in milk

A multiplex loop-mediated isothermal amplification-RFLP (mLAMP-RFLP) was developed and validated for simultaneous detection of Salmonella strains and Shigella strains in milk. In this system, two sets of LAMP primers were designed to specifically target invA of Salmonella spp. and ipaH of Shigella spp. Under isothermal conditions at 63 °C, ladder pattern of DNA bands could be amplified within 60 min in the presence of genomic DNAs of Salmonella strains and Shigella strains, which could be distinguished between Salmonella spp. and Shigella spp. simultaneously based on the different ladder pattern of DNA bands and subsequent restriction enzyme analysis. The overall analysis time was approximately 20 h including the enrichment of the bacterial cells, which greatly saved detection time. The sensitivity of mLAMP was found to be 100 fg DNA/tube with genomic DNAs of Salmonella strains and Shigella strains, comparatively, multiplex PCR was 1 pg DNA/tube. The mLAMP allowed the detection of milk sample artificially contaminated by Salmonella strains and Shigella strains at initial inoculation levels of approximate 5CFU/10 mL. In conclusion, the mLAMP described here can potentially facilitate simultaneous monitoring of Salmonella and Shigella in a large number of food samples, which could be used as a primary screening method and as a supplement to classical detection method.

Salmonella sp e Listeria monocytogenes em presunto suíno comercializado em supermercados de Fortaleza (CE, Brasil): fator de risco para a saúde pública

O objetivo deste trabalho foi avaliar a ocorrência de Salmonella sp. e Listeria spp. em presunto suíno cozido sem capa de gordura, mantido sob temperatura de refrigeração, comercializado em supermercados de Fortaleza (CE). O material estudado compreendeu quarenta amostras, provenientes de oito marcas comerciais, coletadas em 26 estabelecimentos. A pesquisa de Salmonella sp. e Listeria spp. foi efetuada segundo APHA e HBP, respectivamente. Foi constatado que 30% das amostras estavam contaminadas por Salmonella sp. e 42,50%, 22,50% e 2,5% por L. monocytogenes, L. innocua e L. welshimeri, respectivamente. Foram observadas, ainda, falhas na aplicação das boas práticas de manipulação na área de frios dos supermercados. Verificou-se que 34,61%, 57,69% e 15,38% dos estabelecimentos apresentaram alguma amostra contaminada por Salmonella sp., L. monocytogenes e ambos os microrganismos, respectivamente, abrangendo a área de fiscalização das seis Secretarias Executivas Regionais (SER) do município de Fortaleza. Estes dados mostram a necessidade de um aperfeiçoamento quanto ao controle de qualidade em todo elo da cadeia alimentar como fator fundamental na prevenção de enfermidades transmitidas por alimentos (ETA).

Rapid and simultaneous quantitation of Escherichia coli 0157:H7, Salmonella, and Shigella in ground beef by multiplex real-time PCR and immunomagnetic separation

The objective of this study was to establish a multiplex real-time PCR for the simultaneous quantitation of Escherichia coli O157:H7, Salmonella, and Shigella. Genomic DNA for the real-time PCR was extracted by the boiling method. Three sets of primers and corresponding TaqMan probes were designed to target these three pathogenic bacteria. Multiplex real-time PCR was performed with TaqMan Universal PCR Master Mix in an ABI Prism 7700 Sequence Detection System. Final standard curves were calculated for each pathogen by plotting the threshold cycle value against the bacterial number (log CFU per milliliter) via linear regression. With optimized conditions, the quantitative detection range of the real-time multiplex PCR for pure cultures was 10(2) to 10(9) CFU/ml for E. coli O157:H7, 10(3) to 10(9) CFU/ml for Salmonella, and 10(1) to 10(8) CFU/ml for Shigella. When the established multiplex real-time PCR system was applied to artificially contaminated ground beef, the detection limit was 10(5) CFU/g for E. coli O157:H7, 10(3) CFU/g for Salmonella, and 10(4) CFU/g for Shigella. Immunomagnetic separation (IMS) was further used to separate E. coli O157:H7 and Salmonella from the beef samples. With the additional use of IMS, the detection limit was 10(3) CFU/g for both pathogens. Results from this study showed that TaqMan real-time PCR, combined with IMS, is potentially an effective method for the rapid and reliable quantitation of E. coli 0157:H7, Salmonella, and Shigella in food.