Comparison of primers for the detection of Salmonella enterica serovars using real-time PCR

Cecal microbiome profile of Hawaiian feral chickens and pasture-raised broiler (commercial) chickens determined using 16S rRNA amplicon sequencing

This study investigated the taxonomic profile and abundance distribution of the bacterial community in the ceca of feral and pasture-raised broiler (commercial) chickens. Cecal content from feral and commercial chickens (n = 7 each) was collected, and total DNA was isolated. Next-Generation Sequencing (Illumina MiSeq) was performed to characterize the cecal microbiota. Specific bacteria explored were: Bacteroides, Bifidobacterium, Lactobacillus, Enterococcus, Escherichia, and Clostridium. At the phylum level, 92% of the bacteria belonged to Firmicutes, Bacteroidetes, and Proteobacteria for both feral and commercial chickens. The proportional abundance of Firmicutes was 55.3% and 63.3%, Bacteroidetes was 32.5% and 24.4%, and Proteobacteria was 7.0% and 5.9% in the feral and commercial chickens, respectively. The alpha-diversity Shannon index (P = 0.017) and Simpson index (P = 0.038) were significantly higher for commercial than for feral chickens. Predictive functional profiling by PICRUSt showed enriched microbial metabolic pathways for L-proline biosynthesis in the feral group (P < 0.01). There were a greater percentage of specific bacteria in the feral than commercial chickens, albeit with lower diversity but a more functional microbiota. In conclusion, feral birds have distinguished microbial communities, and further microbiome analysis is mandated to know the specific functional role of individual microbiota. The difference in microbiota level between feral and commercial birds could be accounted to the scavenging nature, diverse feed ingredients, and distinct rearing localities.

Multiplex Detection of Salmonella spp., E. coli O157 and L. monocytogenes by qPCR Melt Curve Analysis in Spiked Infant Formula

Food poisoning continue to be a threat in the food industry showing a need to improve the detection of the pathogen responsible for the hospitalization cases and death. DNA-based techniques represent a real advantage and allow the detection of several targets at the same time, reducing cost and time of analysis. The development of new methodology using SYBR Green qPCR for the detection of L. monocytogenes, Salmonella spp. and E. coli O157 simultaneously was developed and a non-competitive internal amplification control (NC-IAC) was implemented to detect reaction inhibition. The formulation and supplementation of the enrichment medium was also optimized to allow the growth of all pathogens. The limit of detection (LoD) 95% obtained was <1 CFU/25 g for E. coli O157, and 2 CFU/25 g for Salmonella spp. and L. monocytogenes and regarding the multiplex detection a LoD 95% of 1.7 CFU/25 g was observed. The specificity, relative sensitivity and accuracy of full methodology were 100% and the use of the NC-IAC allowed the reliability of the results without interfering with the sensitivity of the methodology. The described study proved to obtain results comparable to those of probe-based qPCR, and more economically than classical high resolution melting qPCR, being both important aspects for its implementation in the food industry.

Recent advances in the development of nucleic acid diagnostics

Since the early 1970s, the use of nucleic acid sequences for specific diagnostic applications has followed a somewhat linear pattern of development. Early methods for restriction enzyme digestion, as well as reverse transcription, were followed in the late 1970s by Southern, northern and dot blotting, as well as DNA sequencing. In 1985, the description of PCR and the routine laboratory manipulation of sufficient quantities of DNA for diagnostics, resulted in the exponential growth of molecular biology. Subsequently, alternative DNA and RNA amplification protocols followed. The last 10 years have seen the second explosion in molecular biology with the development of real-time quantitative PCR and oligonucleotide microarrays. This advancement continues with the development of methods for 'direct' nucleic acid target detection from samples without in vitro amplification, and enhanced transduction elements for improved sensitivity of nucleic acid detection. In this article, we will describe the current state of the art in nucleic acid diagnostics, the use of nucleic acid-based diagnostics in clinical practice and the emerging technologies in the field. Finally, we will describe future trends and expected advances in the field.

Effect of enrichment medium on real-time detection of Salmonella enterica from lettuce and tomato enrichment cultures

Three enrichment broths commonly used for detection of Salmonella (buffered peptone water [BPW], tryptic soy broth [TSB], and universal preenrichment broth [UPB]) were compared for use in real-time SYBR Green PCR detection of Salmonella introduced into enrichment cultures made from store-bought lettuce and tomatoes. The produce served as a source of normal plant microbiota to measure how well DNA-based detection methods for Salmonella work in a suspension of plant-associated bacteria that may be closely related to Salmonella. A qualitative assessment of the background microbiota that grew in the three enrichment broths cultures from tomato and lettuce samples revealed that different bacteria predominated in the different broths. Results obtained with five produce-related outbreak Salmonella strains and PCR primers directed toward three different Salmonella genes suggest that the ability to detect Salmonella from these enrichment cultures by real-time PCR was 10 to 1,000 times better with TSB enrichment cultures. Detection levels were similar between the different enrichment media when an immunomagnetic separation method was used; however, the immunological technique did not enhance detection from TSB enrichment cultures. Detection could be affected by the medium and by the background microbiota. An immunomagnetic separation method may be useful in BPW and UPB enrichment cultures but not in TSB enrichment cultures.

Molecular beacon-based real-time PCR detection of primary isolates of Salmonella Typhimurium and Salmonella Enteritidis in environmental and clinical samples

Background

A fast and simple two-step multiplex real-time PCR assay has been developed to replace the traditional, laborious Salmonella serotyping procedure. Molecular beacons were incorporated into the assay as probes for target DNA. Target sequences were regions of the invA, prot6E and fliC genes specific for Salmonella spp. Salmonella Enteritidis and Salmonella Typhimurium, respectively, the two most clinically relevant serotypes. An internal amplification positive control was included in the experiment to ensure the optimal functioning of the PCR and detect possible PCR inhibition. Three sets of primers were used for the amplification of the target sequences. The results were compared to those of the Kauffmann-White antigenic classification scheme.

Results

The assay was 100% sensitive and specific, correctly identifying all 44 Salmonella strains, all 21 samples of S. Enteritidis and all 17 samples of S. Typhimurium tested in this work. Therefore, the entire experiment had specificity and sensitivity of 100%. The detection limit was down to 10 copies of DNA target per 25 μl reaction.

Conclusion

The assay can amplify and analyse a large number of samples in approximately 8 hours, compared to the 4 to 5 days conventional identification takes, and is thus considered a very promising method for detecting the two major serotypes of Salmonella quickly and accurately from clinical and environmental samples.

Rapid quantification of Salmonella typhimurium inoculated to meat products by real-time PCR

The objective of this study was to use a 5'-nuclease (TaqMan) real-time PCR method with primers and probe specific to the spaQ gene as a rapid approach to quantitatively determine Salmonella Typhimurium. The result showed that the correlation coefficient between real-time PCR estimates and bovine serum albumin (BSA) plate counts of S. Typhimurium was 0.99, independently of 10(5)-fold numbers of bystander Escherichia coli O157:H7 or total viable counts. The sensitivity of the real-time quantitative PCR assay was 10 CFU/mL for pure S. Typhimurium culture without enrichment. A known number of S. Typhimurium target cells were inoculated to dumpling fillings and chicken nuggets and DNA was extracted for real-time PCR analysis. The sensitivity was 60 CFU/g for S. Typhimurium inoculated to the food samples without any preceding procedure of enrichment. The duration of the entire experiment from DNA isolation and purification to PCR amplification was less than 12 h. This study demonstrated that real-time PCR is a rapid and reliable technique for quantifying S. Typhimurium possessing the spaQ gene in pure culture and in meat products.

Detection of salmonella by flow-through immunocapture real-time PCR in selected foods within 8 hours

This study investigated flow-through immunocapture (FTI), using the Pathatrix device, followed by plating on xylose lysine desoxycholate (XLD) agar (FTI-XLD) or analysis by real-time PCR (FTI-PCR) for the detection of Salmonella on smooth tomato surfaces and in potato salad and ground beef within 8 h. Food samples were inoculated with an appropriate dilution of a five-serovar Salmonella cocktail and enriched for 5 h. Following enrichment, samples were analyzed by the FTI-XLD and FTI-PCR methods. Food samples were also analyzed by a modified U.S. Food and Drug Administration Bacteriological Analytical Manual (BAM) Salmonella culture method for comparison. Salmonella inoculated at 10(0) CFU per tomato or 10(0) CFU/25 g was detected by the FTI-XLD method in 6, 8, and 4 of 10 samples for tomatoes, potato salad, and ground beef, respectively. Salmonella inoculated at 10(0) CFU per tomato or 10(0) CFU/25 g was detected by the FTI-PCR method in 8, 9, and 9 of 10 samples for tomatoes, potato salad, and ground beef, respectively. The FTI-PCR method achieved significantly higher (P < 0.05) detection of Salmonella on tomatoes, whereas the FTI-XLD method achieved significantly lower (P < 0.05) detection of Salmonella in ground beef when compared with the modified BAM Salmonella culture method; however, all other comparisons to the modified BAM method were not significantly different. The FTI-XLD method demonstrated the ability to isolate presumptive Salmonella colonies up to 48 hfaster than did the modified BAM Salmonella culture method.

Preliminary evaluation of flow-through immunocapture followed by real-time PCR for the detection of Salmonella serovars on tomato surfaces within 8 hours

This study reports a preliminary evaluation of flow-through immunocapture (FTI) followed by real-time PCR (FTI-PCR) for the detection of Salmonella serovars on tomato surfaces within 8 h. The FTI-PCR method was compared with real-time PCR, direct plating of FTI beads on xylose lysine desoxycholate (XLD), and the conventional culture method for Salmonella found in the U.S. Food and Drug Administration's (FDA) Bacteriological Analytical Manual (BAM). Unwaxed green tomatoes were spot inoculated with a five-serovar Salmonella cocktail on smooth surfaces at levels of 10(0) to 10(4) CFU per tomato and washed in lactose broth (LB) using a shake-rub method. The resulting LB rinse was incubated at 37 degrees C for 4 h prior to analysis by FTI-XLD, real-time PCR, or FTI-PCR and for 24 h as the first step in the BAM Salmonella culture method. For FTI-XLD, the observed lowest detection level (LDL) was 4.6 x 10(1) CFU per tomato. There was no significant difference in performance between the FTI-XLD method and the BAM Salmonella culture method (P > 0.05); however, the FTI-XLD method reduced the overall assay time by 48 h. For real-time PCR and FTI-PCR, the observed LDLs were 4.6 x 10(1) and 9.2 x 10(0) CFU per tomato, respectively. The FTI-PCR method was superior to the BAM Salmonella culture method (P < 0.05) for the detection of Salmonella serovars on tomato surfaces and was completed within 8 h.

Comparison of primers for the detection of pathogenic Escherichia coli using real-time PCR

AIMS

To evaluate PCR primers for the detection of pathogenic Escherichia coli in a real-time PCR assay and determine their utility in produce irrigation water testing.

METHODS AND RESULTS

Three previously published PCR primer sets and one set designed for this study were tested for their ability to produce amplification products for several pathogenic E. coli serotypes from whole cells as template. Two of the previously published primer sets were chosen for real-time PCR detection limit determination. The coneaeA and PEH detection limit of E. coli O157:H7 was 10(0) and 10(1) CFU rxn(-1) in sterile water respectively. To detect E. coli O157:H7 in sprout irrigation water, the water required dilution due to PCR inhibitors. The detection limit of the coneaeA and PEH was 10(1) and between 10(2) and 10(3) CFU rxn(-1) in diluted sprout irrigation water respectively.

CONCLUSIONS

The primer set coneaeA was able to produce an amplification product from each E. coli serotype, except O128:H7 and most sensitive for real-time PCR detection of pathogenic E. coli in diluted sprout irrigation water.

SIGNIFICANCE AND IMPACT OF THE STUDY

The necessity of a dissociation analysis to distinguish positive samples from those with fluorescence of random dsDNA generation for real-time PCR in a complex background was established.