Messenger RNA-based RT-PCR detection of viable Salmonella

Relative accuracy, specificity and sensitivity of a 5' nuclease real-time PCR assay for Salmonella detection in naturally contaminated pork cuts

In the present study the relative sensitivity, specificity and accuracy of a Real-Time PCR assay for Salmonella detection in naturally contaminated pork cuts were evaluated in comparison with the ISO 6579:2004 reference culture method. Meat samples were collected from packaging up to the end of shelf life from 10 different lots over a year. The PCR method included an 18 h pre-enrichment step in buffered peptone water, a DNA extraction step, and a final 5' nuclease Real-Time PCR assay, including an Internal Amplification Control (IAC) and targeting the ttrRSBCA locus. Based on the analysis of 480 sub-units (three sub-units for each sample), the relative sensitivity, specificity and accuracy of the Real-Time PCR assay were 90, 78.7, and 82.9% respectively, corresponding to a Cohen's kappa value of 0.81 (very good agreement). These results suggest the PCR method as a rapid and accurate method for the quick check of meat lots before distribution. The ISO reference method might be applied only on positive Real-Time PCR samples for confirmatory and isolation purposes, mandatory in epidemiological investigations.

Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains

Background

The central role of Type III secretion systems (T3SS) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. Some Pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second T3SS (T3SS-2) in addition to the well characterized Hrc1 T3SS which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. The aim of this study is to perform an in silico analysis of T3SS-2, and to compare it with other known T3SSs.

Results

Based on phylogenetic analysis and gene organization comparisons, the T3SS-2 cluster of the P. syringae pv. phaseolicola strain is grouped with a second T3SS found in the pNGR234b plasmid of Rhizobium sp. These additional T3SS gene clusters define a subgroup within the Rhizobium T3SS family. Although, T3SS-2 is not distributed as widely as the Hrc1 T3SS in P. syringae strains, it was found to be constitutively expressed in P. syringae pv phaseolicola through RT-PCR experiments.

Conclusions

The relatedness of the P. syringae T3SS-2 to a second T3SS from the pNGR234b plasmid of Rhizobium sp., member of subgroup II of the rhizobial T3SS family, indicates common ancestry and/or possible horizontal transfer events between these species. Functional analysis and genome sequencing of more rhizobia and P. syringae pathovars may shed light into why these bacteria maintain a second T3SS gene cluster in their genome.

Reverse transcriptase real-time PCR for detection and quantification of viable Campylobacter jejuni directly from poultry faecal samples

Campylobacter spp. is the most common cause of bacterial diarrhoea in humans worldwide. Therefore, rapid and reliable methods for detection and quantification of this pathogen are required. In this study, we have developed a reverse transcription quantitative real-time PCR (RT-qPCR) for detection and quantification of viable Campylobacter jejuni directly from chicken faecal samples. The results of this method and a DNA-based quantitative real-time PCR (qPCR) method were compared with those of a bacterial culture method. Using bacterial culture and RT-qPCR methods, viable C. jejuni cells could be detected for up to 5 days in both the C. jejuni spiked and the naturally contaminated faecal samples. We found that no RT-qPCR signals were obtained when viable C. jejuni cells could not be counted by the culture method. In contrast, using a DNA-based qPCR method, dead or non-viable Campylobacter cells were detected, and all tested samples were positive, even after 20 days of storage. The developed method for detection and quantification of viable C. jejuni cells directly from chicken faecal samples can be used for further research on the survival of Campylobacter in the environment.

Growth and virulence properties of biofilm-forming Salmonella enterica serovar typhimurium under different acidic conditions

This study was designed to characterize the viability and potential virulence of bofilm-forming Salmonella enterica serovar Typhimurium under different pH levels, ranging from 5 to 7. The plate count method and real-time reverse transcription-PCR (RT-PCR) were used to evaluate the survival of S. Typhimurium grown in Trypticase soy broth (TSB) adjusted to pH 5, 6, and 7 (TSB-5, TSB-6, and TSB-7, respectively) at 37°C for 10 days. In TSB-5 and TSB-6, the numbers of viable cells estimated by using the real-time RT-PCR were greater than the culturable counts enumerated by the plate count method. Reflectance micro-Fourier transform infrared (micro-FTIR) spectroscopy was used to evaluate the biochemical changes in biofilm cells. Considerable changes in chemical components were observed in the biofilm cells grown in TSB-5 and TSB-6 when compared to the cells grown in TSB-7. The enterotoxin production and invasive ability of planktonic and biofilm S. Typhimurium cells were inferred by the relative levels of expression of stn and invA. The levels of expression of stn and invA were significantly increased in biofilm S. Typhimurium cells grown in TSB-5 (1.9-fold and 3.2-fold) and TSB-6 (2.1-fold and 22.3-fold) after 10 days of incubation. These results suggest that the biofilm-forming S. Typhimurium under different pH levels might change the virulence production and stress response mechanisms.

Development of a real-time NASBA assay for the detection of Campylobacter jejuni cells

The objectives of this study were the development of a real-time NASBA assay for the detection of Campylobacter jejuni mRNA and the evaluation of its potential to determine the viability of the detected C. jejuni cells. A set of specific primers and probes was chosen to amplify the mRNA of the tuf-gene and the GTPase-gene. Only the tuf-assay was able to detect as low as 10(2) cells per NASBA reaction and was specific for Campylobacter. However, as the assay was able to detect dead cells, it cannot be used to demonstrate the viability of C. jejuni cells. The tuf-gene mRNA is no good viability indicator due to its stability.