Enrica Omiccioli

A new platform for Real-Time PCR detection of Salmonella spp., Listeria monocytogenes and Escherichia coli O157 in milk

Intoxications and infections caused by food-borne pathogens represent an increasing public health problem, and diagnostic tests in multiplex format are needed for the rapid identification of food contaminations caused by more than one microbial species. We have developed a multiple PCR-based platform for the simultaneous detection of the widespread milk-associated pathogens Salmonella spp., Listeria monocytogenes and Escherichia coli O157. The assay combines an enrichment step in a medium properly formulated for the simultaneous growth of target pathogens, a DNA isolation method, and a multiplex Real-Time PCR detection system based either on dual-labelled probes (mRT-PCR), or on melting curve analysis (mHRM). The second, producing a distinct peak for each amplification product, allows the qualitative assessment of pathogen presence. Moreover, the internal amplification control (IAC) included in the reaction, ensuring the reliability of results, complies with quality management programmes. Inclusivity and exclusivity were 100% each, with a detection limit of 1 CFU for each pathogen in a total of five 25 ml-aliquots of raw milk, and a duration of two working days. The assay represents an alternative approach for the qualitative detection of the cited bacterial species, suitable for a relatively inexpensive screening of several milk samples, reducing the turnaround time and the workload.

Development of a magnetic capture hybridization-PCR assay for Listeria monocytogenes direct detection in milk samples.

Aims:  A rapid and sensitive method for Listeria monocytogenes direct detection from milk was developed. It is based on a magnetic capture hybridization procedure for selective DNA purification, followed by PCR identification. A comparison with two similar commercial systems from Dynal (Dynabeads) was carried out.

A multiplex magnetic capture hybridisation and multiplex Real-Time PCR protocol for pathogen detection in seafood

Seafood could become a source of bacterial pathogens by exposure to contaminated water or through processing practices, thus representing a public health hazard. Conventional culture-based analytical methods take several days to be completed, while the molecular rapid identification of bacterial pathogens is crucial for effective disease control. The developed application consist of a multiplex magnetic capture hybridisation (mMCH) assay for the simultaneous isolation of Salmonella spp. and Listeria monocytogenes DNA from seafood, using paramagnetic amino-modified nanoparticles with capture oligonucleotides, and a triplex Real-Time PCR with an Internal Amplification Control (IAC), in accordance with ISO 22174. The detection probability was 100% with 10 genome equivalents of each target species co-amplified in the same reaction. The complete molecular procedure was tested on raw and smoked salmon fillets artificially contaminated with known amounts of one or both target bacteria (1-10(3)cfu/g), directly or after culture enrichment, and compared for equivalence with the standard methods. Results revealed a complete agreement between the two approaches, with a sensitivity of 1 cfu/g, in enriched samples, and higher sensitivity (10(2)-10(3)cfu/g) of the molecular method in samples examined before culture enrichment. The proposed procedure was also able to identify a natural contamination by L. monocytogenes in smoked salmon with a considerable shortening of time.

Microbiological Surveillance of a Bovine Raw Milk Farm Through Multiplex Real-Time PCR

Raw milk is increasingly appreciated by consumers but can be contaminated by a variety of zoonotic pathogens. Therefore, preventive measures, such as on-farm hazard analysis critical control point (HACCP) programs, must be applied to protect consumers. The aim of the present study was the comparison of a multiplex real-time polymerase chain reaction (PCR) assay with a culture-based approach in an on-farm quality assurance program for the detection of Escherichia coli O157, Salmonella spp., and Listeria monocytogenes in bulk tank milk, in-line milk filters, manure, and feces. Results revealed that the real-time PCR was more sensitive in detecting E. coli O157 than the culture method in filters (48% vs. 4% positive), manure (93% vs. 7% positive) and feces (60% vs. 4% positive). The two methods were equally efficient in detecting L. monocytogenes (8% of filters), while Salmonella spp. was not detected in any sample. In conclusion, the real-time PCR, by reducing analysis time to two working days, can be proposed as a useful tool in the raw milk primary production setting as a rapid and user-friendly screening method.

Validation according to ISO/TS 12869:2012 of a molecular method for the isolation and quantification of Legionella spp. in water

The aim of the present work was to validate the performances of a new molecular method comprehensive of water sample filtration, DNA extraction and Real-Time PCR for the quantification of Legionella spp. in clear water samples, in accordance with the recent ISO Technical Specification 12869:2012. All criteria and requirements were verified considering inclusivity and exclusivity, check of the calibration function, limit of detection and limit of quantification, recovery calculation, robustness and uncertainty of the entire method. The performances were validated as all parameters resulted to be in compliance with values detailed by the above mentioned standard. The described method proved to be specific, sensitive, accurate and it has been fully validated according to ISO/TS 12869:2012. The possibility of using a validated molecular method will improve the reliability of the results making it a promising tool that should be used in addition to cultural analysis. Moreover, these findings make it particularly suitable for a relatively inexpensive screening of water samples, reducing the turnaround time and the workload.

Validation and application of a quantitative real-time PCR assay to detect common wheat adulteration of durum wheat for pasta production

Pasta is the Italian product par excellence and it is now popular worldwide. Pasta of a superior quality is made with pure durum wheat. In Italy, addition of Triticum aestivum (common wheat) during manufacturing is not allowed and, without adequate labeling, its presence is considered an adulteration. PCR-related techniques can be employed for the detection of common wheat contaminations. In this work, we demonstrated that a previously published method for the detection of T. aestivum, based on the gliadin gene, is inadequate. Moreover, a new molecular method, based on DNA extraction from semolina and real-time PCR determination of T. aestivum in Triticum spp., was validated. This multiplex real-time PCR, based on the dual-labeled probe strategy, guarantees target detection specificity and sensitivity in a short period of time. Moreover, the molecular analysis of common wheat contamination in commercial wheat and flours is described for the first time.

Detection of Shiga toxin-producing Escherichia coli (STEC) in ground beef and bean sprouts: Evaluation of culture enrichment conditions

The main purpose of this work was to evaluate culture enrichment conditions, with particular regard to those reported in ISO/TS 13136:2012, for STEC detection in food. The culture media evaluated included mTSB with novobiocin 0-16mg/l (mTSB+N0-16) or acriflavin 12mg/l (mTSB+A12); BPW; mBPWp with acriflavin 10mg/l, cefsulodin 10mg/l, vancomycin 8mg/l (mBPWp+ACV); and mBPWp with cefsulodin 10mg/l, vancomycin 8mg/l (mBPWp+CV). They were used for the growth of STEC O157, O26, O103, O111, O145 and O104 in pure cultures or in artificially contaminated food matrices (ground beef, mung bean sprouts). STEC detection was accomplished using commercially available multiplex real-time PCR assays targeting stx1-stx2 and eae, and serogroup-associated genes. More rapid multiplication of STEC in pure cultures occurred in mBPWp+CV, while an inhibitory effect of novobiocin and acriflavin was observed for some STEC serogroups in media with these selective agents. mBPWp+CV allowed the detection of all serogroups in bean sprouts when inoculated at levels as low as 1CFU/25g. A reduced novobiocin concentration of 2mg/l in mTSB was required for STEC detection in ground beef samples. A temperature of 42°C for the entire duration of the enrichment or 44°C after an initial phase of 6h at 37°C was important to limit the multiplication of non-target bacteria. Results of this study suggest that media and protocols should be adapted to the food being analyzed, since protocols provided in official reference methods may produce insufficient sensitivity.

Comparative analysis of the standard PCR-Based Replicon Typing (PBRT) with the commercial PBRT-KIT

Plasmids are the main vectors of resistance and virulence genes in Enterobacteriaceae and plasmid typing is essential for the analysis of evolution, epidemiology and spread of antibacterial resistance. The PCR-Based Replicon Typing (PBRT), developed by Carattoli et al. in 2005, was an efficient method for plasmid identification and typing in Enterobacteriaceae. The 2005 PBRT scheme detected 18 replicons in 8 PCR reactions. Recently, the identification of novel replicons and plasmid types requested an update of the PBRT scheme. A commercial PBRT-KIT was devised for the identification of 28 different replicons in 8 multiplex PCRs. Here we report sensitivity and specificity of the PBRT-KIT carried out in comparison with the 2005 PBRT. The analysis of plasmid content was performed on forty-two enterobacterial strains from different sources, containing different replicon content. The 2005 PBRT identified replicons in 76.2% of the strains. The PBRT-KIT detected replicons in 100% of the analyzed strains, demonstrating increasing sensitivity and specificity of the commercial test with respect to the former 2005 PBRT scheme.