Development and validation of a rapid real-time PCR based method for the specific detection of Salmonella on fresh meat

In this study, a combined enrichment/real-time PCR method for the rapid detection of Salmonella on fresh meat carcasses, was designed, developed and validated in-house following requirements outlined in ISO 16140:2003. The method included an 18 h non-selective enrichment in buffered peptone water (BPW) and a 6 h selective enrichment in Rappaport Vasilliadis Soya (RVS) broth, based on the traditional culture method, ISO 6579:2002. The real-time PCR assay included an internal amplification control (IAC), was 100% specific and was sensitive to one cell equivalent. The alternative method was validated against the traditional culture method and relative accuracy of 94.9%, sensitivity of 94.7% and specificity of 100% were determined using 150 fresh meat carcass swabs. This alternative method had a detection limit of 1–10 CFU/100 cm² for fresh meat carcass swabs and was performed in 26 h. Following further inter-laboratory studies, this alternative method could be suitable for implementation in testing laboratories for the analysis of carcass swabs.     

Evaluation of the ISO 10273:2003 method for the isolation of human pathogenic Yersinia enterocolitica from pig carcasses and minced meat

Pig carcass swabs (n = 254) and minced meat samples (n = 82) were examined for pathogenic Yersinia enterocolitica using different routinely used enrichment protocols. All samples were obtained in the context of the official Yersinia monitoring program in Belgium. In total, 28 carcasses (11.0%) were contaminated with Y. enterocolitica bioserotype 4/O:3 and one (0.4%) with bioserotype 2/O:9. Four minced meat samples (4.9%) tested positive for Y. enterocolitica bioserotype 4/O:3. Using the ISO 10273:2003 method, eight out of the 29 Yersinia-positive carcasses (27.6%) and none of the contaminated minced meat samples (0.0%) were detected. Reducing the enrichment time in PSB from 5 to 2 days increased the number of positive samples. Overall, enrichment in PSB at 25 °C recovered more positive carcasses and minced meat samples than selective enrichment and cold enrichment. As the exclusive use of the ISO 10273:2003 method results in a strong underestimation of Y. enterocolitica positive carcasses and minced meats, efforts are needed to optimize the current version of the ISO method. In addition, isolation of pathogenic Y. enterocolitica requires experience and the use of a stereomicroscope to avoid false negative results.     

Development of multiplex real-time PCR with Internal amplification control for simultaneous detection of Salmonella and Cronobacter in powdered infant formula

Contamination of powdered infant formula (PIF) by the bacteria Cronobacter spp. and Salmonella enterica was deemed a matter of great concern by the World Health Organization and the Food and Agriculture Organization of the United Nations in 2004. Therefore, we developed a rapid and sensitive multiplex real-time PCR assay for the simultaneous detection of Cronobacter and Salmonella in PIF. In addition, an internal amplification control (IAC) was also included for exclusion of false negative results in this study. The quantitative detection range for pure cultures in this optimized multiplex real-time PCR assay was 10³ to 10⁸ CFU/ml for both Salmonella and Cronobacter. When our established multiplex real-time PCR system was applied to artificially contaminated PIF, the detection limit was 10³ CFU/ml for Salmonella and Cronobacter without enrichment. The commercial PIF was then inoculated with Salmonella and Cronobacter at 10, 1 and 0.1 CFU per gram of formula and the single enrichment broth samples were analyzed by multiplex real-time PCR after enrichment for 9, 12, and 24 h. At 12 h post-enrichment, we could detect Salmonella and Cronobacter at initial inoculation levels of approximately 0.1 CFU/g in PIF. Additionally, stable fluorescent IAC signals could be assessed between 29 and 34 cycles of PCR amplification. Results from this study showed that the multiplex real-time PCR assay is an effective method for the rapid and simultaneous detection and quantification of Cronobacter and Salmonella in PIF.     

Multiplex fiber optic biosensor for detection of Listeria monocytogenes, Escherichia coli O157:H7 and Salmonella enterica from ready-to-eat meat samples

Listeria monocytogenes, Escherichia coli O157:H7 and Salmonella enterica are the most common foodborne bacterial pathogens and are responsible for many outbreaks. Therefore, multiplex detection of these three using a single assay platform is highly desirable. The objective was to develop and optimize a fiber optic sensor for simultaneous detection of these three from food. The streptavidin coated optical waveguides were immobilized with biotinylated polyclonal antibodies and exposed to the bacterial suspensions or enriched food samples for 2 h. Pathogens were detected after reacting with Alexa-Fluor 647-labeled monoclonal antibodies. Ready-to-eat beef, chicken and turkey meats were inoculated with each pathogen (∼100 cfu/25 g), enriched in SEL (Salmonella, E. coli, Listeria), a multipathogen selective enrichment broth for 18 h and tested with the biosensor. The biosensor was able to detect each pathogen, individually or in a mixture with very little cross-reactivity. The limit of detection for the sensor was ∼10³ cfu/ml for all three pathogens. Furthermore, the biosensor successfully detected each pathogen, grown in a mixture from enriched meat samples under 24 h. The pathogen presence was further verified by PCR and immunofluorescence assay. The multiplex fiber optic sensor shows promise for detection of the three pathogens if present in the same sample eliminating the use of multiple single pathogen detection platforms.     

Effect of sample preparation and bacterial concentration on Salmonella enterica detection in poultry meat using culture methods and PCR assaying of preenrichment broths

We evaluated the sensitivity of a PCR assay in the detection of Salmonella enterica at the broth preenrichment step of poultry meat. A total of 162 retail poultry meat samples, which were prepared by manual massaging, stomacher or no homogenization were compared for Salmonella recovery. Using these homogenization methods, the PCR assay at the broth preenrichment step detected Salmonella in, respectively, 48.9%, 62.2% and 50.0% of meat and giblet samples detected as Salmonella-positive using the culture method. In ground chicken, however, Salmonella was detected in 21.7% of samples treated by stomacher homogenization, compared to 40.7% and 48% of untreated and hand-massaged samples, respectively. These results suggest that stomaching of ground chicken causes excessive effusion of food constituents, which affects PCR results. Using the most probable number (MPN) technique, Salmonella was detected at under 1.0 CFU/g in 12 ground chicken samples and under 10³ CFU/ml of broth in seven of the 12 broth-enriched samples, which considered the minimum concentration detectable by PCR assay. These results show that Salmonella detection using routine PCR assays is difficult in poultry meat, and in particular ground chicken, due to low amounts of Salmonella and the presence of inhibitors.     

Prevalence of Salmonella enterica in bulk tank milk from US dairies as determined by polymerase chain reaction

Samples of bulk tank milk from dairies across the United States, taken as part of the National Animal Health Monitoring System Dairy 2002 survey, were analyzed for the presence of Salmonella enterica using a commercially available real-time polymerase chain reaction (PCR) kit. Samples from 854 farms in 21 states were collected and enriched in tetrathionate broth to amplify any salmonellae present, and DNA was isolated from the resulting biomass. One hundred one samples (11.8%) were shown to contain Salmonella enterica using the real-time PCR assay, whereas conventional culture techniques detected the pathogen in only 22 (2.6%) of the samples. A conventional PCR assay targeting a different gene from Salmonella enterica confirmed the presence of the organism in 94 of the real-time PCR-positive samples. Thus, assay of milk samples by real-time PCR indicates that the prevalence of Salmonella enterica in US bulk tank milk is substantially higher than previously reported.     

Investigation of Salmonella enterica in Sardinian slaughter pigs: prevalence, serotype and genotype characterization

In order to improve the knowledge about the presence of Salmonella in pork meat in Sardinia (Italy), the prevalence and the sources of Salmonella at 5 pig slaughterhouses (slaughtered pigs and environment) were investigated and the isolates were characterised. A total of 462 samples were collected, 425 from pigs at slaughter and 41 from the slaughterhouse environment. Salmonella was isolated from 26/85 (30.5%) mesenteric lymph nodes, 14/85 (16.4%) colon contents, and from 12/85 (14.1%) carcasses and livers. Salmonella prevalence was 38% (8/21) in samples from surfaces not in contact with meat, and 35% (7/20) in those from surfaces in contact with meat. Thirty-one pigs were identified as carriers of Salmonella in lymph nodes and/or colon content, but of these, only 8 carcasses were positive. A total of 103 Salmonella isolates were serotyped and genotyped. Eight different serotypes were detected; the most common were S. Derby (44/103, 42.7%) and S. Typhimurium (24/103, 23.3%). The most prevalent S. Typhimurium phage type was DT193. Thirty-two isolates were found to be resistant to more than one antimicrobial (MDR). Pulse-field gel electrophoresis (PFGE) permitted the resolution of XbaI macrorestriction fragments of the Salmonella strains into 20 distinct pulsotypes. Combined application of a plasmid profiling assay (PPA) and PFGE gave useful additional information to assist in tracing the routes of Salmonella contamination in abattoirs. To reduce Salmonella prevalence some preventive measures should be encouraged: the origin of infected slaughter animals should be identified and direct and cross-contamination of carcasses should be avoided by adhering to HACCP principles in association with good hygiene procedures (GHP).     

Inhibition of polymerase chain reaction for the detection of Escherichia coli O157:H7 and Salmonella enterica on walnut kernels

The aim of this study was to determine whether Escherichia coli O157:H7 can be reliably detected and isolated from walnut kernels using standard methods of analysis. The limit of detection approached 1 cell per analytical unit (25 g) for E. coli O157:H7 on walnut kernels enriched in modified tryptic soy broth with 20 μg/ml novobiocin and plating onto selective agar media. The presence of PCR inhibitors in walnut kernels was indicated by the failure to detect E. coli O157:H7 from culture positive enrichment broths analysed by PCR, with two separate polymerase and reagent compositions (Dupont BAX E. coli O157:H7 MP system, Promega GoTaq Green for stx) and three methods of template preparation (DuPont BAX, Qiagen DNeasy, Bio-Rad InstaGene). PCR inhibition was overcome by 1:100 dilution in TE buffer of the DNeasy or InstaGene template. PCR inhibition was not relieved by dilution of the BAX template. Similar results were observed for walnut kernels inoculated with Salmonella enterica and analysed for invA, indicating that PCR inhibition is not specific to the organism or primer/template. These results indicate that analysis of walnut kernels for pathogens should be with culture based methods or use protocols for DNA template preparation modified to remove or dilute inhibitors and the need for internal amplification controls in PCR methods.     

Evaluation of ISO 10272:2006 standard versus alternative enrichment and plating combinations for enumeration and detection of Campylobacter in chicken meat

In the present study, we evaluate the recommended ISO 10272:2006 versus alternative procedures for Campylobacter enumeration and enrichment in naturally contaminated chicken meat samples (n = 49). Three enrichment media were evaluated; Bolton broth, Preston broth and CampyFood broth^® (bioMérieux SA, Marcy l’Etoile, France). In addition, three selective plating agars were compared; modified charcoal cefoperazone deoxycholate agar (mCCDA), CampyFood agar^® (CFA; bioMérieux SA) and Brilliance CampyCount agar^® (BCC; Oxoid, Basingstoke, England). Direct plating on CFA provided the highest number of Campylobacter positive samples (17/49); however this was not statistically different (P > 0.05) from numbers of positive samples recovered by direct plating on mCCDA (15/49) or BCC agars (14/49). Also, there was no significant difference between Campylobacter counts on the three compared media (P > 0.05). The coloured colonies of Campylobacter on CFA and BCC were easier to record and count than those on mCCDA. Enrichment of chicken meat samples in Bolton broth for 48 h and subsequent plating on CFA provided significantly higher (P < 0.05) Campylobacter detection compared to the other broth-agar combinations. Enrichment in Preston broth for 24 h followed by plating on mCCDA gave a higher number of positive samples (20/49) than 48 h enrichment in Bolton broth and plating on mCCDA (15/49). Enrichment in Bolton broth for 48 h followed by plating on CFA recovered 35% of samples below the limit for quantifications (<10 CFU/g, n = 34), as identified by direct plating on mCCDA. Compared to the current ISO method, some alternative combinations of enrichment and agar media could provide significantly better detection and enumeration of Campylobacter in chicken meat.     

Response of two Salmonella enterica strains inoculated in model cheese treated with high hydrostatic pressure

The aim of this work was to determine the response to high hydrostatic pressure and the ability for survival, recovery, and growth of 2 strains of Salmonella enterica (Salmonella enteritidis and Salmonella typhimurium) inoculated in a washed-curd model cheese produced with and without starter culture. Inoculated samples were treated at 300 and 400 MPa for 10 min at room temperature and analyzed after treatment and after 1, 7, and 15 d of storage at 12° C to study the behavior of the Salmonella population. Cheese samples produced with starter culture and treated at 300 and 400 MPa showed maximum lethality; no significant differences in the baroresistant behavior of both strains were detected. Nevertheless, when starter culture was not present, the maximum lethality was only observed in cheese samples treated at 400 MPa, in the case of S. enteritidis. Ability to repair and grow was not observed in model cheese produced with starter culture and cell counts of treated samples decreased after 15 d of storage at 12° C. In cheese produced without starter culture, Salmonella cells showed the ability to repair and grow during the storage period, reaching counts over 3 log₁₀ (cfu/mL) in both applied treatments and serotypes. These results suggest that high hydrostatic pressure treatments are effective to reduce Salmonella population in this type of cheese, but the presence of the starter culture affects the ability of this microorganism to repair and grow during the storage period.     

Effect of the growth environment on the strain variability of Salmonella enterica kinetic behavior

Intra-species variability of microbial growth kinetic behavior is an event with important implications for food safety research. Aiming at the evaluation of the growth variability among Salmonella enterica strains as affected by the growth environment, the kinetic behavior of 60 isolates of the pathogen was assessed at 37 °C in tryptone soy broth of different pH values (4.3-7.0) and NaCl concentrations (0.5-6.0%). Maximum specific growth rate (μ_max) values corresponding to each strain and growth condition were estimated by means of absorbance detection times of serially decimally diluted cultures using the automated turbidimetric system Bioscreen C. A total of 9600 optical density curves were generated for the strains and the growth conditions tested. The variability of μ_max among the S. enterica strains was important and greater than that observed within the strains (i.e. among replicates). Moreover, strain variability increased as the growth conditions became more stressful both in terms of pH and NaCl. The coefficient of variation of μ_max among the tested strains at pH 7.0-0.5% NaCl was 6.1%, while at pH 4.3-0.5% NaCl and pH 7.0-6.0% NaCl was 11.8% and 23.5%, respectively. Beyond the scientific interest in understanding strain variability, the findings of this study should be useful in strain selection for exploitation in food safety challenge studies as well as in incorporating strain variability in predictive microbiology and microbial risk assessment.     

Modeling the growth rate and lag time of different strains of Salmonella enterica and Listeria monocytogenes in ready-to-eat lettuce

The growth parameters (growth rate, μ and lag time, λ) of three different strains each of Salmonella enterica and Listeria monocytogenes in minimally processed lettuce (MPL) and their changes as a function of temperature were modeled. MPL were packed under modified atmosphere (5% O₂, 15% CO₂ and 80% N₂), stored at 7–30 °C and samples collected at different time intervals were enumerated for S. enterica and L. monocytogenes. Growth curves and equations describing the relationship between μ and λ as a function of temperature were constructed using the DMFit Excel add-in and through linear regression, respectively. The predicted growth parameters for the pathogens observed in this study were compared to ComBase, Pathogen modeling program (PMP) and data from the literature. High R² values (0.97 and 0.93) were observed for average growth curves of different strains of pathogens grown on MPL. Secondary models of μ and λ for both pathogens followed a linear trend with high R² values (>0.90). Root mean square error (RMSE) showed that the models obtained are accurate and suitable for modeling the growth of S. enterica and L. monocytogenes in MP lettuce. The current study provides growth models for these foodborne pathogens that can be used in microbial risk assessment.     

Evaluation of the strain variability of Salmonella enterica acid and heat resistance

The inherent acid and heat resistances of 60 Salmonella enterica strains were assessed in tryptone soy broth without dextrose acidified to pH 3.0 or heated at 57 °C. A total of 360 inactivation curves were generated. Regarding the acid challenge experiments, the inactivation rate (k_acid), estimated using the log–linear model, ranged from 0.47 to 3.25 h⁻¹. A log–linear model with a “survival tail” was used to describe the thermal inactivation of the strains, and the estimated inactivation rate (k_heat) ranged from 0.42 to 1.33 min⁻¹. The strain variability of k_acid was considerably higher than that of k_heat with the coefficient of variation of this kinetic parameter among the tested strains being 39.0% and 18.3%, respectively. No correlation was observed between the estimated k_acid and k_heat values of the 60 S. enterica strains. Furthermore, no trends among the tested strains related to origin, serotype or antibiotic resistance profile were evident. The present study is the first one to comparatively evaluate the inherent acid and heat resistance profiles of multiple S. enterica strains. Beyond their value in strain selection for use in food safety challenge studies, the collected data should be useful in describing and integrating the strain variability of S. enterica acid and heat resistance profiles in quantitative microbial risk assessment.     

Salmonella, Escherichia coli O157:H7 and E. coli biotype 1 in a pilot survey of imported and New Zealand pig meats

A pilot survey for the pathogens Salmonella and Escherichia coli O157:H7, and E. coli biotype 1 was conducted on 100 New Zealand-produced (domestic) pig carcasses and 110 imported pig meat samples over an 8-month period to assess the likelihood of introduction of novel pathogen strains into New Zealand (NZ), and as a guide for development of a domestic pork National Microbiological Database programme. Salmonella was not isolated from domestic pig carcasses or from pig meat imported from Canada and the USA. The prevalence of Salmonella in imported pig meat was 3.6% (95% CI 1.0–9.0) with positive samples detected from Australian pig meat. The prevalence of E. coli O157:H7 on domestic pig carcasses was 1% (95% CI 0.03–5.4) while the overall prevalence of E. coli O157:H7 in imported pig meat was 1.8% (95% CI 0.2–6.4), detected mainly from Australian but not from Canadian or US pork. All except three samples have an E. coli biotype 1 count of <100 CFU cm⁻² or g⁻¹, indicating good hygiene quality of domestic and imported pig meat. The results demonstrated that importation of uncooked pig meat is a potential route for the introduction of new clones of Salmonella and E. coli O157:H7 into New Zealand.     

Salmonella on feces,hides and carcasses in beef slaughter facilities in Venezuela

This study determined Salmonella prevalence at different stages during the slaughtering in three beef slaughter plants (A, B and C) located in the western region of Venezuela (Zulia and Lara states). Each facility was visited three times at monthly intervals, from the months October through December of 2006. Samples were collected from hides (n = 80), fecal grabs (n = 80) and carcasses (n = 80) at the phases of pre-evisceration, after-evisceration and pre-cooler at three sampling sites on the animals (rump, flank and brisket). Salmonella prevalence was higher on hides (36.3%) than on feces (13.8%) (P < 0.05). Differences among slaughter plants for overall Salmonella prevalence were observed (P = 0.001; A: 3.5%, B: 11.1%, C: 4.4%). From the isolated strains, Salmonella enterica subspecies enterica ser. Saintpaul, Salmonella ser. Javiana and Salmonella ser. Weltevreden were identified. Cattle feces and hides might be considered as important sources of Salmonella for carcass contamination at different slaughter stages. The presence of potentially pathogenic Salmonella serotypes at the slaughtering stages is an evidence of the circulation of this pathogen in the food environment; its presence could increase consumers' risks of infection if proper food handling and preparation techniques are not followed. These data should serve as a baseline for future comparisons in Salmonella prevalence on beef carcasses to be used by the government and industry in order to establish preventive measures and to better address the risks of Salmonella contamination.     

A filtration-based real-time PCR method for the quantitative detection of viable Salmonella enterica and Listeria monocytogenes in food samples

We developed a novel filtration-based method that can eliminate dead or severally damaged Salmonella enterica and Listeria monocytogenes in food samples. This new method can recover all viable bacteria in less than 30 min, and can be coupled with a subsequent bacterial DNA extraction and real-time PCR. No statically significant differences (p < 0.01) were found between real-time PCR results obtained separately from S. enterica and L. monocytogenes when different ratios of living and dead cells were used. The analytical sensitivity in both cases was 1 genome equivalent (GE), and the quantification was linear (R² > 0.9969) over a 5-log dynamic range with PCR efficiencies >0.9754. When compared with the standard microbiological methods for the detection of these foodborne pathogens, the relative accuracy was excellent ranging from 95.72% to 104.48%. Finally, we applied the pre-treatment method to the direct detection of viable forms of these foodborne pathogens in food samples using yogurt as a model, the results being similar to those obtained using pure cultures.     

The evaluation of a PCR-based method for identification of Salmonella enterica serotypes from environmental samples and various food matrices

The most commonly used method for serotyping Salmonella spp. is based on the Kaufmann–White scheme, and is composed of serological reactions using antibodies to LPS agglutinins. The multiplex PCR used in this investigation was established by Kim et al. to serotype the 30 most common clinical Salmonella serotypes, as determined by CDC. The PCR assay consists of two five-plex reactions and a single two-plex PCR reaction, based on six genetic loci from Salmonella enterica serotype Typhimurium and four loci from S. enterica serotype Typhi. In this investigation, we further evaluated the method for serotyping Salmonella spp. using a reference collection, environmental samples collected from a Mid-Atlantic region tomato farm study, four food matrices spiked with different Salmonella serotypes and a proficiency test. The PCR assay was first evaluated using DNA isolated from pure cultures of isolates obtained from various clinical and environmental samples, and then DNA isolated from broth cultures of food matrices of “Red round” and Roma tomatoes, Romaine lettuce, green onions and Serrano peppers spiked with serotypes Newport, Typhimurium, Javiana and Saintpaul, respectively. The results showed that the PCR assay correctly serotyped Salmonella spp. from the clinical, environmental, spiked food matrices, and proficiency test samples. These findings are significant because the PCR assay was successful in the identification of Salmonella in the spiked samples in a broth culture containing other non-salmonella organism. This method may be a useful resource for the food safety community.     

Verocytotoxigenic Escherichia coli O157 in beef and sheep abattoirs in Ireland and characterisation of isolates by Pulsed-Field Gel Electrophoresis and Multi-Locus Variable Number of Tandem Repeat Analysis

This study aimed to investigate verocytotoxigenic Escherichia coli O157 in the largest beef and sheep slaughter plants in Ireland over a one-year period. Samples consisted of pooled rectal swabs (n = 407) and pooled carcass swabs (n = 407) from 5 animals belonging to the same herd or flock and minced meat (n = 91) from the same sampling date. E. coli O157 isolates were characterised using PCR for a range of genes, i.e. 16S, rfbE, fliC, vtx1, vtx2, eaeA and confirmed VTEC O157 isolates were tested for antimicrobial susceptibility and typed using Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA). VTEC O157 was isolated from 7.6% and 3.9% of bovine rectal and carcass swab samples and from 5.8% and 2.9% of ovine rectal and carcass swab samples respectively. None of the bovine minced meat samples (n = 77) and only one of the 14 ovine minced meat samples was positive for VTEC O157. Following PFGE and MLVA, cross contamination from faeces to carcasses was identified. While PFGE and MLVA identified the same clusters for highly related strains, MLVA discriminated better than PFGE in addition to being more rapid and less labour intensive. Results showed that cattle and sheep presented for slaughter in Ireland harbour VTEC O157, and although the levels entering the food chain are low, this should not be overlooked as possible sources of zoonotic infection; molecular typing was able to demonstrate relationships among strains and could be used to elucidate the sources of human infection.     

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 (1–10³ 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 (10²–10³ 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.