Assessment of food safety using a new real-time PCR assay for detection and quantification of virulence factors of enterococci in food samples.

AIMS: Development of Taqman MGB real-time PCR (q-PCR) assays for the quantitative detection of virulence factor genes in pure culture and food samples with regard to food safety assessment. METHODS AND RESULTS: New Taqman primers and probes were designed for the ace, esp and gelE genes based on the determinants of virulence profiles of enterococcal strains from GenBank. The high specificity and accuracy of the Taqman probe assay was confirmed. The limit of detection for the different virulence genes was 102  CFU ml-1 or CFU g-1 for pure culture and meat samples, and 103  CFU g-1 for cheese samples. CONCLUSION: This method provides the specific and rapid detection and quantification of ace, esp and gelE genes compared to conventional PCR assays, thus allowing the rapid and direct safety assessment of Enterococcus genus in food samples. SIGNIFICANCE AND IMPACT OF THE STUDY: This study presents efficient methods that can be used directly on food products for the rapid quantification and tracing of virulence genes, regarding food safety assessment. Moreover, this is the first study to quantify these virulence factors using a specific Taqman q-PCR assay in food samples.

Detection and quantification of spoilage and pathogenic Bacillus cereus, Bacillus subtilis and Bacillus licheniformis by real-time PCR.

A new primer-probe set for the detection and quantification of Bacillus cereus, Bacillus licheniformis and Bacillus subtilis by real-time PCR (Rti-PCR) was developed. For it, forty-eight strains belonging to these species were considered. The DNA of these strains was isolated and a fragment of the 16S rRNA gene amplified. The amplicons were sequenced and the obtained sequences were aligned with reference sequences from the GenBank. For the development of the Real-Time PCR (RTi-PCR) methodology based on TaqMan probes, a primer pair and probe, specific for the studied Bacillus spp., were designed. To establish the quantification method, two RTi-PCR standard curves were constructed; one with DNA extracted from a serially-diluted B. cereus culture and a second curve with DNA extracted from a sterilised food product inoculated with serial dilutions of B. cereus. The curves exhibited R(2) values of 0.9969 and 0.9958 respectively. Linear correlations between the log(10) input DNA concentration and the threshold cycle (Ct) values were observed with a magnitude of linearity in the range of 1.65 × 10(1) CFU/mL to 1.65 × 10(6) CFU/mL for both standard curves. The specificity of the designed primers and probe was tested with DNA extracted from B. cereus, B. licheniformis and B. subtilis strains, which gave Ct values between 14 and 15, whereas non-specific amplifications of the DNA from other microbial species of food interest exhibited a Ct value above 28.5. To our knowledge, this method represents the first study about the quantification of spoilage and/or pathogenic B. cereus, B. licheniformis and B. subtilis in food products, with the aim to prevent the presence of these undesirable species in the food chain.

Real-time polymerase chain reaction for the quantitative detection of tetA and tetB bacterial tetracycline resistance genes in food.

A new, rapid, sensitive and specific method was developed to directly detect and quantify tetA and tetB in food. Both tet genes are two of the most frequently present tetracycline resistance genes in gram-negative bacteria. A set of primers and Taqman probes was designed for each gene. The standard curves were performed using Escherichia coli BM13 (C600 RifR)/RP4 and E. coli NCTC 50365, which carry tetA and tetB, respectively. Meat and fish samples inoculated with these reference strains were used as a matrix to construct the standard curves for the analysis of 20 samples of chicken meat and 10 samples of hake (Merlucius merlucius). The limits of detection in pure culture were 5 cfu/mL (0.7 log cfu/mL) in the case of tetA, 50 cfu/mL (1.7log cfu/mL) for tetB and 5×10(2)cfu/g (2.7 log cfu/g) for both genes in food samples. The results obtained by real-time quantitative polymerase chain reaction (qPCR) were compared to counts of tetracycline-resistant bacteria obtained by plating extracts of poultry and hake samples in culture media supplemented with 16 mg/L of tetracycline. Counts of tetracycline-resistant bacteria obtained by qPCR showed a positive correlation, especially interesting when compared with microbiological counts of tetracycline-resistant Enterobacteriaceae in poultry meat (r=0.5509) and with tetracycline-resistant mesophilic aerobic bacteria in hake samples (r=0.7146). The obtained results demonstrate that this method could be a useful tool for the direct quantification of the amount of bacterial strains that carry tetA and/or tetB genes in food samples.

Prevalence and antimicrobial resistance patterns of Salmonella from different raw foods in Mexico.

The presence of Salmonella was determined in 116 samples of poultry meat, 81 samples of pork, 73 samples of beef, 33 samples of cheese, 61 samples of fish, and 78 samples of vegetables collected from retail stores and supermarkets in Hidalgo State (Mexico). Ninety-three Salmonella strains isolated from raw foods were characterized, and MICs were determined for 10 antimicrobials. Salmonella was detected in 35.3% of poultry meat, 30.3% of cheese, 21.8% of vegetable, 17.3% of pork, and 15.1% of beef samples, but no Salmonella was detected in fish samples. Significantly higher counts were obtained in chicken meat (P = 0.0001), pork (P = 0.0116), cheese (P = 0.0228), and vegetables (P = 0.0072) obtained from retail stores compared with those samples obtained from supermarkets. Salmonella isolates had high levels of resistance to ampicillin (66.7% of isolates), tetracycline (61.3%), and chloramphenicol (64.5%) and low levels of resistance to cefotaxime (0%), gentamicin (3.2%), and kanamycin (4.3%). Higher levels of quinolone resistance were found in isolates from poultry meat and vegetables compared with that in other foods tested. High levels of multiresistant strains were found in all foods tested except fish, ranging from 100% of pork samples to 47.1% of vegetable samples. The present study revealed that Salmonella prevalence was higher in foods from retail stores than in foods from supermarkets. Resistance rates observed for Salmonella were largely comparable to those reported in other countries for most antimicrobials, although resistance to chloramphenicol tended to be higher.

Antimicrobial resistance in Enterococcus spp. strains isolated from organic chicken, conventional chicken, and turkey meat: a comparative survey.

The mean counts of Enterococcus spp. were determined for 30 samples each of organic chicken meat, conventional chicken meat, and turkey meat, and differences for Enterococcus contamination in meat were determined. Two enterococci strains from each sample were isolated to obtain a total of 180 strains, and resistance to ampicillin, chloramphenicol, doxycycline, ciprofloxacin, erythromycin, gentamicin, nitrofurantoin, and vancomycin was determined by a disk diffusion method. Average counts obtained showed that Enterococcus mean counts from organic chicken meat (3.18 log CFU/g) were significantly higher than those obtained from conventional chicken meat (2.06 log CFU/g) or conventional turkey meat (1.23 log CFU/g). However, the resistance data obtained showed that isolates from organic chicken meat were less resistant than enterococci isolates from conventional chicken meat to ampicillin (P = 0.0067), chloramphenicol (P = 0.0154), doxycycline (P = 0.0277), ciprofloxacin (P = 0.0024), erythromycin (P = 0.0028), and vancomycin (P = 0.0241). In addition, isolates from organic chicken were less resistant than conventional turkey meat isolates to ciprofloxacin (P = 0.001) and erythromycin (P = 0.0137). Multidrug-resistant isolates were found in every group tested, but rates of multidrug-resistant strains were significantly higher in conventional chicken and turkey than those obtained from organic chicken meat. Enterococcus faecalis was the most common species isolated from organic chicken (36.67%), whereas Enterococcus durans was the most common species isolated from conventional chicken (58.33%) and turkey (56.67%). The rates obtained for antimicrobial resistance suggest that although organic chicken meat may have higher numbers of Enterococcus, these bacteria present a lower level of antimicrobial resistance.