Strategies to accelerate the applicability of gene amplification protocols for pathogen detection in meat and meat products

Evaluation of Effects of Primary and Secondary Enrichment for the Detection ofListeria monocytogenesby Real-Time PCR in Retail Ground Chicken Meat

A SYBR Green I based real-time PCR assay with inlA-specific oligonucleotide primers was developed for easy and rapid detection of Listeria monocytogenes in a model food that usually has a high incidence of contamination with this pathogen. Results with pure cultures and artificially contaminated chicken meat samples indicate that the PCR assay was highly specific and sensitive. The melting point analysis of the 160 bp amplified DNA fragment was different for L. monocytogenes isolates of the two major phylogenetic divisions of the species, 1 and 2. The assay was then used to survey retail ground chicken meat for contamination with L. monocytogenes. Thirty-seven samples were enriched according to the United States Department of Agriculture culture assays to detect L. monocytogenes on meat. The use and efficiency of PCR assay was examined following both primary and secondary enrichments, which were also plated on chromogenic agar for enumeration of L. monocytogenes and nonpathogenic Listeria spp. to investigate the discrepancies between culture and PCR. Overall, L. monocytogenes was detected in 75% of the samples. Primary enrichment yielded detection rates of 70% and 37% for culture and PCR, respectively. The corresponding rates for secondary enrichment were 54% and 70%, respectively. Test sensitivity is therefore influenced by the type of enrichment and is probably related not only to the limited growth of L. monocytogenes in the primary enrichment media (false-negative PCR results), but also to the high populations of nonpathogenic Listeria spp. in the secondary enrichment broths (false-negative culture results). The main challenge of rapid PCR-based detection of L. monocytogenes from food is the poor sensitivity of primary enrichment media. The improvement of enrichment conditions may help increase assay sensitivity.

Polymerase chain reaction detection of foodborne Salmonella spp. in animal feeds

Foodborne salmonellosis continues to be a public health issue of considerable concern. Animal feed has been a major link in pre-harvest food animal production. Although monitoring systems and control measures are available to limit Salmonella spp. contamination on animal feeds detection methodology is relatively time consuming in the context of time inputs for feed processing and mixing. Current cultural methods of Salmonella spp. detection in feeds require several days for confirmation. This amount of time represents significant problems if control measures are to be effectively implemented in a fashion that keeps feed processing costs low. Molecular methods offer improved sensitivity and potential reduction in assay time. In particular, several commercial polymerase chain reaction (PCR) assays, and combined PCR-hybridization assays have been suggested as possible means to implement more rapid detection of Salmonella spp. extracted from animal feeds. It has now become possible to rapidly detect and confirm the presence of foodborne Salmonella spp. in feed matrices by commercial amplification detection systems. The primary challenges remaining are to develop more reliable recovery and extraction procedures for routine processing of samples from a wide variety of feed matrices and apply molecular techniques for assessing physiological status of Salmonella spp. contaminants in animal feeds.

A real-time PCR assay for the detection of Campylobacter jejuni in foods after enrichment culture

A real-time PCR assay was developed for the quantitative detection of Campylobacter jejuni in foods after enrichment culture. The specificity of the assay for C. jejuni was demonstrated with a diverse range of Campylobacter species, related organisms, and unrelated genera. The assay had a linear range of quantification over six orders of magnitude, and the limit of detection was approximately 12 genome equivalents. The assay was used to detect C. jejuni in both naturally and artificially contaminated food samples. Ninety-seven foods, including raw poultry meat, offal, raw shellfish, and milk samples, were enriched in blood-free Campylobacter enrichment broth at 37 degrees C for 24 h, followed by 42 degrees C for 24 h. Enrichment cultures were subcultured to Campylobacter charcoal-cefoperazone-deoxycholate blood-free selective agar, and presumptive Campylobacter isolates were identified with phenotypic methods. DNA was extracted from enrichment cultures with a rapid lysis method and used as the template in the real-time PCR assay. A total of 66 samples were positive for C. jejuni by either method, with 57 samples positive for C. jejuni by subculture to selective agar medium and 63 samples positive in the real-time PCR assay. The results of both methods were concordant for 84 of the samples. The total time taken for detection from enrichment broth samples was approximately 3 h for the real-time PCR assay, with the results being available immediately at the end of PCR cycling, compared to 48 h for subculture to selective agar. This assay significantly reduces the total time taken for the detection of C. jejuni in foods and is an important model for other food-borne pathogens.

Detection of Campylobacter jejuni and Campylobacter coli in foods by enrichment culture and polymerase chain reaction enzyme-linked immunosorbent assay

A polymerase chain reaction (PCR) assay based on a solution hybridization format with colorimetric end-point detection (PCR ELISA) was investigated for the specific detection of Campylobacter jejuni and Campylobacter coli in food samples following enrichment culture. One hundred fifteen samples of raw meat and offal (poultry, porcine, ovine, and bovine), raw shellfish, and artificially contaminated milk were enriched in blood-free Campylobacter Enrichment Broth for 48 h. Enrichment cultures were subcultured to Campylobacter blood-free selective agar plates, and presumptive isolates were identified by phenotypic methods. DNA was extracted from 1-ml aliquots of the enrichment cultures using a rapid extraction method, and the DNA was used as the template in a PCR ELISA. A comparison of the PCR ELISA with the enrichment culture and subculture to selective agar method showed that the results of 112 of the 115 samples tested were in agreement by both methods. Seventy-one of the various food samples were positive in the PCR ELISA, and 70 samples were positive by culture. The PCR ELISA had a sensitivity of 99% and a specificity of 96%, with a positive predictive value of 97% and a negative predictive value of 98%. The PCR ELISA is a rapid, sensitive, and specific method for the detection of C. jejuni and C. coli in foods following enrichment culture and significantly reduces the time required for their detection.

Efficacy of a commercial polymerase chain reaction-based assay for detection of Salmonella spp. in animal feeds

Salmonellosis is a cyclic problem in the food industry, to which animal feed has been contributory. Current conventional methods of Salmonella spp. detection require 96 h for detection and confirmation. With modern and just-in-time production schedules, a 96-h hold represents a significant expense in storage and decontamination. The commercially available assay, 'BAX for Screening/Salmonella' (BAX), is based on the principle of the polymerase chain reaction and may represent a significant decrease in assay time. Seven fresh feed formulations, two fresh feed ingredients, seven stored feeds and two stored feed ingredients were artificially contaminated with a primary poultry isolate of Salmonella typhimurium and analysed by conventional and BAX methodology. The results of BAX agreed with conventional plating results for 16 of 18 samples spiked with 1200 cfu 10 g(-1) of feed and 13 of 18 samples spiked with 40 cfu 10 g(-1) of feed. Indigenous Salmonella spp. were detected in five of eight samples of poultry diets by conventional methods. With BAX, Salmonella spp. could not be detected in any of the samples after only 7 h of enrichment but could be detected in two dietary samples after 13 h of enrichment and four dietary samples after 24 h of enrichment. Specific sequences of salmonella DNA that were extracted from poultry diets could be detected with BAX.

Conventional and molecular methods for understanding probiotic bacteria functionality in gastrointestinal tracts

The recent successes of probiotic application to limit colonization of foodborne pathogens in the gastrointestinal tracts of food animals ensures continued commercialization and widespread use of such cultures. Given that the the fermentation response and ecological balance of the probiotic consortium appears to be essential for the effectiveness of the cultures, it is essential to develop a methodology to accurately identify and quantitate these organisms during commercial production as well as successful in vivo colonization after administration. However, if further optimization of the effectiveness of defined cultures is to be achieved, methods to assess expression of key metabolic processes occurring during establishment of the probiotic culture as well as its subsequent ability to limit foodborne pathogen colonization are needed. Conventional methods to study individual probiotic gastrointestinal organisms include selective plating to identify specific nutritional groups, but the requirement of strict anaerobiosis for the obligate anaerobic members of these cultures can confound sample handling and preparation. Immunological methods can circumvent some of these problems but are somewhat limited for assessing functionality. The main advantage of using molecular tools is that the genetic diversity of the microflora, as well as their gene activity data are obtainable, both at the community level and at the single species level. Methods are currently available that permit studying individual members of microbial consortia, fluxes in community diversity, spatial distribution of consortia members, and the expression of specific microbial genes within communities. These methods involve the utilization of both DNA- and RNA-targeted probes, gene amplification protocols, and mRNA analysis. The study of mechanisms and functionality can only enhance the potential of probiotic cultures for limiting foodborne pathogen colonization.

Direct quantification of the enteric bacterium Oxalobacter formigenes in human fecal samples by quantitative competitive-template PCR

Homeostasis of oxalic acid appears to be regulated, in part, by the gut-associated bacterium Oxalobacter formigenes. The loss of this bacterium from the gut flora is associated with an increased susceptibility to hyperoxaluria, a condition which can lead to the formation of calcium oxalate crystalluria and kidney stones. In order to identify and quantify the presence of O. formigenes in clinical specimens, a quantitative-PCR-based assay system utilizing a competitive DNA template as an internal standard was developed. This quantitative competitive-template PCR test allows for the rapid, highly specific, and reproducible quantification of O. formigenes in fecal samples and provides a prototype for development of DNA-based quantitative assays for enteric bacteria.

Rapid molecular detection of microbial pathogens: breakthroughs and challenges

Microbiological contamination of foods and drinking water is a global problem, and a significant amount of expense is being incurred as a result of such contamination. The microorganisms associated with almost half of all disease outbreaks still go unidentified, primarily as a result of inadequate monitoring and surveillance. Though significant improvements have been made in refining molecular methods for detecting infectious agents, a majority of these methods are being employed only on clinical samples where pathogen densities are much higher than those found in environmental and food samples. Comparative evaluations of the various protocols in terms of cost, sensitivity, specificity, speed, and reproducibility need to be undertaken so that the true applicability of these methods can determined. In the future, molecular methods, especially gene amplifications and in situ hybridizations, will find increasing applications in the differentiation of viable and non-viable organisms, in predicting antimicrobial resistance, and in the identification and characterization of unculturable microorganisms. Though molecular detection methods will not totally replace conventional methods, they will significantly enhance our ability to detect microbial pathogens rapidly.