Detection of thermophilic Campylobacter spp. in blood-free enriched samples of inoculated foods by the polymerase chain reaction

The detection of thermophilic Campylobacter spp., as represented by Campylobacter jejuni, by the polymerase chain reaction (PCR) was investigated and compared with the selective agar isolation (SAI) method. Stationary-phase cultures of C. jejuni were inoculated into either blood-free enrichment broth (BFEB) or BFEB that contained 10% broccoli, crabmeat, mushroom, raw milk, and raw oyster rinses. Following a 48-h enrichment period, aliquots of food test portions were removed for simultaneous analysis by PCR and SAI. It was determined that the presence of charcoal and iron in the enrichment broth interfered with the PCR assay. Therefore, three DNA extraction techniques were developed and evaluated using a 16S rRNA primer pair in the PCR assay. The 50% end point (DL50) values (determined upon six initial C. jejuni spiking levels) were used to assess the frequency of isolation utilizing PCR versus SAI for the detection of this organism in the enrichment matrices. There were virtually no differences in detection of C. jejuni among enriched samples analyzed by PCR and SAI. Mean DL50 values (n = 3) for plain BFEB, broccoli, crabmeat, mushroom, raw milk, and raw oyster were, respectively, 0.02 (PCR) versus 0.01 (SAI), 0.01 versus 0.06, 0.07 versus 0.04, 0.03 versus 0.08, 0.01 versus 0.01, and 0.01 versus 0.01 CFU/5 g food. Significant variability in the detection limit of C. jejuni by PCR in the food enrichments was observed among DNA extraction techniques. Using 48-h enrichment cultures followed by PCR analysis could save 1 day of the time required for the presumptive identification of C. jejuni in suspected foods.     

Application of an indirect ELISA and a PCR technique for detection of cows’ milk in sheep's and goats’ milk cheeses

We have applied a polymerase chain reaction (PCR) procedure and an indirect enzyme-linked immunosorbent assay (ELISA) for detecting the presence of cows’ milk in sheeps’ and goats’ milk cheeses. The PCR used a cattle-specific primer set targeting a 223 bp fragment from the mitochondrial 12S rRNA gene. This technique was applied to experimental cheese mixtures, industrial cheeses produced with known amounts of cow's milk, and several commercial cheeses, enabling the detection of low percentages of cows’ milk (1%). An indirect ELISA using a monoclonal antibody (AH4) against bovine β-casein was also assayed in this study for the specific detection of bovine milk in cheese. Results suggested that both ELISA and PCR may provide specific and reliable tools for detection of low percentages of undeclared cows’ milk in sheeps’ and/or goats’ milk cheeses and other dairy products.     

Application of a polymerase chain reaction to detect adulteration of ovine cheeses with caprine milk

A polymerase chain reaction (PCR) procedure has been applied for the detection of caprine milk in ovine cheeses by using primers targeting the mitochondrial 12S ribosomal RNA gene. The use of a primer pair specific for goat in PCR analysis of cheese samples, enabled the amplification of a goat 122 bp fragment with a sensitivity threshold of approximately 1%, whereas no amplification signal was achieved with sheep's, cow's and water buffalo's milk DNA. This study demonstrates the usefulness of the proposed PCR assay for the qualitative detection of goats’ milk in ewes’ cheeses, and may therefore provide a simple and accurate approach applicable to the authentication of cheese or other dairy products in routine monitoring programs.     

A multiplex PCR assay based on 16S rRNA and hly for rapid detection of L. monocytogenes in Milk

A multiplex PCR assay was developed by targeting ‘16S rRNA’ and ‘hly’ genes for detection of Listeria or Listeria monocytogenes in dairy foods on the basis of amplification of 1200 and 713 bp products, respectively. The assay conditions were optimized to make it truly rapid and to cut down the cost. The authenticity of the multiplex PCR was ascertained by using Nested PCR targeted against internal region of ‘hly’ gene that produced an amplified product of 188 bp. The multiplex PCR assay was found to be specific for detection of L. monocytogenes only since none of the non-listerial cultures gave positive signal. The sensitivity of the multiplex PCR was limited to 10 ng pure DNA and 1–10 cells of L. monocytogenes after 4–6 h enrichment in Listeria enrichment broth. When applied to 20 raw milk and 10 pasteurized milk samples, L. monocytogenes could not be detected in any of the samples by the multiplex PCR assay. This assay could find potential application in dairy industry for monitoring dairy foods for this high risk food pathogen on routine basis.     

Multiplex polymerase chain reaction assay for simultaneous detection of Staphylococcus aureus and streptococcal causes of bovine mastitis

To improve diagnosis of mastitis in dairy cattle, a multiplex polymerase chain reaction (PCR) assay was developed for the simultaneous detection of the four major bacterial causes of bovine mastitis, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, and Streptococcus uberis. The target sequence was the 16S to 23S rRNA spacer regions. The performance of the assay was examined with 117 milk samples collected from a subclinically infected herd, and the diagnostic specificities and sensitivities of the multiplex PCR were compared with conventional culture. PCR was significantly more sensitive than culture for detection of S. aureus and S. uberis, but there were no significant differences in sensitivities between PCR and culture for the detection of S. agalactiae and S. dysgalactiae. The results suggest that this multiplex PCR assay could be used as an alternative method in routine diagnosis for rapid, sensitive, and specific simultaneous detection of S. aureus, S. agalactiae, S. dysgalactiae, and S. uberis in milk samples.     

The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR

The purpose of this work was to study the bacterial communities in raw milk and in Danish raw milk cheeses using pyrosequencing of tagged amplicons of the V3 and V4 regions of the 16S rDNA and cDNA. Furthermore, the effects of acidification and ripening starter cultures, cooking temperatures and rate of acidification on survival of added Escherichia coli, Listeria innocua and Staphylococcus aureus in cheeses at different stages of ripening were studied by pyrosequencing and quantitative real time (qRT)-PCR. A high diversity of bacterial species was detected in raw milk. Lactococcus lactis, Streptococcus thermophilus, Lactobacillus casei and Lactobacillus rhamnosus were the main bacteria detected in raw milk and cheeses. Bacteria belonging to the genera Brevibacterium, Staphylococcus, Escherichia, Weissella, Leuconostoc, Pediococcus were also detected in both 16S rDNA and cDNA obtained from raw milk and cheeses. E. coli, which was added to milk used for production of some cheeses, was detected in both DNA and RNA extracted from cheeses at different stages of ripening showing the highest percentage of the total sequence reads at 7 days of ripening and decreased again in the later ripening stages. Growth of E. coli in cheeses appeared to be affected by the cooking temperature and the rate of acidification but not by the ripening starter cultures applied or the indigenous microbiota of raw milk. Growth of L. innocua and S. aureus added to milks was inhibited in all cheeses at different stages of ripening. The use of 16S rRNA gene pyrosequencing and qRT-PCR allows a deeper understanding of the behavior of indigenous microbiota, starter cultures and pathogenic bacteria in raw milk and cheeses.     

Rapid detection of cows' milk in sheeps' and goats' milk by a species-specific polymerase chain reaction technique

A polymerase chain reaction (PCR) assay was developed for the specific identification of cows' milk in sheep's and goats' milk by using primers targeting the mitochondrial 12S rRNA gene. The use of a forward primer complementary to a conserved DNA sequence, along with a reverse primer specific for cow, yielded a 223-bp fragment from cows' milk DNA, whereas no amplification signal was obtained in sheep's and goats' milk DNA. The technique was applied to raw, pasteurized, and sterilized milk binary mixtures of cow-sheep and cow-goat, enabling the specific detection of cows' milk with a good sensitivity threshold (0.1%). The proposed PCR assay represents a rapid and straightforward method applicable to the authentication of milk and other dairy products in routine analysis.     

Artisanal and experimental Pecorino Siciliano cheese: microbial dynamics during manufacture assessed by culturing and PCR-DGGE analyses

Traditional artisanal Pecorino Siciliano (PS) cheeses, and two experimental PS cheeses were manufactured using either raw or pasteurised ewes' milk with the addition of starter cultures. The bacterial diversity and dynamics of the different cheese types were evaluated both by culturing and characterisation of isolates, and a culture-independent approach based on the 16S ribosomal RNA (rRNA) gene. Following cultivation, artisanal and experimental cheese types showed similar microbial counts, and isolates belonging to Lactococcus lactis, Streptococcus thermophilus, Enterococcus faecalis and Leuconostoc mesenteroides were identified by phenotypic characterisation and comparison of the restriction fragment length polymorphism (RFLP) of the 16S rRNA gene to that of reference species. The culture-independent fingerprinting technique PCR and denaturing gradient gel electrophoresis (DGGE) of V6 to V8 regions of the 16S rRNA gene of samples taken during artisanal PS cheese manufacture, from raw milk to the ripened cheese, indicated relevant shifts in the microbial community structure. The dominance of Streptococcus bovis and Lactococcus lactis species in the traditional artisanal PS was revealed by 16S rRNA gene sequencing. Comparison of DGGE profiles of samples from milk to ripened cheese, derived from artisanal procedure and the two experimental PS cheeses during production showed similar trends with the presence of intense bands in common. Nevertheless, the profiles of several artisanal cheeses from different farms appeared more diverse, and these additional species are probably responsible for the generally superior flavour and aroma development of traditional PS cheese.     

A multiplex polymerase chain reaction for the identification of cows’, goats’ and sheep's milk in dairy products

A multiplex PCR able to identify cows’, goats’ and sheep's milk in dairy products was developed. Specific primers were designed in the mitochondrial 12s and 16s rRNA genes so as to generate fragments of different length.The assay was applied to 19 cheeses from the retail trade in order to verify the label statements. The multiplex PCR results were confirmed by PCR-restriction fragment length polymorphism.The proposed multiplex PCR represents a rapid and sensitive method applicable on a routine basis. In fact it enables to detect, in a single step, goats’, sheep's and cows’ milk in dairy products with a good sensitivity threshold (0.5%).     

Development and evaluation of a Mycobacterium avium subspecies paratuberculosis (MAP) specific multiplex PCR assay

There are specificity questions inherent in most of the current PCR systems that amplify the MAP IS900 sequence as an indicator for Mycobacterium avium subspecies paratuberculosis (MAP) presence due to false positives associated with IS900-like sequences that exists in other Mycobacterium species besides MAP. We developed a multiplex PCR system designed to enhance specificity for MAP detection in a single PCR reaction. This PCR assay co-amplifies the mycobacterium species 16S rRNA gene, MAP IS900 and f57 sequences. The assay incorporates an internal PCR amplification control (IC) template system enabling PCR amplification conditions to be assessed in each reaction. The assay's specificity was confirmed by testing 10 isolates of MAP and 59 isolates of other bacterial species. In parallel we also applied on the same samples, one of the established nested PCR systems that targets only the IS900 sequence. The multiplex PCR assay was highly specific for MAP, the nested PCR system was also positive with several other mycobacterium species. In this context, we report for the first time false positive IS900 PCR signals in Mycobacterium chelonae, Mycobacterium terrae and Mycobacterium xenopi strains associated with one of the established PCR systems widely used for MAP detection. Finally, the potential application of this multiplex PCR system in milk analysis is demonstrated through analysis of raw milk samples artificially contaminated with MAP.     

一种快速定性和定量检测发酵乳中L.fermentum的方法

通过比对发酵乳杆菌(L.fermentum)与其他乳酸菌的16S rRNA基因序列的异同,设计出L.fermentum的种属特异性引物,应用此引物进行种属特异性PCR和实时荧光定量PCR反应,通过琼脂糖凝胶电泳图谱和实时荧光定量PCR图谱分析,建立一种快速检测发酵乳中L.fermentum定性和定量测定方法.     

HYGIENIC PARAMETERS, TOXINS AND PATHOGEN OCCURRENCE IN RAW MILK CHEESES

In total, 71 samples of retail raw milk cheeses produced or imported in Belgium and samples of Belgian farmhouse cheeses were examined for cotiforms, β-glucuronidase positive Escherichia coli, Escherichia coli O157 , Staphylococcus aureus, Salmonella spp. , Listeria spp. and Listeria monocytogenes. The presence of staphylococcal enterotoxins was investigated on samples with S. aureus counts higher than 10³ cfu/g. The incidence of coliforms, β-glucuronidase positive E. coli and S. aureus was higher in soft than in blue veined, semi-hard, hard and fresh cheeses. Four mold-ripened soft cheeses were positive for E. coli O157. One of the 4 cheeses was positive for verotoxin VT2. Staphylococcal enterotoxins were detected in 1 soft redsmear cheese, which was positive for L. monocytogenes. L. monocytogenes was also detected in one fresh cheese . Salmonella was not detected in any of the 71 raw milk cheeses.     

多重PCR检测婴幼儿配方奶粉中3种食源性致病菌

为建立一种能够同时检测婴幼儿配方奶粉(Powdered Infant Formula,PIF)中克罗诺杆菌、沙门氏菌和金黄色葡萄球菌3种食源性致病菌的多重PCR检测方法。通过单重PCR验证了9对引物的特异性,筛选出其中3对特异性好的引物建立了多重PCR体系,对其特异性和灵敏度进行评价,并将其应用于人工污染PIF中3种食源性致病菌的检测。结果表明,针对克罗诺杆菌、沙门氏菌和金黄色葡萄球菌等3种食源性致病菌所筛选的3对引物分别能扩增出469、638和796 bp的目的条带,具有高度特异性。多重PCR检测体系的最佳退火温度为55℃,最佳Mg2+浓度为2.00 mmol/L,最佳引物浓度为400 nmol/L。在此条件下3种目的菌在102 CFU/mL均可同时扩增出较清晰条带。将建立的多重PCR检测体系应用于人工污染PIF中3种食源性致病菌的检测,其检出限达到103 CFU/g。本研究初步建立了一种能准确、快速、特异性的检测PIF中克罗诺杆菌、沙门氏菌和金黄色葡萄球菌的多重PCR方法,适用于PIF中3种常见的食源性致病菌的快速检测。     

原料乳中多种致病菌的快速过滤富集及多重PCR检测

针对目前原料乳中致病菌的检测方法繁琐费时耗力的缺点,建立一种能同时检测原料乳中多种致病菌的快速检测方法,采用多重PCR快速灵敏检测技术与一种不需要预增菌就可以直接从原料乳中快速过滤富集菌体的技术相结合来同时检测原料乳中主要致病菌——沙门氏菌、大肠杆菌O157:H7、金黄色葡萄球菌、单增李斯特氏菌和蜡样芽孢杆菌。整个过程只需7～8h即可完成,且检测灵敏度可达102cfu/mL。这种方法是对传统检测方法的有效改进,并且达到了原料乳检测快速、准确、灵敏的要求。     

Detection of banned ruminant-derived material in industrial feedstuffs by TaqMan real-time PCR Assay

A ruminant-specific real-time PCR system was designed and applied for the detection of processed animal protein from ruminants in industrial feedstuffs. The assay includes a primer pair and a TaqMan probe selectively targeting mitochondrial 16S rRNA gene sequences from the ruminant group and another primer-probe set based on the eukaryotic nuclear 18S rRNA gene (positive amplification control). Both ruminant and eukaryotic PCR systems generated short PCR amplicons of 79 and 77 bp, respectively. To evaluate the suitability of the real-time PCR assay for the detection of banned by-products of ruminant origin, 126 feed samples subjected to rendering under current European legislation regulations were analyzed. The assay achieved 100% success in classifying the samples as positive or negative in terms of qualitative ruminant composition, with a detection limit of 0.1%. The quantitative ability of the assay is however restricted by variations in the composition and treatment of the feeds, which affect the amount and quality of amplifiable DNA.     

An improved PCR primer pair based on 16S rDNA for the specific detection of Salmonella serovars in food samples

Salmonella serovars are some of the major bacterial pathogens that can cause sporadic cases and outbreaks of foodborne illness. Based on the sequence data in the V3 region of the 16S rRNA gene, two PCR primer pairs have been designed for the detection of all serovars of Salmonella. However, none of these primers were specific for Salmonella because complete sequence homology with certain non-Salmonella strains has been found within each of them. Thus, the specificities of these two primer pairs could not rely on only one of the two primers. In this study, we modified our previous 16SFI primer by extending one base at the 5' end and three bases at the 3' end. The modified primer, 16S-Sal, was designed with one or more mismatched bases near the 3' end of the primer annealing to the corresponding sequences of non-Salmonella strains. Such modification eliminates interference from Citrobacter freundii and Enterobacter cloacae as occurs with the 16SFI primer. When 16S-Sal and a degenerate primer, 16S-CCR, were used as a primer pair, detection specificity of Salmonella serovars was achieved. Because this primer pair was used for PCR detection of the salmonellae in food samples, such as whole milk and chicken meat, as low as 1 to 9 CFU/g (ml) of the food sample could be detected when a 8-h preculture step was performed prior to the PCR. For chicken meat, the endogenous microflora did not interfere with the PCR results.     

Detection, quantification and vitality of Listeria monocytogenes in food as determined by quantitative PCR

In this paper we describe the development of a quantitative PCR (qPCR) technique to detect, quantify and determine the vitality of Listeria monocytogenes in foods. The method was based on the amplification of the intergenic region spacer (IGS) between the 16S and 23S rRNA genes. A panel of more than 100 strains of Listeria spp. and non-Listeria was used in order to verify the specificity of the primers and Taqman probe and amplification signals were obtained only when L. monocytogenes DNA and RNA were loaded in the qPCR mix. Standard curves were constructed in several food matrices (milk, meat, soft cheese, fermented sausage, cured ham and ready-to-eat salad). The quantification limit was of 10(3)-10(4) cfu/g or ml, while for the determination of vitality it was 10(4)-10(5) cfu/g or ml. After an overnight enrichment in BHI at 37 degrees C also 10 cfu/g or ml could be detected in all the matrices used in this study. When we applied the protocol to food samples collected from the market or from small food processing plants, on a total number of 66 samples, 4 fresh cheeses from raw milk gave positive results prior to the overnight incubation, while 9 samples, of which only one represented by fresh meat and the others by cheeses from raw milk, were positive after the enrichment. Out of the 4 positive samples, only one could be quantified and it was determined to contain 4x10(3) cfu/g.     

Molecular differentiation of clostridia associated with "blown pack" spoilage of vacuum-packed meats using internal transcribed spacer polymorphism analysis

The 16S-23S rDNA internal transcribed spacer (ITS) polymorphism analysis was assessed for its suitability in rapid discrimination between species of psychrophilic and psychrotolerant clostridia associated with "blown pack" spoilage of vacuum-packed meats. DNA isolated from 10 reference and 20 meat strains of psychrophilic and psychrotolerant clostridia were used as templates in PCR amplification with primers complementary to conserved regions of the 3' end of the 16S rRNA and 5' end of the 23S rRNA genes directly flanking the spacer. The majority of strains showed multi-band ITS patterns when products of spacer amplification were visualised on an agarose gel. With the majority of meat strains, PCR amplification generated single banding pattern for a single clostridial species. However, meat strains of Cl. algidicarnis produced four different ITS banding patterns. With reference strains of psychrophilic and psychrotolerant clostridia, variation in spacer length was also observed between nonproteolytic Cl. botulinum type B (17B), E (Beluga) and F (202F). On the other hand, the number and size of the ITS amplification products could not be used for a differentiation of Cl. laramiense ATCC 51254(T) from Cl. estertheticum DSM 8809(T), Cl. putrefaciens DSM 1291(T) from Cl. algidicarnis NCFB 2931(T), or Cl. frigidicarnis strains from nonproteolytic Cl. botulinum type B (17B). The presence of interstrain, and lack of interspecies, ITS polymorphism observed in the present study with some clostridial species may preclude the use of 16S-23S rDNA spacer amplification for species-level discrimination and identification, respectively, of psychrophilic and psychrotolerant clostridia associated with meat spoilage. However, where interstrain, intraspecies heterogeneity of ITS amplification products exists, ITS analysis could be useful for tracing back psychrophilic and psychrotolerant clostridia responsible for meat spoilage to their meat plant sources.     

High resolution melting analysis for quantitative detection of bovine milk in pure water buffalo mozzarella and other buffalo dairy products

Identification of buffalo dairy products has become an important issue to ascertain product quality, consumer rights and absence of food-borne allergic reactions. A polymerase chain reaction (PCR) followed by a high resolution melting (HRM) analysis was developed and applied for species specific detection of bovine milk in nine different commercial buffalo dairy products. A specific buffalo 12S rRNA and a bovine d-loop primer pair, targeting the mitochondrial genome, were employed in a duplex PCR assay. The analysis developed was found capable of identifying the presence of bovine milk down to 1% in commercial buffalo milk products and also of quantifying the ratio of bovine into buffalo milk. HRM was proven to be a fast and accurate technique for a routine authentication testing of mozzarella and other buffalo milk products.     

A PCR-based method for the detection of Streptococcus agalactiae in milk

Bovine mastitis caused by Streptococcus agalactiae is mainly subclinical and therefore can be diagnosed only in the laboratory. We developed a polymerase chain reaction (PCR)-based method for specific and sensitive detection of S. agalactiae in raw milk. The specificity of the PCR reaction is based on unique S. agalactiae DNA sequences within the 16S subunit of the rRNA genes. Two pairs of sequences were used as positive controls; general streptococci primers, which anneal to conserved areas within the 16S rRNA subunit gene, and primers, which anneal to sequences within bovine mitochondrial DNA. The method of detection includes selective enrichment of S. agalactiae in the milk sample, followed by DNA extraction using a rapid and simple procedure developed for this purpose, and specific PCR reaction with appropriate controls. The method enables the detection of one bacterium in 1 ml of raw milk. The method developed can be easily incorporated as part of routine screening of bulk milk collection tanks for early detection of infected cows in a herd.