Technical note: Improved method for rapid DNA extraction of mastitis pathogens directly from milk

Efficient control against bovine mastitis requires sensitive, rapid, and specific tests to detect and identify the main bacteria that cause heavy losses to the dairy industry. Molecular detection of pathogenic microorganisms is based on DNA amplification of the target pathogen. Therefore, efficient extraction of DNA from pathogenic bacteria is a major step. In this study, we aimed to develop a specific, sensitive, and rapid method to extract DNA directly from the main gram-positive bacteria known to cause bovine mastitis (Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, and Streptococcus uberis) found in milk samples. The DNA extraction method is based on the lysing and nuclease-inactivating properties of the chaotropic agent, guanidinium thiocyanate, together with the nucleic acid-binding properties of the silica particles. An efficient protocol consisting of 6 basic steps (3 of which were done twice) was developed and applied directly to milk samples. Absence of PCR inhibitors and DNA quality were evaluated by PCR amplification of the species-specific DNA sequences of the target bacteria. The level of sensitivity achieved in our experiments is applicable to milk sample analysis without sample enrichment.     

PCR detection of cows’ milk in water buffalo milk and mozzarella cheese

Polymerase chain reaction (PCR) has been applied for the specific detection of cows’ DNA in water buffalo milk and mozzarella cheese by using primers targeting the mitochondrial 12S ribosomal RNA gene. The use of specific primers for cow yielded a 346 bp fragment from cows’ milk DNA, whereas no amplification signal was obtained in sheep's, goats’ and water buffalo's milk DNA. Analysis of both buffalo milk and buffalo mozzarella cheese mixtures containing different percentages of cows’ milk or bovine mozzarella cheese, enabled the specific detection of cow's DNA with a sensitivity threshold of 0.1%. The proposed PCR assay represents a rapid and straightforward method for the detection of adulterations in water buffalo milk and mozzarella cheese.     

Detection of cow milk adulteration in yak milk by ELISA

In the current study, a simple, sensitive, and specific ELISA assay using a high-affinity anti-bovine β-casein monoclonal antibody was developed for the rapid detection of cow milk in adulterated yak milk. The developed ELISA was highly specific and could be applied to detect bovine β-casein (10–8,000 μg/mL) and cow milk (1:1,300 to 1:2 dilution) in yak milk. Cross-reactivity was <1% when tested against yak milk. The linear range of adulterant concentration was 1 to 80% (vol/vol) and the minimum detection limit was 1% (vol/vol) cow milk in yak milk. Different treatments, including heating, acidification, and rennet addition, did not interfere with the assay. Moreover, the results were highly reproducible (coefficient of variation <10%) and we detected no significant differences between known and estimated values. Therefore, this assay is appropriate for the routine analysis of yak milk adulterated with cow milk.     

Application of polymerase chain reaction to detect adulteration of sheep's milk with goats' milk

The polymerase chain reaction has been applied for the specific detection of goats’ milk in sheep's milk using primers targeting the mitochondrial 12S ribosomal RNA gene. The use of goat-specific primers yielded a 122-bp fragment from goats’ milk DNA, whereas no amplification signal was obtained in sheep's, cows’, and water buffaloes’ milk DNA. Polymerase chain reaction analysis of raw and heat-treated milk binary mixtures of sheep/goat enabled the specific detection of goats’ milk with a sensitivity threshold of 0.1%. This study demonstrates the usefulness of the proposed polymerase chain reaction assay for authentication of milk products in routine analysis.     

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.     

Real-time TaqMan PCR for quantitative detection of cows’ milk in ewes’ milk mixtures

A real-time PCR based on the amplification of a fragment of the mitochondrial 12S ribosomal RNA gene was developed and evaluated for the detection and quantification of cows’ milk in raw and heat-treated cow/sheep milk mixtures. The method combines the use of cow-specific primers that amplify a 252 bp fragment from cow DNA, and mammalian-specific primers amplifying a 428 bp fragment from mammalian species DNA, which is used as an endogenous control. The method measures PCR product accumulation through a 6-carboxyfluorescein-labeled fluorogenic probe (TaqMan). A comparison of the cycle number at which mammalian and cow-specific PCR products were first detected, in combination with the use of reference standards of known bovine content, allowed the determination of the percentage of cows’ milk in mixtures. Experimental raw and heat-treated binary mixtures were analyzed, demonstrating the specificity and sensitivity of the assay for detection and quantification of cows’ milk in the range 0.5–10%.     

Simultaneous detection of cow and buffalo species in milk from China, India, and Pakistan using multiplex real-time PCR

Asian countries are major producers of cow and buffalo milk. For quality and authenticity purposes, a multiplex real-time PCR assay was developed to specifically and simultaneously detect DNA from these 2 bovine species. Targeting the cytochrome b gene of mitochondrial DNA, common PCR primers amplified a 105-bp fragment, and 2 fluorescent probes specific to either cow or buffalo were designed for their identification. Specificity was successfully tested on 6 other species, including sheep and goat, and sensitivity reached 1% of cow DNA in buffalo DNA and vice versa. As an evaluation, the method was tested using 119 freeze-dried Asian milk samples from regional industrial milk facilities. Although these samples did not cover the entire Asian zone, the multiplex assay indicated that approximately 20% of the samples (mainly from India) showed high levels of cross-contamination of cow milk by buffalo milk, and vice versa. Fast, sensitive, and straightforward, this method is fit-for-purpose for the authenticity control of Asian milk.     

Development of a novel loop-mediated isothermal amplification assay for the detection of lipolytic Pseudomonas fluorescens in raw cow milk from north China

Lipases secreted by psychrotrophic bacteria are known to be heat resistant and can remain active even after the thermal processing of milk products. Such enzymes are able to destabilize the quality of milk products by causing a rancid flavor. Rapid detection of a small amount of heat-resistant lipase-producing psychrotrophic bacteria is crucial for reducing their adverse effects on milk quality. In this study, we established and optimized a novel loop-mediated isothermal amplification (LAMP) assay for the detection of Pseudomonas fluorescens in raw cow milk, as the most frequently reported heat-resistant lipase-producing bacterial species. Pseudomonas fluorescens-specific DNA primers for LAMP were designed based on the lipase gene sequence. Reaction conditions of the LAMP assay were tested and optimized. The detection limit of the optimized LAMP assay was found to be lower than that of a conventional PCR-based method. In pure culture, the detection limit of the LAMP assay was found to be 4.8 × 10¹ cfu/reaction of the template DNA, whereas the detection limit of the PCR method was 4.8 × 10² cfu/reaction. Evaluation of the performance of the method in P. fluorescens-contaminated pasteurized cow milk revealed a detection limit of 7.4 × 10¹ cfu/reaction, which was 10² lower than that of the PCR-based method. If further developed, the LAMP assay could offer a favorable on-farm alternative to existing technologies for the detection of psychotrophic bacterial contamination of milk, enabling improved quality control of milk and milk products.     

Development of a highly sensitive and specific assay to detect Staphylococcus aureus in bovine mastitic milk

Diagnosis of udder infections with Staphylococcus aureus by bacteriological milk testing of quarter milk samples is often not satisfactory. To get reliable results, repeated sampling is necessary, which is normally too expensive. Therefore, we developed a test that allows the highly specific detection of Staph. aureus in bovine milk samples at very low concentrations. It is based on a fast procedure to prepare bacteria from milk, followed by DNA extraction and quantitative PCR. The whole analysis is done within 5 h. For clinical milk samples, the analytical sensitivity of the assay was 50.7 times and 507 times higher than conventional bacteriology with 100 and 10 μL, respectively. The diagnostic specificity was 100%. The test is further characterized by a low intra- and interassay variability as well as by a good recovery of Staph. aureus from raw milk. Furthermore, a high correlation (R = 0.925) between the agar plate counts and the quantitative PCR methodology over the whole range of measurement was found. In addition, our test revealed considerably more positive results than bacteriology. Due to its favorable properties, the assay might become an important diagnostic tool in the context of bovine mastitis caused by Staph. aureus.     

Development and comparison of loop-mediated isothermal amplification and quantitative polymerase chain reaction assays for the detection of Mycoplasma bovis in milk

Bovine mastitis is an economic burden for dairies worldwide. Mycoplasma species, and especially Mycoplasma bovis, are among the most important causative agents, and rapid, precise, and low-cost methods for Mycoplasma detection are urgently needed. For this purpose, loop-mediated isothermal amplification (LAMP) and quantitative PCR (qPCR) assays were developed and compared. The LAMP assay was designed and primer concentrations optimized to M. bovis oppD, encoding oligopeptide permease D. For qPCR, a Taqman assay (Applied Biosystems, Carlsbad, CA) targeting M. bovis gltX, encoding glutamate transfer RNA ligase, was optimized for primer concentration, annealing temperature, and DNA polymerase. Both assays were similarly sensitive, with a detection limit of approximately 10⁴ to 10⁵ M. bovis cells/mL. Both assays were also successful in confirming M. bovis identity in laboratory culture suspensions and in bovine milk. The LAMP and qPCR assays combined with the MoBio DNA extraction kit (MoBio Laboratories Inc., Carlsbad, CA) resulted in the correct detection of 13 out of 13 M. bovis isolates and 14 out of 16 M. bovis-positive milk samples collected from commercial dairies in California. When combined with the PrepMan Ultra reagent (Applied Biosystems), the qPCR assay resulted in confirming 21 out of 21 M. bovis-positive milk samples. Comparison of the assays to milk containing either Mycoplasma arginini, Mycoplasma bovigenitalium, Mycoplasma californicum, M. alkalescens, or Acholeplasma laidlawii or milk lacking any detectable Mycoplasma species or relatives resulted in 3 out of 17 (LAMP with MoBio), 1 out of 17 (qPCR with MoBio), and 2 out of 36 (qPCR with PrepMan Ultra) false positives. Overall, the qPCR assay was more robust than LAMP and could be used on DNA recovered from milk prepared with the PrepMan Ultra reagent, a method that does not include a DNA purification step. The use of this qPCR method enables M. bovis detection in bovine milk in 40 to 55 min, and therefore provides new opportunities to accelerate and simplify M. bovis detection in unpasteurized milk to reduce the incidence of M. bovis mastitis outbreaks.     

Comparison of DNA quality in raw and reconstituted milk during sterilization

Responses to milk sterilization are usually evaluated only in terms of physicochemical properties and microbial safety, thus undervaluing the importance of DNA quality in an authentication process by methods based on PCR. Because DNA is a heat-sensitive molecule, we hypothesized that the heating process may impair the detection or quantification of DNA in raw fresh milk (FM) or reconstituted milk (RM), and that differences in DNA quality might exist between FM and RM. We thus investigated the effects of sterilization on the quality of DNA extracted from FM or RM; differences in DNA quality between FM and RM were also evaluated. The quality of extracted DNA from FM or RM was assessed by the specific detection of FM or RM composition in goat milk mixtures using primers targeting the bovine 12S gene, as well as by monitoring DNA yield, purity, ratio of mitochondrial (mt) to nuclear (n) DNA, and the level of DNA degradation. Polymerase chain reaction readily detected both untreated and heat-treated FM or RM in cow-goat milk mixtures, and gave a good sensitivity threshold (0.1%) under all sterilization conditions. The DNA yield and mtDNA:nDNA ratio of FM and RM varied significantly during the sterilization process. These results demonstrated that the sterilization altered the quantification of DNA in FM or RM during sterilization, but DNA could still be readily detected in sterilized FM or RM by PCR. Furthermore, we noted significant differences in DNA integrity, yield, and mtDNA:nDNA ratio between FM and RM during sterilization, which may have potential as a means to distinguish FM and RM.     

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.     

Analysis and comparison of key proteins in Maiwa yak and bovine milk using high-performance liquid chromatography mass spectrometry

Yak milk is an essential and predominant food resource for Tibetan people for subsistence purposes and to combat altitude-induced challenges. Due to its unique qualities, yak milk has recently been gaining broader attention from consumers across China as well in other parts of the world. One of the key characteristics of yak milk is the protein content, which is about 40 to 60% higher than that of native bovine milk. In this work, a sensitive and reproducible high-throughput analytical method was developed employing both ultra high-performance liquid chromatography Orbitrap (Thermo Fisher Scientific) high-resolution accurate mass spectroscopy (UHPLC-HRAM-MS) and UHPLC coupled with triple quadrupole tandem MS (UHPLC-QqQ-MS) to simultaneously analyze 8 milk proteins. A total of 15 Maiwa yak milk samples and 15 bovine milk samples were qualitatively and quantitatively analyzed using targeted proteomics and compared for α-lactalbumin, β-lactoglobulin, α_S1-casein, α_S2-casein, β-casein, κ-casein, lactoferrin, and osteopontin. Peptides of β-lactoglobulin were used to specifically distinguish yak and bovine milk. The results showed that this novel detection method could quantitatively detect these major and minor milk proteins with >0.99 linear correlation coefficient and a recovery rate between 90 and 120%, with relative standard deviations typically less than 10%. The data revealed that yak milk not only had higher overall milk protein content than bovine milk but higher lactoferrin and osteopontin contents as well. The lactoferrin content of yak milk was about 30% higher than that of bovine milk, and the osteopontin content of yak milk was nearly twice that of bovine milk. The application of this method demonstrates that UHPLC-HRAM-MS and UHPLC-QqQ-MS are suitable for high-throughput qualitative and quantitative analysis of major and minor proteins of yak and bovine milk.     

基于三重实时荧光聚合酶链反应构建黄牛和牦牛源性成分同步检测方法

目的 建立一种拥有内源质控的三重实时荧光聚合酶链反应(polymerase chain reaction,PCR)技术,用以快速鉴定肉和乳中黄牛和牦牛的源性成分。方法 首先对黄牛肉、牦牛肉、黄牛奶、牦牛奶等7种动物产品进行特异性检测,同时通过稀释梯度方法验证此方法的绝对检出限(limit of detection, LOD),最后通过黄牛和牦牛肉掺假模拟试验确定该方法的相对灵敏度。结果 该方法的特异性强,能特异性地检测到来源于黄牛和牦牛肉和乳的DNA,稳定扩增的内源质控有效地避免了假阴性结果,本方法针对黄牛奶的绝对LOD为2.5×10^-3～5.0×10^-3 ng,针对牦牛奶的绝对LOD为2.5×10^-3～5.0×10^-2 ng,本方法对黄牛肉和牦牛肉混合肉的相对灵敏度可达0.1%牦牛肉。结论 所建立的三重实时荧光PCR方法特异性强、灵敏度高,可实现黄牛和牦牛源性以及内源质控的同步检测,又能通过内源质控排除实验假阴性结果。     

Novel extraction method of genomic DNA suitable for long-fragment amplification from small amounts of milk

Isolation of genomic DNA is a prerequisite for assessment of milk quality. As a source of genomic DNA, milk somatic cells from milking ruminants are practical, animal friendly, and cost-effective sources. Extracting DNA from milk can avoid the stress response caused by blood and tissue sampling of cows. In this study, we optimized a novel DNA extraction method for amplifying long (>1,000 bp) DNA fragments and used it to evaluate the isolation of DNA from small amounts of milk. The techniques used for the separation of milk somatic cell were explored and combined with a sodium dodecyl sulfate (SDS)-phenol method for optimizing DNA extraction from milk. Spectrophotometry was used to determine the concentration and purity of the extracted DNA. Gel electrophoresis and DNA amplification technologies were used for to determine DNA size and quality. The DNA of 112 cows was obtained from milk (samples of 13 ± 1 mL) and the corresponding optical density ratios at 260:280 nm were between 1.65 and 1.75. Concentrations were between 12 and 45 μg/μL and DNA size and quality were acceptable. The specific PCR amplification of 1,019- and 729-bp bovine DNA fragments was successfully carried out. This novel method can be used as a practical, fast, and economical mean for long genomic DNA extraction from a small amount of milk.     

Development of a real-time PCR assay for the detection of cow and donkey milk

A real-time PCR allelic discrimination TaqMan assay based on the analysis of a single nucleotide polymorphism enabling the differentiation of cow (Bos taurus) and donkey (Equus asinus) milk was developed. Specific primers and probes were designed on the mitochondrial cytochrome c oxidase subunit I gene. The primers were designed upstream and downstream the chosen diagnosis site in a conserved region. Two probes were designed to specifically hybridise to B. taurus and E. asinus sequences. The test allowed the discrimination of bovine and donkey DNA in all blood and pure milk samples giving an unambiguous result plot of rapid and easy interpretation. The detection threshold was 2?% of cow milk in donkey milk. The applicability of the method to matrices containing degraded DNA was demonstrated by analysing samples of raw donkey and cow milk autoclave-treated (121?°C for 15?min). Finally, the assay when applied to milk samples collected from the retail trade has confirmed the species indicated in the label. Furthermore, the assay represents a potentially valuable diagnostic tool for species identification in dairy products for allergic people.     

Mastitis diagnostics: quantitative PCR for Staphylococcus aureus genotype B in bulk tank milk

A novel real-time quantitative PCR assay for detecting the pathogenic and contagious Staphylococcus aureus genotype B (GTB) in bulk tank milk was developed and evaluated. The detection of this pathogen in bulk tank milk would greatly facilitate its control, as it is responsible for great economic loss in Swiss dairy herds. The assay is based on the simultaneous detection of 3 GTB-typical target sequences, including 2 enterotoxin genes and a polymorphism within the leucotoxin E gene. A variety of mastitis-associated bacteria was used to validate the assays, resulting in an analytical specificity of 100% and high repeatability. The analytical sensitivity in milk was 40 cfu/mL. An exponential association between simulated cow prevalence and quantitative PCR result was observed. An initial field study revealed 1 GTB-positive herd among the 33 studied herds. This novel assay for bulk tank milk analysis is suitable for routine purposes and is expected to be an effective tool for minimizing Staph. aureus GTB in Swiss dairy herds.     

Development of multiplex loop-mediated isothermal amplification-RFLP (mLAMP-RFLP) to detect Salmonella spp. and Shigella spp. in milk

A multiplex loop-mediated isothermal amplification-RFLP (mLAMP-RFLP) was developed and validated for simultaneous detection of Salmonella strains and Shigella strains in milk. In this system, two sets of LAMP primers were designed to specifically target invA of Salmonella spp. and ipaH of Shigella spp. Under isothermal conditions at 63 °C, ladder pattern of DNA bands could be amplified within 60 min in the presence of genomic DNAs of Salmonella strains and Shigella strains, which could be distinguished between Salmonella spp. and Shigella spp. simultaneously based on the different ladder pattern of DNA bands and subsequent restriction enzyme analysis. The overall analysis time was approximately 20 h including the enrichment of the bacterial cells, which greatly saved detection time. The sensitivity of mLAMP was found to be 100 fg DNA/tube with genomic DNAs of Salmonella strains and Shigella strains, comparatively, multiplex PCR was 1 pg DNA/tube. The mLAMP allowed the detection of milk sample artificially contaminated by Salmonella strains and Shigella strains at initial inoculation levels of approximate 5 CFU/10 mL. In conclusion, the mLAMP described here can potentially facilitate simultaneous monitoring of Salmonella and Shigella in a large number of food samples, which could be used as a primary screening method and as a supplement to classical detection method.     

多重PCR快速检测婴幼儿奶粉中的病原菌

为了建立同时检测婴幼儿奶粉中阪崎肠杆菌、金黄色葡萄球菌、蜡样芽孢杆菌的多重PCR方法,根据阪崎肠杆菌ompA基因、金黄色葡萄球菌nuc基因、蜡样芽孢杆菌hblA基因分别设计3对引物进行多重PCR扩增,并对反应条件进行优化。结果多重PCR扩增出长度为514、156、235bp的特异性目的条带。不增菌的情况下,多重PCR同时检测3种病原菌的灵敏度是103cfu/mL,3种病原菌在奶粉中的检出限是104cfu/g。建立的多重PCR反应准确、快速、高效,为同时检测婴幼儿奶粉中的阪崎肠杆菌、金黄色葡萄球菌、蜡样芽孢杆菌提供了新方法。