Detection and quantification of viable Bacillus cereus group species in milk by propidium monoazide quantitative real-time PCR

Establishment and application of quantitative detection of Bacillus velezensis HMB26553, a biocontrol agent against cotton damping-off caused by Rhizoctonia

A highly sensitive quantitative PCR (qPCR) method was developed for detection and quantification of Bacillus velezensis HMB26553 in cotton rhizosphere. The study aimed to develop a quantitative detection method for the strain HMB26553, and explore the relationship between its colonization of the cotton rhizosphere and its control effect. The whole genome sequence of strain HMB26553 was obtained by genome sequencing and a unique specific sequence pB-gene0026 on plasmid plaBV2 was identified by using high-throughput alignment against NCBI. Plasmid plaBV2 could be stably genetically inherited. Based on this sequence, specific primers for amplifying 106 bp and a minor groove binder (MGB) TaqMan probe for enhancing sensitivity were designed. The copy number of plaBV2 in strain HMB26553, which was 2, was confirmed by internal reference primers and the MGB TaqMan probe based on housekeeping gene gyrB. The established detection technique based on these primers and probes had high specificity and sensitivity compared to traditional plate counting method, with a detection limit of 1.5 copy genome. Using this method, the study discovered a likely correlation between the quantity of colonization in cotton rhizosphere and efficacy against cotton damping-off caused by Rhizoctonia after seed soaking and irrigation with strain HMB26553. Thus, this method provides scientific support for the rational application of strain HMB26553 in the future.

Detection of Viable Streptococcus equi equi Using Propidium Monoazide Polymerase Chain Reaction

There is debate around the clinical significance of Streptococcus equi subsp. equi detection in low numbers using quantitative real-time PCR (qPCR). Propidium monoazide (PMA) qPCR has been used to differentiate DNA from viable and nonviable bacterial cells. The aim of this study was to evaluate the ability of PMA eqbE SEQ2190 triplex qPCR to differentiate DNA from viable and nonviable S. equi in positive and suspect positive clinical specimens. Fifty-seven stored (frozen and refrigerated) positive (36) or suspect positive (21) clinical specimens (determined via SeeI qPCR as the gold standard) were tested using eqbE SEQ2190 triplex qPCR with (+) and without (-) PMA pretreatment. Cycle thresholds were higher when using PMA indicating a mixture of heat killed and viable cells. Number of S. equi positive specimens were as follows: 6/57 eqbE + PMA, 13/57 eqbE -PMA (Chi- squared 3.1, p = .079); 10/57 SEQ2190 +PMA, 53/57 SEQ2190 -PMA (Chi- squared 65.6, p < .0001). The mean cycle thresholds were as follows: 23.88 eqbE -PMA, 29.89 eqbE + PMA (p = .04); 24.9 SEQ2190 -PMA, 31.9 SEQ2190 +PMA (p < .0001). PMA qPCR can be used to determine S. equi viability, but testing should be performed on fresh specimens.

Conventional and advanced detection techniques of foodborne pathogens: A comprehensive review

Foodborne pathogens are a major public health concern and have a significant economic impact globally. From harvesting to consumption stages, food is generally contaminated by viruses, parasites, and bacteria, which causes foodborne diseases such as hemorrhagic colitis, hemolytic uremic syndrome (HUS), typhoid, acute, gastroenteritis, diarrhea, and thrombotic thrombocytopenic purpura (TTP). Hence, early detection of foodborne pathogenic microbes is essential to ensure a safe food supply and to prevent foodborne diseases. The identification of foodborne pathogens is associated with conventional (e.g., culture-based, biochemical test-based, immunological-based, and nucleic acid-based methods) and advances (e.g., hybridization-based, array-based, spectroscopy-based, and biosensor-based process) techniques. For industrial food applications, detection methods could meet parameters such as accuracy level, efficiency, quickness, specificity, sensitivity, and non-labor intensive. This review provides an overview of conventional and advanced techniques used to detect foodborne pathogens over the years. Therefore, the scientific community, policymakers, and food and agriculture industries can choose an appropriate method for better results.

qPCR detection of viable Bacillus cereus group cells in cosmetic products

Reference methods for microbiological safety assessments of cosmetics rely on culture methods that reveal colonies of live microorganisms on growth media. Rapid molecular technologies, such as qPCR, detects the presence of target DNA in samples from dead and viable cells. DNA intercalating dyes, such as propidium monoazide (PMAxx), are capable of restricting PCR amplification to viable microbial cells. Here we developed singleplex and multiplex real time (qPCR) assays for the detection of Bacillus cereus (B. cereus) using 16S rRNA and phosphatidylcholine-specific phospholipase C (PLC) gene specific sequences coupled with PMAxx. The limit of detection was determined to be ~ 1 log CFU/ml for 16S rRNA and 3 log CFU/ml for PLC detection in pure culture using an eye shadow isolate, B. cereus 3A. We assessed the inclusivity and exclusivity of our qPCR assays using 212 strains, including 143 members of B. cereus, 38 non- B. cereus. and 31 non-Bacillus species; inclusivity was 100% for the 16S rRNA and 97.9% for the PLC targets; the exclusivity was 100% for 16S rRNA and 98.6% for PLC targets. These qPCR assays were then used to assess samples of commercial cosmetics: one set of liquid face toners (N = 3), artificially contaminated with B. cereus 3A, and one set of powdered cosmetics (N = 8), previously determined to be contaminated with B. cereus. For some samples, test portions were analyzed by qPCR in parallel, with and without PMAxx treatment. All test portions were simultaneously streaked on BACARA plates to confirm viable cells of B. cereus, according to the culture method. We found no difference in sensitivity between the singleplex and the multiplex qPCR assays (P > 0.05). Inoculated samples that did not recover B. cereus on plates still showed amplification of the DNA targets. However, that amplification was significantly delayed in PMAxx -treated samples (P < 0.0001) with C_T value differences of 7.82 for 16S rRNA and 7.22 for PLC. Likewise, amplification delay was significant (P < 0.0001) with inoculated samples that recovered B. cereus on plates with C_T value differences of 2.96 and 2.36 for 16S rRNA and PLC, respectively, demonstrating the presence of dead cells in the samples. All our qPCR results correlated with detection on BACARA plates (kappa, k = 0.99), independently of the presence of PMAxx in the PCR assays. Nevertheless, the amplification threshold with PMAxx dyes was significantly higher than the non-PMAxx dyes. Our findings confirm qPCR can be used for more rapid detection of microorganisms in cosmetics, including B. cereus, and selective detection of viable cells can be improved using PMAxx dyes.

Current Perspectives on Viable but Non-Culturable Foodborne Pathogenic Bacteria: A Review

Foodborne diseases caused by foodborne pathogens pose risks to food safety. Effective detection and efficient inactivation of pathogenic bacteria has always been a research hotspot in the field of food safety. Complicating these goals, bacteria can be induced to adopt a viable but non-culturable (VBNC) state under adverse external environmental stresses. When in the VBNC state, pathogens cannot form visible colonies during traditional culture but remain metabolically active and toxic. The resulting false negative results in growth-related assays can jeopardize food safety. This review summarizes the latest research on VBNC foodborne pathogens, including induction conditions, detection methods, mechanism of VBNC formation, and possible control strategies. It is hoped that this review can provide ideas and methods for future research on VBNC foodborne pathogenic bacteria.

Identification of cry genes in Bacillus thuringiensis by multiplex real-time PCR

Bacillus thuringiensis is an important bacterium of the group Bacillus cereus sensu lato due to its insecticidal properties. This microorganism has high genetic variability and its strains produce different Cry toxins, known as δ-endotoxins, which are mainly responsible for its toxic effect on insects that are agricultural pests or vector human diseases. Each strain can express a variety of cry genes, out of a total of 789 cry genes described so far. The detection of these genes is very important to characterize strains, as they may indicate their toxic potential. Several methods have been used to characterize B. thuringiensis strains, but one of the most common techniques is Polymerase Chain Reaction (PCR) from primers that detect the presence of cry genes. This technique has been optimized to make real-time multiplex quantitative PCR (qPCR) assays faster, more efficient, and safer, because the presence of three genes can be detected in a single reaction. In this work, a multiplex assay was developed to identify the presence of genes from the cry1A, cry1C, and cry1F families whose respective toxins are present in both bioinsecticides, and commercial transgenic plants used to control caterpillars. Specific primers were designed to identify the families of the cited genes and the system was validated with samples that were sequenced by next-generation sequencing (NGS). The system was implemented and used to characterize 214 strains. Of these, eight were submitted to conventional PCR, and the results matched, again validating the system. Thus, the application of the proposed technique allows the reliable evaluation through this system to detect the presence of the genes of the families cry1A, cry1C, and cry1F in samples of B. thuringiensis.

Rapid, Sensitive, and Selective Quantification of Bacillus cereus Spores Using xMAP Technology

Bacillus cereus is a spore-forming ubiquitous bacterium notable as a food poisoning agent. Detection of B. cereus spores using selective media is laborious and non-specific. Herein, the quantitative detection of B. cereus spores was investigated with commercial antibodies and published aptamer sequences. Several detection reagents were screened for affinity to Bacillus collagen-like protein A (BclA), an abundant exosporium glycoprotein. Sensitivity and selectivity toward B. cereus spores were tested using immunoassays and multi-analyte profiling (xMAP). A recombinant antibody developed in llama against BclA protein showed B. cereus spore selectivity and sensitivity between 10² and 10⁵ spores/mL using xMAP. DNA aptamer sequences demonstrated sensitivity from 10³ to 10⁷ spores/mL and no cross-reaction to B. megaterium and B. subtilis. Selectivity for B. cereus spores was also demonstrated in a mixture of several diverse microorganisms and within a food sample with no compromise of sensitivity. As proof of concept for multiplexed measurement of human pathogens, B. cereus and three other microorganisms, E. coli, P. aeruginosa, and S. cerevisiae, were simultaneously detected using xMAP. These data support the development of a rapid, sensitive, and selective system for quantitation of B. cereus spores and multiplexed monitoring of human pathogens in complex matrices.

An Improved Method for Quantification of Viable Fusarium Cells in Infected Soil Products by Propidium Monoazide Coupled with Real-Time PCR

Fusarium is a soil-borne pathogen that causes root rot disease in cucumber. To date, quantitative real-time PCR (qPCR) is a common tool to detect the content of Fusarium in soil. However, qPCR cannot distinguish between viable and nonviable cells. The aim of this study was to develop a detection technique to pretreat tissue fluid with propidium monoazide (PMA) followed by extract DNA, and then to quantify viable Fusarium cells in contaminated soil. In this work, the specific primer pair F8-1/F8-2 was designed based on the translation elongation factor (EF) gene and a PMA-qPCR assay was established to amplify and quantify soils of viable Fusarium cells. The PMA pretreatment test was optimized, which indicated that the optimal PMA concentration and light exposure time were 50 mmol L⁻¹ and 15 min, respectively. The lowest limit of viable cells in suspension detected and soil by PMA-qPCR were 82 spore mL⁻¹ and 91.24 spore g⁻¹, respectively. For naturally contaminated soil, viable Fusarium cells were detected in eight of the 18 samples, and the Fusarium amount ranged from 10⁴ to 10⁶ spore g⁻¹. In conclusion, the PMA-qPCR method has the characteristics of high sensitivity, efficiency, and time saving, which could support nursery plants to avoid Fusarium infection and agro-industry losses.

A Novel Propidium Monoazide-Based PCR Assay Can Measure Viable Uropathogenic E. coli In Vitro and In Vivo

Background

Polymerase chain reaction (PCR) is an important means by which to study the urine microbiome and is emerging as possible alternative to urine cultures to identify pathogens that cause urinary tract infection (UTI). However, PCR is limited by its inability to differentiate DNA originating from viable, metabolically active versus non-viable, inactive bacteria. This drawback has led to concerns that urobiome studies and PCR-based diagnosis of UTI are confounded by the presence of relic DNA from non-viable bacteria in urine. Propidium monoazide (PMA) dye can penetrate cells with compromised cell membranes and covalently bind to DNA, rendering it inaccessible to amplification by PCR. Although PMA has been shown to differentiate between non-viable and viable bacteria in various settings, its effectiveness in urine has not been previously studied. We sought to investigate the ability of PMA to differentiate between viable and non-viable bacteria in urine.

Methods

Varying amounts of viable or non-viable uropathogenic E. coli (UTI89) or buffer control were titrated with mouse urine. The samples were centrifuged to collect urine sediment or not centrifuged. Urine samples were incubated with PMA and DNA cross-linked using blue LED light. DNA was isolated and uidA gene-specific PCR was performed. For in vivo studies, mice were inoculated with UTI89, followed by ciprofloxacin treatment or no treatment. After the completion of ciprofloxacin treatment, an aliquot of urine was plated on non-selective LB agar and another aliquot was treated with PMA and subjected to uidA-specific PCR.

Results

PMA’s efficiency in excluding DNA signal from non-viable bacteria was significantly higher in bacterial samples in phosphate-buffered saline (PBS, dC_T=13.69) versus bacterial samples in unspun urine (dC_T=1.58). This discrepancy was diminished by spinning down urine-based bacterial samples to collect sediment and resuspending it in PBS prior to PMA treatment. In 3 of 5 replicate groups of UTI89-infected mice, no bacteria grew in culture; however, there was PCR amplification of E. coli after PMA treatment in 2 of those 3 groups.

Conclusion

We have successfully developed PMA-based PCR methods for amplifying DNA from live bacteria in urine. Our results suggest that non-PMA bound DNA from live bacteria can be present in urine, even after antibiotic treatment. This indicates that viable but non-culturable E. coli can be present following treatment of UTI, and may explain why some patients have persistent symptoms but negative urine cultures following UTI treatment.

Characterization of Chemical and Bacterial Concentrations in Floor Dust Samples in Southeast Texas Households

Indoor dust can be a major source of heavy metals, nutrients, and bacterial contamination in residential environments and may cause serious health problems. The goal of this research is to characterize chemical and bacterial contaminants of indoor, settled house dust in the Houston Metropolitan region. To achieve this, a total of 31 indoor dust samples were collected, along with household survey data, which were subsequently analyzed for elemental and bacterial concentrations. Microscopic and geospatial analysis was conducted to characterize and map potential hotspots of contamination. Interestingly Cd, Cr, Cu, Pb, and Zn concentrations of all 31 indoor dust samples were significantly enriched and exceeded soil background concentrations. Furthermore, As, Cd, Pb, and Zn concentrations in the dust samples were significantly correlated to the enteric bacterial load concentrations. Human health assessment revealed that cancer risk values via ingestion for Cd, Cr, and Ni were greater than the acceptable range. Of our 31 dust sample isolates, three Gram-negative and 16 Gram-positive pathogenic bacteria were identified, capable of causing a wide range of diseases. Our results demonstrate that both chemical and bacterial characterization of indoor dust coupled with spatial mapping is essential to assess and monitor human and ecological health risks.

Paper-based sensor from pyrrolidinyl peptide nucleic acid for the efficient detection of Bacillus cereus

Bacillus cereus is one of the most common foodborne pathogens found in various kinds of staple foods such as rice and wheat. A rapid and accurate detection method for this pathogen is highly desirable for the sustainable production of relevant food products. While several classical and molecular-based detection methods are available for the identification of B. cereus, they suffered one or more limitations such as the requirement for a tedious and time-consuming process, less than ideal specificity, and the lack of portability. Herein, we developed the first paper-based sensing device that exhibits high species specificity with sufficiently low limit of detection for the visual detection of specific DNA sequences of B. cereus. The success is attributed to the strategic planning of fabrication in various dimensions including thorough bioinformatics search for highly specific genes, the use of the pyrrolidinyl peptide nucleic acid (PNA) probe whose selectivity advantage is well documented, and an effective PNA immobilization and DNA-binding visualization method with an internal cross-checking system for validating the results. Testing in rice matrices indicates that the sensor is capable of detecting and distinguishing B. cereus from other bacterial species. Hence, this paper-based sensor has potential to be adopted as a practical means to detect B. cereus in food industries.

Incidence of Bacillus cereus, Bacillus sporothermodurans and Geobacillus stearothermophilus in ultra-high temperature milk and biofilm formation capacity of isolates

The presence of mesophilic and thermophilic spore-forming bacteria in UHT milk, as well as biofilm formation in dairy plants, are concerning. The current study explored the spore-forming bacilli diversity in 100 samples of UHT milk (skimmed and whole). Through this work, a total of 239 isolates from UHT milk samples were obtained. B. cereus s.s. was isolated from 7 samples, B. sporothermodurans from 19 and, G. stearothermophilus from 25 samples. Genes encoding hemolysin (HBL), and non-hemolytic (NHE) enterotoxins were detected in B. cereus s.s. isolates. All isolates of B. cereus s.s. (12) B. sporothermodurans (38), and G. stearothermophilus (47) were selected to verify the ability of biofilm formation in microtiter plates. The results showed all isolates could form biofilms. The OD₅₉₅ values of biofilm formation varied between 0.14 and 1.04 for B. cereus, 0.20 to 1.87 for B. sporothermodurans, and 0.49 to 2.77 for G. stearothermophilus. The data highlights that the dairy industry needs to reinforce control in the initial quality of the raw material and in CIP cleaning procedures; avoiding biofilm formation and consequently a persistent microbiota in processing plants, which can shelter pathogenic species such as B. cereus s.s.

Predominant Mycotoxins, Pathogenesis, Control Measures, and Detection Methods in Fermented Pastes

Fermented pastes are some of the most popular traditional products in China. Many studies reported a strong possibility that fermented pastes promote exposure to mycotoxins, including aflatoxins, ochratoxins, and cereulide, which were proven to be carcinogenic and neurotoxic to humans. The primary mechanism of pathogenicity is by inhibiting protein synthesis and inducing oxidative stress using cytochrome P450 (CYP) enzymes. The level of mycotoxin production is dependent on the pre-harvest or post-harvest stage. It is possible to implement methods to control mycotoxins by using appropriate antagonistic microorganisms, such as Aspergillus niger, Lactobacillus plantarum, and Saccharomyces cerevisiae isolated from ordinary foods. Also, drying products as soon as possible to avoid condensation or moisture absorption in order to reduce the water activity to lower than 0.82 during storage is also effective. Furthermore, organic acid treatment during the soaking process reduces toxins by more than 90%. Some novel detection technologies based on magnetic adsorption, aptamer probes, and molecular-based methods were applied to rapidly and accurately detect mycotoxins in fermented pastes.

Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products

With the abolition of milk quotas in the European Union in 2015, several member states including Ireland, Luxembourg, and Belgium have seen year on year bi-monthly milk deliveries to dairies increase by up to 35%. Milk production has also increased outside of Europe in the past number of years. Unsurprisingly, there has been a corresponding increased focus on the production of dried milk products for improved shelf life. These powders are used in a wide variety of products, including confectionery, infant formula, sports dietary supplements and supplements for health recovery. To ensure quality and safety standards in the dairy sector, strict controls are in place with respect to the acceptable quantity and species of microorganisms present in these products. A particular emphasis on spore-forming bacteria is necessary due to their inherent ability to survive extreme processing conditions. Traditional microbiological detection methods used in industry have limitations in terms of time, efficiency, accuracy, and sensitivity. The following review will explore the common spore-forming bacterial contaminants of milk powders, will review the guidelines with respect to the acceptable limits of these microorganisms and will provide an insight into recent advances in methods for detecting these microbes. The various advantages and limitations with respect to the application of these diagnostics approaches for dairy food will be provided. It is anticipated that the optimization and application of these methods in appropriate ways can ensure that the enhanced pressures associated with increased production will not result in any lessening of safety and quality standards.

Advances and Challenges in Viability Detection of Foodborne Pathogens

Foodborne outbreaks are a serious public health and food safety concern worldwide. There is a great demand for rapid, sensitive, specific, and accurate methods to detect microbial pathogens in foods. Conventional methods based on cultivation of pathogens have been the gold standard protocols; however, they take up to a week to complete. Molecular assays such as polymerase chain reaction (PCR), sequencing, microarray technologies have been widely used in detection of foodborne pathogens. Among molecular assays, PCR technology [conventional and real-time PCR (qPCR)] is most commonly used in the foodborne pathogen detection because of its high sensitivity and specificity. However, a major drawback of PCR is its inability to differentiate the DNA from dead and viable cells, and this is a critical factor for the food industry, regulatory agencies and the consumer. To remedy this shortcoming, researchers have used biological dyes such as ethidium monoazide and propidium monoazide (PMA) to pretreat samples before DNA extraction to intercalate the DNA of dead cells in food samples, and then proceed with regular DNA preparation and qPCR. By combining PMA treatment with qPCR (PMA-qPCR), scientists have applied this technology to detect viable cells of various bacterial pathogens in foods. The incorporation of PMA into PCR-based assays for viability detection of pathogens in foods has increased significantly in the last decade. On the other hand, some downsides with this approach have been noted, particularly to achieve complete suppression of signal of DNA from the dead cells present in some particular food matrix. Nowadays, there is a tendency of more and more researchers adapting this approach for viability detection; and a few commercial kits based on PMA are available in the market. As time goes on, more scientists apply this approach to a broader range of pathogen detections, this viability approach (PMA or other chemicals such as platinum compound) may eventually become a common methodology for the rapid, sensitive, and accurate detection of foodborne pathogens. In this review, we summarize the development in the field including progress and challenges and give our perspective in this area.