Specific biomarker mining and rapid detection of Burkholderia cepacia complex by recombinase polymerase amplification.

Objective: To mine specific proteins and their protein-coding genes as suitable molecular biomarkers for the Burkholderia cepacia Complex (BCC) bacteria detection based on mega analysis of microbial proteomic and genomic data comparisons and to develop a real-time recombinase polymerase amplification (rt-RPA) assay for rapid isothermal screening for pharmaceutical and personal care products. Methods: We constructed an automatic screening framework based on Python to compare the microbial proteomes of 78 BCC strains and 263 non-BCC strains to identify BCC-specific protein sequences. In addition, the specific protein-coding gene and its core DNA sequence were validated in silico with a self-built genome database containing 158 thousand bacteria. The appropriate methodology for BCC detection using rt-RPA was evaluated by 58 strains in pure culture and 33 batches of artificially contaminated pharmaceutical and personal care products. Results: We identified the protein SecY and its protein-coding gene secY through the automatic comparison framework. The virtual evaluation of the conserved region of the secY gene showed more than 99.8% specificity from the genome database, and it can distinguish all known BCC species from other bacteria by phylogenetic analysis. Furthermore, the detection limit of the rt-RPA assay targeting the secY gene was 5.6 × 102 CFU of BCC bacteria in pure culture or 1.2 pg of BCC bacteria genomic DNA within 30 min. It was validated to detect <1 CFU/portion of BCC bacteria from artificially contaminated samples after a pre-enrichment process. The relative trueness and sensitivity of the rt-RPA assay were 100% in practice compared to the reference methods. Conclusion: The automatic comparison framework for molecular biomarker mining is straightforward, universal, applicable, and efficient. Based on recognizing the BCC-specific protein SecY and its gene, we successfully established the rt-RPA assay for rapid detection in pharmaceutical and personal care products.

Exopolysaccharides from Lactobacillus plantarum reduces cadmium uptake and mitigates cadmium toxicity in rice seedlings.

Exopolysaccharides (EPSs) can be used as effective exogenous substances to alleviate the toxic effect of cadmium (Cd) on rice and other crops, thus improving plant growth characteristics under stress conditions, and reducing the accumulation of Cd in grains, but the underlying mechanism is still unclear. In the present work, the effects of EPSs from Lactobacillus plantarum on the efficiency of Cd absorption and distribution in rice seedlings under Cd stress were investigated. The results revealed that growth of rice seedlings was severely inhibited by exposure to Cd, resulting in the decrease of plant height, leaf length and biomass. This inhibition phenomenon was alleviated by the addition of EPSs from L. plantarum LPC-1. The underlying mechanism might be that EPSs could facilitate the accumulation efficiency of Cd in rice roots and reduce the transportation rate of Cd from root to leaves, therefore decreasing the Cd content in leaves. Further research showed that Cd contents in the cell wall fraction of the rice seedling root were increased by the addition of EPSs, while the proportions of Cd in the cell organelle and cell soluble component were reduced. Application of EPSs promotes the proportion of pectate- and protein- integrated Cd in rice roots. While the content of water-soluble Cd, which is more toxic to plants, decreased continuously both in roots and leaves. Our study clearly confirmed the positive effects of EPSs on alleviating Cd toxicity and decreasing Cd translocation in rice above-ground parts. Furthermore, the subcellular distribution and chemical forms of Cd in different rice seedlings parts were also affected by the addition of EPSs, which might be an important potential mechanism for EPSs in respect of alleviating Cd toxicity for rice. These findings provided a foundation for the application of exogenous substances on improving the growth performance of crops under heavy metal stress.

Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol.

Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species. Paenibacillus polymyxa is a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representative P. polymyxa strains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome of P. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification of P. polymyxa strains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, the nif cluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable in P. polymyxa. Analysis of antibiotic gene clusters in P. polymyxa revealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis of P. polymyxa will help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use of P. polymyxa in agriculture.

Extractive biodegradation and bioavailability assessment of phenanthrene in the cloud point system by Sphingomonas polyaromaticivorans.

The biological treatment of polycyclic aromatic hydrocarbons is an important issue. Most microbes have limited practical applications because of the poor bioavailability of polycyclic aromatic hydrocarbons. In this study, the extractive biodegradation of phenanthrene by Sphingomonas polyaromaticivorans was conducted by introducing the cloud point system. The cloud point system is composed of a mixture of (40 g/L) Brij 30 and Tergitol TMN-3, which are nonionic surfactants, in equal proportions. After phenanthrene degradation, a higher wet cell weight and lower phenanthrene residue were obtained in the cloud point system than that in the control system. According to the results of high-performance liquid chromatography, the residual phenanthrene preferred to partition from the dilute phase into the coacervate phase. The concentration of residual phenanthrene in the dilute phase (below 0.001 mg/L) is lower than its solubility in water (1.18 mg/L) after extractive biodegradation. Therefore, dilute phase detoxification was achieved, thus indicating that the dilute phase could be discharged without causing phenanthrene pollution. Bioavailability was assessed by introducing the apparent logP in the cloud point system. Apparent logP decreased significantly, thus indicating that the bioavailability of phenanthrene increased remarkably in the system. This study provides a potential application of biological treatment in water and soil contaminated by phenanthrene.

Screening of lignan patterns in Schisandra species using ultrasonic assisted temperature switch ionic liquid microextraction followed by UPLC-MS/MS analysis.

The ultrasonic assisted temperature-switch ionic liquid microextraction (UATS-ILME) has been successfully applied in extracting of seven lignans from Schisandra. 1-Butyl-3-methylimidazolium tetrafluoroborate ([C4MIM][BF4]) aqueous solution was selected for extracting the target analytes in raw material at 80°C. The lignans were deposited into a single drop by in situ forming 1-butyl-3-methylimidazolium hexafluorophosphate ([C4MIM][PF6]) by cooling down to 0°C and centrifuging for 10min. The extracts were analyzed by ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) in a robust multiple-reaction monitoring (MRM) mode in five minutes. Meanwhile, the proposed method was validated and successfully applied to the determination of seven lignans in twelve Schisandra species. The results indicated that UATS-ILME combined with UPLC-MS/MS is a powerful and practical tool, which has great potential for comprehensive quality control of herbal medicines.

Polymerase chain reaction-based serotyping of pathogenic bacteria in food.

Serotyping analysis of bacterial pathogens in food products is important for foodborne disease surveillance and outbreak investigations. Traditional immunological techniques are labor-intensive and time-consuming, whereas polymerase chain r eaction (PCR)-based techniques are more robust, consistent and rapid. PCR-based methods also provide easier standardization and better reproducibility. Here, we summarize some recent developments and applications of PCR-based serotyping for common foodborne pathogens, and provide a list of available bioinformatics tools for developing PCR-based serotyping assays.

Inactivation and sublethal injury kinetics of Staphylococcus aureus in broth at low temperature storage.

Low temperatures are widely used to ensure food quality and safety. However, sublethally injured Staphylococcus aureus is an important microbiological safety concern in low temperature food. The objective of this study was to develop predictive inactivation kinetic models for the inactivation and sublethal injury of S. aureus in broth at different temperatures (4 to -18°C) and time points. S. aureus was diluted in tryptic soy broth plus 0.6% (wt/vol) yeast extract (TSBYE) to obtain approximately 10(8) CFU/ml and was stored separately at 4, -3, -11, and -18°C. After specific time points within 96 days, survival of S. aureus was determined on TSBYE and TSBYE agar plus 10% NaCl for enumeration of the total viable and noninjured cell numbers, respectively. Linear, Weibull, and modified Gompertz models were applied to determine survival curve regression. The combination of low temperature and time resulted in S. aureus inactivation, although the cells were able to survive in this sublethal state. Storage temperature was the critical parameter in survival of S. aureus. The modified Weibull model successfully described a second model of noninjured S. aureus cell survival at different low temperatures, whereas only the linear model was able to fit the total viable cells. The predictive model may be used to estimate the level of S. aureus contamination in food at low storage temperatures and times, and it provides new insight into the sublethally injured survival state of S. aureus in low temperature food.

Comparative Genomic Analysis of Two-Component Signal Transduction Systems in Probiotic Lactobacillus casei.

Lactobacillus casei has traditionally been recognized as a probiotic, thus needing to survive the industrial production processes and transit through the gastrointestinal tract before providing benefit to human health. The two-component signal transduction system (TCS) plays important roles in sensing and reacting to environmental changes, which consists of a histidine kinase (HK) and a response regulator (RR). In this study we identified HKs and RRs of six sequenced L. casei strains. Ortholog analysis revealed 15 TCS clusters (HK-RR pairs), one orphan HKs and three orphan RRs, of which 12 TCS clusters were common to all six strains, three were absent in one strain. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. Some TCS clusters are involved with the response under the stress of the bile salts, acid, or oxidative, which contribute to survive the difficult journey through the human gastrointestinal tract. Computational predictions of 15 TCSs were verified by PCR experiments. This genomic level study of TCSs should provide valuable insights into the conservation and divergence of TCS proteins in the L. casei strains.

A putative MerR family regulator involved in biofilm formation in Listeria monocytogenes 4b G.

The capability of forming biofilm makes the foodborne pathogen Listeria monocytogenes more resistant to environmental stresses. To examine the mechanism of biofilm formation, L. monocytogenes transposon mutant strain GB8 with decreased ability to form biofilm was characterized in this study. Southern blot assay revealed a single copy of transposon in the GB8 chromosome, and the insertion site was identified by inverse polymerase chain reaction (IPCR). The expression of lm.G_1497 was found to be inactivated by the transposon insertion, and the gene was identical to gene LMOf2365_1497 in the sequenced strain L. monocytogenes strain 4b F2365, encoding a MerR family protein. The ability of producing biofilm was recovered in revertant GBR8. It was confirmed by quantitative real-time PCR that the transcription of the gene flanking lm.G_1497 was not affected by Tn917 insertion. These results suggested that lm.G_1497 was responsible for the positive regulation of biofilm formation in L. monocytogenes 4b G. Moreover, the failure of lm.G_1497 expression resulted in a decrease of the autolysis rate, while no effect on cell growth and motility in L. monocytogenes GB8, which might imply that the reduction in biofilm was caused by the difference in cell autolysis.

The synergistic effects of low-dose irinotecan and TRAIL on TRAIL-resistant HT-29 colon carcinoma in vitro and in vivo.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a member of the tumor necrosis factor superfamily that induces apoptosis in a broad range of human cancer cell lines while sparing most normal cell types. However, many tumors remain resistant to treatment with TRAIL. In this study, we investigated the synergistic effects of low-dose irinotecan (CPT-11) and TRAIL on TRAIL­resistant HT-29 colon carcinoma cells and explored potential mechanisms of apoptosis. Cell viability was analyzed by sulforhodamine B (SRB) assay and apoptosis was evaluated by flow cytometry and DNA ladder assay. The mRNA expression of TRAIL receptors death receptor 4 (DR4) and DR5 were determined by reverse transcription polymerase chain reaction (RT-PCR). The changes of Bax and caspase-9 in protein levels were also detected by western blotting. Tumor growth curves were depicted and tumor inhibitive rates were calculated. Our results showed that the antitumor effect of TRAIL could be enhanced significantly by low-dose CPT-11 on TRAIL-resistant HT-29 cells both in vitro and in vivo. The synergistic apoptotic effect of CPT-11 and TRAIL was proposed to be mediated by upregulating DR5 mRNA expression and increasing expression of Bax and caspase-9 proteins. The data suggest that the combination of TRAIL with low-dose CPT-11 could be an effective therapeutic approach for HT-29 colon carcinoma.

Development of a real time PCR assay for rapid detection of Vibrio parahaemolyticus from seafood.

A real time PCR assay for the detection of Vibrio parahaemolyticus in seafood samples was developed using a novel specific target and a competitive internal amplification control (IAC). The specificity of this assay was evaluated using 390 bacterial strains including V. parahaemolyticus, and other strains belonging to Vibrio and non-Vibrio species. The real time PCR assay unambiguously distinguished V. parahaemolyticus with a detection sensitivity of 4.8 fg per PCR with purified genomic DNA or 1 CFU per reaction by counting V. parahaemolyticus colonies. The assays of avoiding interference demonstrated that, even in the presence of 2.1 µg genomic DNA or 10(7) CFU background bacteria, V. parahaemolyticus could still be accurately detected. In addition, the IAC was used to indicate false-negative results, and lower than 94 copies of IAC per reaction had no influence on the detection limit. Ninety-six seafood samples were tested, of which 58 (60.4%) were positive, including 3 false negative results. Consequently, the real time PCR assay is effective for the rapid detection of V. parahaemotyticus contaminants in seafood.

Diversity of Salmonella isolates using serotyping and multilocus sequence typing.

One hundred and twenty-one Salmonella isolates were obtained from food, feed, and live chicken samples derived from 13 countries or regions. In this study, their subtypes were evaluated by serotyping and multilocus sequence typing (MLST), and their genetic profiles were also characterized. It was demonstrated by serotyping on these isolates that 36 various serovars were obtained in this study, of which three serotypes S. Babelsberg, S. Fresno, and S. II were first found in mainland China. Based on Simpson's index of diversity, the serotyping method had a 0.943 discriminatory power. Meanwhile, there were a total of 42 unique sequence types (STs) characterized by MLST, and the discriminatory power of MLST (D = 0.947) was close to that of the serotyping method. In MLST, hisD revealed the highest levels of nucleotide diversity. In addition, ST-92 was the most common ST represented by 16 Salmonella isolates, followed by ST-367 which was represented by 14 isolates. Seven new alleles were identified, which were associated with other alleles and resulted in the assignment of nine new STs. It was concluded from the results that MLST was generally associated with serotype, but not associated with the epidemiological source of the samples, and antimicrobial resistance patterns.

SMM-system: A mining tool to identify specific markers in Salmonella enterica.

This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html.

Development of a single base extension-tag microarray for the detection of pathogenic Vibrio species in seafood.

In this study, a single base extension-tag array on glass slides (SBE-TAGS) microarray was established to detect the seven leading seafood-borne pathogens, including Vibrio parahaemolyticus, Vibrio cholerae, Vibrio vulnificus, Vibrio mimicus, Vibrio alginolyticus, Vibrio anguillarum, and Vibrio harveyi. Three multiplex PCR assays were developed to specifically target the following species with individual gene markers, which are aadS, tdh, and trh for V. parahaemolyticus; col, toxR, and vvh for V. alginolyticus, V. mimicus, and V. vulnificus; and empA, vhh1, and tcpA for V. anguillarum, V. harveyi, and V. cholerae, respectively. The purified PCR products were used as template DNA for single base extension-tag reactions, labeled with Cy3 fluorescent dye and hybridized to DNA microarrays. The detection specificity of this microarray method was 100%, with the sensitivity for pure genomic DNA at 200 fg to 2 pg per reaction. Application of the DNA microarray methodology to 55 naturally contaminated seafood samples (shrimp, fish, and oysters) revealed the presence of V. parahaemolyticus at 50.9% and V. alginolyticus at 32.7%. This corresponds with traditional assays (microbiological and biochemical tests) except one sample which was identified as negative in V. parahaemolyticus by the microarray assay but as positive by the conventional method. Therefore, a combination of multiplex PCR with DNA microarray hybridization based on SBE-TAGS ensures rapid and accurate detection of pathogenic Vibrio species in seafood, thereby providing safer seafood products for consumers at a low financial burden to the aquaculture industry.

Species-specific PCR detection of the food-borne pathogen Vibrio parahaemolyticus using the irgB gene identified by comparative genomic analysis.

Vibrio parahaemolyticus is an enteric pathogen, which can cause acute gastroenteritis in humans after consumption of raw or partially cooked seafood, and specific molecular markers are necessary for its accurate identification by PCR methods. In the present study, 23 protein-coding sequences were identified by the comparative genomics method as V. parahaemolyticus-specific candidate markers. We targeted the irgB gene (vp2603), coding for iron-regulated virulence regulatory protein IrgB, in order to develop a PCR method for the detection of V. parahaemolyticus. PCR specificity was identified by amplification of 293 V. parahaemolyticus templates and by the loss of a PCR product with 11 strains from other Vibrio species and 35 non-Vibrio bacterial strains. The PCR assay had the 369-bp fragment and the sensitivity of 0.17 pg purified genomic DNA from V. parahaemolyticus. Furthermore, a multiplex PCR assay for the detection of total and virulent strains of V. parahaemolyticus was developed by targeting irgB, tdh and trh genes. These data indicated that the irgB gene is a new and effective marker for the detection of V. parahaemolyticus. In addition, this study demonstrates that genome sequence comparison has a powerful application in identifying specific markers for the detection and identification of bacterial pathogens.

Retention of Vibrio parahaemolyticus in oyster tissues after chlorine dioxide treatment.

Vibrio parahaemolyticus is an important food-borne bacterium that is closely related to food poisoning from consumption of raw or lightly-cooked oysters. Therefore, intensive efforts must be taken to depurate the contaminated oysters. Chlorine dioxide (ClO2) is considered to be a safe and effective disinfectant and is routinely applied for treatment of drinking water and seafood. However, the retention of V. parahaemolyticus in oyster tissues has not yet been explored after using ClO2 as a disinfectant. To address this lack of information, oysters (Crassostrea gigas) were artificially contaminated with V. parahaemolyticus (ATCC 17802). Individual oysters, the gills and the digestive glands were analyzed by spreading supernatants from homogenized tissues onto thiosulfate-citrate-bile-salt sucrose agar and polymerase chain reaction assays on the resulting bacterial colonies. V. parahaemolyticus that bioaccumulated in different oyster tissues could be disinfected completely after 6h of treatment with 20mg/L of ClO2. Thus, ClO2 appears to be a candidate disinfectant for V. parahaemolyticus depuration in oysters. The digestive glands appear to be a promising target tissue for detection of bacterial pathogens in oysters, using either conventional methods or molecular assays. The shelf life of oysters was extended to at least 12days following 6h of ClO2 treatment at 4 degrees C.