Development of a high resolution melting method based on a novel molecular target for discrimination between Bacillus cereus and Bacillus thuringiensis

A novel method of species-specific molecular target mining and accurate discrimination of Bacillus cereus sensu lato

Bacillus cereus, a member of the Bacillus cereus sensu lato (B. cereus s.l.), is widely distributed in nature and can contaminate a variety of foods, leading to foodborne illnesses and substantial losses in the food industry. Although culture-based methods remain the gold standard for identifying B. cereus due to their high sensitivity under specific conditions, they are often complex and labor-intensive to implement. Furthermore, the high genetic similarity among certain members of the B. cereus s.l. makes it challenging to identify species-specific molecular targets, hindering the rapid and accurate differentiation of these bacteria. In this study, we introduce a novel method, comparative analysis based on whole genome slices (CAWGS), combined with the Basic Local Alignment Search Tool (BLAST) for efficient molecular target mining. Using CAWGS-BLAST and pan-genome analysis, we successfully identified new molecular targets for B. cereus, Bacillus thuringiensis, emetic B. cereus, Bacillus anthracis, Bacillus mycoides, Bacillus weihenstephanensis, and Bacillus megaterium. Based on these newly discovered targets, we developed a PCR-CRISPR/Cas12a method for detecting B. cereus s.l. and related species. Our research not only provides a rapid and accurate approach for discriminating B. cereus s.l. and related species, but also offers a universal and valuable reference for detecting foodborne pathogens, especially those with highly similar phenotypic and genetic characteristics.

Development of a High-Resolution Melting Method for the Detection of Clarithromycin-Resistant Helicobacter pylori in the Gastric Microbiome

Background: The issue of Helicobacter pylori (H. pylori) resistance to clarithromycin (CLR) has consistently posed challenges for clinical treatment. Hence, a rapid susceptibility testing (AST) method urgently needs to be developed. Methods: In the present study, 35 isolates of H. pylori were isolated from 203 gastritis patients of the Guangzhou cohort, and the antimicrobial resistance phenotypes were associated with their genomes to analyze the relevant mutations. Based on these mutations, a rapid detection system utilizing high-resolution melting (HRM) curve analysis was designed and verified by the Shenzhen cohort, which consisted of 38 H. pylori strains. Results: Genomic analysis identified the mutation of the 2143 allele from A to G (A2143G) of 23S rRNA as the most relevant mutation with CLR resistance (p < 0.01). In the HRM system, the wild-type H. pylori showed a melting temperature (Tm) of 79.28 ± 0.01 °C, while the mutant type exhibited a Tm of 79.96 ± 0.01 °C. These differences enabled a rapid distinction between two types of H. pylori (p < 0.01). Verification examinations showed that this system could detect target DNA as low as 0.005 ng/μL in samples without being affected by other gastric microorganisms. The method also showed a good performance in the Shenzhen validation cohort, with 81.58% accuracy, and 100% specificity. Conclusions: We have developed an HRM system that can accurately and quickly detect CLR resistance in H. pylori. This method can be directly used for the detection of gastric microbiota samples and provides a new benchmark for the simple detection of H. pylori resistance.

An overview of the production and use of Bacillus thuringiensis toxin

The widespread utilization of traditional chemical pesticides has given rise to numerous negative impacts, leading to a surge in interest in exploring environmentally friendly alternatives. Bacillus thuringiensis (Bt), a bacterium renowned for its insecticidal properties, produces Cry proteins during its lifecycle. These proteins have distinct advantages over traditional chemical pesticides, including higher environmental safety, broader insecticidal spectra, and lower pesticide residues. Consequently, the discovery and application of Bt hold immense significance in plant disease and pest management, as well as in plant protection. Currently, Bt preparations occupy a prominent position as the world's largest and most widely used biopesticides. This article comprehensively reviews the fundamental aspects, insecticidal mechanisms, practical applications, and fermentation technologies related to Bt.

A novel multiplex PCR based method for the detection of Listeria monocytogenes clonal complex 8

Listeria monocytogenes is an important foodborne pathogen worldwide, which could cause listeriosis with a 20-30 % fatality rate in immunocompromised individuals. Listeria monocytogenes MLST clonal complex (CC) 8 strain is a common clone in food and clinical cases. The aim of this study was to develop multiplex PCR (mPCR) and high-resolution melting (HRM) qPCR to simultaneously detect L. monocytogenes CC8 and the other L. monocytogenes strains based on pan-genome analysis. A novel multiplex PCR and HRM qPCR targeted for the genes LM5578_1180 (specific for CC8) and LM5578_2262 (for L. monocytogenes) were developed. The specificity of this multiplex PCR and HRM qPCR were verified with other CCs of L. monocytogenes and other species strains. The detection limit of this multiplex PCR and HRM qPCR is 2.1 × 103 CFU/mL and 2.1 × 100 CFU/mL, respectively. This multiplex PCR and HRM qPCR could accurately detect CC8 strains with the interference of different ratios of L. monocytogenes CC9, CC87, CC121, CC155, and L. innocua strains. Subsequently, the detection ability of mPCR and HRM qPCR were also evaluated in spiked samples. The mPCR method could successfully detect 6.2 × 103 CFU/mL of CC8 L. monocytogenes after 6 h enrichment while the multiplex HRM qPCR method could successfully detect 6.2 × 104 CFU/mL of CC8 L. monocytogenes after 3 h enrichment. The feasibility of these methods were satisfactory in terms of sensitivity, specificity, and efficiency after evaluating 12 mushroom samples and was consistent with that of the National Standard Detection Method (GB4789.30-2016). In conclusion, the developed assays could be applied for rapid screening and detection of L. monocytogenes CC8 strains both in food and food production environments, providing accurate results to adopt monitoring measures to improve microbiological safety.

Are Bacillus thuringiensis strains like any other Bacillus cereus strains? Phenotypic-based tools to locate Bacillus thuringiensis in the diversity of the Bacillus cereus sensu lato group

Some Bacillus thuringiensis (Bt) strains are used as pesticide agent. This species belongs to Bacillus cereus (Bc) group which contains many species with a high phenotypic diversity, and could be pathogenic like B. cereus. The aim of this study was to characterize the phenotype of 90 strains belonging to Bc group, half of which were Bt. Knowing that Bt strains belong to different phylogenetic Bc groups, do Bt strains have the same phenotype than other Bc group strains? Five phenotypic parameters were estimated for 90 strains in the Bc group, of which 43 were Bt strains: minimal, maximal and optimal growth temperature, cytotoxicity on Caco-2 cells, heat resistance of spores. The dataset was processed by principal component analysis, showing that 53% of the variance of the profiles corresponded to factors linked to growth, heat resistance and cytotoxicity. The phenotype followed the phylogenetic groups based on panC. Bt strains showed similar behavior to other strains in the Bc group, in our experimental conditions. Commercial bio-insecticide strains were mesophilic with low heat resistance.

Genomic–proteomic analysis of a novel Bacillus thuringiensis strain: toxicity against two lepidopteran pests, abundance of Cry1Ac5 toxin, and presence of InhA1 virulence factor

Bacillus thuringiensis (Bt) is a biological alternative to the indiscriminate use of chemical insecticides in agriculture. Due to resistance development on insect pests to Bt crops, isolating novel Bt strains is a strategy for screening new pesticidal proteins or strains containing toxin profile variety that can delay resistance. Besides, the combined genomic and proteomic approaches allow identifying pesticidal proteins and virulence factors accurately. Here, the genome of a novel Bt strain (Bt TOL651) was sequenced, and the proteins from the spore-crystal mixture were identified by proteomic analysis. Toxicity bioassays with the spore-crystal mixture against larvae of Diatraea saccharalis and Anticarsia gemmatalis, key pests of sugarcane and soybean, respectively, were performed. The toxicity of Bt TOL651 varies with the insect; A. gemmatalis (LC₅₀ = 1.45 ng cm^-2) is more susceptible than D. saccharalis (LC₅₀ = 73.77 ng cm^-2). Phylogenetic analysis of the gyrB gene indicates that TOL651 is related to Bt kenyae strains. The genomic analysis revealed the presence of cry1Aa18, cry1Ac5, cry1Ia44, and cry2Aa9 pesticidal genes. Virulence factor genes such as phospholipases (plcA, piplc), metalloproteases (inhA), hemolysins (cytK, hlyIII, hblA, hblC, hblD), and enterotoxins (nheA, nheB, nheC) were also identified. The combined use of the genomic and proteomic data indicated the expression of Cry1Aa18, Cry1Ac5, and Cry2Aa9 proteins, with Cry1Ac5 being the most abundant. InhA1 also was expressed and may contribute to Bt TOL651 pathogenicity. These results provide Bt TOL651 as a new tool for the biocontrol of lepidopteran pests.

Construction and optimization of a multiplex PMAxx-qPCR assay for viable Bacillus cereus and development of a detection kit

In this study, a PMAxx-qPCR method for the detection and quantification of viable Bacillus cereus (B. cereus) was established based on the cesA gene that is involved in cereulide synthesis, enterotoxin gene bceT and hemolytic enterotoxin gene hblD combined with modified propidium monoazide (PMAxx). The sensitivity detection limit of the method was as follows: the DNA extracted by the kit reached 140 fg/μL, and the bacterial suspension without enrichment reached 2.24 × 10¹ CFU/mL; 14 nonB. cereus strains of the 17 tested strains all tested as negative, whereas the 2 strains of B. cereus carrying the target virulence gene(s) could be accurately detected. In terms of application, we assembled the constructed PMAxx-qPCR reaction into a detection kit and evaluated its application performance. The results showed that the detection kit has high sensitivity, strong anti-interference capability, and has good application potential. The purpose of this study is to provide a reliable detection method for the prevention and traceability of B. cereus infections.

Efficient and Scalable Process to Produce Novel and Highly Bioactive Purified Cytosolic Crystals from Bacillus thuringiensis

Bacillus thuringiensis (Bt) is a Gram-positive soil bacterium that is widely and safely applied in the environment as an insecticide for combatting insect pests that damage crops or are disease vectors. Dominant active ingredients made by Bt are insect-killing crystal (Cry) proteins released as crystalline inclusions upon bacterial sporulation. Some Bt Cry proteins, e.g., Cry5B (formally Cry5Ba1), target nematodes (roundworms) and show exceptional promise as anthelmintics (cures for parasitic nematode diseases). We have recently described inactivated bacteria with cytosolic crystal(s) (IBaCC) in which bioactive Bt Cry crystals (containing Cry5B) are fully contained within the cytosol of dead bacterial ghosts. Here, we demonstrate that these IBaCC-trapped Cry5B crystals can be liberated and purified away from cellular constituents, yielding purified cytosolic crystals (PCC). Cry5B PCC contains ~95% Cry5B protein out of the total protein content. Cry5B PCC is highly bioactive against parasitic nematode larvae and adults in vitro. Cry5B PCC is also highly active in vivo against experimental human hookworm and Ascaris infections in rodents. The process was scaled up to the 100-liter scale to produce PCC for a pilot study to treat two foals infected with the ascarid Parascaris spp. Single-dose Cry5B PCC brought the fecal egg counts of both foals to zero. These studies describe the process for the scalable production of purified Bt crystals and define a new and attractive pharmaceutical ingredient form of Bt Cry proteins.

IMPORTANCEBacillus thuringiensis crystal proteins are widely and safely used as insecticides. Recent studies have shown they also can cure gastrointestinal parasitic worm (nematode) infections when ingested. However, reproducible, scalable, and practical techniques for purifying these proteins have been lacking. Here, we address this severe limitation and present scalable and practical methods for large-scale purification of potently bioactive B. thuringiensis crystals and crystal proteins. The resultant product, called purified cytosolic crystals (PCC), is highly compatible with ingestible drug delivery and formulation. Furthermore, there are growing applications in agriculture and insect control where access to large quantities of purified crystal proteins is desirable and where these methods will find great utility.

A Visualized Isothermal Amplification Method for Rapid and Specific Detection of Emetic and Non-emetic Bacillus cereus in Dairy Products

Bacillus cereus is widely distributed in foods, especially dairy products, and can lead to diarrhea (non-emetic B. cereus) and emesis (emetic B. cereus). Although diarrhea due to B. cereus is usually mild, emesis can lead to acute encephalopathy and even death. To develop rapid and sensitive detection methods for B. cereus in foods, specific primers targeting the gyrase B (gyrB) and cereulide synthetase (ces) genes were designed and screened using recombinase polymerase amplification (RPA). Probes and base substitutions were introduced to improve specificity and eliminate primer-dependent artifacts. The 5' ends of the reverse primers and probes were modified with biotin and fluorescein isothiocyanate for detection of RPA products on a lateral flow strip (LFS). The developed RPA-LFS assay allows detection within 20 min at 37°C with no cross-reactivity with other foodborne pathogens. The limit of detection was 10⁴ copies/ml and 10² CFU/ml in pure cultures and milk, respectively. Comparisons with established methods using cream obtained similar results. A specific, rapid, and sensitive RPA-LFS assay was successfully developed for on-site detection of B. cereus in dairy products to distinguish emetic from non-emetic strains.