Incorporating germination-induction into decontamination strategies for bacterial spores

Thioflavin-T does not report on electrochemical potential and memory of dormant or germinating bacterial spores

IMPORTANCE

Bacillus and Clostridium spores cause food spoilage and disease because of spores' dormancy and resistance to microbicides. However, when spores "come back to life" in germination, their resistance properties are lost. Thus, understanding the mechanisms of spore germination could facilitate the development of "germinate to eradicate" strategies. One germination feature is the memory of a pulsed germinant stimulus leading to greater germination following a second pulse. Recent observations of increases in spore binding of the potentiometric dye thioflavin-T early in their germination of spores led to the suggestion that increasing electrochemical potential is how spores "remember" germinant pulses. However, new work finds no increased thioflavin-T binding in the physiological germination of Coatless spores or of intact spores germinating with dodecylamine, even though spore memory is seen in both cases. Thus, using thioflavin-T uptake by germinating spores to assess the involvement of electrochemical potential in memory of germinant exposure, as suggested recently, is questionable.

Bacillus spore germination: mechanisms, identification, and antibacterial strategies

Bacterial spores are metabolically inactive and highly resistant to harsh environmental conditions in nature and during decontamination processes in food and related industries. However, inducing germination using specific germinants in dormant spores can convert them into vegetative cells which are metabolically active and fragile. The potential utility of a "germinate to eradicate" strategy, also known as germination-inactivation, has been validated in foods. Meanwhile, the strategy has sparked much interest in triggering and maximizing spore germination. Although many details of the spore germination process have been identified over the past decades, there remain many uncertainties, including some signal transduction mechanisms involved in germination. In addition, the successful implementation of the germination-inactivation strategy relies on the sensitive detection of germinative biomarkers within minutes of germination initiation and the optimal timing for the subsequent inactivation step. Meanwhile, the emergence of biomarkers has renewed attention to the practical application of the spore germination process. Here, this review presents the current knowledge of the germination mechanisms of Bacillus spore, influencing factors, and germination biomarkers. It also covers a detailed discussion on the development of germination-inactivation as a spore eradication strategy.

The underlying mechanism of bacterial spore germination: An update review

Bacterial spores are highly resilient and universally present on earth and can irreversibly enter the food chain to cause food spoilage or foodborne illness once revived to resume vegetative growth. Traditionally, extensive thermal processing has been employed to efficiently kill spores; however, the relatively high thermal load adversely affects food quality attributes. In recent years, the germination-inactivation strategy has been developed to mildly kill spores based on the circumstance that germination can decrease spore-resilient properties. However, the failure to induce all spores to geminate, mainly owing to the heterogeneous germination behavior of spores, hampers the success of applying this strategy in the food industry. Undoubtedly, elucidating the detailed germination pathway and underlying mechanism can fill the gap in our understanding of germination heterogeneity, thereby facilitating the development of full-scale germination regimes to mildly kill spores. In this review, we comprehensively discuss the mechanisms of spore germination of Bacillus and Clostridium species, and update the molecular basis of the early germination events, for example, the activation of germination receptors, ion release, Ca-DPA release, and molecular events, combined with the latest research evidence. Moreover, high hydrostatic pressure (HHP), an advanced non-thermal food processing technology, can also trigger spore germination, providing a basis for the application of a germination-inactivation strategy in HHP processing. Here, we also summarize the diverse germination behaviors and mechanisms of spores of Bacillus and Clostridium species under HHP, with the aim of facilitating HHP as a mild processing technology with possible applications in food sterilization. Practical Application: This work provides fundamental basis for developing efficient killing strategies of bacterial spores in food industry.

Dose-response analysis of Bacillus thuringiensis HD-1 cry- spore reduction on surfaces using formaldehyde with pre-germination

AIM

To establish a basis for rapid remediation of large areas contaminated with Bacillus anthracis spores.

METHODS AND RESULTS

Representative surfaces of wood, steel and cement were coated by nebulization with B. thuringiensis HD-1 cry- (a simulant for B. anthracis) at 5.9 ± 0.2, 6.3 ± 0.2 and 5.8 ± 0.2 log10 CFU per cm² , respectively. These were sprayed with formaldehyde, either with or without pre-germination. Low volume (equivalent to ≤2500 L ha^-1 ) applications of formaldehyde at 30 g l^-1 to steel or cement surfaces resulted in ≥4 or ≤2 log10 CFU per cm² reductions respectively, after 2 h exposure. Pre-germinating spores (500 mmol l^-1 l-alanine and 25 mmol l^-1 inosine, pH 7) followed by formaldehyde application showed higher levels of spore inactivation than formaldehyde alone with gains of up to 3.4 log10 CFU per cm² for a given dose. No loss in B. thuringiensis cry- viability was measured after the 2 h germination period, however, a pre-heat shock log10 reduction was seen for B. anthracis strains: LSU149 (1.7 log10), Vollum and LSU465 (both 0.9 log10), LSU442 (0.2 log10), Sterne (0.8 log10) and Ames (0.6 log10).

CONCLUSIONS

A methodology was developed to produce representative spore contamination of surfaces along with a laboratory-based technique to measure the efficacy of decontamination. Dose-response analysis was used to optimize decontamination. Pre-germinating spores was found to increase effectiveness of decontamination but requires careful consideration of total volume used (germinant and decontaminant) by surface type.

SIGNIFICANCE AND IMPACT OF THE STUDY

To be practically achievable, decontamination of a wide area contaminated with B. anthracis spores must be effective, timely and minimize the amount of materials required. This study uses systematic dose-response methodology to demonstrate that such an approach is feasible.

Inhibitory activities of propolis, nisin, melittin and essential oil compounds on Paenibacillus alvei and Bacillus subtilis

Background

Natural products represent important sources of antimicrobial compounds. Propolis and compounds from essential oils comprise good examples of such substances because of their inhibitory effects on bacterial spores, including bee pathogens.

Methods

Ethanol extracts of propolis (EEP) from Apis mellifera were prepared using different methods: double ultrasonication, double maceration and maceration associated with ultrasonication. Together with the antimicrobial peptides nisin and melittin, and compounds present in the essential oils of clove (Syzygium aromaticum) and cinnamon (Cinnamomum zeylanicum), assays were carried out on one Bacillus subtilis isolate and Paenibacillus alvei (ATCC 6344) against vegetative and sporulated forms, using the resazurin microtiter assay. Synergism with all the antimicrobials in association with tetracycline was verified by the time-kill curve method. Potassium and phosphate efflux, release of proteins and nucleic acids were investigated.

Results

EEPs showed the same MIC, 156.25 µg/mL against B. subtilis and 78.12 µg/mL against P. alvei. The peptides showed better activities against B. subtilis (MIC of 12 µg/mL for melittin and 37.50 µg/mL for nisin). Antimicrobials showed similar inhibitory effects, but cinnamaldehyde (39.06 µg/mL) showed the best action against P. alvei. Melittin and nisin showed the greatest capacity to reduce spores, regarding B. subtilis there was a 100% reduction at 6.25 and 0.78 µg/mL, respectively. Concerning P. alvei, the reduction was 93 and 98% at concentrations of 80 µg/mL of melittin and 15 µg/mL of nisin. EEPs showed the highest effects on the protein release against B. subtilis and P. alvei. Nucleic acid release, phosphate and potassium efflux assays indicated bacterial cell membrane damage. Synergism between antimicrobials and tetracycline was demonstrated against both bacteria.

Conclusion

All antimicrobials tested showed antibacterial activities against vegetative and sporulated forms of P. alvei and B. subtilis, especially nisin and melittin. Synergism with tetracycline and damage on bacterial cell membrane also occurred.

Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage

Members of the genus Clostridium are frequently associated with meat spoilage. The ability for low numbers of spores of certain Clostridium species to germinate in cold-stored vacuum-packed meat can result in blown pack spoilage. However, little is known about the germination process of these clostridia, despite this characteristic being important for their ability to cause spoilage. This study sought to determine the genomic conditions for germination of 37 representative Clostridium strains from seven species (C. estertheticum, C. tagluense, C. frigoris, C. gasigenes, C. putrefaciens, C. aligidicarnis and C. frigdicarnis) by comparison with previously characterized germination genes from C. perfringens, C. sporogenes and C. botulinum. All the genomes analysed contained at least one gerX operon. Seven different gerX operon configuration types were identified across genomes from C. estertheticum, C. tagluense and C. gasigenes. Differences arose between the C. gasigenes genomes and those belonging to C. tagluense/C. estertheticum in the number and type of genes coding for cortex lytic enzymes, suggesting the germination pathway of C. gasigenes is different. However, the core components of the germination pathway were conserved in all the Clostridium genomes analysed, suggesting that these species undergo the same major steps as Bacillus subtilis for germination to occur.

Clostridioides difficile spore germination: initiation to DPA release

Germination by Clostridioides difficile spores is an essential step in pathogenesis. Spores are metabolically dormant forms of bacteria that resist severe conditions. Work over the last 10 years has elucidated that C. difficile spores germinate thorough a novel pathway. This review summarizes our understanding of C. difficile spore germination and the factors involved in germinant recognition, cortex degradation and DPA release.

Where Does the Peanut Smut Pathogen, Thecaphora frezii, Fit in the Spectrum of Smut Diseases?

Smut fungi, such as Ustilago maydis, have been studied extensively as a model for plant-pathogenic basidiomycetes. However, little attention has been paid to smut diseases of agronomic importance that are caused by species of the genus Thecaphora, probably due to their more localized distribution. Peanut smut incited by Thecaphora frezii has been reported only in South America, and Argentina is the only country where this disease has been noted in commercial peanut production. In this work, important advances in deciphering T. frezii specific biology/pathobiology in relation to potato (T. solani), wheat (U. tritici), and barley (U. nuda) smuts are presented. We summarize the state of knowledge of fungal effectors, functionally characterized to date in U. maydis and most recently in T. thlaspeos, as well as the potential to be present in other Thecaphora species involved in dicot-host interactions like T. frezii-peanut. We also discuss applicability and limitations of currently available methods for identification of smut fungi in different situations and management strategies to reduce their impact on agri-food quality. We conclude by describing some of the challenges in elucidating T. frezii strategies that allow it to infect the host and tolerate or evade plant immune defense mechanisms, and assessing other aspects related to pest control and their implications for human health.

Impact of Heating Rates on Alicyclobacillus acidoterrestris Heat Resistance under Non-Isothermal Treatments and Use of Mathematical Modelling to Optimize Orange Juice Processing

Alicyclobacillus acidoterrestris is a spoilage microorganism responsible for relevant product and economic losses in the beverage and juice industry. Spores of this microorganism can survive industrial heat treatments and cause spoilage during posterior storage. Therefore, an effective design of processing treatments requires an accurate understanding of the heat resistance of this microorganism. Considering that industrial treatments are dynamic; this understanding must include how the heat resistance of the microorganism is affected by the heating rate during the heating and cooling phases. The main objective of this study was to establish the effect of heating rates and complex thermal treatments on the inactivation kinetics of A. acidoterrestris. Isothermal experiments between 90 and 105 °C were carried out in a Mastia thermoresistometer, as well as four different dynamic treatments. Although most of the inactivation takes place during the holding phase, our results indicate the relevance of the heating phase for the effectiveness of the treatment. The thermal resistance of A. acidoterrestris is affected by the heating rate during the heating phase. Specifically, higher heating rates resulted in an increased microbial inactivation with respect to the one predicted based on isothermal experiments. These results provide novel information regarding the heat response of this microorganism, which can be valuable for the design of effective heat treatments to improve product safety and stability. Moreover, it highlights the need to incorporate experimental data based on dynamic treatments in process design, as heating rates can have a very significant effect on the thermal resistance of microorganisms.

Graphene-Based and Surface-Enhanced Raman Spectroscopy for Monitoring the Physio-Chemical Response of Thermophilic Bacterial Spores to Low Temperatures Exposure

Monitoring the spore life cycle is one of the main issues in several fields including environmental control, sustainable ecosystems, food security, and healthcare systems. In this framework, the study of the living organism resistance to extreme conditions like those mimicking space environments is particularly interesting. The assessment of the local change of the pH level can be extremely useful for this purpose. An optical physiometer method based on the Raman response of the graphene, which is able to locally sense pH of a fluid on a micrometric scale, has been recently proposed. Due to the presence of π-bonds at the surface, the electronic doping of graphene is determined by the external conditions and can be electrochemically controlled or altered by the contact with an acid or alkaline fluid. The doping level affects the vibrational energies of the graphene that can be monitored by conventional Raman spectroscopy. In addition, Surface-Enhanced Raman Spectroscopy (SERS) can give direct information on the biochemical changes occurring in spore components. In this work, we propose the joint use of Graphene-Based Raman Spectroscopy (GbRS) and SERS for the monitoring of the response of spores to exposure to low temperatures down to 100 K. The spores of the thermophilic bacterium Parageobacillus thermantarcticus isolated from an active volcano of Antarctica (Mt. Melbourne) were investigated. These spores are particularly resistant to several stressing stimuli and able to adapt to extreme conditions like low temperatures, UV irradiation, and γ-rays exposure. The results obtained showed that the joint use of GbRS and SERS represents a valuable tool for monitoring the physio-chemical response of bacterial spores upon exposure to stressing stimuli.

Bacillus spore germination: Knowns, unknowns and what we need to learn

How might a microbial cell that is entirely metabolically dormant - and which has the ability to remain so for extended periods of time - irreversibly commit itself to resuming vegetative growth within seconds of being exposed to certain amino acids or sugars? That this process takes place in the absence of any detectable ATP or de novo protein synthesis, and relies upon a pre-formed apparatus that is immobilised, respectively, in a semi-crystalline membrane or multi-layered proteinaceous coat, only exacerbates the challenge facing spores of Bacillales species when stimulated to germinate. Whereas the process by which spores are formed in response to nutrient starvation - sporulation - involves the orchestrated interplay between hundreds of distinct proteins, the process by which spores return to life - germination - is a much simpler affair, requiring a handful of receptor and channel proteins complemented with specialized peptidoglycan lysins. Despite this relative simplicity, and research effort spanning many decades, comprehensive understanding of key molecular and biochemical details and, in particular signal transduction mechanisms associated with spore germination, has remained elusive. In this review we provide an up to date overview of the field while identifying what we consider to be the key gaps in knowledge associated with germination of Bacillales spores, suggesting also technical approaches that may provide fresh insight to this unique biological process.

Biological Validation of a Chemical Effluent Decontamination System

Introduction:

Failure of an existing effluent decontamination system (EDS) prompted the consideration of commercial off-the-shelf solutions for decontamination of containment laboratory waste. A bleach-based chemical EDS was purchased to serve as an interim solution.

Methods:

Studies were conducted in the laboratory to validate inactivation of Bacillus spores with bleach in complex matrices containing organic simulants including fetal bovine serum, humic acid, and animal room sanitation effluent.

Results:

These studies demonstrated effective decontamination of >106 spores at a free chlorine concentration of ≥5700 parts per million with a 2-hour contact time. Translation of these results to biological validation of the bleach-based chemical EDS required some modifications to the system and its operation.

Discussion:

The chemical EDS was validated for the treatment of biosafety levels 3 and 4 waste effluent using laboratory-prepared spore packets along with commercial biological indicators; however, several issues and lessons learned identified during the process of onboarding are also discussed, including bleach product source, method of validation, dechlorination, and treated waste disposal.

DNA Damage Kills Bacterial Spores and Cells Exposed to 222-Nanometer UV Radiation

This study examined the microbicidal activity of 222-nm UV radiation (UV₂₂₂), which is potentially a safer alternative to the 254-nm UV radiation (UV₂₅₄) that is often used for surface decontamination. Spores and/or growing and stationary-phase cells of Bacillus cereus, Bacillus subtilis, Bacillus thuringiensis, Staphylococcus aureus, and Clostridioides difficile and a herpesvirus were all killed or inactivated by UV₂₂₂ and at lower fluences than with UV₂₅₄B. subtilis spores and cells lacking the major DNA repair protein RecA were more sensitive to UV₂₂₂, as were spores lacking their DNA-protective proteins, the α/β-type small, acid-soluble spore proteins. The spore cores' large amount of Ca²⁺-dipicolinic acid (∼25% of the core dry weight) also protected B. subtilis and C. difficile spores against UV₂₂₂, while spores' proteinaceous coat may have given some slight protection against UV₂₂₂ Survivors among B. subtilis spores treated with UV₂₂₂ acquired a large number of mutations, and this radiation generated known mutagenic photoproducts in spore and cell DNA, primarily cyclobutane-type pyrimidine dimers in growing cells and an α-thyminyl-thymine adduct termed the spore photoproduct (SP) in spores. Notably, the loss of a key SP repair protein markedly decreased spore UV₂₂₂ resistance. UV₂₂₂-treated B. subtilis spores germinated relatively normally, and the generation of colonies from these germinated spores was not salt sensitive. The latter two findings suggest that UV₂₂₂ does not kill spores by general protein damage, and thus, the new results are consistent with the notion that DNA damage is responsible for the killing of spores and cells by UV₂₂₂IMPORTANCE Spores of a variety of bacteria are resistant to common decontamination agents, and many of them are major causes of food spoilage and some serious human diseases, including anthrax caused by spores of Bacillus anthracis Consequently, there is an ongoing need for efficient methods for spore eradication, in particular methods that have minimal deleterious effects on people or the environment. UV radiation at 254 nm (UV₂₅₄) is sporicidal and commonly used for surface decontamination but can cause deleterious effects in humans. Recent work, however, suggests that 222-nm UV (UV₂₂₂) may be less harmful to people than UV₂₅₄ yet may still kill bacteria and at lower fluences than UV₂₅₄ The present work has identified the damage by UV₂₂₂ that leads to the killing of growing cells and spores of some bacteria, many of which are human pathogens, and UV₂₂₂ also inactivates a herpesvirus.

Structural and functional analyses of the N-terminal domain of the A subunit of a Bacillus megaterium spore germinant receptor

Germination of Bacillus spores is induced by the interaction of specific nutrient molecules with germinant receptors (GRs) localized in the spore's inner membrane. GRs typically consist of three subunits referred to as A, B, and C, although functions of individual subunits are not known. Here we present the crystal structure of the N-terminal domain (NTD) of the A subunit of the Bacillus megaterium GerK₃ GR, revealing two distinct globular subdomains bisected by a cleft, a fold with strong homology to substrate-binding proteins in bacterial ABC transporters. Molecular docking, chemical shift perturbation measurement, and mutagenesis coupled with spore germination analyses support a proposed model that the interface between the two subdomains in the NTD of GR A subunits serves as the germinant binding site and plays a critical role in spore germination. Our findings provide a conceptual framework for understanding the germinant recruitment mechanism by which GRs trigger spore germination.

Inactivation of Bacillus cereus ATCC 14579 Spore on Garlic with Combination Treatments of Germinant Compounds and Superheated Steam

HIGHLIGHTS

Germinant compounds were combined with SHS to inactivate B. cereus spores. B. cereus spores were inactivated effectively by SHS after Ala+IMP treatment. Inactivation trend was analyzed by the Weibull model, and t₃ d values were determined. Sublethal injury was not observed by SHS after Ala+IMP treatment.

Colony-Forming Unit Spreadplate Assay versus Liquid Culture Enrichment-Polymerase Chain Reaction Assay for the Detection of Bacillus Endospores in Soils

A liquid culture enrichment-polymerase chain reaction (E-PCR) assay was investigated as a potential tool to overcome inhibition by chemical component, debris, and background biological impurities in soil that were affecting detection assay performance for soil samples containing Bacillus atrophaeus subsp. globigii (a surrogate for B. anthracis). To evaluate this assay, 9 g of matched sets of three different soil types (loamy sand [sand], sandy loam [loam] and clay) was spiked with 0, ~4.5, 45, 225, 675 and 1350 endospores. One matched set was evaluated using a previously published endospore concentration and colony-forming unit spreadplate (CFU-S) assay and the other matched set was evaluated using an E-PCR assay to investigate differences in limits of detection between the two assays. Data illustrated that detection using the CFU-S assay at the 45-endospore spike level started to become sporadic whereas the E-PCR assay produced repeatable detection at the ~4.5-endospore spike concentration. The E-PCR produced an ~2-log increase in sensitivity and required slightly less time to complete than the CFU-S assay. This study also investigated differences in recovery among pure and blended sand and clay soils and found potential activation of B. anthracis in predominately clay-based soils.

A Standard Method To Inactivate Bacillus anthracis Spores to Sterility via Gamma Irradiation

In 2015, a laboratory of the United States Department of Defense (DoD) inadvertently shipped preparations of gamma-irradiated spores of Bacillus anthracis that contained live spores. In response, a systematic evidence-based method for preparing, concentrating, irradiating, and verifying the inactivation of spore materials was developed. We demonstrate the consistency of spore preparations across multiple biological replicates and show that two different DoD institutions independently obtained comparable dose-inactivation curves for a monodisperse suspension of B. anthracis spores containing 3 × 10¹⁰ CFU. Spore preparations from three different institutions and three strain backgrounds yielded similar decimal reduction (D₁₀) values and irradiation doses required to ensure sterility (D_SAL) to the point at which the probability of detecting a viable spore is 10^-6 Furthermore, spores of a genetically tagged strain of B. anthracis strain Sterne were used to show that high densities of dead spores suppress the recovery of viable spores. Together, we present an integrated method for preparing, irradiating, and verifying the inactivation of spores of B. anthracis for use as standard reagents for testing and evaluating detection and diagnostic devices and techniques.IMPORTANCE The inadvertent shipment by a U.S. Department of Defense (DoD) laboratory of live Bacillus anthracis (anthrax) spores to U.S. and international destinations revealed the need to standardize inactivation methods for materials derived from biological select agents and toxins (BSAT) and for the development of evidence-based methods to prevent the recurrence of such an event. Following a retrospective analysis of the procedures previously employed to generate inactivated B. anthracis spores, a study was commissioned by the DoD to provide data required to support the production of inactivated spores for the biodefense community. The results of this work are presented in this publication, which details the method by which spores can be prepared, irradiated, and tested, such that the chance of finding residual living spores in any given preparation is 1/1,000,000. These irradiated spores are used to test equipment and methods for the detection of agents of biological warfare and bioterrorism.

Enhancing Whole Phage Therapy and Their Derived Antimicrobial Enzymes through Complex Formulation

The resurgence of research into phage biology and therapy is, in part, due to the increasing need for novel agents to treat multidrug-resistant infections. Despite a long clinical history in Eastern Europe and initial success within the food industry, commercialized phage products have yet to enter other sectors. This relative lack of success is, in part, due to the inherent biological limitations of whole phages. These include (but are not limited to) reaching target sites at sufficiently high concentrations to establish an infection which produces enough progeny phages to reduce the bacterial population in a clinically meaningful manner and the limited host range of some phages. Conversely, parallels can be drawn between antimicrobial enzymes derived from phages and conventional antibiotics. In the current article the biological limitations of whole phage-based therapeutics and their derived antimicrobial enzymes will be discussed. In addition, the ability of more complex formulations to address these issues, in the context of medical and non-medical applications, will also be included.

A fluorescence in situ staining method for investigating spores and vegetative cells of Clostridia by confocal laser scanning microscopy and structured illuminated microscopy

Non-pathogenic spore-forming Clostridia are of increasing interest due to their application in biogas production and their capability to spoil different food products. The life cycle for Clostridium includes a spore stage that can assist in survival under environmentally stressful conditions, such as extremes of temperature or pH. Due to their size, spores can be investigated by a range of microscopic techniques, many of which involve sample pre-treatment. We have developed a quick, simple and non-destructive fluorescent staining procedure that allows a clear differentiation between spores and vegetative cells and effectively stains spores, allowing recovery and tracking in subsequent experiments. Hoechst 34580, Propidium iodide and wheat germ agglutinin WGA 488 were used in combination to stain four strains of Clostridia at different life cycle stages. Staining was conducted without drying the sample, preventing changes induced by dehydration and cells observed by confocal laser scanner microscopy or using a super-resolution microscope equipped with a 3D-structured illumination module. Dual staining with Hoechst/Propidium iodide differentiated spores from vegetative cells, provided information on the viability of cells and was successfully applied to follow spore production induced by heating. Super-resolution microscopy of spores probed by Hoechst 34580 also allowed chromatin to be visualised. Direct staining of a cheese specimen using Nile Red and Fast Green allowed in situ observation of spores within the cheese and their position within the cheese matrix. The proposed staining method has broad applicability and can potentially be applied to follow Clostridium spore behaviour in a range of different environments.